WO2001004311A1 - Secreted and transmembrane polypeptides and nucleic acids encoding the same - Google Patents

Secreted and transmembrane polypeptides and nucleic acids encoding the same Download PDF

Info

Publication number
WO2001004311A1
WO2001004311A1 PCT/US2000/004414 US0004414W WO0104311A1 WO 2001004311 A1 WO2001004311 A1 WO 2001004311A1 US 0004414 W US0004414 W US 0004414W WO 0104311 A1 WO0104311 A1 WO 0104311A1
Authority
WO
WIPO (PCT)
Prior art keywords
seq
atcc
polypeptide
amino acid
acid sequence
Prior art date
Application number
PCT/US2000/004414
Other languages
French (fr)
Inventor
Avi J. Ashkenazi
David Botstein
Luc Desnoyers
Dan L. Eaton
Napoleone Ferrara
Ellen Filvaroff
Sherman Fong
Wei-Qiang Gao
Hanspeter Gerber
Mary E. Gerritsen
Audrey Goddard
Paul J. Godowski
Christopher J. Grimaldi
Austin L. Gurney
Kenneth J. Hillan
Ivar J. Kljavin
Jennie P. Mather
James Pan
Nicholas F. Paoni
Margaret Ann Roy
Timothy A. Stewart
Daniel Tumas
P. Mickey Williams
William I. Wood
Original Assignee
Genentech, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from PCT/US1999/020594 external-priority patent/WO2000015666A2/en
Priority claimed from PCT/US1999/020944 external-priority patent/WO2000015792A2/en
Priority claimed from PCT/US1999/021090 external-priority patent/WO2000015796A2/en
Priority claimed from PCT/US1999/021547 external-priority patent/WO2000015797A2/en
Priority claimed from PCT/US1999/023089 external-priority patent/WO2000021996A2/en
Priority claimed from PCT/US1999/028214 external-priority patent/WO2001019987A1/en
Priority claimed from PCT/US1999/028313 external-priority patent/WO2000032221A2/en
Priority claimed from PCT/US1999/028565 external-priority patent/WO2000037638A2/en
Priority claimed from PCT/US1999/028564 external-priority patent/WO2000055319A1/en
Priority claimed from PCT/US1999/030095 external-priority patent/WO2000037640A2/en
Priority claimed from PCT/US1999/030911 external-priority patent/WO2000075316A1/en
Priority claimed from PCT/US1999/030999 external-priority patent/WO2001005836A1/en
Priority claimed from PCT/US2000/000219 external-priority patent/WO2000053753A2/en
Priority to AU28839/00A priority Critical patent/AU2883900A/en
Application filed by Genentech, Inc. filed Critical Genentech, Inc.
Priority to KR1020017011378D priority patent/KR20010104373A/en
Priority to KR1020017011378A priority patent/KR100553300B1/en
Priority to AU33816/00A priority patent/AU768694B2/en
Priority to PCT/US2000/005004 priority patent/WO2000053757A2/en
Priority to EP00912015A priority patent/EP1159419A1/en
Priority to CA002361849A priority patent/CA2361849A1/en
Priority to JP2000603378A priority patent/JP2003531811A/en
Priority to KR1020017011406A priority patent/KR20010103046A/en
Priority to PCT/US2000/005841 priority patent/WO2000053758A2/en
Priority to AU35144/00A priority patent/AU3514400A/en
Priority to CA002362427A priority patent/CA2362427A1/en
Priority to JP2000603379A priority patent/JP2004516227A/en
Priority to EP00913764A priority patent/EP1220905A2/en
Priority to EP00917878A priority patent/EP1214409B1/en
Priority to PT00917878T priority patent/PT1214409E/en
Priority to CNA2004100465359A priority patent/CN1560249A/en
Priority to AU38784/00A priority patent/AU783117B2/en
Priority to IL14818800A priority patent/IL148188A0/en
Priority to PCT/US2000/006471 priority patent/WO2001018210A1/en
Priority to DK00917878T priority patent/DK1214409T3/en
Priority to AT00917878T priority patent/ATE326532T1/en
Priority to MXPA02002491A priority patent/MXPA02002491A/en
Priority to JP2001521746A priority patent/JP2004500037A/en
Priority to SI200030879T priority patent/SI1214409T1/en
Priority to CN00815274A priority patent/CN1387570A/en
Priority to DE60028054T priority patent/DE60028054T2/en
Priority to CA002384089A priority patent/CA2384089A1/en
Priority to ES00917878T priority patent/ES2264929T3/en
Priority to KR1020027003131A priority patent/KR20020059591A/en
Priority to PCT/US2000/008439 priority patent/WO2000073454A1/en
Priority to AU37743/00A priority patent/AU3774300A/en
Priority to EP00916675A priority patent/EP1210418B1/en
Priority to JP2001500766A priority patent/JP2004522402A/en
Priority to CA002383254A priority patent/CA2383254A1/en
Priority to AT00916675T priority patent/ATE478145T1/en
Priority to JP2001503894A priority patent/JP2003529324A/en
Priority to PCT/US2000/014042 priority patent/WO2000077037A2/en
Priority to EP07025117A priority patent/EP1978029A3/en
Priority to AT07025116T priority patent/ATE449109T1/en
Priority to AU51527/00A priority patent/AU5152700A/en
Priority to EP00936172A priority patent/EP1208195A2/en
Priority to EP07025118A priority patent/EP1956030B1/en
Priority to CA2372511A priority patent/CA2372511C/en
Priority to AT07025118T priority patent/ATE448246T1/en
Priority to EP07025116A priority patent/EP1953173B1/en
Priority to PCT/US2000/015264 priority patent/WO2000073452A2/en
Priority to PCT/US2000/020710 priority patent/WO2001009327A2/en
Priority to AU63910/00A priority patent/AU6391000A/en
Priority to EP05019540A priority patent/EP1621620A3/en
Priority to EP05019539A priority patent/EP1623993A3/en
Priority to AU75730/00A priority patent/AU7573000A/en
Priority to DE60043951T priority patent/DE60043951D1/en
Priority to PCT/US2000/023328 priority patent/WO2001016318A2/en
Priority to JP2001520864A priority patent/JP3951035B2/en
Priority to EP00964919A priority patent/EP1208202A2/en
Priority to EP05019536A priority patent/EP1623991A3/en
Priority to EP05019538A priority patent/EP1623992A3/en
Priority to CA002645727A priority patent/CA2645727A1/en
Priority to CA002380355A priority patent/CA2380355A1/en
Priority to ES05019537T priority patent/ES2341257T3/en
Priority to EP07019808A priority patent/EP1892249A1/en
Priority to AT05019537T priority patent/ATE459645T1/en
Priority to EP05019537A priority patent/EP1637541B1/en
Priority to EP10005292A priority patent/EP2228446A1/en
Priority to EP06000583A priority patent/EP1686134A3/en
Priority to EP06000581A priority patent/EP1666494A1/en
Priority to CA002491258A priority patent/CA2491258A1/en
Priority to CA2709291A priority patent/CA2709291A1/en
Priority to JP2001542531A priority patent/JP2004522404A/en
Priority to CA002491433A priority patent/CA2491433A1/en
Priority to EP05025102A priority patent/EP1672070A3/en
Priority to EP06000585A priority patent/EP1661996A1/en
Priority to EP06000584A priority patent/EP1669371A3/en
Priority to CA002496312A priority patent/CA2496312A1/en
Priority to EP06000582A priority patent/EP1666495A1/en
Priority to CA002491610A priority patent/CA2491610A1/en
Priority to EP00983846A priority patent/EP1250426A2/en
Priority to PCT/US2000/032678 priority patent/WO2001040466A2/en
Priority to EP06000586A priority patent/EP1688497A1/en
Priority to AU20554/01A priority patent/AU2055401A/en
Priority to CA002490853A priority patent/CA2490853A1/en
Priority to CA002391455A priority patent/CA2391455A1/en
Priority to CA002490909A priority patent/CA2490909A1/en
Priority to EP06000588A priority patent/EP1690873A3/en
Priority to CA002494705A priority patent/CA2494705A1/en
Priority to CA002492070A priority patent/CA2492070A1/en
Priority to CA002492049A priority patent/CA2492049A1/en
Priority to EP06000589A priority patent/EP1661997A1/en
Priority to EP06000587A priority patent/EP1690872A3/en
Publication of WO2001004311A1 publication Critical patent/WO2001004311A1/en
Priority to US09/767,609 priority patent/US20020042367A1/en
Priority to US09/828,366 priority patent/US20020010137A1/en
Priority to US09/866,028 priority patent/US6642360B2/en
Priority to US09/902,759 priority patent/US20030077654A1/en
Priority to US09/902,692 priority patent/US20030054400A1/en
Priority to US09/902,736 priority patent/US6894148B2/en
Priority to US09/902,736 priority patent/US20030049676A1/en
Priority to US09/902,775 priority patent/US6686451B1/en
Priority to US09/902,853 priority patent/US20020192659A1/en
Priority to US09/902,903 priority patent/US20030044839A1/en
Priority to US09/902,615 priority patent/US20030092002A1/en
Priority to US09/902,979 priority patent/US20030113718A1/en
Priority to US09/902,634 priority patent/US20030082540A1/en
Priority to US09/902,572 priority patent/US20030108983A1/en
Priority to US09/902,713 priority patent/US20030082541A1/en
Priority to US09/903,640 priority patent/US7208308B2/en
Priority to US09/903,786 priority patent/US20030044793A1/en
Priority to US09/903,520 priority patent/US20030054401A1/en
Priority to US09/903,749 priority patent/US7147853B2/en
Priority to US09/904,011 priority patent/US20030003530A1/en
Priority to US09/903,925 priority patent/US20030096233A1/en
Priority to US09/903,562 priority patent/US6965015B2/en
Priority to US09/903,823 priority patent/US20030104381A1/en
Priority to US09/903,943 priority patent/US20030054349A1/en
Priority to US09/903,603 priority patent/US6767995B2/en
Priority to US09/904,119 priority patent/US20030049621A1/en
Priority to US09/903,806 priority patent/US20030130489A1/en
Priority to US09/903,603 priority patent/US20030148419A1/en
Priority to US09/904,766 priority patent/US20030152999A1/en
Priority to US09/904,859 priority patent/US20030036060A1/en
Priority to US09/904,805 priority patent/US20030211568A1/en
Priority to US09/904,938 priority patent/US20030211569A1/en
Priority to US09/905,125 priority patent/US6664376B2/en
Priority to US09/904,877 priority patent/US20030186358A1/en
Priority to US09/905,088 priority patent/US20030073077A1/en
Priority to US09/905,291 priority patent/US20020160374A1/en
Priority to US09/905,056 priority patent/US20030054441A1/en
Priority to US09/904,992 priority patent/US20030135025A1/en
Priority to US09/904,786 priority patent/US7557192B2/en
Priority to US09/905,449 priority patent/US6965011B2/en
Priority to US09/905,381 priority patent/US6818746B2/en
Priority to US09/904,553 priority patent/US20030059828A1/en
Priority to US09/904,820 priority patent/US20030036094A1/en
Priority to US09/904,532 priority patent/US7151160B2/en
Priority to US09/905,348 priority patent/US20030064923A1/en
Priority to US09/904,838 priority patent/US20030148370A1/en
Priority to US09/904,920 priority patent/US6806352B2/en
Priority to US09/905,075 priority patent/US7169906B2/en
Priority to US09/904,462 priority patent/US6878807B2/en
Priority to US09/904,485 priority patent/US20030064367A1/en
Priority to US09/904,956 priority patent/US20030049622A1/en
Priority to US09/906,722 priority patent/US6946262B2/en
Priority to US09/906,700 priority patent/US6723535B2/en
Priority to US09/906,742 priority patent/US20030023054A1/en
Priority to US09/906,760 priority patent/US20030096340A1/en
Priority to US09/906,646 priority patent/US6852848B2/en
Priority to US09/906,679 priority patent/US6974689B1/en
Priority to US09/906,838 priority patent/US7070979B2/en
Priority to US09/906,777 priority patent/US20030148371A1/en
Priority to US09/906,815 priority patent/US7094567B2/en
Priority to US09/906,618 priority patent/US6828146B2/en
Priority to US09/907,575 priority patent/US20030073079A1/en
Priority to US09/907,728 priority patent/US20030190611A1/en
Priority to US09/907,841 priority patent/US7033825B2/en
Priority to US09/907,925 priority patent/US20030054352A1/en
Priority to US09/907,652 priority patent/US20030104469A1/en
Priority to US09/907,942 priority patent/US7087738B2/en
Priority to US09/907,824 priority patent/US20020197671A1/en
Priority to US09/907,979 priority patent/US20030082542A1/en
Priority to US09/907,613 priority patent/US20030027145A1/en
Priority to US09/907,794 priority patent/US6635468B2/en
Priority to US09/908,093 priority patent/US20030017498A1/en
Priority to US09/908,576 priority patent/US20040005553A1/en
Priority to US09/909,320 priority patent/US7074592B2/en
Priority to US09/909,204 priority patent/US20030036061A1/en
Priority to US09/909,064 priority patent/US6818449B2/en
Priority to US09/909,088 priority patent/US20020146709A1/en
Priority to US09/924,647 priority patent/US20020155543A1/en
Priority to US09/941,992 priority patent/US20030082546A1/en
Priority to US09/943,851 priority patent/US20020150976A1/en
Priority to US09/944,413 priority patent/US20020156004A1/en
Priority to US09/944,457 priority patent/US6734288B2/en
Priority to US09/943,762 priority patent/US20020142958A1/en
Priority to US09/944,432 priority patent/US20020142419A1/en
Priority to US09/944,403 priority patent/US20020165143A1/en
Priority to US09/944,396 priority patent/US20020132981A1/en
Priority to US09/944,449 priority patent/US20020102647A1/en
Priority to US09/943,664 priority patent/US20040091972A1/en
Priority to US09/943,780 priority patent/US20030096742A1/en
Priority to US09/944,907 priority patent/US20020198147A1/en
Priority to US09/944,654 priority patent/US20020142959A1/en
Priority to US09/944,896 priority patent/US7189566B2/en
Priority to US09/944,884 priority patent/US7018837B2/en
Priority to US09/944,862 priority patent/US20020115145A1/en
Priority to US09/944,852 priority patent/US20030083479A1/en
Priority to US09/945,584 priority patent/US6908993B2/en
Priority to US09/945,587 priority patent/US6936254B2/en
Priority to US09/944,929 priority patent/US7550573B2/en
Priority to US09/944,944 priority patent/US6929947B2/en
Priority to US09/945,015 priority patent/US20020132768A1/en
Priority to US09/991,073 priority patent/US20020127576A1/en
Priority to US09/990,444 priority patent/US6930170B2/en
Priority to US09/990,456 priority patent/US20020137890A1/en
Priority to US09/990,443 priority patent/US20030054987A1/en
Priority to US09/990,438 priority patent/US20030027754A1/en
Priority to US09/990,562 priority patent/US20030027985A1/en
Priority to US09/990,436 priority patent/US20020198148A1/en
Priority to US09/993,748 priority patent/US20030069403A1/en
Priority to US09/993,687 priority patent/US20020198149A1/en
Priority to US09/990,726 priority patent/US20030054359A1/en
Priority to US09/993,667 priority patent/US20030022187A1/en
Priority to US09/990,711 priority patent/US20030032023A1/en
Priority to US09/990,442 priority patent/US20020132252A1/en
Priority to US09/992,598 priority patent/US6956108B2/en
Priority to US09/990,427 priority patent/US20030073809A1/en
Priority to US09/992,521 priority patent/US20030083461A1/en
Priority to US09/990,440 priority patent/US20030060407A1/en
Priority to US09/993,469 priority patent/US20030068623A1/en
Priority to US09/991,854 priority patent/US20030059780A1/en
Priority to US09/991,163 priority patent/US20020132253A1/en
Priority to US09/993,583 priority patent/US7074897B2/en
Priority to US09/997,666 priority patent/US20030027163A1/en
Priority to US09/997,666 priority patent/US7244816B2/en
Priority to US09/997,440 priority patent/US20030059833A1/en
Priority to US09/997,559 priority patent/US20030054403A1/en
Priority to US09/997,641 priority patent/US20030224358A1/en
Priority to US09/998,041 priority patent/US20030119001A1/en
Priority to US09/997,601 priority patent/US7189814B2/en
Priority to US09/997,529 priority patent/US7309761B2/en
Priority to US09/997,514 priority patent/US7019116B2/en
Priority to US09/997,384 priority patent/US20030087305A1/en
Priority to US09/997,641 priority patent/US7112656B2/en
Priority to US09/998,041 priority patent/US7309775B2/en
Priority to US09/997,857 priority patent/US20030064375A1/en
Priority to US09/998,156 priority patent/US20030044806A1/en
Priority to US09/997,653 priority patent/US7034122B2/en
Priority to US09/997,585 priority patent/US20030119055A1/en
Priority to US09/997,585 priority patent/US7166282B2/en
Priority to US09/997,529 priority patent/US20030134284A1/en
Priority to US09/997,573 priority patent/US20030049682A1/en
Priority to US09/997,628 priority patent/US20030059782A1/en
Priority to US09/997,384 priority patent/US7119177B2/en
Priority to US09/997,683 priority patent/US20030059783A1/en
Priority to US09/997,542 priority patent/US20030068647A1/en
Priority to US09/997,428 priority patent/US20030027162A1/en
Priority to US09/997,614 priority patent/US20030124531A1/en
Priority to US10/002,796 priority patent/US20030032057A1/en
Priority to US09/997,601 priority patent/US20030054404A1/en
Priority to US09/997,349 priority patent/US7034106B2/en
Priority to US09/997,333 priority patent/US6953836B2/en
Priority to US09/990,437 priority patent/US20030045463A1/en
Priority to US09/991,181 priority patent/US6913919B2/en
Priority to US09/991,157 priority patent/US7101687B2/en
Priority to US09/991,172 priority patent/US20030050457A1/en
Priority to US09/990,441 priority patent/US7041804B2/en
Priority to US09/991,150 priority patent/US20030194760A1/en
Priority to US09/989,726 priority patent/US7018811B2/en
Priority to US09/989,723 priority patent/US20020072092A1/en
Priority to US09/989,862 priority patent/US20030130182A1/en
Priority to US09/989,732 priority patent/US7037679B2/en
Priority to US09/989,722 priority patent/US20020072067A1/en
Priority to US09/989,729 priority patent/US20030059831A1/en
Priority to US09/989,735 priority patent/US6972185B2/en
Priority to US09/989,328 priority patent/US7056736B2/en
Priority to US09/989,734 priority patent/US7491529B2/en
Priority to US09/989,727 priority patent/US20020072497A1/en
Priority to US09/989,279 priority patent/US7083978B2/en
Priority to US09/989,721 priority patent/US20020142961A1/en
Priority to US09/989,725 priority patent/US20030139329A1/en
Priority to US09/989,730 priority patent/US7157247B2/en
Priority to US09/989,728 priority patent/US7029873B2/en
Priority to US09/989,731 priority patent/US20020103125A1/en
Priority to US09/989,293 priority patent/US7034136B2/en
Priority to US10/006,867 priority patent/US7160985B2/en
Priority to US10/028,072 priority patent/US20030004311A1/en
Priority to US10/032,996 priority patent/US20030054447A1/en
Priority to US10/033,301 priority patent/US20020098506A1/en
Priority to US10/033,326 priority patent/US20020098507A1/en
Priority to US10/033,223 priority patent/US20020164646A1/en
Priority to US10/033,245 priority patent/US20020160392A1/en
Priority to US10/032,990 priority patent/US20030032060A1/en
Priority to US10/033,435 priority patent/US20030027256A1/en
Priority to US10/033,396 priority patent/US20030077657A1/en
Priority to US10/033,167 priority patent/US20020182618A1/en
Priority to US10/033,244 priority patent/US20020192668A1/en
Priority to US10/033,246 priority patent/US20020098505A1/en
Priority to US10/052,586 priority patent/US20020127584A1/en
Priority to US10/066,273 priority patent/US7317092B2/en
Priority to US10/066,193 priority patent/US20030044902A1/en
Priority to US10/066,203 priority patent/US20030180796A1/en
Priority to US10/066,211 priority patent/US20030044844A1/en
Priority to US10/066,198 priority patent/US20030170721A1/en
Priority to US10/066,494 priority patent/US20030032063A1/en
Priority to US10/066,500 priority patent/US20020177165A1/en
Priority to US10/066,269 priority patent/US20030040014A1/en
Priority to US10/081,056 priority patent/US20040043927A1/en
Priority to US10/119,480 priority patent/US20040087769A1/en
Priority to US10/121,044 priority patent/US20030190717A1/en
Priority to US10/121,047 priority patent/US20030077778A1/en
Priority to US10/121,045 priority patent/US20030073210A1/en
Priority to US10/121,042 priority patent/US20030096386A1/en
Priority to US10/121,059 priority patent/US20030190721A1/en
Priority to US10/121,051 priority patent/US20030092147A1/en
Priority to US10/121,040 priority patent/US20030082759A1/en
Priority to US10/121,041 priority patent/US20030077776A1/en
Priority to US10/121,046 priority patent/US20030194791A1/en
Priority to US10/121,050 priority patent/US20030054516A1/en
Priority to US10/121,048 priority patent/US20030199051A1/en
Priority to US10/121,055 priority patent/US20030190718A1/en
Priority to US10/121,053 priority patent/US20030199053A1/en
Priority to US10/121,056 priority patent/US20030082760A1/en
Priority to US10/121,057 priority patent/US20030190719A1/en
Priority to US10/121,043 priority patent/US7220831B2/en
Priority to US10/121,052 priority patent/US20030199052A1/en
Priority to US10/121,060 priority patent/US20030190722A1/en
Priority to US10/121,061 priority patent/US20030082761A1/en
Priority to US10/121,049 priority patent/US20030022239A1/en
Priority to US10/121,062 priority patent/US20030077779A1/en
Priority to US10/121,063 priority patent/US20030199055A1/en
Priority to US10/121,054 priority patent/US20030199054A1/en
Priority to US10/121,058 priority patent/US20030190720A1/en
Priority to US10/123,292 priority patent/US20030073211A1/en
Priority to US10/123,771 priority patent/US20030199060A1/en
Priority to US10/123,262 priority patent/US20030049816A1/en
Priority to US10/123,261 priority patent/US20030068796A1/en
Priority to US10/123,154 priority patent/US20030190724A1/en
Priority to US10/123,236 priority patent/US20030068795A1/en
Priority to US10/123,292 priority patent/US7045603B2/en
Priority to US10/123,109 priority patent/US20030190723A1/en
Priority to US10/123,214 priority patent/US7343721B2/en
Priority to US10/123,215 priority patent/US7291329B2/en
Priority to US10/123,322 priority patent/US20030199059A1/en
Priority to US10/123,155 priority patent/US20030068794A1/en
Priority to US10/123,235 priority patent/US20030082762A1/en
Priority to US10/123,291 priority patent/US20030199058A1/en
Priority to US10/123,157 priority patent/US20030190725A1/en
Priority to US10/123,156 priority patent/US20030194792A1/en
Priority to US10/123,213 priority patent/US20030199057A1/en
Priority to US10/123,108 priority patent/US7635478B2/en
Priority to US10/123,213 priority patent/US7193048B2/en
Priority to US10/123,212 priority patent/US7276577B2/en
Priority to US10/123,913 priority patent/US20030203462A1/en
Priority to US10/123,905 priority patent/US7285625B2/en
Priority to US10/123,911 priority patent/US7408032B2/en
Priority to US10/123,908 priority patent/US7335728B2/en
Priority to US10/123,903 priority patent/US20030073212A1/en
Priority to US10/123,909 priority patent/US7193049B2/en
Priority to US10/123,904 priority patent/US20030022328A1/en
Priority to US10/123,907 priority patent/US7084258B2/en
Priority to US10/123,905 priority patent/US20030087344A1/en
Priority to US10/123,912 priority patent/US20030100087A1/en
Priority to US10/123,910 priority patent/US7329404B2/en
Priority to US10/123,906 priority patent/US20030190726A1/en
Priority to US10/123,902 priority patent/US20030077781A1/en
Priority to US10/125,805 priority patent/US20030194794A1/en
Priority to US10/124,823 priority patent/US20030199062A1/en
Priority to US10/125,704 priority patent/US7357926B2/en
Priority to US10/124,819 priority patent/US7285626B2/en
Priority to US10/124,818 priority patent/US20030082763A1/en
Priority to US10/124,821 priority patent/US20030199023A1/en
Priority to US10/125,795 priority patent/US7304131B2/en
Priority to US10/124,817 priority patent/US20030077786A1/en
Priority to US10/124,822 priority patent/US7109305B2/en
Priority to US10/124,814 priority patent/US7105335B2/en
Priority to US10/124,820 priority patent/US20030190729A1/en
Priority to US10/124,813 priority patent/US7312307B2/en
Priority to US10/124,824 priority patent/US20030077659A1/en
Priority to US10/124,816 priority patent/US20030190728A1/en
Priority to US10/125,166 priority patent/US20030039648A1/en
Priority to US10/125,932 priority patent/US7317079B2/en
Priority to US10/125,924 priority patent/US7342097B2/en
Priority to US10/125,927 priority patent/US20030190731A1/en
Priority to US10/125,931 priority patent/US20030199063A1/en
Priority to US10/125,922 priority patent/US7309762B2/en
Priority to US10/127,831 priority patent/US20030082689A1/en
Priority to US10/128,689 priority patent/US20030087365A1/en
Priority to US10/131,823 priority patent/US7304132B2/en
Priority to US10/131,817 priority patent/US7291701B2/en
Priority to US10/131,815 priority patent/US20030092103A1/en
Priority to US10/131,825 priority patent/US7282566B2/en
Priority to US10/137,865 priority patent/US20030032155A1/en
Priority to US10/137,867 priority patent/US20030207349A1/en
Priority to US10/137,868 priority patent/US20030082764A1/en
Priority to US10/140,023 priority patent/US20030207416A1/en
Priority to US10/140,020 priority patent/US20030207415A1/en
Priority to US10/140,474 priority patent/US20030032156A1/en
Priority to US10/139,963 priority patent/US7288625B2/en
Priority to US10/140,024 priority patent/US20040058424A1/en
Priority to US10/139,980 priority patent/US7247710B2/en
Priority to US10/140,470 priority patent/US20030022331A1/en
Priority to US10/140,928 priority patent/US20030068798A1/en
Priority to US10/140,865 priority patent/US20030207420A1/en
Priority to US10/140,864 priority patent/US20030207419A1/en
Priority to US10/140,805 priority patent/US20030207417A1/en
Priority to US10/140,808 priority patent/US7425621B2/en
Priority to US10/140,925 priority patent/US20030073215A1/en
Priority to US10/140,809 priority patent/US20030207418A1/en
Priority to US10/140,860 priority patent/US7307151B2/en
Priority to US10/140,921 priority patent/US7317080B2/en
Priority to US10/063,651 priority patent/US7193057B2/en
Priority to US10/141,760 priority patent/US7342104B2/en
Priority to US10/141,756 priority patent/US7488586B2/en
Priority to US10/141,701 priority patent/US20030207421A1/en
Priority to US10/141,754 priority patent/US7361732B2/en
Priority to US10/141,755 priority patent/US7297764B2/en
Priority to US10/142,425 priority patent/US20030207424A1/en
Priority to US10/143,114 priority patent/US20030036180A1/en
Priority to US10/142,430 priority patent/US7309766B2/en
Priority to US10/143,113 priority patent/US7329730B2/en
Priority to US10/142,417 priority patent/US7304133B2/en
Priority to US10/142,423 priority patent/US20030049817A1/en
Priority to US10/142,431 priority patent/US7285629B2/en
Priority to US10/143,032 priority patent/US7408033B2/en
Priority to US10/142,419 priority patent/US7153941B2/en
Priority to US10/145,627 priority patent/US20030180869A1/en
Priority to US10/145,753 priority patent/US20030207372A1/en
Priority to US10/145,876 priority patent/US20030134371A1/en
Priority to US10/145,875 priority patent/US20030166079A1/en
Priority to US10/146,792 priority patent/US20030207428A1/en
Priority to US10/146,786 priority patent/US20030203438A1/en
Priority to US10/146,730 priority patent/US20030207427A1/en
Priority to US10/146,794 priority patent/US20030207375A1/en
Priority to US10/146,789 priority patent/US20030180872A1/en
Priority to US10/147,528 priority patent/US20030219885A1/en
Priority to US10/147,519 priority patent/US20030077791A1/en
Priority to US10/147,492 priority patent/US20030082765A1/en
Priority to US10/147,536 priority patent/US20040077064A1/en
Priority to US10/152,373 priority patent/US20030186367A1/en
Priority to US10/152,395 priority patent/US7189534B2/en
Priority to US10/153,934 priority patent/US20030129695A1/en
Priority to US10/156,843 priority patent/US20030207805A1/en
Priority to US10/157,782 priority patent/US20030077792A1/en
Priority to US10/157,786 priority patent/US20030208055A1/en
Priority to US10/158,791 priority patent/US20030207429A1/en
Priority to US10/158,782 priority patent/US20030082766A1/en
Priority to US10/160,498 priority patent/US20030073216A1/en
Priority to US10/173,689 priority patent/US20030166104A1/en
Priority to US10/173,694 priority patent/US20030166107A1/en
Priority to US10/173,695 priority patent/US20030032101A1/en
Priority to US10/173,699 priority patent/US20030166109A1/en
Priority to US10/173,693 priority patent/US20030073169A1/en
Priority to US10/173,706 priority patent/US20030022293A1/en
Priority to US10/173,707 priority patent/US20030166110A1/en
Priority to US10/173,708 priority patent/US20030040053A1/en
Priority to US10/173,690 priority patent/US20030166105A1/en
Priority to US10/173,702 priority patent/US20030170793A1/en
Priority to US10/173,698 priority patent/US20030166108A1/en
Priority to US10/173,692 priority patent/US20030166188A1/en
Priority to US10/173,691 priority patent/US20030166106A1/en
Priority to US10/173,700 priority patent/US20030027262A1/en
Priority to US10/173,697 priority patent/US20030032102A1/en
Priority to US10/173,696 priority patent/US20030082767A1/en
Priority to US10/173,703 priority patent/US20030170794A1/en
Priority to US10/173,701 priority patent/US20030104538A1/en
Priority to US10/173,705 priority patent/US20030032103A1/en
Priority to US10/173,704 priority patent/US20030170795A1/en
Priority to US10/174,570 priority patent/US20030211572A1/en
Priority to US10/174,578 priority patent/US20030073170A1/en
Priority to US10/174,590 priority patent/US20030008352A1/en
Priority to US10/174,579 priority patent/US20030027264A1/en
Priority to US10/174,569 priority patent/US20030166111A1/en
Priority to US10/174,589 priority patent/US20030166114A1/en
Priority to US10/174,588 priority patent/US20030027266A1/en
Priority to US10/174,576 priority patent/US7125962B2/en
Priority to US10/174,582 priority patent/US20030027265A1/en
Priority to US10/174,587 priority patent/US20030166113A1/en
Priority to US10/174,572 priority patent/US20030027263A1/en
Priority to US10/174,591 priority patent/US20030166115A1/en
Priority to US10/174,574 priority patent/US20030170796A1/en
Priority to US10/175,740 priority patent/US20030027268A1/en
Priority to US10/174,586 priority patent/US20030032106A1/en
Priority to US10/174,585 priority patent/US20030032105A1/en
Priority to US10/174,581 priority patent/US7153939B2/en
Priority to US10/174,583 priority patent/US7211645B2/en
Priority to US10/175,738 priority patent/US20030022294A1/en
Priority to US10/175,751 priority patent/US20030166122A1/en
Priority to US10/175,736 priority patent/US20030166117A1/en
Priority to US10/175,749 priority patent/US20050196832A1/en
Priority to US10/175,747 priority patent/US20030032107A1/en
Priority to US10/175,739 priority patent/US20030027267A1/en
Priority to US10/175,752 priority patent/US20030022295A1/en
Priority to US10/175,750 priority patent/US20030073172A1/en
Priority to US10/175,753 priority patent/US20030077732A1/en
Priority to US10/175,735 priority patent/US20030082715A1/en
Priority to US10/175,748 priority patent/US20030166121A1/en
Priority to US10/175,744 priority patent/US20030166119A1/en
Priority to US10/175,745 priority patent/US20030166120A1/en
Priority to US10/175,754 priority patent/US20030166123A1/en
Priority to US10/175,742 priority patent/US20030166118A1/en
Priority to US10/175,746 priority patent/US20030027270A1/en
Priority to US10/175,737 priority patent/US20030013153A1/en
Priority to US10/175,741 priority patent/US20030073171A1/en
Priority to US10/175,743 priority patent/US20030027269A1/en
Priority to US10/176,491 priority patent/US20030087373A1/en
Priority to US10/176,487 priority patent/US20030032110A1/en
Priority to US10/176,483 priority patent/US20030017541A1/en
Priority to US10/176,746 priority patent/US20030068680A1/en
Priority to US10/176,484 priority patent/US20030059876A9/en
Priority to US10/176,988 priority patent/US20030170802A1/en
Priority to US10/176,918 priority patent/US7495083B2/en
Priority to US10/176,753 priority patent/US20030044917A1/en
Priority to US10/176,919 priority patent/US20030032114A1/en
Priority to US10/176,749 priority patent/US20030017542A1/en
Priority to US10/176,989 priority patent/US20030170803A1/en
Priority to US10/176,759 priority patent/US20030166128A1/en
Priority to US10/176,485 priority patent/US20030032109A1/en
Priority to US10/176,993 priority patent/US20030027280A1/en
Priority to US10/176,911 priority patent/US20030032113A1/en
Priority to US10/176,493 priority patent/US20030032111A1/en
Priority to US10/176,914 priority patent/US20030017543A1/en
Priority to US10/176,479 priority patent/US20030040054A1/en
Priority to US10/176,757 priority patent/US7317082B2/en
Priority to US10/176,917 priority patent/US20030044918A1/en
Priority to US10/176,921 priority patent/US20030027276A1/en
Priority to US10/176,747 priority patent/US20030027273A1/en
Priority to US10/176,754 priority patent/US7709602B2/en
Priority to US10/176,490 priority patent/US20030170798A1/en
Priority to US10/176,913 priority patent/US20030022298A1/en
Priority to US10/176,981 priority patent/US20030170800A1/en
Priority to US10/176,920 priority patent/US20030166129A1/en
Priority to US10/176,990 priority patent/US20030036119A1/en
Priority to US10/176,482 priority patent/US20030022296A1/en
Priority to US10/176,991 priority patent/US20030027324A1/en
Priority to US10/176,922 priority patent/US20030166130A1/en
Priority to US10/176,480 priority patent/US20030166124A1/en
Priority to US10/176,986 priority patent/US20030073173A1/en
Priority to US10/176,481 priority patent/US20030032108A1/en
Priority to US10/176,751 priority patent/US20030036117A1/en
Priority to US10/176,752 priority patent/US20030170799A1/en
Priority to US10/176,756 priority patent/US20030032112A1/en
Priority to US10/176,925 priority patent/US20030032115A1/en
Priority to US10/176,992 priority patent/US20030027279A1/en
Priority to US10/176,923 priority patent/US20030068681A1/en
Priority to US10/176,924 priority patent/US20030166131A1/en
Priority to US10/176,916 priority patent/US20030040056A1/en
Priority to US10/176,760 priority patent/US7339033B2/en
Priority to US10/176,915 priority patent/US20030017544A1/en
Priority to US10/176,978 priority patent/US20030032116A1/en
Priority to US10/176,985 priority patent/US20030027277A1/en
Priority to US10/176,750 priority patent/US20030027274A1/en
Priority to US10/176,987 priority patent/US20030027278A1/en
Priority to US10/176,982 priority patent/US20030044919A1/en
Priority to US10/176,486 priority patent/US7354999B2/en
Priority to US10/176,748 priority patent/US20030040055A1/en
Priority to US10/176,979 priority patent/US20030087374A1/en
Priority to US10/176,755 priority patent/US20030166127A1/en
Priority to US10/176,758 priority patent/US20030008353A1/en
Priority to US10/176,983 priority patent/US20030170801A1/en
Priority to US10/176,488 priority patent/US20030027271A1/en
Priority to US10/176,489 priority patent/US20030166125A1/en
Priority to US10/176,492 priority patent/US20030027272A1/en
Priority to US10/179,506 priority patent/US20030044920A1/en
Priority to US10/179,525 priority patent/US20030040060A1/en
Priority to US10/179,521 priority patent/US20030170806A1/en
Priority to US10/179,519 priority patent/US7339024B2/en
Priority to US10/179,515 priority patent/US20030166135A1/en
Priority to US10/179,507 priority patent/US20030040057A1/en
Priority to US10/179,513 priority patent/US20030044921A1/en
Priority to US10/179,523 priority patent/US20030215909A1/en
Priority to US10/179,511 priority patent/US20030104539A1/en
Priority to US10/179,522 priority patent/US20030044923A1/en
Priority to US10/179,516 priority patent/US20030040058A1/en
Priority to US10/179,514 priority patent/US20030044922A1/en
Priority to US10/179,508 priority patent/US20030166133A1/en
Priority to US10/179,520 priority patent/US20030096353A1/en
Priority to US10/179,517 priority patent/US20030170805A1/en
Priority to US10/179,526 priority patent/US20030100061A1/en
Priority to US10/179,510 priority patent/US20030032117A1/en
Priority to US10/179,509 priority patent/US20030207392A1/en
Priority to US10/179,512 priority patent/US20030166134A1/en
Priority to US10/179,518 priority patent/US20030104540A1/en
Priority to US10/180,551 priority patent/US20030036123A1/en
Priority to US10/180,549 priority patent/US20030032122A1/en
Priority to US10/180,557 priority patent/US20030022301A1/en
Priority to US10/180,540 priority patent/US20030040061A1/en
Priority to US10/180,555 priority patent/US20030032123A1/en
Priority to US10/180,541 priority patent/US20030036120A1/en
Priority to US10/180,544 priority patent/US20030032119A1/en
Priority to US10/180,543 priority patent/US20030032118A1/en
Priority to US10/180,554 priority patent/US20050202526A1/en
Priority to US10/180,560 priority patent/US20030044925A1/en
Priority to US10/180,548 priority patent/US7696319B2/en
Priority to US10/180,546 priority patent/US20030032120A1/en
Priority to US10/180,545 priority patent/US20030040062A1/en
Priority to US10/180,552 priority patent/US7348415B2/en
Priority to US10/180,542 priority patent/US20030036121A1/en
Priority to US10/180,553 priority patent/US7365156B2/en
Priority to US10/180,550 priority patent/US20030064440A1/en
Priority to US10/180,547 priority patent/US20030032121A1/en
Priority to US10/180,556 priority patent/US7355000B2/en
Priority to US10/180,559 priority patent/US20030032124A1/en
Priority to US10/183,018 priority patent/US20030104541A1/en
Priority to US10/183,010 priority patent/US20030032126A1/en
Priority to US10/183,008 priority patent/US20030040064A1/en
Priority to US10/183,005 priority patent/US7317093B2/en
Priority to US10/183,002 priority patent/US20030054454A1/en
Priority to US10/183,003 priority patent/US20030082716A1/en
Priority to US10/183,011 priority patent/US20030068682A1/en
Priority to US10/183,016 priority patent/US20030082717A1/en
Priority to US10/183,017 priority patent/US20030040065A1/en
Priority to US10/183,013 priority patent/US7309769B2/en
Priority to US10/183,006 priority patent/US7297776B2/en
Priority to US10/183,014 priority patent/US20030064441A1/en
Priority to US10/181,000 priority patent/US7319137B2/en
Priority to US10/183,015 priority patent/US20030044926A1/en
Priority to US10/180,998 priority patent/US7087421B2/en
Priority to US10/183,019 priority patent/US7425605B2/en
Priority to US10/183,012 priority patent/US7718770B2/en
Priority to US10/183,009 priority patent/US7339034B2/en
Priority to US10/183,001 priority patent/US7084255B2/en
Priority to US10/180,999 priority patent/US7297767B2/en
Priority to US10/184,618 priority patent/US7393917B2/en
Priority to US10/184,638 priority patent/US20030054456A1/en
Priority to US10/184,612 priority patent/US20030036127A1/en
Priority to US10/184,628 priority patent/US7309770B2/en
Priority to US10/184,633 priority patent/US20030068683A1/en
Priority to US10/184,631 priority patent/US20030036134A1/en
Priority to US10/184,641 priority patent/US20030073174A1/en
Priority to US10/184,615 priority patent/US20030044927A1/en
Priority to US10/184,627 priority patent/US7282569B2/en
Priority to US10/184,640 priority patent/US7271250B2/en
Priority to US10/184,619 priority patent/US20030049738A1/en
Priority to US10/184,630 priority patent/US7304143B2/en
Priority to US10/184,654 priority patent/US7378486B2/en
Priority to US10/184,616 priority patent/US20030036128A1/en
Priority to US10/184,614 priority patent/US20030032128A1/en
Priority to US10/184,627 priority patent/US20030040070A1/en
Priority to US10/184,613 priority patent/US20030119105A1/en
Priority to US10/184,652 priority patent/US20030032134A1/en
Priority to US10/184,630 priority patent/US20030036133A1/en
Priority to US10/184,651 priority patent/US7291704B2/en
Priority to US10/184,642 priority patent/US7332573B2/en
Priority to US10/184,658 priority patent/US20030027281A1/en
Priority to US10/184,629 priority patent/US20030036132A1/en
Priority to US10/184,625 priority patent/US20030040068A1/en
Priority to US10/184,623 priority patent/US20030032129A1/en
Priority to US10/184,632 priority patent/US20030036135A1/en
Priority to US10/184,655 priority patent/US20030040073A1/en
Priority to US10/184,645 priority patent/US7291718B2/en
Priority to US10/184,650 priority patent/US20030036138A1/en
Priority to US10/184,647 priority patent/US20030032133A1/en
Priority to US10/184,656 priority patent/US20030044931A1/en
Priority to US10/184,635 priority patent/US20030032130A1/en
Priority to US10/184,643 priority patent/US20030044929A1/en
Priority to US10/184,617 priority patent/US20030036129A1/en
Priority to US10/184,644 priority patent/US20030044930A1/en
Priority to US10/184,646 priority patent/US20030032132A1/en
Priority to US10/184,634 priority patent/US20030068684A1/en
Priority to US10/184,624 priority patent/US20030104542A1/en
Priority to US10/184,621 priority patent/US20030054455A1/en
Priority to US10/184,620 priority patent/US20030044928A1/en
Priority to US10/184,657 priority patent/US20030104543A1/en
Priority to US10/184,636 priority patent/US20030036136A1/en
Priority to US10/184,626 priority patent/US20030040069A1/en
Priority to US10/184,637 priority patent/US20030032131A1/en
Priority to US10/184,622 priority patent/US20030036130A1/en
Priority to US10/187,597 priority patent/US20030036141A1/en
Priority to US10/187,739 priority patent/US7291706B2/en
Priority to US10/187,747 priority patent/US7291707B2/en
Priority to US10/187,884 priority patent/US20030036155A1/en
Priority to US10/187,886 priority patent/US7291708B2/en
Priority to US10/187,588 priority patent/US7351795B2/en
Priority to US10/187,598 priority patent/US20030036142A1/en
Priority to US10/187,601 priority patent/US7291705B2/en
Priority to US10/187,887 priority patent/US7285645B2/en
Priority to US10/187,594 priority patent/US7294335B2/en
Priority to US10/188,766 priority patent/US7351804B2/en
Priority to US10/187,741 priority patent/US20030036147A1/en
Priority to US10/187,600 priority patent/US20030036143A1/en
Priority to US10/188,775 priority patent/US20030040075A1/en
Priority to US10/188,781 priority patent/US20030036160A1/en
Priority to US10/187,602 priority patent/US20030036145A1/en
Priority to US10/187,747 priority patent/US20030036150A1/en
Priority to US10/188,769 priority patent/US20030036157A1/en
Priority to US10/188,780 priority patent/US7268217B2/en
Priority to US10/187,885 priority patent/US20030032138A1/en
Priority to US10/187,757 priority patent/US7276578B2/en
Priority to US10/188,767 priority patent/US7312310B2/en
Priority to US10/187,751 priority patent/US20030036151A1/en
Priority to US10/187,754 priority patent/US20030036153A1/en
Priority to US10/188,773 priority patent/US20030036159A1/en
Priority to US10/187,753 priority patent/US20030036152A1/en
Priority to US10/188,770 priority patent/US7358340B2/en
Priority to US10/187,743 priority patent/US20030036148A1/en
Priority to US10/187,603 priority patent/US20030036146A1/en
Priority to US10/187,746 priority patent/US20030036149A1/en
Priority to US10/187,745 priority patent/US7250490B2/en
Priority to US10/188,774 priority patent/US20030040074A1/en
Priority to US10/187,596 priority patent/US20030032136A1/en
Priority to US10/192,010 priority patent/US20030044932A1/en
Priority to US10/194,461 priority patent/US20030054459A1/en
Priority to US10/194,462 priority patent/US7388073B2/en
Priority to US10/194,423 priority patent/US7339025B2/en
Priority to US10/194,365 priority patent/US7381791B2/en
Priority to US10/194,361 priority patent/US20030036161A1/en
Priority to US10/195,892 priority patent/US7385033B2/en
Priority to US10/195,883 priority patent/US20060073544A1/en
Priority to US10/195,894 priority patent/US20030043176A1/en
Priority to US10/195,893 priority patent/US20030206188A1/en
Priority to US10/195,902 priority patent/US20030038826A1/en
Priority to US10/195,901 priority patent/US20030036165A1/en
Priority to US10/195,897 priority patent/US20030036164A1/en
Priority to US10/195,889 priority patent/US7534856B2/en
Priority to US10/195,888 priority patent/US20060073545A1/en
Priority to US10/196,759 priority patent/US20030071835A1/en
Priority to US10/196,756 priority patent/US7304145B2/en
Priority to US10/196,760 priority patent/US7408034B2/en
Priority to US10/196,743 priority patent/US20030038827A1/en
Priority to US10/196,762 priority patent/US20030040078A1/en
Priority to US10/196,745 priority patent/US7423120B2/en
Priority to US10/199,462 priority patent/US20030054468A1/en
Priority to US10/198,768 priority patent/US20030049756A1/en
Priority to US10/199,464 priority patent/US20030032140A1/en
Priority to US10/199,316 priority patent/US20030068726A1/en
Priority to US10/202,938 priority patent/US20030104551A1/en
Priority to US10/205,904 priority patent/US20030073813A1/en
Priority to US10/215,371 priority patent/US20040137561A1/en
Priority to US10/226,739 priority patent/US7390879B2/en
Priority to JP2002341509A priority patent/JP4017507B2/en
Priority to US10/265,542 priority patent/US20030171568A1/en
Priority to US10/298,993 priority patent/US20030211576A1/en
Priority to US10/299,976 priority patent/US20030180312A1/en
Priority to US10/299,937 priority patent/US20030185846A1/en
Priority to US10/336,979 priority patent/US20050026243A1/en
Priority to US10/425,447 priority patent/US20040023331A1/en
Priority to US10/429,667 priority patent/US20030207401A1/en
Priority to US10/439,249 priority patent/US20030228664A1/en
Priority to US10/448,923 priority patent/US7241865B2/en
Priority to US10/448,580 priority patent/US7208312B1/en
Priority to US10/449,656 priority patent/US20040005665A1/en
Priority to US10/448,713 priority patent/US20040006211A1/en
Priority to US10/633,008 priority patent/US7192589B2/en
Priority to US10/712,560 priority patent/US20040146908A1/en
Priority to US10/735,014 priority patent/US7442772B2/en
Priority to JP2003420475A priority patent/JP2004154140A/en
Priority to US10/771,187 priority patent/US7355002B2/en
Priority to US10/797,366 priority patent/US7378507B2/en
Priority to US10/855,211 priority patent/US20050026832A1/en
Priority to US10/916,250 priority patent/US7368250B2/en
Priority to US10/943,353 priority patent/US20050059115A1/en
Priority to US10/955,952 priority patent/US20050153396A1/en
Priority to US10/963,467 priority patent/US7223586B2/en
Priority to US10/964,241 priority patent/US20070026487A1/en
Priority to US10/970,823 priority patent/US7307152B2/en
Priority to US10/972,317 priority patent/US7208321B2/en
Priority to US11/050,154 priority patent/US7122631B2/en
Priority to US11/050,559 priority patent/US7157267B2/en
Priority to US11/057,268 priority patent/US20060084144A1/en
Priority to US11/057,966 priority patent/US20050187379A1/en
Priority to JP2005054646A priority patent/JP2005224245A/en
Priority to US11/080,062 priority patent/US7619062B2/en
Priority to US11/081,485 priority patent/US20050170465A1/en
Priority to US11/100,159 priority patent/US7425613B2/en
Priority to JP2005118579A priority patent/JP2005253468A/en
Priority to JP2005118701A priority patent/JP2005253469A/en
Priority to JP2005118968A priority patent/JP2005270107A/en
Priority to JP2005118817A priority patent/JP2005245460A/en
Priority to JP2005119030A priority patent/JP2005261437A/en
Priority to US11/110,133 priority patent/US20050181445A1/en
Priority to US11/176,863 priority patent/US20050266490A1/en
Priority to US11/189,442 priority patent/US20060246465A1/en
Priority to JP2005235120A priority patent/JP2006068006A/en
Priority to JP2005264293A priority patent/JP2006068016A/en
Priority to JP2005238266A priority patent/JP2006025795A/en
Priority to JP2005238244A priority patent/JP2006061156A/en
Priority to JP2005238217A priority patent/JP2006051031A/en
Priority to JP2005238274A priority patent/JP2006051032A/en
Priority to US11/240,891 priority patent/US20060246540A1/en
Priority to US11/283,473 priority patent/US20090142800A1/en
Priority to US11/296,155 priority patent/US20060127983A1/en
Priority to US11/323,117 priority patent/US20070092941A1/en
Priority to US11/341,175 priority patent/US7468427B2/en
Priority to US11/353,554 priority patent/US7417126B2/en
Priority to US11/355,441 priority patent/US7449551B2/en
Priority to US11/471,396 priority patent/US20060233803A1/en
Priority to US11/518,609 priority patent/US20070077623A1/en
Priority to US11/542,578 priority patent/US20070031405A1/en
Priority to US11/642,816 priority patent/US20070088151A1/en
Priority to US11/725,027 priority patent/US20080312421A1/en
Priority to US11/725,063 priority patent/US7741056B2/en
Priority to US11/725,076 priority patent/US20070190049A1/en
Priority to JP2007172879A priority patent/JP5512073B2/en
Priority to JP2007326613A priority patent/JP2008161190A/en
Priority to JP2007326609A priority patent/JP2008148701A/en
Priority to JP2007325484A priority patent/JP2008148699A/en
Priority to JP2007326424A priority patent/JP2008167749A/en
Priority to US12/031,612 priority patent/US7514538B2/en
Priority to US12/079,178 priority patent/US20090170158A1/en
Priority to JP2008256822A priority patent/JP2009095345A/en
Priority to US12/393,224 priority patent/US20090227776A1/en
Priority to JP2011138276A priority patent/JP2011236224A/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals

Definitions

  • the present invention relates generally to the identification and isolation of novel DNA and to the recombinant production of novel polypeptides.
  • Extracellular proteins play important roles in, among other things, the formation, differentiation and maintenance of multicellular organisms.
  • secreted polypeptides or signaling molecules normally pass through the cellular secretory pathway to reach their site of action in the extracellular environment.
  • Secreted proteins have various industrial applications, including as pharmaceuticals, diagnostics, biosensors and bioreactors.
  • Most protein drugs available at present, such as thrombolytic agents, interferons, interleukins, erythropoietins, colony stimulating factors, and various other cytokines, are secretory proteins.
  • Their receptors, which are membrane proteins, also have potential as therapeutic or diagnostic agents.
  • Efforts are being undertaken by both industry and proficient to identify new, native secreted proteins. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)].
  • Membrane-bound proteins and receptors can play important roles in, among other things, the formation, differentiation and maintenance of multicellular organisms.
  • membrane-bound proteins and cell receptors include, but are not limited to, cytokine receptors, receptor kinases, receptor phosphatases, receptors involved in cell-cell interactions, and cellular adhesin molecules like selectins and integrins. For instance, transduction of signals that regulate cell growth and differentiation is regulated in part by phosphorylation of various cellular proteins. Protein tyrosine kinases, enzymes that catalyze that process, can also act as growth factor receptors. Examples include fibroblast growth factor receptor and nerve growth factor receptor.
  • Membrane-bound proteins and receptor molecules have various industrial applications, including as pharmaceutical and diagnostic agents. Receptor immunoadhesins, for instance, can be employed as therapeutic agents to block receptor-ligand interactions. The membrane-bound proteins can also be employed for screening of potential peptide or small molecule inhibitors of the relevant receptor/ligand interaction.
  • EGF Epidermal growth factor
  • EGFR EGF receptor
  • CNS central nervous system
  • EGF acts directly on cultured cerebral cortical and cerebellar neurons, enhancing neurite outgrowth and survival.
  • EGF also acts on other cell types, including septal cholinergic and mesencephalic dopaminergic neurons, indirectly through glial cells.
  • Evidence of the effects of EGF on neurons in the CNS is accumulating, but the mechanisms of action remain essentially unknown.
  • EGF-induced signaling in mitotic cells is better understood than in postmitotic neurons.
  • Studies of cloned pheochromocytoma PC 12 cells and cultured cerebral cortical neurons have suggested that the EGF-induced neurotrophic actions are mediated by sustained activation of the EGFR and mitogen-activated protein kinase (MAPK) in response to EGF.
  • MAPK mitogen-activated protein kinase
  • EGF is a multi-potent growth factor that acts upon various types of cells including mitotic cells and postmitotic neurons.
  • EGF is produced by the salivary and Brunner's glands of the gastrointestinal system, kidney, pancreas, thyroid gland, pituitary gland, and the nervous system, and is found in body fluids such as saliva, blood, cerebrospinal fluid (CSF), urine, amniotic fluid, prostatic fluid, pancreatic juice, and breast milk, Plata-Salaman, Peptides 12: 653-663 (1991).
  • EGF is mediated by its membrane specific receptor, which contains an intrinsic tyrosine kinase.
  • EGF is believed to function by binding to the extracellular portion of its receptor which induces a transmembrane signal that activates the intrinsic tyrosine kinase.
  • Non isolated peptides having this motif include TGF- ⁇ , amphiregulin, schwannoma-derived growth factor (SDGF), heparin-binding EGF-like growth factors and certain virally encoded peptides (e.g., Vaccinia virus, Reisner, Nature 313: 801-803 (1985), Shope fibroma virus, Chang et al., Mol Cell Biol. 7: 535-540 (1987), Molluscum contagiosum, Porter and Archard, J. Gen. Virol. 68: 673-682 (1987), and Myxoma virus, Upton et al., J. Virol. 6J.: 1271-1275 (1987), Prigent and Lemoine, Prog. Growth Factor Res. 4: 1-24 (1992).
  • EGF-like domains are not confined to growth factors but have been observed in a variety of cell-surface and extracellular proteins which have interesting properties in cell adhesion, protein-protein interaction and development, Laurence and Gusterson, Tumor Biol. IT : 229-261 (1990). These proteins include blood coagulation factors (factors VI, IX, X, XII, protein C, protein S, protein Z, tissue plasminogen activator, urokinase), extracellular matrix components (laminin, cytotactin, entactin), cell surface receptors (LDL receptor, thrombomodulin receptor) and immunity-related proteins (complement Clr, uromodulin).
  • blood coagulation factors factors VI, IX, X, XII, protein C, protein S, protein Z, tissue plasminogen activator, urokinase
  • extracellular matrix components laminin, cytotactin, entactin
  • LDL receptor thrombomodulin receptor
  • immunity-related proteins complement
  • EGF-like precursors are preserved through lower organisms as well as in mammalian cells.
  • a number of genes with developmental significance have been identified in invertebrates with EGF-like repeats.
  • the notch gene of Drosophila encodes 36 tandemly arranged 40 amino acid repeats which show homology to EGF, Wharton et al., Cell 43: 557-581 (1985).
  • Hydropathy plots indicate a putative membrane spanning domain, with the EGF-related sequences being located on the extracellular side of the membrane.
  • EGF EGF-like repeats
  • Delta Delta
  • 95F 5ZD
  • Lin-12 nematode gene Lin-12 which encodes a putative receptor for a developmental signal transmitted between two specified cells.
  • EGF has been shown to have potential in the preservation and maintenance of gastrointestinal mucosa and the repair of acute and chronic mucosal lesions, Konturek et al, Eur. J. Gastroenterol Hepatol. 7 (10), 933-37 (1995), including the treatment of necrotizing enterocolitis, Zollinger- Ellison syndrome, gastrointestinal ulceration gastrointestinal ulcerations and congenital microvillus atrophy, Guglietta and Sullivan, Eur. J.
  • EGF is also implicated various skin disease characterized by abnormal keratinocyte differentiation, e.g. , psoriasis, epithelial cancers such as squamous cell carcinomas of the lung, epidermoid carcinoma of the vulva and gliomas. King et al, Am. J. Med. Sci. 296: 154-158 (1988).
  • Nephritis is a condition characterized by inflammation of the kidney affecting the structure and normal function of the kidney. This condition can be chronic or acute and is generally caused by infection, degenerative process or vascular disease. In all cases, early detection is desirable so that the patient with nephritis can begin treatment of the condition.
  • TIN-ag tubulointerstitial nephritis antigen
  • the rabbit TIN-ag has a domain in the amino-terminal region containing an epidermal growth factor-like motif that shares homology with laminin A and S chains, alpha 1 chain of type I collagen, von Willebrand's factor and mucin, indicating structural and functional similarities. Studies have also been conducted in mice. However, it is desirable to identify tubulointerstitial nephritis antigens in humans to aid in the development of early detection methods and treatment of nephritis.
  • Proteins which have homology to tubulointerstitial nephritis antigens are of particular interest to the medical and industrial communities. Often, proteins having homology to each other have similar function. It is also of interest when proteins having homology do not have similar functions, indicating that certain structural motifs identify information other than function, such as locality of function.
  • hgerein a novel polypeptide, designated hgerein as PRO230, which has homology to tubulointerstitial nephritis antigens.
  • Stem cells are undifferentiated cells capable of (a) proliferation, (b) self maintenance, (c) the production of a large number of differentiated functional progeny, (d) regeneration of tissue after injury and/or (e) a flexibility in the use of these options.
  • Stem cells often express cell surface antigens which are capable of serving as cell specific markers that can be exploited to identify stem cells, thereby providing a means for identifying and isolating specific stem cell populations.
  • stem cell populations Having possession of different stem cell populations will allow for a number of important applications. For example, possessing a specific stem cell population will allow for the identification of growth factors and other proteins which are involved in their proliferation and differentiation. In addition, there may be as yet undiscovered proteins which are associated with (1) the early steps of dedication of the stem cell to a particular lineage, (2) prevention of such dedication, and (3) negative control of stem cell proliferation, all of which may be identified if one has possession of the stem cell population. Moreover, stem cells are important and ideal targets for gene therapy where the inserted genes promote the health of the individual into whom the stem cells are transplanted. Finally, stem cells may play important roles in transplantation of organs or tissues, for example liver regeneration and skin grafting.
  • PRQ187 Growth factors are molecular signals or mediators that enhance cell growth or proliferation, alone or in concert, by binding to specific cell surface receptors. However, there are other cellular reactions than only growth upon expression to growth factors. As a result, growth factors are better characterized as multifunctional and potent cellular regulators. Their biological effects include proliferation, chemotaxis and stimulation of extracellular matrix production. Growth factors can have both stimulatory and inhibitory effects. For example, transforming growth factor (TGF- ⁇ ) is highly pleiotropic and can stimulate proliferation in some cells, especially connective tissue, while being a potent inhibitor of proliferation in others, such as lymphocytes and epithelial cells.
  • TGF- ⁇ transforming growth factor
  • Peptide growth factors are elements of a complex biological language, providing the basis for intercellular communication. They permit cells to convey information between each other, mediate interaction between cells and change gene expression. The effect of these multifunctional and pluripotent factors is dependent on the presence or absence of other peptides.
  • FGF-8 is a member of the fibroblast growth factors (FGFs) which are a family of heparin-binding, potent mitogens for both normal diploid fibroblasts and established cell lines, Gospodarowicz et al. ( 1984), Proc. Natl. Acad. Sci. USA 81:6963.
  • the FGF family comprises acidic FGF (FGF-1), basic FGF (FGF-2), INT-2 (FGF-3), K-FGF/HST (FGF-4), FGF-5, FGF-6, KGF (FGF-7), AIGF (FGF-8) among others. All FGFs have two conserved cysteine residues and share 30-50% sequence homology at the amino acid level.
  • Fibroblast growth factors can also stimulate a large number of cell types in a non-mitogenic manner. These activities include promotion of cell migration into wound area (chemotaxis), initiation of new blood vessel formulation (angiogenesis), modulation of nerve regeneration and survival (neurotrophism), modulation of endocrine functions, and stimulation or suppression of specific cellular protein expression, extracellular matrix production and cell survival. Baird & Bohlen, Handbook of Exp. Pharmacol. 95(1): 369-418, Springer, (1990). These properties provide a basis for using fibroblast growth factors in therapeutic approaches to accelerate wound healing, nerve repair, collateral blood vessel formation, and the like. For example, fibroblast growth factors have been suggested to minimize myocardium damage in heart disease and surgery (U.S. P.
  • FGF-8 also known as androgen-induced growth factor (AIGF)
  • AIGF androgen-induced growth factor
  • FGF-8 has been proposed to be under androgenic regulation and induction in the mouse mammary carcinoma cell line SC3. Tanaka et al., Proc. Natl. Acad. Sci. USA 89: .8928-8932 (1992); Sato et al, J. Steroid Biochem. Molec. Biol. £7: 91-98 (1993).
  • FGF-8 may have a local role in the prostate, which is known to be an androgen-responsive organ.
  • FGF-8 can also be oncogenic, as it displays transforming activity when transfected into NIH-3T3 fibroblasts. Kouhara et al., Oncogene 9455-462 (1994). While FGF-8 has been detected in heart, brain, lung, kidney, testis, prostate and ovary, expression was also detected in the absence of exogenous androgens. Schmitt et al., J. Steroid Biochem. Mol. Biol. 57 (3-4): 173-78 (1996).
  • FGF-8 shares the property with several other FGFs of being expressed at a variety of stages of murine embryogenesis, which supports the theory that the various FGFs have multiple and perhaps coordinated roles in differentiation and embryogenesis. Moreover, FGF-8 has also been identified as a protooncogene that cooperates with Wnt-1 in the process of mammary tumorigenesis (Shackleford et ⁇ /., Proc. Natl. Acad. Sci. USA 90, 740-744 (1993); Heikinheimo et al, Mech. Dev. 48: 129-138 (1994)).
  • FGF-8 exists as three protein isoforms, as a result of alternative splicing of the primary transcript. Tanaka et al., supra. Normal adult expression of FGF-8 is weak and confined to gonadal tissue, however northern blot analysis has indicated that FGF-8 mRNA is present from day 10 through day 12 or murine gestation, which suggests that FGF-8 is important to normal development. Heikinheimo et al., Mech Dev. 48(2): 129-38 (1994).
  • FGF-8 has a unique temporal and spatial pattern in embryogenesis and suggests a role for this growth factor in multiple regions of ectodermal differentiation in the post-gastrulation embryo.
  • novel poypeptides having homology to FGF-8 wherein those polypeptides are heein designated PRO 187 polypeptides.
  • Protein-protein interactions include receptor and antigen complexes and signaling mechanisms. As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction.
  • Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations.
  • the crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglubular shape.
  • von Willebrand factor is a protein which plays an important role in the maintenence of hemostasis. More specifically, von Willebrand factor is a protein which is known to participate in platelet-vessel wall interactions at the site of vascular injury via its ability to interact and form a complex with Factor VIII. The absence of von Willebrand factor in the blood causes an abnormality with the blood platelets that prevents platelet adhesion to the vascular wall at the site of the vascular injury. The result is the propensity for brusing, nose bleeds, intestinal bleeding, and the like comprising von Willebrand's disease.
  • the cell surface protein HCAR is a membrane-bound protein that acts as a receptor for subgroup C of the adenoviruses and subgroup B of the coxsackieviruses.
  • HCAR may provide a means for mediating viral infection of cells in that the presence of the HCAR receptor on the cellular surface provides a binding site for viral particles, thereby facilitating viral infection.
  • CD97 is a seven-span transmembrane receptor which has a cellular ligand, CD55, DAF. Hamann, et al., J. Exp. Med. (U.S.), 184(3): 1189 (1996). Additionally, CD97 has been reported as being a dedifferentiation marker in human thyroid carcinomas and as associated with inflammation. Aust, et al. , Cancer Res. (U.S.), 57(9): 1798 (1997); Gray, et al., J. Immunol. (U.S.), 157(12):5438 (1996).
  • CD97 has also been reported as being related to the secretin receptor superfamily, but unlike known members of that family, CD97 and EMRl have extended extracellular regions that possess several EGF domains at the N-terminus.
  • EMRl is further described in Lin, et al., Genomics. 41(3):301 (1997) and Baud, et al., Genomics. 26(2):334 (1995).
  • CD97 and EMRl appear to be related to the secretin receptors
  • a known member of the secretin family of G protein-coupled receptors includes the alpha-latroxin receptor, latrophilin, which has been described as calcium independent and abundant among neuronal tissues.
  • latrophilin alpha-latroxin receptor
  • Both members of the secretin receptor superfamily and non-members which are related to the secretin receptor superfamily, or CRF and calcitonin receptors are of interest. In particular, new members of these families, identified by their homology to known proteins, are of interest.
  • Growth factors are molecular signals or mediators that enhance cell growth or proliferation, alone or in concert, by binding to specific cell surface receptors, however, there are other cellular reactions than only growth upon expression to growth factors. As a result, growth factors are better characterized as multifunctional and potent cellular regulators. Their biological effects include proliferation, chemotaxis and stimulation of extracellular matrix production. Growth factors can have both stimulatory and inhibitory effects.
  • TGF- ⁇ transforming growth factors
  • TGF- ⁇ is highly pleiotropic and can stimulate proliferation in some cells, especially connective tissues, while being a potent inhibitor of proliferation in others, such as lymphocytes and epithelial cells.
  • Peptide growth factors are elements of a complex biological language, providing the basis for intercellular communication. They permit cells to convey information between each other, mediate interaction between cells and change gene expression, the effect of these multifunctional and pluripotent factors is dependent on the presence or absence of other peptides.
  • Fibroblast growth factors are a family of heparin-binding, potent mitogens for both normal diploid fibroblasts and established cell lines, Godpodarowicz, D. et al. (1984), Proc. Natl. Acad. Sci. USA 81: 6983.
  • the FGF family comprises acidic FGF (FGF-1), basic FGF (FGF-2), INT-2 (FGF-3), K-FGF/HST (FGF- ' 4), FGF-5, FGF-6, KGF (FGF-7), AIGF (FGF-8) among others. All FGFs have two conserved cysteine residues and share 30-50% sequence homology at the amino acid level.
  • Fibroblast growth factors can also stimulate a large number of cell types in a non-mitogenic manner. These activities include promotion of cell migration into a wound area (chemotaxis), initiation of new blood vessel formulation (angiogenesis), modulation of nerve regeneration and survival (neurotrophism), modulation of endocrine functions, and stimulation or suppression of specific cellular protein expression, extracellular matrix production and cell survival. Baird, A. & Bohlen, P., Handbook of Exp. Phrmacol. 95(1): 369-418 (1990). These properties provide a basis for using fibroblast growth factors in therapeutic approaches to accelerate wound healing, nerve repair, collateral blood vessel formation, and the like.
  • fibroblast growth factors have been suggested to minimize myocardium damage in heart disease and surgery (U.S. P. 4,378,437).
  • PR0533 polypeptides have been suggested to minimize myocardium damage in heart disease and surgery.
  • Some of the most important proteins involved in the above described regulation and modulation of cellular processes are the enzymes which regulate levels of protein phosphorylation in the cell.
  • the enzymes that catalyze these processes include the protein kinases, which function to phosphorylate various cellular proteins, and the protein phosphatases, which function to remove phosphate residues from various cellular proteins. The balance of the level of protein phosphorylation in the cell is thus mediated by the relative activities of these two types of enzymes.
  • Protein-protein interactions include receptor and antigen complexes and signaling mechanisms. As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction. Thus, the underlying mechanisms of protein-protein interactions are of interest to the scientific and medical community.
  • Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations.
  • the crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglubular shape.
  • Immunoglobulins are antibody molecules, the proteins that function both as receptors for antigen on the B-cell membrane and as the secreted products of the plasma cell. Like all antibody molecules, immunoglobulins perform two major functions: they bind specifically to an antigen and they participate in a limited number of biological effector functions. Therefore, new members of the Ig superfamily are always of interest. Molecules which act as receptors by various viruses and those which act to regulate immune function are of particular interest. Also of particular interest are those molecules which have homology to known Ig family members which act as virus receptors or regulate immune function. Thus, molecules having homology to poliovirus receptors, CRTAM and CD166 (a ligand for lymphocyte antigen CD6) are of particular interest.
  • Extracellular and membrane-bound proteins play important roles in the formation, differentiation and maintenance of multicellular organisms.
  • secreted polypeptides or signaling molecules normally pass through the cellular secretory pathway to reach their site of action in the extracellular environment, usually at a membrane-bound receptor protein.
  • PR0258 polypeptides have homology to CRT AM, designated herein as PR0258 polypeptides.
  • Protein-protein interactions include receptor and antigen complexes and signaling mechanisms. As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction. Thus, the underlying mechanisms of protein-protein interactions are of interest to the scientific and medical community.
  • Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations.
  • the crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglobular shape.
  • Thrombomodulin binds to and regulates the activity of thrombin. It is important in the control of blood coagulation. Thrombomodulin functions as a natural anticoagulant by accelerating the activation of protein C by thrombin. Soluble thrombomodulin may have therapeutic use as an antithrombotic agent with reduced risk for hemorrhage as compared with heparin. Thrombomodulin is a cell surface trans-membrane glycoprotein, present on endothelial cells and platelets. A smaller, functionally active form of thrombomodulin circulates in the plasma and is also found in urine. (In Haeberli, A., Human Protein Data, VCH Oub., N.Y., 1992). Peptides having homology to thrombomodulin are particularly desirable.
  • PR0269 polypeptides having homology to thrombomodulin, designated herein as PR0269 polypeptides.
  • PRQ287 Procollagen C-proteinase enhancer protein binds to and enhances the activity of bone morphogenic protein "BMP1 "/procollagen C-proteinase (PCP). It plays a role in extracellular matrix deposition. BMP1 proteins may be used to induce bone and/or cartilage formation and in wound healing and tissue repair. Therefore, procollagen C-proteinase enhancer protein, BMP1 and proteins having homology thereto, are of interest to the scientific and medical communities. We herein describe the identification and characterization of novel polypeptides having homology to procollagen C-proteinase enhancer protein precursor and procollagen C-proteinase enhancer protein, designated herein as PR0287 polypeptides.
  • PRQ214 Growth factors are molecular signals or mediators that enhances cell growth or proliferation, alone or in concert, by binding to specific cell surface receptors. However, there are other cellular reactions than only growth upon expression to growth factors. As a result, growth factors are better characterized as multifunctional and potent cellular regulators. Their biological effects include proliferation, chemotaxis and stimulation of extracellular matrix production. Growth factors can have both stimulatory and inhibitory effects. For example, transforming growth factor ⁇ (TGF- ⁇ ) is highly pleiotropic and can stimulate proliferation in some cells, especially connective tissue, while being a potent inhibitor of proliferation in others, such as lymphocytes and epithelial cells.
  • TGF- ⁇ transforming growth factor ⁇
  • Peptide growth factors are elements of a complex biological language, providing the basis for intercellular communication. They permit cells to convey information between each other, mediate interaction between cells and change gene expression. The effect of these multifunctional and pluripotent factors is dependent on the presence or absence of other peptides.
  • Epidermal growth factor is a conventional mitogenic factor that stimulates the proliferation of various types of cells including epithelial cells and fibroblasts. EGF binds to and activates the EGF receptor (EGFR), which initiates intracellular signaling and subsequent effects.
  • EGFR EGF receptor
  • the EGFR is expressed in neurons of the cerebral cortex, cerebellum, and hippocampus in addition to other regions of the central nervous system (CNS). In addition, EGF is also expressed in various regions of the CNS. Therefore, EGF acts not only on mitotic cells, but also on postmitotic neurons. In fact, many studies have indicated that EGF has neurotrophic or neuromodulatory effects on various types of neurons in the CNS.
  • EGF acts directly on cultured cerebral cortical and cerebellar neurons, enhancing neurite outgrowth and survival.
  • EGF also acts on other cell types, including septal cholinergic and mesencephalic dopaminergic neurons, indirectly through glial cells.
  • Evidence of the effects of EGF on neurons in the CNS is accumulating, but the mechanisms of action remain essentially unknown.
  • EGF-induced signaling in mitotic cells is better understood than in postmitotic neurons.
  • Studies of cloned pheochromocytoma PC12 cells and cultured cerebral cortical neurons have suggested that the EGF-induced neurotrophic actions are mediated by sustained activation of the EGFR and mitogen-activated protein kinase (MAPK) in response to EGF.
  • MAPK mitogen-activated protein kinase
  • EGF is a multi-potent growth factor that acts upon various types of cells including mitotic cells and postmitotic neurons.
  • EGF is produced by the salivary and Brunner's glands of the gastrointestinal system, kidney, pancreas, thyroid gland, pituitary gland, and the nervous system, and is found in body fluids such as saliva, blood, cerebrospinal fluid (CSF), urine, amniotic fluid, prostatic fluid, pancreatic juice, and breast milk, Plata-Salaman, CR Peptides 12: 653-663 (1991).
  • body fluids such as saliva, blood, cerebrospinal fluid (CSF), urine, amniotic fluid, prostatic fluid, pancreatic juice, and breast milk, Plata-Salaman, CR Peptides 12: 653-663 (1991).
  • EGF is mediated by its membrane specific receptor, which contains an intrinsic tyrosine kinase. Stoscheck CM et al., J. Cell Biochem. 31: 135-152 (1986). EGF is believed to function by binding to the extracellular portion of its receptor which induces a transmembrane signal that activates the intrinsic tyrosine kinase.
  • Non isolated peptides having this motif include TGF-a, amphiregulin, schwannoma-derived growth factor (SDGF), heparin-binding EGF-like growth factors and certain virally encoded peptides (e.g., Vaccinia virus, Reisner AH, Nature 313: 801-803 (1985), Shope fibroma virus, Chang W. , et al. , Mol Cell Biol. 7: 535-540 (1987), Molluscum contagiosum, Porter CD & Archard LC, /. Gen. Virol. 68: 673-682 (1987), and Myxoma virus, Upton C e/ ⁇ /., . Virol. 61 : 1271-1275 (1987).
  • EGF-like domains are not confined to growth factors but have been observed in a variety of cell-surface and extracellular proteins which have interesting properties in cell adhesion, protein-protein interaction and development, Laurence DJR & Gusterson BA, Tumor Biol. 11 : 229-261 (1990).
  • proteins include blood coagulation factors (factors VI, IX, X, XII, protein C, protein S, protein Z, tissue plasminogen activator, urokinase), extracellular matrix components (laminin, cytotactin, entactin), cell surface receptors (LDL receptor, thrombomodulin receptor) and immunity-related proteins (complement Clr, uromodulin).
  • EGF-like precursors are preserved through lower organisms as well as in mammalian cells.
  • a number of genes with developmental significance have been identified in invertebrates with EGF-like repeats.
  • the notch gene of Drosophila encodes 36 tandemly arranged 40 amino acid repeats which show homology to EGF, Wharton W et al., Cell 43: 557-581 (1985).
  • Hydropathy plots indicate a putative membrane spanning domain, with the EGF-related sequences being located on the extracellular side of the membrane.
  • Other homeotic genes with EGF-like repeats include Delta, 95F and 5ZD which were identified using probes based on Notch, and the nematode gene Lin-12 which encodes a putative receptor for a developmental signal transmitted between two specified cells.
  • EGF has been shown to have potential in the preservation and maintenance of gastrointestinal mucosa and the repair of acute and chronic mucosal lesions, Konturek, PC et al, Eur. J. Gastroenterol Hepatol. 7 (10), 933-37 (1995), including the treatment of necrotizing enterocolitis, Zollinger- Ellison syndrome, gastrointestinal ulceration gastrointestinal ulcerations and congenital microvillus atrophy, A. Guglietta & PB Sullivan, Eur. J. Gastroenterol Hepatol, 7(10), 945-50 (1995). Additionally, EGF has been implicated in hair follicle differentiation; CL. du Cros, . Invest. Dermatol.
  • EGF is also implicated various skin disease characterized by abnormal keratinocyte differentiation, e.g., psoriasis, epithelial cancers such as squamous cell carcinomas of the lung, epidermoid carcinoma of the vulva and gliomas. King, LE et al., Am. J. Med. Sci. 296: 154-158 (1988).
  • TGF- ⁇ supergene family or simply TGF- ⁇ superfamily, a group of secreted proteins, includes a large number of related growth and differentiation factors expressed in virtually all phyla.
  • Superfamily members bind to specific cell surface receptors that activate signal transduction mechanisms to elicit their multifunctional cytokine effects. Kolodziejczyk and Hall, Biochem. Cell. Biol.. 74: 299-314 (1996); Attisano and Wrana, Cytokine Growth Factor Rev.. 7: 327-339 (1996); and Hill, Cellular Signaling. 8: 533-544 (1996).
  • Members of this family include five distinct forms of TGF- ⁇ (Sporn and Roberts, in Peptide Growth Factors and Their Receptors.
  • the proteins of the TGF- ⁇ superfamily are disulfide-linked homo- or heterodimers encoded by larger precursor polypeptide chains containing a hydrophobic signal sequence, a long and relatively poorly conserved N-terminal pro region of several hundred amino acids, a cleavage site (usually polybasic), and a shorter and more highly conserved C-terminal region.
  • This C-terminal region corresponds to the processed mature protein and contains approximately 100 amino acids with a characteristic cysteine motif, i. e. , the conservation of seven of the nine cysteine residues of TGF- ⁇ among all known family members.
  • TGF- ⁇ Although the position of the cleavage site between the mature and pro regions varies among the family members, the C-terminus of all of the proteins is in the identical position, ending in the sequence Cys-X-Cys-X, but differing in every case from the TGF- ⁇ consensus C-terminus of Cys-Lys-Cys-Ser. Sporn and Roberts, 1990, supra.
  • TGF- ⁇ l There are at least five forms of TGF- ⁇ currently identified, TGF- ⁇ l, TGF- ⁇ 2, TGF- ⁇ 3, TGF- ⁇ 4, and
  • the activated form of TGF- ⁇ l is a homodimer formed by dimerization of the carboxy-terminal 112 amino acids of a 390 amino acid precursor.
  • Recombinant TGF- ⁇ l has been cloned (Derynck et al, Nature. 316:701-705 (1985)) and expressed in Chinese hamster ovary cells (Gentry etal., Mol. Cell. Biol..7: 3418-3427 (1987)). Additionally, recombinant human TGF- ⁇ 2 (deMartin et al , EMBO J.. 6: 3673 (1987)), as well as human and porcine TGF- ⁇ 3 (Derynck etal. , EMBOJ..
  • TGF- ⁇ 2 has a precursor form of 414 amino acids and is also processed to a homodimer from the carboxy-terminal 112 amino acids that shares approximately 70% homology with the active form of TGF- ⁇ l (Marquardt et al. , J. Biol. Chem.. 262: 12127 (1987)). See also EP 200,341; 169,016; 268,561; and 267,463; U.S. Pat. No. 4,774,322; Cheifetz etal.
  • TGF- ⁇ 4 and TGF- ⁇ 5 were cloned from a chicken chondrocyte cDNA library (Jakowlew et al. , Molec. Endocrinol.. 2: 1186-1195 (1988)) and from a frog oocyte cDNA library, respectively.
  • the pro region of TGF- ⁇ associates non-covalently with the mature TGF- ⁇ dimer (Wakefield et al. , J. Biol. Chem.. 263: 7646-7654 (1988); Wakefield et al , Growth Factors. 1: 203-218 (1989)), and the pro regions are found to be necessary for proper folding and secretion of the active mature dimers of both TGF- ⁇ and activin (Gray and Mason, Science. 247: 1328-1330 (1990)).
  • the association between the mature and pro regions of TGF- ⁇ masks the biological activity of the mature dimer, resulting in formation of an inactive latent form.
  • Latency is not a constant of the TGF- ⁇ superfamily, since the presence of the pro region has no effect on activin or inhibin biological activity.
  • a unifying feature of the biology of the proteins from the TGF- ⁇ superfamily is their ability to regulate developmental processes.
  • TGF- ⁇ has been shown to have numerous regulatory actions on a wide variety of both normal and neoplastic cells. TGF- ⁇ is multifunctional, as it can either stimulate or inhibit cell proliferation, differentiation, and other critical processes in cell function (Sporn and Roberts, supra).
  • EBAF TGF- ⁇ superfamily
  • the predicted protein sequence of EBAF showed a strong homology to the protein encoded by mouse lefty IstraS of the TGF- ⁇ superfamily.
  • a motif search revealed that the predicted EBAF protein contains most of the cysteine residues which are conserved among the TGF- ⁇ -related proteins and which are necessary for the formation of the cysteine knot structure.
  • the EBAF sequence contains an additional cysteine residue, 12 amino acids upstream from the first conserved cysteine residue.
  • the only other family members known to contain an additional cysteine residue are TGF- ⁇ s, inhibins, and GDF-3.
  • EBAF similar to LEFTY, GDF-3/Vgr2, and GDF-9, lacks the cysteine residue that is known to form the intermolecular disulfide bond.
  • EBAF appears to be an additional member of the TGF- ⁇ superfamily with an unpaired cysteine residue that may not exist as a dimer.
  • hydrophobic contacts between the two monomer subunits may promote dimer formation.
  • Fluorescence in situ hybridization showed that the ebaf gene is located on human chromosome 1 at band q42.1.
  • TGF- ⁇ superfamily such as those related to EBAF
  • PR0317 polypeptides Additional members of the TGF- ⁇ superfamily, such as those related to EBAF, are being searched for by industry and academics.
  • PR0317 polypeptides novel polypeptides having homology to EBAF, designated herein as PR0317 polypeptides.
  • mAbs cancer specific monoclonal antibodies
  • Such mAbs which can distinguish between normal and cancerous cells are useful in the diagnosis, prognosis and treatment of the disease.
  • antigens are known to be associated with neoplastic diseases, such as colorectal cancer.
  • the A33 antigen is expressed in more than 90% of primary or metastatic colon cancers as well as normal colon epithelium. Since colon cancer is a widespread disease, early diagnosis and treatment is an important medical goal. Diagnosis and treatment of colon cancer can be implemented using monoclonal antibodies (mAbs) specific therefore having fluorescent, nuclear magnetic or radioactive tags. Radioactive gene, toxins and/or drug tagged mAbs can be used for treatment in situ with minimal patient description. mAbs can also be used to diagnose during the diagnosis and treatment of colon cancers. For example, when the serum levels of the A33 antigen are elevated in a patient, a drop of the levels after surgery would indicate the mmor resection was successful.
  • mAbs monoclonal antibodies
  • adenovirus-derived vectors have been proposed as a means of inserting antisense nucleic acids into tumors (U.S. P. 5,518,885).
  • antisense nucleic acids U.S. P. 5,518,885
  • PRO301 polypeptides having homology to certain cancer-associated antigens, designated herein as PRO301 polypeptides.
  • Cholesterol uptake can have serious implications on one's health. Cholesterol uptake provides cells with most of the cholesterol they require for membrane synthesis. If this uptake is blocked, cholesterol accumulates in the blood and can contribute to the formation of atherosclerotic plaques in blood vessel walls. Most cholesterol is transported in the blood bound to protein in the form of complexes known as low-density lipoproteins (LDLs). LDLs are endocytosed into cells via LDL receptor proteins. Therefore, LDL receptor proteins, and proteins having homology thereto, are of interest to the scientific and medical communities.
  • LDLs low-density lipoproteins
  • Membrane-bound proteins and receptors can play an important role in the formation, differentiation and maintenance of multicellular organisms.
  • the LDL receptors are an example of membrane-bound proteins which are involved in the synthesis and formation of cell membranes, wherein the health of an individual is affected directly and indirectly by its function.
  • Many membrane-bound proteins act as receptors such as the LDL receptor. These receptors can function to endocytose substrates or they can function as a receptor for a channel.
  • Other membrane-bound proteins function as signals or antigens.
  • Membrane-bound proteins and receptor molecules have various industrial applications, including as pharmaceutical and diagnostic agents.
  • the membrane-bound proteins can also be employed for screening of potential peptide or small molecule regulators of the relevant receptor/ligand interaction.
  • LDL receptor In the case of the LDL receptor, it is desirable to find molecules which enhance endocytosis so as to lower blood cholesterol levels and plaque formation. It is also desirable to identify molecules which inhibit endocytosis so that these molecules can be avoided or regulated by individuals having high blood cholesterol.
  • Polypeptides which are homologous to lipoprotein receptors but which do not function as lipoprotein receptors are also of interest in the determination of the function of the fragments which show homology.
  • Complement is a group of proteins found in the blood that are important in humoral immunity and inflammation. Complement proteins are sequentially activated by antigen-antibody complexes or by proteolytic enzymes. When activated, complement proteins kill bacteria and other microorganisms, affect vascular permeability, release histamine and attract white blood cells. Complement also enhances phagocytosis when bound to target cells. In order to prevent harm to autologous cells, the complement activation pathway is tightly regulated.
  • Deficiencies in the regulation of complement activation or in the complement proteins themselves may lead to immune-complex diseases, such as systemic lupus erythematosus, and may result in increased susceptibility to bacterial infection. In all cases, early detection of complement deficiency is desirable so that the patient can begin treatment. Thus, research efforts are currently directed toward identification of soluble and membrane proteins that regulate complement activation.
  • Factor H is a 150 kD soluble serum protein that interacts with complement protein C3b to accelerate the decay of C3 convertase and acts as a cofactor for Factor I-mediated cleavage of complement protein C4b.
  • Complement receptor type 1 is a 190-280 kD membrane bound protein found in mast cells and most blood cells.
  • CRl interacts with complement proteins C3b, C4b, and iC3b to accelerate dissociation of C3 convertases, acts as a cofactor for Factor I-mediated cleavage of C3b and C4b, and binds immune complexes and promotes their dissolution and phagocytosis.
  • Proteins which have homology to complement proteins are of particular interest to the medical and industrial communities. Often, proteins having homology to each other have similar function. It is also of interest when proteins having homology do not have similar functions, indicating that certain structural motifs identify information other than function, such as locality of function.
  • PR0222 polypeptides having homology to complement receptors, designated herein as PR0222 polypeptides.
  • oligosaccharide structures can be created through the differential activities of a smaller number of glycosyltransferases.
  • the diverse structures of oligosaccharides can be generated by transcription of relatively few gene products, which suggests that the oligosaccharides are a plausible mechanism by which is directed a wide range of cell-cell interactions. Examples of differential expression of cell surface carbohydrates and putative carbohydrate binding proteins (lectins) on interacting cells have been described (J. Dodd & T.M. Jessel, /. Neurosci. 5: 3278 (1985); L.J. Regan et al, Proc. Natl. Acad. Sci. USA 83: 2248 (1986); M.
  • cell adhesion molecules that are involved in the interaction between leukocytes and the endothelium during an inflammatory response currently stands at four: (1) selectins; (2) (carbohydrate and glycoprotein) ligands for selectins; (3) integrins; and (4) integrin ligands, which are members of the immunoglobulin gene superfamily.
  • selectins are cell adhesion molecules that are unified both structurally and functionally. Structurally, selectins are characterized by the inclusion of a domain with homology to a calcium-dependent lectin (C -lectins), an epidermal growth factor (egf)-like domain and several complement binding-like domains, Bevilacqua, M.P. et al, Science 243: 1160-1165 (1989); Johnston et al., Cell 56: 1033-1044 (1989); Lasky et al, Cell 56: 1045-1055 (1989); Siegalman, M. et al, Science 243: 1165-1172 (1989); Stoolman, L.M., Ce// 56: 907-910 (1989).
  • C -lectins calcium-dependent lectin
  • egf epidermal growth factor
  • selectins share the common property of their ability to mediate cell binding through interactions between their lectin domains and cell surface carbohydrate ligands (Brandley , B, et al. , Cell 63, 861-863 (1990); Springer, T. and Lasky, L.A. , Nature 349. 19-197 (1991); Bevilacqua, M.P. and Nelson, R.M., /. Clin. Invest. 91 379-387 (1993) and Tedder et al, J. Exp. Med. 170: 123-133 (1989).
  • L-selectin also called peripheral lymph node homing receptor (pnHR), LEC-CAM-1 , LAM-1, gp90 MEL , gpl00 MEL , gpl 10 MEL , MEL-14 antigen, Leu-8 antigen, TQ-1 antigen, DREG antigen
  • E-selectin LEC-CAM-2, LECAM-2, ELAM-1
  • P-selectin LEC-CAM-3, LECAM-3, GMP-140, PADGEM
  • E-selectin is believed to recognize the carbohydrate sequence NeuNAc 2-3Gal ⁇ l-4(Fuc ⁇ l-3)GlcNAc (sialyl-Lewis x, or sLe x ) and related oligosaccharides, Berg et al, J. Biol. Chem. 265: 14869-14872 (1991); Lowe etal, Cell ⁇ : 475-484 (1990); Phillips etal, Science 250: 1130- 1132 (1990); Tiemeyer et al, Proc. Natl. Acad. Sci. USA SS: 1138-1142 (1991).
  • L-selectin which comprises a lectin domain, performs its adhesive function by recognizing carbohydrate-containing ligands on endothelial cells. L-selectin is expressed on the surface of leukocytes, such as lymphocytes, neutrophils, monocytes and eosinophils, and is involved with the trafficking of lymphocytes to peripheral lymphoid tissues (Gallatin et al, Nature 303: 30-34 (1983)) and with acute neutrophil-medicated inflammatory responses (Watson, S.R., Nature 349: 164-167 (1991)).
  • leukocytes such as lymphocytes, neutrophils, monocytes and eosinophils
  • the amino acid sequence of L-selectin and the encoding nucleic acid sequence are, for example, disclosed in U.S. patent No. 5,098,833 issued 24 March 1992.
  • L-selectin (LECAM-1) is particularly interesting because of its ability to block neutrophil influx (Watson et al, Nature 349: 164-167 (1991). It is expressed in chronic lymphocytic leukemia cells which bind to HEV (Spertini et al, Nature 349: 691-694 (1991). It is also believed that HEV structures at sites of chronic inflammation are associated with the symptoms of diseases such as rheumatoid arthritis, psoriasis and multiple sclerosis.
  • E-selectin is particularly interesting because of its transient expression on endothelial cells in response to IL-1 or TNF. Bevilacqua et al., Science 243: 1160 (1989). The time course of this induced expression (2-8 h) suggests a role for this receptor in initial neutrophil induced extravasation in response to infection and injury. It has further been reported that anti-ELAM-1 antibody blocks the influx of neutrophils in a primate asthma model and thus is beneficial for preventing airway obstruction resulting from the inflammatory response. Gundel et al, J. Clin. Invest. 88: 1407 (1991). The adhesion of circulating neutrophils to stimulated vascular endothelium is a primary event of the inflammatory response.
  • P-selectin has been reported to recognize the Lewis x structure (Gal ⁇ l-4(Fuc ⁇ l-3) GlcNAc), Larsen et al, Cell 63: 467-474(1990). Others report that an additional terminal linked sialic acid is required for high affinity binding, Moore et al, J. Cell. Biol. ⁇ 2: 491-499 (1991). P-selectin has been shown to be significant in acute lung injury. Anti-P-selectin antibody has been shown to have strong protective effects in a rodent lung injury model. M.S. Mulligan et al, J. Clin. Invest. 90: 1600 (1991).
  • PR0234 polypeptides having homology to lectin proteins, herein designated as PR0234 polypeptides. 22. PRQ231
  • Some of the most important proteins involved in the above described regulation and modulation of cellular processes are the enzymes which regulate levels of protein phosphorylation in the cell.
  • the enzymes that catalyze these processes include the protein kinases, which function to phosphorylate various cellular proteins, and the protein phosphatases, which function to remove phosphate residues from various cellular proteins. The balance of the level of protein phosphorylation in the cell is thus mediated by the relative activities of these two types of enzymes.
  • Protein phosphatases represent a growing family of enzymes that are found in many diverse forms, including both membrane-bound and soluble forms. While many protein phosphatases have been described, the functions of only a very few are beginning to be understood (Tonks, Semin. Cell Biol. 4:373-453 (1993) and Dixon, Recent Prog. Horm. Res. 51 :405-414 (1996)). However, in general, it appears that many of the protein phosphatases function to modulate the positive or negative signals induced by various protein kinases. Therefore, it is likely that protein phosphatases play critical roles in numerous and diverse cellular processes. Given the physiological importance of the protein phosphatases, efforts are being undertaken by both industry and academia to identify new, native phosphatase proteins.
  • Scavenger receptors are known to protect IgG molecules from catabolic degradation. Riechmann and Hollinger, Nature Biotechnology. 15:617 (1997). In particular, studies of the CH2 and CH3 domains have shown that specific sequences of these domains are important in determining the half-lives of antibodies. Ellerson, et al., J. Immunol.. 116: 510 (1976); Yasmeen, et al., J. Immunol. 116: 518 (1976; Pollock, et al., Eur. J. Immunol .. 20: 2021 (1990). Scavenger receptor proteins and antibodies thereto are further reported in U.S. Patent No. 5,510,466 to Krieger, et al. Due to the ability of scavenger receptors to increase the half-life of polypeptides and their involvement in immune function, molecules having homology to scavenger receptors are of importance to the scientific and medical community.
  • Oxygen free radicals and antioxidants appear to play an important role in the central nervous system after cerebral ischemia and reperfusion. Moreover, cardiac injury, related to ischaemia and reperfusion has been reported to be caused by the action of free radicals. Additionally, studies have reported that the redox state of the cell is a pivotal determinant of the fate of the cells. Furthermore, reactive oxygen species have been reported to be cytotoxic, causing inflammatory disease, including tissue necrosis, organ failure, atherosclerosis, infertility, birth defects, premature aging, mutations and malignancy. Thus, the control of oxidation and reduction is important for a number of reasons including for control and prevention of strokes, heart attacks, oxidative stress and hypertension.
  • reductases and particularly, oxidoreductases, are of interest.
  • Publications further describing this subject matter include Kelsey, et al., Br. J. Cancer. 76(7):852-4 (1997); Friedrich and Weiss, J. Theor. Biol.. 187(4):529-40 (1997) and Pieulle, et al., J. Bacteriol.. 179(18):5684-92 (1997).
  • Oxygen free radicals and antioxidants appear to play an important role in the central nervous system after cerebral ischemia and reperfusion. Moreover, cardiac injury, related to ischaemia and reperfusion has been reported to be caused by the action of free radicals.
  • reductases and particularly, oxidoreductases
  • the transcription factors, NF-kappa B and AP-1 are known to be regulated by redox state and to affect the expression of a large variety of genes thought to be involved in the pathogenesis of AIDS, cancer, atherosclerosis and diabetic complications. Publications further describing this subject matter include Kelsey, et al. , Br. J. Cancer. 76(7):852-4 (1997); Friedrich and Weiss, J. Theor. Biol.. 187(4):529-40 (1997) and Pieulle, et al., J. Bacteriol.. 179(18): 5684-92 (1997).
  • PR0233 polypeptides which have homology to reductase
  • the carboxypeptidase family of exopeptidases constitutes a diverse group of enzymes that hydrolyze carboxyl-terminal amide bonds in polypeptides, wherein a large number of mammalian tissues produce these enzymes.
  • Many of the carboxypeptidase enzymes that have been identified to date exhibit rather strong cleavage specificities for certain amino acids in polypeptides.
  • carboxypeptidase enzymes have been identified which prefer lysine, arginine, serine or amino acids with either aromatic or branched aliphatic side chains as substrates at the carboxyl terminus of the polypeptide.
  • serine carboxypeptidases such amino acid specific enzymes have been identified from a variety of different mammalian and non-mammalian organisms.
  • the mammalian serine carboxypeptidase enzymes play important roles in many different biological processes including, for example, protein digestion, activation, inactivation, or modulation of peptide hormone activity, and alteration of the physical properties of proteins and enzymes.
  • efforts are being undertaken by both industry and proficient to identify new, native secreted and membrane-bound receptor proteins and specifically novel carboxypeptidases. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound receptor proteins.
  • novel polypeptides having homology to one or more serine carboxypeptidase polypeptides, designated herein as PR0223 polypeptides.
  • Plexin was first identified in Xenopus tadpole nervous system as a membrane glycoprotein which was shown to mediate cell adhesion via a homophilic binding mechanism in the presence of calcium ions. Strong evolutionary conservation between Xenopus, mouse and human homologs of plexin has been observed. [Kaneyama et al., Biochem. And Biophys. Res. Comm. 226: 524-529 (1996)]. Given the physiological importance of cell adhesion mechanisms in vivo, efforts are currently being under taken to identify new, native proteins which are involved in cell adhesion. We describe herein the identification of a novel polypeptide which has homology to plexin, designated herein as PR0235.
  • PRQ236 and PRQ262 ⁇ -galactosidase is a well known enzymatic protein which functions to hydrolyze ⁇ -galactoside molecules
  • ⁇ -galactosidase has been employed for a variety of different applications, both in vitro and in vivo and has proven to be an extremely useful research tool. As such, there is an interest in obtaining novel polypeptides which exhibit homology to the ⁇ -galactosidase polypeptide.
  • Densin is a glycoprotein which has been isolated from the brain which has all the hallmarks of an adhesion molecule. It is highly concentrated at synaptic sites in the brain and is expressed prominently in dendritic processes in developing neurons. Densin has been characterized as a member of the O-linked sialoglycoproteins. Densin has relevance to medically important processes such as regeneration. Given the physiological importance of synaptic processes and cell adhesion mechanisms in vivo, efforts are currently being under taken to identify new, native proteins which are involved in synaptic machinery and cell adhesion. We describe herein the identification of novel polypeptides which have homology to densin, designated herein as PR0239 polypeptides.
  • Ebnerin is a cell surface protein associated with von Ebner glands in mammals. Efforts are being undertaken by both industry and proficient to identify new, native cell surface receptor proteins and specifically those which possess sequence homology to cell surface proteins such as ebnerin. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel receptor proteins. We herein describe the identification of novel polypeptides having significant homology to the von Ebner's gland-associated protein ebnerin, designated herein as PR0257 polypeptides.
  • PRO260 Fucosidases are enzymes that remove fucose residues from fucose containing proteoglycans. In some pathological conditions, such as cancer, rheumatoid arthritis, and diabetes, there is an abnormal fucosylation of serum proteins. Therefore, fucosidases, and proteins having homology to fucosidase, are of importance to the study and abrogation of these conditions. In particular, proteins having homology to the al ⁇ ha-1-fucosidase precursor are of interest. Fucosidases and fucosidase inhibitors are further described in U.S. Patent Nos.
  • PRO260 polypeptides having homology to fucosidases
  • PRQ263 CD44 is a cell surface adhesion molecule involved in cell-cell and cell-matrix interactions.
  • Hyaluronic acid a component of the extracellular matrix is a major ligand.
  • Other ligands include collagen, fibronectin, laminin, chrondroitin sulfate, mucosal addressin, serglycin and osteoponin.
  • CD44 is also important in regulating cell traffic, lymph node homing, transmission of growth signals, and presentation of chemokines and growth factors to traveling cells.
  • CD44 surface proteins are associated with metastatic tumors and CD44 has been used as a marker for HIV infection. Certain splice variants are associated with metastasis and poor prognosis of cancer patients.
  • CD44 molecules having homology with CD44 are of particular interest, as their homology indicates that they may have functions related to those functions of CD44.
  • CD44 is further described in U.S. Patent Nos. 5,506, 119, 5,504,194 and 5, 108,904; Gerberick, et al. , Toxicol. Appl. Pharmacol.. 146(1): 1 (1997); Wittig, et al.. Immunol. Letters (Netherlands), 57(1-3):217 (1997); and Oliveira and Odell, Oral Oncol. (England), 33(4):260 (1997).
  • PR0263 polypeptides having homology to CD44 antigen, designated herein as PR0263 polypeptides.
  • Thioredoxins effect reduction-oxidation (redox) state. Many diseases are potentially related to redox state and reactive oxygen species may play a role in many important biological processes.
  • the transcription factors, NF-kappa B and AP-1 are regulated by redox state and are known to affect the expression of a large variety of genes thought to be involved in the pathogenesis of AIDS, cancer, atherosclerosis and diabetic complications.
  • Such proteins may also play a role in cellular antioxidant defense, and in pathological conditions involving oxidative stress such as stroke and inflammation in addition to having a role in apoptosis. Therefore, thioredoxins, and proteins having homology thereto, are of interest to the scientific and medical communities. We herein describe the identification and characterization of novel polypeptides having homology to thioredoxin, designated herein as PRO270 polypeptides.
  • the proteoglycan link protein is a protein which is intimately associated with various extracellular matrix proteins and more specifically with proteins such as collagen.
  • one primary component of collagen is a large proteoglycan called aggrecan.
  • aggrecan a large proteoglycan called aggrecan.
  • This molecule is retained by binding to the glycosaminoglycan hyaluronan through the amino terminal Gl globular domain of the core protein. This binding is stabilized by the proteoglycan link protein which is a protein that is also associated with other tissues containing hyaluronan binding proteoglycans such as versican.
  • Link protein has been identified as a potential target for autoimmune antibodies in individuals who suffer from juvenile rheumatoid arthritis (see Guerassimov et al., J. Rheumatology 24(5):959-964 (1997)). As such, there is strong interest in identifying novel proteins having homology to link protein. We herein describe the identification and characterization of novel polypeptides having such homology, designated herein as PR0271 polypeptides.
  • Reticulocalbin is an endoplasmic reticular protein which may be involved in protein transport and luminal protein processing. Reticulocalbin resides in the lumen of the endopladsmic rerticulum, is known to bind calcium, and may be involved in a luminal retention mechanism of the endoplasmic reticulum. It contains six domains of the EF-hand motif associated with high affinity calcium binding. We describe herein the identification and characterization of a novel polypeptide which has homology to the reticulocalbin protein, designated herein as PR0272.
  • PRQ294 Collagen, a naturally occurring protein, finds wide application in industry. Chemically hydrolyzed natural collagen can be denatured and renatured by heating and cooling to produce gelatin, which is used in photographic and medical, among other applications. Collagen has important properties such as the ability to form interchain aggregates having a conformation designated as a triple helix. We herein describe the identification and characterization of a novel polypeptide which has homology to portions of the collagen molecule, designated herein as PR0294.
  • the integrins comprise a supergene family of cell-surface glycoprotein receptors that promote cellular adhesion. Each cell has numerous receptors that define its cell adhesive capabilities. Integrins are involved in a wide variety of interaction between cells and other cells or matrix components . The integrins are of particular importance in regulating movement and function of immune system cells The platelet Hb/IIIA integrin complex is of particular importance in regulating platelet aggregation. A member of the integrin family, integrin ⁇ -6, is expressed on epithelial cells and modulates epithelial inflammation. Another integrin, leucocyte-associated antigen- 1 (LFA-1) is important in the adhesion of lymphocytes during an immune response.
  • LFA-1 leucocyte-associated antigen- 1
  • integrins are expressed as heterodimers of non-covalently associated alpha and beta subunits.
  • PR0295 The integrins are expressed as heterodimers of non-covalently associated alpha and beta subunits.
  • Protein-protein interactions include receptor and antigen complexes and signaling mechanisms. As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction.
  • Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations.
  • the crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglubular shape.
  • PR0293 leucine rich repeat proteins
  • Protein-protein interactions include receptor and antigen complexes and signaling mechanisms . As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction. Thus, the underlying mechanisms of protein-protein interactions are of interest to the scientific and medical community. All proteins containing leucine-rich repeats are thought to be involved in protein-protein interactions.
  • Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations.
  • the crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglubular shape.
  • Densin is a glycoprotein which has been isolated from the brain which has all the hallmarks of an adhesion molecule. It is highly concentrated at synaptic sites in the brain and is expressed prominently in dendritic processes in developing neurons. Densin has been characterized as a member of the O-linked sialoglycoproteins. Densin has relevance to medically important processes such as regeneration. Given the physiological importance of synaptic processes and cell adhesion mechanisms in vivo, efforts are currently being under taken to identify new, native proteins which are involved in synaptic machinery and cell adhesion. Densin is further described in Kennedy, M.B, Trends Neurosci. (England), 20(6):264 (1997) and Apperson, et al., L Neurosci.. 16(21):6839 (1996).
  • PR0247 leucine rich repeat proteins
  • Proteases are enzymatic proteins which are involved in a large number of very important biological processes in mammalian and non-mammalian organisms. Numerous different protease enzymes from a variety of different mammalian and non-mammalian organisms have been both identified and characterized. The mammalian protease enzymes play important roles in many different biological processes including, for example, protein digestion, activation, inactivation, or modulation of peptide hormone activity, and alteration of the physical properties of proteins and enzymes.
  • the GLIP protein family has been characterized as comprising zinc-finger proteins which play important roles in embryogenesis. These proteins may function as transcriptional regulatory proteins and are known to be amplified in a subset of human tumors.
  • Glioma pathogenesis protein is structurally related to a group of plant pathogenesis-related proteins. It is highly expressed in glioblastoma. See US Pat. Nos. 5,582,981 (issued Dec. 10, 1996) and 5,322,801 (issued June 21 , 1996), Ellington, A.D. et al., Nature. 346:818 (1990), Grindley, J.C. et al., Dev. Biol..
  • CRISP or cysteine rich secretory protein family are a group of proteins which are also structurally related to a group of plant pathogenesis proteins. [Schwidetzky, U., Biochem. J.. 321:325 (1997), Pfisterer, P., Mol. Cell Biol.. 16(11):6160 (1996), Kratzschmar, J., Eur. J. Biochem.. 236(3): 827 (1996)].
  • PR0328 polypeptides a novel polypeptide which has homology to GLIP and CRISP
  • Protein-protein interactions include receptor and antigen complexes and signal ing mechanisms . As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction. Thus, the underlying mechanisms of protein-protein interactions are of interest to the scientific and medical community. All proteins containing leucine-rich repeats are thought to be involved in protein-protein interactions.
  • Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations.
  • the crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglubular shape.
  • IGF insulin like growth factor
  • the acid labile subunit of IGF is also of interest in that it increases the half-life of IGF and is part of the IGF complex in vivo.
  • Another protein which has been reported to have leucine-rich repeats is the SLIT protein which has been reported to be useful in treating neuro-degenerative diseases such as Alzheimer's disease, nerve damage such as in Parkinson's disease, and for diagnosis of cancer, see, Artavanistsakonas, S. and Rothberg, J. M., W09210518- A 1 by Yale University .
  • LIG- 1 a membrane glycoprotein that is expressed specifically in glial cells in the mouse brain, and has leucine rich repeats and immunoglobulin-like domains. Suzuki, et al., J.
  • proteoglycans comprising a repeat characterized by an arrangement of conserved leucine residues (leucine-rich repeat motif) have diverse biological roles.
  • Certain proteoglycans such as biglycan, fibromodulin and decorin, are, for example, characterized by the presence of a leucine-rich repeat of about 24 amino acids [Ruoslahti, Ann. Rev. Cell. Biol. 4 229-255 (1988); Oldberg et al , EMBO J. 8, 2601-2604 (1989)].
  • proteoglycans are believed to play a role in regulating extracellular matrix, cartilage or bone function.
  • the proteoglycan decorin binds to collagen type I and II and affects the rate of fibril formation.
  • Fibromodulin also binds collagen and delays fibril formation. Both fibromodulin and decorin inhibit the activity of transforming growth factor beta (TGF- ⁇ ) (U.S. Patent No. 5,583, 103 issued December 10, 1996). TGF- ⁇ is known to play a key role in the induction of extracellular matrix and has been implicated in the development of fibrotic diseases, such as cancer and glomerulonephritis. Accordingly, proteoglycans have been proposed for the treatment of fibrotic cancer, based upon their ability to inhibit TGF- ⁇ 's growth stimulating activity on the cancer cell.
  • TGF- ⁇ transforming growth factor beta
  • Proteoglycans have also been described as potentially useful in the treatment of other proliferative pathologies, including rheumatoid arthritis, arteriosclerosis, adult respiratory distress syndrome, cirrhosis of the liver, fibrosis of the lungs, post-myocardial infarction, cardiac fibrosis, post-angioplasty restenosis, renal interstitial fibrosis and certain dermal fibrotic conditions, such as keloids and scarring, which might result from burn injuries, other invasive skin injuries, or cosmetic or reconstructive surgery (U.S. Patent No. 5,654,270, issued August 5, 1997).
  • PR0332 polypeptides which have homology to proteins of the leucine rich repeat superfamily, designated herein as PR0332 polypeptides.
  • Fibrillin microfibrils define the continuous elastic network of skin, and are present in dermis as microfibril bundles devoid of measurable elastin extending from the dermal-epithelial junction and as components of the thick elastic fibres present in the deep reticular dermis.
  • Marfan syndrome has been linked to mutations which interfere with multimerization of fibrillin monomers or other connective tissue elements.
  • Fibulin-1 is a modular glycoprotein with amino-terminal anaphlatoxin-like modules followed by nine epidermal growth factor (EGF)-like modules and, depending on alternative splicing, four possible carboxyl termini.
  • Fibulin-2 is a novel extracellular matrix protein frequently found in close association with microfibrils containing either fibronectin or fibrillin.
  • fibrillin, fibulin, and molecules related thereto are of interest, particularly for the use of preventing skin from being damaged from aging, injuries or the sun, or for restoring skin damaged from same.
  • these molecules are generally of interest in the study of connective tissue and attachment molecules and related mechanisms. Fibrillin, fibulin and related molecules are further described in Adams, et al.. J.
  • PR0334 polypeptides having homology to fibulin and fibrillin, designated herein as PR0334 polypeptides.
  • mAbs tumor or cancer specific monoclonal antibodies
  • Such mAbs which can distinguish between normal and cancerous cells are useful in the diagnosis, prognosis and treatment of the disease.
  • Particular antigens are known to be associated with neoplastic diseases, such as colorectal and breast cancer. Since colon cancer is a widespread disease, early diagnosis and treatment is an important medical goal.
  • Diagnosis and treatment of cancer can be implemented using monoclonal antibodies (mAbs) specific therefore having fluorescent, nuclear magnetic or radioactive tags. Radioactive genes, toxins and/or drug tagged mAbs can be used for treatment in situ with minimal patient description.
  • CEA Carcinoembryonic antigen
  • CEA is a glycoprotein found in human colon cancer and the digestive organs of a 2-6 month human embryos.
  • CEA is a known human mmor marker and is widely used in the diagnosis of neoplastic diseases, such as colon cancer. For example, when the serum levels of CEA are elevated in a patient, a drop of CEA levels after surgery would indicate the mmor resection was successful. On the other hand, a subsequent rise in serum CEA levels after surgery would indicate that metastases of the original mmor may have formed or that new primary tumors may have appeared.
  • CEA may also be a target for mAb, antisense nucleotides
  • Protein disulfide isomerase is an enzymatic protein which is involved in the promotion of correct refolding of proteins through the establishment of correct disulfide bond formation. Protein disulfide isomerase was initially identified based upon its ability to catalyze the renaturation of reduced denatured RNAse (Goldberger et al., J. Biol. Chem. 239: 1406-1410 (1964) and Epstein et al. , Cold Spring Harbor Symp. Quant. Biol. 28:439-449 (1963)).
  • Protein disulfide isomerase has been shown to be a resident enzyme of the endoplasmic reticulum which is retained in the endoplasmic reticulum via a -KDEL or -HDEL amino acid sequence at its C-terminus.
  • disulfide bond-forming enzymes and their potential uses in a number of different applications, for example in increasing the yield of correct refolding of recombinantly produced proteins, efforts are currently being undertaken by both industry and proficient to identify new, native proteins having homology to protein disulfide isomerase. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel protein disulfide isomerase homologs.
  • PR0268 a novel polypeptide having homology to protein disulfide isomerase
  • Prolyl 4-hydroxylase is an enzyme which functions to post-translationally hydroxylate proline residues at the Y position of the amino acid sequence Gly-X-Y, which is a repeating three amino acid sequence found in both collagen and procollagen. Hydroxylation of proline residues at the Y position of the Gly-X-Y amino acid triplet to form 4-hydroxyproline residues at those positions is required before newly synthesized collagen polypeptide chains may fold into their proper three-dimensional triple-helical conformation. If hydroxylation does not occur, synthesized collagen polypeptides remain non-helical, are poorly secreted by cells and cannot assemble into stable functional collagen fibrils. Vuorio et al. , Proc. Natl. Acad. Sci. USA 89:7467-7470 (1992). Prolyl 4-hydroxylase is comprised of at least two different polypeptide subunits, alpha and beta.
  • Fringe is a protein which specifically blocks serrate-mediated activation of notch in the dorsal compartment of the Drosophila wing imaginal disc.
  • novel polypeptides which may have a role in development and/or the regulation of serrate-like molecules.
  • novel polypeptides having homology to fringe as identified and described herein, designated herein as PR0339 and PRO310 polypeptides.
  • Lectins are a class of proteins comprising a region that binds carbohydrates specifically and non- covalently. Numerous lectins have been identified in higher animals, both membrane-bound and soluble, and have been implicated in a variety of cell-recognition phenomena and mmor metastasis.
  • lectins can be classified as either C-type (calcium-dependent) or S-type (thiol -dependent).
  • Lectins are thought to play a role in regulating cellular events that are initiated at the level of the plasma membrane.
  • plasma membrane associated molecules are involved in the activation of various subsets of lymphoid cells, e.g. T-lymphocytes, and it is known that cell surface molecules are responsible for activation of these cells and consequently their response during an immune reaction.
  • a particular group of cell adhesion molecules, selectins belong in the superfamily of C-type lectins.
  • This group includes L-selectin (peripheral lymph node homing receptor (pnHR), LEC-CAM-1 , LAM-1, gp90 MEL , gpl00 MEL , gpl lO ME , MEL-14 antigen, Leu-8 antigen, TQ-1 antigen, DREG antigen), E-selectin (LEC-CAM-2, LECAM-2, ELAM-1), and P-selectin (LEC-CAM-3, LECAM-3, GMP-140, PADGEM).
  • pnHR peripheral lymph node homing receptor
  • LEC-CAM-1 peripheral lymph node homing receptor (pnHR)
  • LAM-1 LAM-1
  • gp90 MEL gpl00 MEL
  • gpl lO ME MEL-14 antigen
  • Leu-8 antigen Leu-8 antigen
  • selectins consist of a C-type lectin (carbohydrate binding) domain, an epidermal growth factor-like (EGF-like) motif, and variable numbers of complement regulatory (CR) motifs.
  • Selectins are associated with leukocyte adhesion, e.g. the attachment of neutrophils to venular endothelial cells adjacent to inflammation (E- selectin), or with the trafficking of lymphocytes from blood to secondary lymphoid organs, e.g. lymph nodes and Peyer's patches (L-selectin).
  • Mac-2 Another exemplary lectin is the cell-associated macrophage antigen, Mac-2 that is believed to be involved in cell adhesion and immune responses. Macrophages also express a lectin that recognizes Tn Ag, a human carcinoma-associated epitope.
  • CD95 Fluorescence-activated protein
  • Apoptosis is a non-necrotic cell death that takes place in metazoan animal cells following activation of an intrinsic cell suicide program.
  • the cloning of Fas antigen is described in PCT publication WO 91/10448, and European patent application EP510691.
  • the mature Fas molecule consists of 319 amino acids of which 157 are extracellular, 17 constimte the transmembrane domain, and 145 are intracellular. Increased levels of Fas expression at T cell surface have been associated with mmor cells and HIV-infected cells. Ligation of CD95 triggers apoptosis in the presence of interleukin-1 (IL-2).
  • IL-1 interleukin-1
  • C-type lectins also include receptors for oxidized low-density lipoprotein (LDL). This suggests a possible role in the pathogenesis of atherosclerosis.
  • LDL low-density lipoprotein
  • Applicants have identified cDNA clones that encode novel polypeptides having homology to EGF, designated in the present application as "PR021 1 " and "PR0217” polypeptides.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0211 or PR0217 polypeptide.
  • the isolated nucleic acid comprises DNA encoding EGF-like homologue PR0211 and PR0217 polypeptides of Fig. 2 (SEQ ID NO:2) and/or 4 (SEQ ID NO:4) indicated in Fig. 1 (SEQ ID NOl) and/or Fig. 3 (SEQ ID NO:3), respectively, or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0211 and PR0217 EGF-like homologue
  • PR0211 and PR0217 polypeptides are isolated native sequence PR0211 and PR0217 EGF-like homologue polypeptides, which in one embodiment, includes an amino acid sequence comprising residues: 1 to 353 of Fig. 2 (SEQ ID NO:2) or (2) 1 to 379 of Fig. 4 (SEQ ID NO: 4).
  • PRO230 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PRO230".
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO230 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PRO230 polypeptide having amino acid residues 1 through 467 of Figure 6 (SEQ ID NO : 12) , or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PRO230 polypeptide.
  • the invention provides isolated native sequence PRO230 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 through 467 of Figure 6 (SEQ ID NO: 12).
  • the invention provides an expressed sequence tag (EST) comprising the nucleotide sequence of SEQ ID NO: 13 ( Figure 7) which is herein designated as DNA20088.
  • EST expressed sequence tag
  • PRQ232 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0232" .
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0232 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0232 polypeptide having amino acid residues 1 to 114 of Figure 9 (SEQ ID NO: 18), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0232 polypeptide.
  • the invention provides isolated native sequence PR0232 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 114 of Figure 9 (SEQ ID NO: 18).
  • PRQ187 Applicants have identified a cDNA clone that encodes a novel polypeptide, designated in the present application as "PRO 187".
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0187 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0187 polypeptide of Figure 11 (SEQ ID NO:23), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides a nucleic acid comprising the coding sequence of Figure 10 (SEQ ID NO: 22) or its complement.
  • the invention provides a nucleic acid of the full length protein of clone DNA27864-1155, deposited with the ATCC under accession number ATCC 209375, alternatively the coding sequence of clone DNA27864-1155, deposited under accession number ATCC 209375.
  • the invention provides isolated PR0187 polypeptide.
  • the invention provides isolated native sequence PRO 187 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 205 of Figure 11 (SEQ ID NO:23).
  • the invention provides a polypeptide encoded by the nucleic acid deposited under accession number ATCC 209375.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0265 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0265 polypeptide having amino acid residues 1 to 660 of Figure 13 (SEQ ID NO: 28), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0265 polypeptide.
  • the invention provides isolated native sequence PR0265 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 660 of Figure 13 (SEQ ID NO:28).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0265 polypeptide.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0219 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0219 polypeptide having amino acid residues 1 to 915 of Figure 15 (SEQ ID NO:34), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0219 polypeptide.
  • the invention provides isolated native sequence PR0219 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 915 of Figure 15 (SEQ ID NO:34).
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0246 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0246 polypeptide having amino acid residues 1 to 390 of Figure 17 (SEQ ID NO:39), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0246 polypeptide.
  • the invention provides isolated native sequence PR0246 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 390 of Figure 17 (SEQ ID NO: 39).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0246 polypeptide.
  • Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to CD97, EMRl and latrophilin, wherein the polypeptide is designated in the present application as "PR0228" .
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0228 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0228 polypeptide having amino acid residues 1 to 690 of Figure 19 (SEQ ID NO:49), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0228 polypeptide.
  • the invention provides isolated native sequence PR0228 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 690 of Figure 19 (SEQ ID NO: 49).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0228 polypeptide.
  • the invention provides an expressed sequence tag (EST) comprising the nucleotide sequence of SEQ ID NO:50, designated herein as DNA21951.
  • EST expressed sequence tag
  • the invention provides an isolated nucleic acid molecule having at least about 80% sequence identity to (a) a DNA molecule encoding a PR0533 polypeptide comprising the sequence of amino acids 23 to 216 of Figure 22 (SEQ ID NO:59), or (b) the complement of the DNA molecule of (a).
  • the sequence identity preferably is about 85 % , more preferably about 90% , most preferably about 95 % .
  • the isolated nucleic acid has at least about 80%, preferably at least about 85 % , more preferably at least about 90% , and most preferably at least about 95% sequence identity with a polypeptide having amino acid residues 23 to 216 of Figure 22 (SEQ ID NO:59).
  • the highest degree of sequence identity occurs within the secreted portion (amino acids 23 to 216 of Figure 22, SEQ ID NO:59).
  • the isolated nucleic acid molecule comprises DNA encoding a PR0533 polypeptide having amino acid residues 1 to 216 of Figure 22 (SEQ ID NO:59), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides a nucleic acid of the full length protein of clone DNA49435-1219, deposited with the ATCC under accession number ATCC 209480.
  • the invention provides isolated PR0533 polypeptide.
  • the invention provides isolated native sequence PR0533 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 23 to 216 of Figure 22 (SEQ ID NO:59).
  • Native PR0533 polypeptides with or without the native signal sequence (amino acids 1 to 22 in Figure 22 (SEQ ID NO:59)), and with or without the initiating methionine are specifically included.
  • the invention provides a PR0533 polypeptide encoded by the nucleic acid deposited under accession number ATCC 209480.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0245 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0245 polypeptide having amino acid residues 1 to 312 of Fig. 24 (SEQ ID NO:64), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0245 polypeptide.
  • the invention provides isolated native sequence PR0245 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 312 of Figure 24 (SEQ ID NO:64).
  • an isolated nucleic acid comprises DNA encoding the PRO220 polypeptide having amino acid residues 1 through 708 of Figure 26 (SEQ ID NO: 69), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • an isolated nucleic acid comprises DNA encoding the PR0221 polypeptide having amino acid residues 1 through 259 of Figure 28 (SEQ ID NO:71), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • an isolated nucleic acid comprises DNA encoding the PR0227 polypeptide having amino acid residues 1 through 620 of Figure 30 (SEQ ID NO:73), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PRO220, PR0221 and PR0227 polypeptides.
  • the isolated native sequence for the PRO220 polypeptide which in one embodiment, includes an amino acid sequence comprising residues 1 to 708 of Figure 26 (SEQ ID NO:69).
  • the isolated native sequence for the PR0221 polypeptide which in one embodiment, includes an amino acid sequence comprising residues 1 to 259 of Figure 28 (SEQ ID NO:71).
  • the isolated native sequence for the PR0227 polypeptide which in one embodiment, includes an amino acid sequence comprising residues 1 to 620 of Figure 30 (SEQ ID NO:73).
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0258 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0258 polypeptide having amino acid residues 1 to 398 of Figure 32 (SEQ ID NO:84), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0258 polypeptide.
  • the invention provides isolated native sequence PR0258 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 398 of Figure 32 (SEQ ID N0:84).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0258 polypeptide.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0266 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0266 polypeptide having amino acid residues 1 to 696 of Figure 34 (SEQ ID NO:91), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0266 polypeptide.
  • the invention provides isolated native sequence PR0266 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 696 of Figure 34 (SEQ ID NO:91).
  • PRQ269 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as PR0269.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0269 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0269 polypeptide having amino acid residues 1 to 490 of Fig. 36 (SEQ ID NO:96), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0269 polypeptide.
  • the invention provides isolated native sequence PR0269 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 490 of Figure 36 (SEQ ID NO:96).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0269 polypeptide.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0287 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0287 polypeptide having amino acid residues 1 to 415 of Fig. 38 (SEQ ID NO: 104), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0287 polypeptide.
  • the invention provides isolated native sequence PR0287 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 415 of Figure 38 (SEQ ID NO: 104).
  • PRQ214 Applicants have identified a cDNA clone that encodes a novel polypeptide, designated in the present application as "PR0214" .
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0214 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0214 polypeptide of Fig. 40 (SEQ ID NO: 109), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides a nucleic acid comprising the coding sequence of Fig. 39 (SEQ ID NO: 108) or its complement.
  • the invention provides a nucleic acid of the full length protein of clone DNA32286-1191 , deposited with ATCC under accession number ATCC 209385.
  • the invention provides isolated PR0214 polypeptide.
  • the invention provides isolated native sequence PR0214 polypeptide, which in one embodiment, includes an amino acid sequence comprising the residues of Figure 40 (SEQ ID NO: 109).
  • the invention provides a polypeptide encoded by the nucleic acid deposited under accession number ATCC 209385.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding PR0317 polypeptide.
  • the isolated nucleic acid comprises DNA (SEQ ID NO: 113) encoding
  • the invention provides isolated PR0317 polypeptide.
  • the invention provides isolated native-sequence PR0317 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 366 of Figure 42 (SEQ ID NO: 114).
  • the invention supplies a method of detecting the presence of PR0317 in a sample, the method comprising: a) contacting a detectable anti-PR0317 antibody with a sample suspected of containing PR0317; and b) detecting binding of the antibody to the sample; wherein the sample is selected from the group consisting of a body fluid, a tissue sample, a cell extract, and a cell culture medium.
  • a method for determining the presence of PR0317 mRNA in a sample comprising: a) contacting a sample suspected of containing PR0317 mRNA with a detectable nucleic acid probe that hybridizes under moderate to stringent conditions to PR0317 mRNA; and b) detecting hybridization of the probe to the sample.
  • the sample is a tissue sample and the detecting step is by in situ hybridization, or the sample is a cell extract and detection is by Northern analysis.
  • the invention provides a method for treating a PR0317-associated disorder comprising administering to a mammal an effective amount of the PR0317 polypeptide or a composition thereof containing a carrier, or with an effective amount of a PR0317 agonist or PR0317 antagonist, such as an antibody which binds specifically to PR0317.
  • PRQ301 Applicants have identified a cDNA clone (DNA40628-1216) that encodes a novel polypeptide, designated in the present application as "PRO301 ".
  • the invention provides an isolated nucleic acid molecule having at least about 80% sequence identity to (a) a DNA molecule encoding a PRO301 polypeptide comprising the sequence of amino acids 28 to 258 of Fig. 44 (SEQ ID NO: 119), or (b) the complement of the DNA molecule of (a).
  • the sequence identity preferably is about 85% , more preferably about 90% , most preferably about 95 % .
  • the isolated nucleic acid has at least about 80 % , preferably at least about 85 % , more preferably at least about 90 % , and most preferably at least about 95 % sequence identity with a polypeptide having amino acid residues 28 to 258 of Fig. 44 (SEQ ID NO: 119).
  • the highest degree of sequence identity occurs within the extracellular domains (amino acids 28 to 258 of Fig. 44, SEQ ID NO: 119).
  • the isolated nucleic acid molecule comprises DNA encoding a PRO301 polypeptide having amino acid residues 28 to 299 of Fig.
  • the invention provides a nucleic acid of the full length protein of clone DNA40628-1216, deposited with the ATCC under accession number ATCC 209432, alternatively the coding sequence of clone DNA40628-1216, deposited under accession number ATCC 209432.
  • the invention provides isolated PRO301 polypeptide.
  • the invention provides isolated native sequence PRO301 polypeptide, which in one embodiment, includes an amino acid sequence comprising the extracellular domain residues 28 to 258 of Figure 44 (SEQ ID NO: 119).
  • Native PRO301 polypeptides with or without the native signal sequence amino acids 1 to 27 in Figure 44 (SEQ ID NO: 119), and with or without the initiating methionine are specifically included.
  • the sequences of the invention may also comprise the transmembrane domain (residues 236 to about 258 in Figure 44; SEQ ID NO: 119) and/or the intracellular domain (about residue 259 to 299 in Figure 44; SEQ ID NO: 119).
  • the invention provides a PRO301 polypeptide encoded by the nucleic acid deposited under accession number ATCC 209432.
  • PRQ224 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0224" .
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0224 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0224 polypeptide having amino acid residues 1 to 282 of Figure 46 (SEQ ID NO: 127), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0224 polypeptide.
  • the invention provides isolated native sequence PR0224 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 282 of Figure 46 (SEQ ID NO: 127). 20. PRQ222
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0222 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0222 polypeptide having amino acid residues 1 to 490 of Fig. 48 (SEQ ID NO: 132), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0222 polypeptide.
  • the invention provides isolated native sequence PR0222 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 490 of Figure 48 (SEQ ID NO: 132).
  • the invention provides an isolated nucleic acid encoding a novel lectin comprising
  • the isolated nucleic acid comprises the DNA encoding PR0234 polypeptides having amino acid residues 1 to 382 of Fig. 50 (SEQ ID NO: 137), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides an isolated nucleic acid molecule comprising the nucleotide sequence of Fig. 49 (SEQ ID NO: 136).
  • the invention provides isolated novel PR0234 polypeptides.
  • the invention provides isolated native sequence PR0234 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 382 of Figure 50 (SEQ ID NO: 137).
  • the invention provides oligonucleotide probes useful for isolating genomic and cDNA nucleotide sequences.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0231 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0231 polypeptide having amino acid residues 1 to 428 of Fig. 52 (SEQ ID NO: 142), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0231 polypeptide.
  • the invention provides isolated native sequence PR0231 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 428 of Figure 52 (SEQ ID NO: 142). 23. PRQ229
  • Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to scavenger receptors wherein the polypeptide is designated in the present application as "PR0229".
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0229 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0229 polypeptide having amino acid residues 1 to 347 of Figure 54 (SEQ ID NO: 148), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0229 polypeptide.
  • the invention provides isolated native sequence PR0229 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 347 of Figure 54 (SEQ ID NO: 148).
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0238 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0238 polypeptide having amino acid residues 1 to 310 of Figure 56 (SEQ ID NO: 153), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0238 polypeptide.
  • the invention provides isolated native sequence PR0238 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 310 of Figure 56 (SEQ ID NO: 153).
  • PRQ233 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0233".
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0233 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0233 polypeptide having amino acid residues 1 to 300 of Figure 58 (SEQ ID NO: 159), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0233 polypeptide.
  • the invention provides isolated native sequence PR0233 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 300 of Figure 58 (SEQ ID NO: 159). 26. PRQ223
  • Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to serine carboxypeptidase polypeptides, wherein the polypeptide is designated in the present application as "PR0223".
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0223 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0223 polypeptide having amino acid residues 1 to 476 of Figure 60 (SEQ ID NO: 164), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0223 polypeptide.
  • the invention provides isolated native sequence PR0223 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 476 of Figure 60 (SEQ ID NO: 164).
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0235 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0235 polypeptide having amino acid residues 1 to 552 of Figure 62 (SEQ ID NO: 170), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0235 polypeptide.
  • the invention provides isolated native sequence PR0235 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 552 of Figure 62 (SEQ ID NO: 170).
  • PRQ236 and PRQ262 Applicants have identified cDNA clones that encode novel polypeptides having homology to ⁇ - galactosidase, wherein those polypeptides are designated in the present application as "PR0236" and "PR0262”.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0236 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0236 polypeptide having amino acid residues 1 to 636 of Figure 64 (SEQ ID NO: 175), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0262 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0262 polypeptide having amino acid residues 1 to 654 of Figure 66 (SEQ ID NO: 177), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0236 polypeptide.
  • the invention provides isolated native sequence PR0236 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 636 of Figure 64 (SEQ ID NO: 175).
  • the invention provides isolated PR0262 polypeptide.
  • the invention provides isolated native sequence PR0262 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 654 of Figure 66 (SEQ ID NO: 177).
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0239 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0239 polypeptide having amino acid residues 1 to 501 of Figure 68 (SEQ ID NO: 185), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0239 polypeptide.
  • the invention provides isolated native sequence PR0239 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 501 of Figure 68 (SEQ ID NO: 185).
  • PRQ257 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0257”.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0257 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0257 polypeptide having amino acid residues 1 to 607 of Figure 70 (SEQ ID NO: 190), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0257 polypeptide.
  • the invention provides isolated native sequence PR0257 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 607 of Figure 70 (SEQ ID NO: 190).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0257 polypeptide.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO260 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PRO260 polypeptide having amino acid residues 1 to 467 of Figure 72 (SEQ ID NO: 195), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PRO260 polypeptide.
  • the invention provides isolated native sequence PRO260 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 467 of Figure 72 (SEQ ID NO: 195).
  • Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to CD44 antigen, wherein the polypeptide is designated in the present application as "PR0263".
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0263 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0263 polypeptide having amino acid residues 1 to 322 of Figure 74 (SEQ ID NO:201), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0263 polypeptide.
  • the invention provides isolated native sequence PR0263 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 322 of Figure 74 (SEQ ID NO: 201).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0263 polypeptide.
  • PRO270 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PRO270".
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO270 polypeptide.
  • the isolated nucleic acid comprises DNA whivch includes the sequence encoding the PRO270 polypeptide having amino acid residues 1 to 296 of Fig. 76 (SEQ ID NO: 207), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PRO270 polypeptide.
  • the invention provides isolated native sequence PRO270 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 296 of Figure 76 (SEQ ID NO: 207).
  • Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to the proteoglycan link protein, wherein the polypeptide is designated in the present application as "PR0271".
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0271 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0271 polypeptide having amino acid residues 1 to 360 of Figure 78 (SEQ ID N0:213), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0271 polypeptide.
  • the invention provides isolated native sequence PR0271 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 360 of Figure 78 (SEQ ID NO:213).
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0272 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0272 polypeptide having amino acid residues 1 to 328 of Figure 80 (SEQ ID NO:221), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0272 polypeptide.
  • the invention provides isolated native sequence PR0272 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 328 of Figure 80 (SEQ ID NO:211).
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0294 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0294 polypeptide having amino acid residues 1 to 550 of Figure 82 (SEQ ID NO:227), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0294 polypeptide.
  • the invention provides isolated native sequence PR0294 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 550 of Figure 82 (SEQ ID NO: 227).
  • PRQ295 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0295" .
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0295 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0295 polypeptide having amino acid residues 1 to 350 of Figure 84 (SEQ ID NO:236), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0295 polypeptide.
  • the invention provides isolated native sequence PR0295 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 350 of Figure 84 (SEQ ID NO: 236).
  • PRQ293 Applicants have identified a cDNA clone that encodes a novel human neuronal leucine rich repeat polypeptide, wherein the polypeptide is designated in the present application as "PR0293" .
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0293 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0293 polypeptide having amino acid residues 1 to 713 of Figure 86 (SEQ ID NO: 245), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0293 polypeptide.
  • the invention provides isolated native sequence PR0293 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 713 of Figure 86 (SEQ ID NO: 245).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0293 polypeptide.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0247 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0247 polypeptide having amino acid residues 1 to 546 of Figure 88 (SEQ ID NO:250), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0247 polypeptide.
  • the invention provides isolated native sequence PR0247 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 546 of Figure 88 (SEQ ID NO:250).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0247 polypeptide.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO302 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PRO302 polypeptide having amino acid residues 1 to 452 of Figure 90 (SEQ ID NO:255), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO303 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PRO303 polypeptide having amino acid residues 1 to 314 of Figure 92 (SEQ ID NO:257), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO304 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PRO304 polypeptide having amino acid residues 1 to 556 of Figure 94 (SEQ ID NO:259), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO307 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PRO307 polypeptide having amino acid residues 1 to 383 of Figure 96 (SEQ ID NO:261), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0343 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0343 polypeptide having amino acid residues 1 to 317 of Figure 98 (SEQ ID NO:263), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PRO302 polypeptide.
  • the invention provides isolated native sequence PRO302 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 452 of Figure 90 (SEQ ID NO:255).
  • the invention provides isolated PRO303 polypeptide.
  • the invention provides isolated native sequence PRO303 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 314 of Figure 92 (SEQ ID NO:257).
  • the invention provides isolated PRO304 polypeptide.
  • the invention provides isolated native sequence PRO304 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 556 of Figure 94 (SEQ ID NO:259).
  • the invention provides isolated PRO307 polypeptide.
  • the invention provides isolated native sequence PRO307 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 383 of Figure 96 (SEQ ID NO:261).
  • the invention provides isolated PR0343 polypeptide.
  • the invention provides isolated native sequence PR0343 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 317 of Figure 98 (SEQ ID NO: 263). 41. PRQ328
  • Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0328" .
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0328 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0328 polypeptide having amino acid residues 1 to 463 of Figure 100 (SEQ ID NO: 285), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0328 polypeptide.
  • the invention provides isolated native sequence PR0328 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 463 of Figure 100 (SEQ ID NO:285).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PRO306 polypeptide.
  • Applicants have identified three cDNA clones that respectively encode three novel polypeptides, each having leucine rich repeats and homology to LIG-1 and ALS. These polypeptides are designated in the present application as PR0335, PR0331 and PR0326, respectively.
  • the invention provides three isolated nucleic acid molecules comprising DNA respectively encoding PR0335, PR0331 and PR0326, respectively.
  • an isolated nucleic acid comprising DNA encoding the PR0335 polypeptide having amino acid residues 1 through 1059 of Figure 102 (SEQ ID NO:290), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate , and optionally , under high stringency conditions .
  • an isolated nucleic acid comprises DNA encoding the PR0331 polypeptide having amino acid residues 1 through 640 of Figure 104 (SEQ ID NO:292), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. Additionally provided herein is an isolated nucleic acid comprises DNA encoding the PR0326 polypeptide having amino acid residues 1 through 1119 of Figure 106 (SEQ ID NO:294), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0335, PR0331 and PR0326 polypeptides or extracellular domains thereof.
  • the invention provides isolated native sequence for the PR0335 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 through 1059 of Figure 102 (SEQ ID NO:290).
  • the isolated native sequence for the PR0331 polypeptide which in one embodiment, includes an amino acid sequence comprising residues 1 through 640 of Figure 104 (SEQ ID NO:292).
  • the isolated native sequence for the PR0326 polypeptide which in one embodiment, includes an amino acid sequence comprising residues 1 through 1119 of Figure 106 (SEQ ID NO:294).
  • the invention provides an isolated nucleic acid molecule comprising DNA having at least about 80% sequence identity to (a) a DNA molecule encoding a PR0358 polypeptide comprising the sequence of amino acids 49 to 642 of Fig. 108 (SEQ ID NO:310), or (b) the complement of the DNA molecule of (a).
  • the sequence identity preferably is about 85 % , more preferably about 90% , most preferably about 95 % .
  • the isolated nucleic acid has at least about 80%, preferably at least about 85% , more preferably at least about 90% , and most preferably at least about 95% sequence identity with a polypeptide having amino acid residues 1 to 642 of Fig. 108 (SEQ ID NO: 310).
  • the highest degree of sequence identity occurs within the leucine-rich repeat domains (amino acids 116 to 624 of Fig. 108, SEQ ID NO:310).
  • the isolated nucleic acid molecule comprises DNA encoding a PR0332 polypeptide having amino acid residues 49 to 642 of Fig. 108 (SEQ ID NO:310), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0332 polypeptides.
  • the invention provides isolated native sequence PR0332 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 49 to 624 of Figure 108 (SEQ ID NO:310).
  • Native PR0332 polypeptides with or without the native signal sequence amino acids 1 to 48 in Figure 108, SEQ ID NO:310, and with or without the initiating methionine are specifically included.
  • Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to fibulin and fibrillin, wherein the polypeptide is designated in the present application as "PR0334".
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0334 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0334 polypeptide having amino acid residues 1 to 509 of Figure 110 (SEQ ID NO:315), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0334 polypeptide.
  • the invention provides isolated native sequence PR0334 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 509 of Figure 110 (SEQ ID NO:315).
  • the invention provides an isolated nucleic acid molecule having at least about 80% sequence identity to (a) a DNA molecule encoding a PR0346 polypeptide comprising the sequence of amino acids 19 to 339 of Fig. 112 (SEQ ID NO: 320), or (b) the complement of the DNA molecule of (a).
  • the sequence identity preferably is about 85%, more preferably about 90%, most preferably about 95 % .
  • the isolated nucleic acid has at least about 80% , preferably at least about 85% , more preferably at least about 90% , and most preferably at least about 95% sequence identity with a polypeptide having amino acid residues 19 to 339 of Fig. 112 (SEQ ID NO:320).
  • the highest degree of sequence identity occurs within the extracellular domains (amino acids 19 to 339 of Fig. 112, SEQ IP NO:320).
  • the polypeptide by which the homology is measured comprises the residues 1-339, 19-360 or 19- 450 of Fig. 112, SEQ IP NO:320).
  • the isolated nucleic acid molecule comprises PNA encoding a PR0346 polypeptide having amino acid residues 19 to 339 of Fig. 112 (SEQ IP NO:320), alternatively residues 1-339, 19-360 or 19-450 of Fig.
  • the invention provides a nucleic acid of the full length protein of clone PNA44167-1243, deposited with the ATCC under accession number ATCC 209434, alternatively the coding sequence of clone DNA44167- 1243, deposited under accession number ATCC 209434.
  • the invention provides isolated PR0346 polypeptide.
  • the invention provides isolated native sequence PR0346 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 19 to 339 of Figure 112 (SEQ ID NO:320).
  • Native PR0346 polypeptides with or without the native signal sequence (residues 1 to 18 in Figure 112 (SEQ ID NO:320), with or without the initiating methionine, with or without the transmembrane domain (residues 340 to 360) and with or without the intracellular domain (residues 361 to 450) are specifically included.
  • the invention provides a PR0346 polypeptide encoded by the nucleic acid deposited under accession number ATCC 209434.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0268 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0268 polypeptide having amino acid residues 1 to 280 of Figure 114 (SEQ ID NO:325), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0268 polypeptide.
  • the invention provides isolated native sequence PR0268 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 280 of Figure 114 (SEQ ID NO:325).
  • An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0268 polypeptide.
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO330 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PRO330 polypeptide having amino acid residues 1 to 533 of Figure 116 (SEQ ID NO:332), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PRO330 polypeptide.
  • the invention provides isolated native sequence PRO330 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 533 of Figure 116 (SEQ ID NO:332).
  • PRQ339 and PRO310 Applicants have identified two cDNA clones wherein each clone encodes a novel polypeptide having homology to fringe, wherein the polypeptides are designated in the present application as "PR0339” and "PRO310" .
  • the invention provides isolated nucleic acid molecules comprising DNA encoding a PR0339 and/or a PR0310 polypeptide.
  • the isolated nucleic acid comprises DNA encoding the PR0339 polypeptide having amino acid residues 1 to 772 of Figure 118 (SEQ ID NO:339), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the isolated nucleic acid comprises DNA encoding the PR0310 polypeptide having amino acid residues 1 to 318 of Figure 120 (SEQ ID NO : 341 ) , or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0339 as well as isolated PRO310 polypeptides.
  • the invention provides isolated native sequence PR0339 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 772 of Figure 118 (SEQ ID NO:339).
  • the invention further provides isolated native sequence PR0310 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 318 of Figure 120 (SEQ ID NO:341).
  • the invention provides an isolated nucleic acid molecule comprising DNA encoding
  • the isolated nucleic acid comprises DNA encoding PR0244 polypeptide having amino acid residues 1 to 219 of Fig. 122 (SEQ ID NO:377), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
  • the invention provides isolated PR0244 polypeptide.
  • the invention provides isolated native sequence PR0244 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 219 of Figure 122 (SEQ ID NO: 377). 50. Additional Embodiments
  • the invention provides vectors comprising DNA encoding any of the herein described polypeptides.
  • Host cell comprising any such vector are also provided.
  • the host cells may be CHO cells, E. coli, or yeast.
  • a process for producing any of the herein described polypeptides is further provided and comprises culturing host cells under conditions suitable for expression of the desired polypeptide and recovering the desired polypeptide from the cell culture.
  • the invention provides chimeric molecules comprising any of the herein described polypeptides fused to a heterologous polypeptide or amino acid sequence.
  • Example of such chimeric molecules comprise any of the herein described polypeptides fused to an epitope tag sequence or a Fc region of an immunoglobulin.
  • the invention provides an antibody which specifically binds to any of the above or below described polypeptides.
  • the antibody is a monoclonal antibody, humanized antibody, antibody fragment or single-chain antibody.
  • the invention provides oligonucleotide probes useful for isolating genomic and cDNA nucleotide sequences, wherein those probes may be derived from any of the above or below described nucleotide sequences.
  • the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence that encodes a PRO polypeptide.
  • the isolated nucleic acid molecule comprises a nucleotide sequence having at least about
  • sequence identity preferably at least about 81 % sequence identity, more preferably at least about 82% sequence identity, yet more preferably at least about 83% sequence identity, yet more preferably at least about
  • sequence identity yet more preferably at least about 85% sequence identity, yet more preferably at least about 86% sequence identity, yet more preferably at least about 87% sequence identity, yet more preferably at least about 88 % sequence identity, yet more preferably at least about 89 % sequence identity, yet more preferably at least about 90% sequence identity, yet more preferably at least about 91 % sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93% sequence identity, yet more preferably at least about 94 % sequence identity, yet more preferably at least about 95 % sequence identity, yet more preferably at least about 96% sequence identity, yet more preferably at least about 97% sequence identity, yet more preferably at least about 98% sequence identity and yet more preferably at least about 99% sequence identity to (a) a DNA molecule encoding a PRO polypeptide having a full-length amino acid sequence as disclosed herein, an amino acid sequence lacking the signal peptide as disclosed herein or an extracellular domain of a transmembrane protein, with or
  • the isolated nucleic acid molecule comprises a nucleotide sequence having at least about
  • sequence identity preferably at least about 81 % sequence identity, more preferably at least about 82% sequence identity, yet more preferably at least about 83% sequence identity, yet more preferably at least about
  • sequence identity yet more preferably at least about 85% sequence identity, yet more preferably at least about 86% sequence identity, yet more preferably at least about 87% sequence identity, yet more preferably at least about 88% sequence identity, yet more preferably at least about 89% sequence identity, yet more preferably at least about 90% sequence identity, yet more preferably at least about 91 % sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93 % sequence identity, yet more preferably at least about 94% sequence identity, yet more preferably at least about 95% sequence identity, yet more preferably at least about 96% sequence identity, yet more preferably at least about 97% sequence identity, yet more preferably at least about 98% sequence identity and yet more preferably at least about 99% sequence identity to (a) a DNA molecule comprising the coding sequence of a full-length PRO polypeptide cDNA as disclosed herein, the coding sequence of a PRO polypeptide lacking the signal peptide as disclosed herein or the coding sequence of an extracellular domain of a trans
  • the invention concerns an isolated nucleic acid molecule comprising a nucleotide sequence having at least about 80% sequence identity, preferably at least about 81 % sequence identity, more preferably at least about 82% sequence identity, yet more preferably at least about 83 % sequence identity, yet more preferably at least about 84% sequence identity, yet more preferably at least about 85 % sequence identity, yet more preferably at least about 86% sequence identity, yet more preferably at least about 87% sequence identity, yet more preferably at least about 88% sequence identity, yet more preferably at least about 89% sequence identity, yet more preferably at least about 90% sequence identity, yet more preferably at least about 91 % sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93% sequence identity, yet more preferably at least about 94% sequence identity, yet more preferably at least about 95 % sequence identity, yet more preferably at least about 96 % sequence identity, yet more preferably at least about 97% sequence identity, yet more preferably at least about 98%
  • Another aspect the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence encoding a PRO polypeptide which is either transmembrane domain-deleted or transmembrane domain- inactivated, or is complementary to such encoding nucleotide sequence, wherein the transmembrane domain(s) of such polypeptide are disclosed herein. Therefore, soluble extracellular domains of the herein described PRO polypeptides are contemplated.
  • Another embodiment is directed to fragments of a PRO polypeptide coding sequence, or the complement thereof, that may find use as, for example, hybridization probes or for encoding fragments of a PRO polypeptide that may optionally encode a polypeptide comprising a binding site for an anti-PRO antibody.
  • nucleic acid fragments are usually at least about 20 nucleotides in length, preferably at least about 30 nucleotides in length, more preferably at least about 40 nucleotides in length, yet more preferably at least about 50 nucleotides in length, yet more preferably at least about 60 nucleotides in length, yet more preferably at least about 70 nucleotides in length, yet more preferably at least about 80 nucleotides in length, yet more preferably at least about 90 nucleotides in length, yet more preferably at least about 100 nucleotides in length, yet more preferably at least about 110 nucleotides in length, yet more preferably at least about 120 nucleotides in length, yet more preferably at least about 130 nucleotides in length, yet more preferably at least about 140 nucleotides in length, yet more preferably at least about 150 nucleotides in length, yet more preferably at least about 160 nucleotides in length, yet more preferably at least about 170 nucleot
  • novel fragments of a PRO polypeptide-encoding nucleotide sequence may be determined in a routine manner by aligning the PRO polypeptide-encoding nucleotide sequence with other known nucleotide sequences using any of a number of well known sequence alignment programs and determining which PRO polypeptide-encoding nucleotide sequence fragment(s) are novel. All of such PRO polypeptide-encoding nucleotide sequences are contemplated herein. Also contemplated are the PRO polypeptide fragments encoded by these nucleotide molecule fragments, preferably those PRO polypeptide fragments that comprise a binding site for an anti-PRO antibody.
  • the invention provides isolated PRO polypeptide encoded by any of the isolated nucleic acid sequences hereinabove identified.
  • the invention concerns an isolated PRO polypeptide, comprising an amino acid sequence having at least about 80% sequence identity, preferably at least about 81 % sequence identity, more preferably at least about 82% sequence identity, yet more preferably at least about 83% sequence identity, yet more preferably at least about 84% sequence identity, yet more preferably at least about 85% sequence identity, yet more preferably at least about 86% sequence identity, yet more preferably at least about 87% sequence identity, yet more preferably at least about 88% sequence identity, yet more preferably at least about 89% sequence identity, yet more preferably at least about 90% sequence identity, yet more preferably at least about 91 % sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93% sequence identity, yet more preferably at least about 94% sequence identity, yet more preferably at least about 95 % sequence identity, yet more preferably at least about 96 % sequence
  • the invention concerns an isolated PRO polypeptide comprising an amino acid sequence having at least about 80% sequence identity, preferably at least about 81 % sequence identity, more preferably at least about 82% sequence identity, yet more preferably at least about 83% sequence identity, yet more preferably at least about 84 % sequence identity, yet more preferably at least about 85 % sequence identity, yet more preferably at least about 86% sequence identity, yet more preferably at least about 87% sequence identity, yet more preferably at least about 88% sequence identity, yet more preferably at least about 89% sequence identity, yet more preferably at least about 90% sequence identity, yet more preferably at least about 91 % sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93% sequence identity, yet more preferably at least about 94% sequence identity, yet more preferably at least about 95 % sequence identity , yet more preferably at least about 96 % sequence identity , yet more preferably at least about 97% sequence identity, yet more preferably at least about 98% sequence identity and yet
  • the invention concerns an isolated PRO polypeptide comprising an amino acid sequence scoring at least about 80% positives, preferably at least about 81 % positives, more preferably at least about 82% positives, yet more preferably at least about 83% positives, yet more preferably at least about 84% positives, yet more preferably at least about 85% positives, yet more preferably at least about 86% positives, yet more preferably at least about 87% positives, yet more preferably at least about 88% positives, yet more preferably at least about 89% positives, yet more preferably at least about 90% positives, yet more preferably at least about 91 % positives, yet more preferably at least about 92% positives, yet more preferably at least about 93% positives, yet more preferably at least about 94% positives, yet more preferably at least about 95% positives, yet more preferably at least about 96% positives, yet more preferably at least about 97% positives, yet more preferably at least about 98% positives and yet more preferably at least about 99%
  • the invention provides an isolated PRO polypeptide without the N-terminal signal sequence and/or the initiating methionine and is encoded by a nucleotide sequence that encodes such an amino acid sequence as hereinbefore described.
  • Processes for producing the same are also herein described, wherein those processes comprise culmring a host cell comprising a vector which comprises the appropriate encoding nucleic acid molecule under conditions suitable for expression of the PRO polypeptide and recovering the PRO polypeptide from the cell culture.
  • Another aspect the invention provides an isolated PRO polypeptide which is either transmembrane domain-deleted or transmembrane domain-inactivated.
  • Processes for producing the same are also herein described, wherein those processes comprise culmring a host cell comprising a vector which comprises the appropriate encoding nucleic acid molecule under conditions suitable for expression of the PRO polypeptide and recovering the PRO polypeptide from the cell culture.
  • the invention concerns agonists and antagonists of a native PRO polypeptide as defined herein.
  • the agonist or antagonist is an anti-PRO antibody or a small molecule.
  • the invention concerns a method of identifying agonists or antagonists to a PRO polypeptide which comprise contacting the PRO polypeptide with a candidate molecule and monitoring a biological activity mediated by said PRO polypeptide.
  • the PRO polypeptide is a native PRO polypeptide.
  • the invention concerns a composition of matter comprising a PRO polypeptide, or an agonist or antagonist of a PRO polypeptide as herein described, or an anti-PRO antibody, in combination with a carrier.
  • the carrier is a pharmaceutically acceptable carrier.
  • Another embodiment of the present invention is directed to the use of a PRO polypeptide, or an agonist or antagonist thereof as hereinbefore described, or an anti-PRO antibody, for the preparation of a medicament useful in the treatment of a condition which is responsive to the PRO polypeptide, an agonist or antagonist thereof or an anti-PRO antibody.
  • Figure 1 shows a nucleotide sequence (SEQ ID NO: l) of a native sequence PR0211 cDNA, wherein SEQ ID NO: l is a clone designated herein as "DNA32292-1131 ".
  • Figure 2 shows the amino acid sequence (SEQ ID NO: 2) derived from the coding sequence of SEQ ID NO: l shown in Figure 1.
  • Figure 3 shows a nucleotide sequence (SEQ ID NO:3) of a native sequence PR0217 cDNA, wherein
  • SEQ ID NO:3 is a clone designated herein as "DNA33094-1131 ".
  • Figure 4 shows the amino acid sequence (SEQ ID NO: 4) derived from the coding sequence of SEQ ID NO: 3 shown in Figure 3.
  • Figure 5 shows a nucleotide sequence (SEQ ID NO: 11) of a native sequence PRO230 cDNA, wherein SEQ ID NO: 11 is a clone designated herein as "DNA33223-1136" .
  • Figure 6 shows the amino acid sequence (SEQ ID NO: 12) derived from the coding sequence of SEQ ID NO: 11 shown in Figure 5.
  • Figure 7 shows a nucleotide sequence designated herein as DNA20088 (SEQ ID NO: 13).
  • Figure 8 shows a nucleotide sequence (SEQ ID NO: 17) of a native sequence PR0232 cDNA, wherein SEQ ID NO: 17 is a clone designated herein as "PNA34435-1140" .
  • Figure 9 shows the amino acid sequence (SEQ IP NO: 18) derived from the coding sequence of SEQ ID NO: 17 shown in Figure 8.
  • Figure 10 shows a nucleotide sequence (SEQ ID NO: 22) of a native sequence PRO 187 cDNA, wherein SEQ ID NO:22 is a clone designated herein as "DNA27864-1155" .
  • Figure 11 shows the amino acid sequence (SEQ ID NO:23) derived from the coding sequence of SEQ
  • Figure 12 shows a nucleotide sequence (SEQ ID NO: 27) of a native sequence PR0265 cDNA, wherein SEQ ID NO:27 is a clone designated herein as "DNA36350-1158" .
  • Figure 13 shows the amino acid sequence (SEQ ID NO: 28) derived from the coding sequence of SEQ ID NO:27 shown in Figure 12.
  • Figure 14 shows a nucleotide sequence (SEQ ID NO:33) of a native sequence PR0219 cDNA, wherein SEQ ID NO:33 is a clone designated herein as "DNA32290-1164" .
  • Figure 15 shows the amino acid sequence (SEQ ID NO: 34) derived from the coding sequence of SEQ ID NO: 33 shown in Figure 14.
  • Figure 16 shows a nucleotide sequence (SEQ ID NO:38) of a native sequence PR0246 cDNA, wherein SEQ ID NO:38 is a clone designated herein as "DNA35639-1172".
  • Figure 17 shows the amino acid sequence (SEQ ID NO:39) derived from the coding sequence of SEQ ID NO:38 shown in Figure 16.
  • Figure 18 shows a nucleotide sequence (SEQ ID NO:48) of a native sequence PR0228 cDNA, wherein SEQ ID NO:48 is a clone designated herein as "DNA33092-1202".
  • Figure 19 shows the amino acid sequence (SEQ ID NO:49) derived from the coding sequence of SEQ ID NO:48 shown in Figure 18.
  • Figure 20 shows a nucleotide sequence designated herein as DNA21951 (SEQ ID NO:50).
  • Figure 21 shows a nucleotide sequence (SEQ ID NO:58) of a native sequence PR0533 cDNA, wherein SEQ ID N0:58 is a clone designated herein as "DNA49435-1219".
  • Figure 22 shows the amino acid sequence (SEQ ID NO:59) derived from the coding sequence of SEQ ID NO:58 shown in Figure 21.
  • Figure 23 shows a nucleotide sequence (SEQ ID NO:63) of a native sequence PR0245 cDNA, wherein
  • SEQ ID NO:63 is a clone designated herein as "DNA35638-1141".
  • Figure 24 shows the amino acid sequence (SEQ ID NO: 64) derived from the coding sequence of SEQ ID NO:63 shown in Figure 23.
  • Figure 25 shows a nucleotide sequence (SEQ ID NO:68) of a native sequence PRO220 cDNA, wherein SEQ ID NO:68 is a clone designated herein as "DNA32298-1132" .
  • Figure 26 shows the amino acid sequence (SEQ ID NO: 69) derived from the coding sequence of SEQ ID NO:68 shown in Figure 25.
  • Figure 27 shows a nucleotide sequence (SEQ ID NO:70) of a native sequence PR0221 cDNA, wherein SEQ ID NO:70 is a clone designated herein as "DNA33089-1132".
  • Figure 28 shows the amino acid sequence (SEQ ID NO:71) derived from the coding sequence of SEQ
  • Figure 29 shows a nucleotide sequence (SEQ ID NO:72) of a native sequence PR0227 cDNA, wherein SEQ ID NO:72 is a clone designated herein as "DNA33786-1132".
  • Figure 30 shows the amino acid sequence (SEQ ID NO:73) derived from the coding sequence of SEQ ID NO:72 shown in Figure 29.
  • Figure 31 shows a nucleotide sequence (SEQ ID NO:83) of a native sequence PR0258 cDNA, wherein SEQ ID NO:83 is a clone designated herein as "DNA35918-1174".
  • Figure 32 shows the amino acid sequence (SEQ ID NO: 84) derived from the coding sequence of SEQ ID NO:83 shown in Figure 31.
  • Figure 33 shows a nucleotide sequence (SEQ ID NO:90) of a native sequence PR0266 cDNA, wherein
  • SEQ ID NO:90 is a clone designated herein as "DNA37150-1178".
  • Figure 34 shows the amino acid sequence (SEQ ID NO:91) derived from the coding sequence of SEQ ID NO: 90 shown in Figure 33.
  • Figure 35 shows a nucleotide sequence (SEQ ID NO:95) of a native sequence PR0269 cDNA, wherein SEQ ID NO:95 is a clone designated herein as "DNA38260-1180".
  • Figure 36 shows the amino acid sequence (SEQ ID NO:96) derived from the coding sequence of SEQ ID NO:95 shown in Figure 35.
  • Figure 37 shows a nucleotide sequence (SEQ ID NO: 103) of a native sequence PR0287 cDNA, wherein SEQ ID NO: 103 is a clone designated herein as "DNA39969-1185".
  • Figure 38 shows the amino acid sequence (SEQ ID NO: 104) derived from the coding sequence of SEQ ID NO: 103 shown in Figure 37.
  • Figure 39 shows a nucleotide sequence (SEQ ID NO: 108) of a native sequence PR0214 cDNA, wherein
  • SEQ ID NO: 108 is a clone designated herein as "DNA32286-1191".
  • Figure 40 shows the amino acid sequence (SEQ ID NO: 109) derived from the coding sequence of SEQ ID NO: 108 shown in Figure 39.
  • Figure 41 shows a nucleotide sequence (SEQ ID NO: 113) of a native sequence PR0317 cDNA, wherein SEQ ID NO: 113 is a clone designated herein as "DNA33461-1199" .
  • Figure 42 shows the amino acid sequence (SEQ ID NO: 114) derived from the coding sequence of SEQ ID NO: 113 shown in Figure 41.
  • Figure 43 shows a nucleotide sequence (SEQ ID NO: 118) of a native sequence PRO301 cDNA, wherein SEQ ID NO: 118 is a clone designated herein as "DNA40628-1216".
  • Figure 44 shows the amino acid sequence (SEQ ID NO: 119) derived from the coding sequence of SEQ ID NO: 118
  • Figure 45 shows a nucleotide sequence (SEQ ID NO: 126) of a native sequence PR0224 cDNA, wherein SEQ ID NO: 126 is a clone designated herein as "DNA33221-1133".
  • Figure 46 shows the amino acid sequence (SEQ ID NO: 127) derived from the coding sequence of SEQ ID NO : 126 shown in Figure 45.
  • Figure 47 shows a nucleotide sequence (SEQ ID NO: 131) of a native sequence PR0222 cDNA, wherein SEQ ID NO:131 is a clone designated herein as "DNA33107-1135".
  • Figure 48 shows the amino acid sequence (SEQ ID NO: 132) derived from the coding sequence of SEQ ID NO: 131 shown in Figure 47.
  • Figure 49 shows a nucleotide sequence (SEQ ID NO: 136) of a native sequence PR0234 cDNA, wherein
  • SEQ ID NO:136 is a clone designated herein as "DNA35557-1137".
  • Figure 50 shows the amino acid sequence (SEQ ID NO: 137) derived from the coding sequence of SEQ ID NO: 136 shown in Figure 49.
  • Figure 51 shows a nucleotide sequence (SEQID NO: 141) of a native sequence PR0231 cDN A , wherein SEQ ID NO: 141 is a clone designated herein as "DNA34434-1139" .
  • Figure 52 shows the amino acid sequence (SEQ ID NO: 142) derived from the coding sequence of SEQ ID NO: 141 shown in Figure 51.
  • Figure 53 shows a nucleotide sequence (SEQ ID NO: 147) of a native sequence PR0229 cDNA, wherein SEQ ID NO:147 is a clone designated herein as "DNA33100-1159".
  • Figure 54 shows the amino acid sequence (SEQ ID NO: 148) derived from the coding sequence of SEQ ID NO: 147 shown in Figure 53.
  • Figure 55 shows a nucleotide sequence (SEQ ID NO: 152) of a native sequence PR0238 cDNA, wherein SEQ ID NO:152 is a clone designated herein as "DNA35600-1162".
  • Figure 56 shows the amino acid sequence (SEQ ID NO: 153) derived from the coding sequence of SEQ ID NO: 152 shown in Figure 55.
  • Figure 57 shows a nucleotide sequence (SEQ ID NO: 158) of a native sequence PR0233 cDNA, wherein SEQ ID NO: 158 is a clone designated herein as "DNA34436-1238".
  • Figure 58 shows the amino acid sequence (SEQ ID NO: 159) derived from the coding sequence of SEQ
  • Figure 59 shows a nucleotide sequence (SEQ ID NO: 163) of a native sequence PR0223 cDNA, wherein SEQ ID NO:163 is a clone designated herein as "DNA33206-1165".
  • Figure 60 shows the amino acid sequence (SEQ ID NO: 164) derived from the coding sequence of SEQ ID NO: 163 shown in Figure 59.
  • Figure 61 shows a nucleotide sequence (SEQ ID NO: 169) of a native sequence PR0235 cDNA, wherein SEQ ID NO:169 is a clone designated herein as "DNA35558-1167".
  • Figure 62 shows the amino acid sequence (SEQ ID NO: 170) derived from the coding sequence of SEQ ID NO: 169 shown in Figure 61.
  • Figure 63 shows a nucleotide sequence (SEQ ID NO: 174) of a native sequence PR0236 cDNA, wherein
  • SEQ ID NO: 174 is a clone designated herein as "DNA35599-1168".
  • Figure 64 shows the amino acid sequence (SEQ ID NO: 175) derived from the coding sequence of SEQ ID NO: 174 shown in Figure 63.
  • Figure 65 shows a nucleotide sequence (SEQ ID NO: 176) of a native sequence PR0262 cDNA, wherein SEQ ID NO: 176 is a clone designated herein as "DNA36992-1168" .
  • Figure 66 shows the amino acid sequence (SEQ ID NO: 177) derived from the coding sequence of SEQ ID NO: 176 shown in Figure 65.
  • Figure 67 shows a nucleotide sequence (SEQ ID NO: 184) of a native sequence PR0239 cDNA, wherein SEQ ID NO: 184 is a clone designated herein as "DNA34407-1169".
  • Figure 68 shows the amino acid sequence (SEQ ID NO: 185) derived from the coding sequence of SEQ
  • Figure 69 shows a nucleotide sequence (SEQ ID NO: 189) of a native sequence PR0257 cDNA, wherein SEQ ID NO: 189 is a clone designated herein as "DNA35841-1173".
  • Figure 70 shows the amino acid sequence (SEQ ID NO: 190) derived from the coding sequence of SEQ ID NO: 189 shown in Figure 69.
  • Figure 71 shows a nucleotide sequence (SEQ ID NO: 194) of a native sequence PRO260 cDNA, wherein SEQ ID NO: 194 is a clone designated herein as "DNA33470-1175".
  • Figure 72 shows the amino acid sequence (SEQ ID NO: 195) derived from the coding sequence of SEQ ID NO: 194 shown in Figure 71.
  • Figure 73 shows a nucleotide sequence (SEQ ID NO: 200) of a native sequence PR0263 cDNA, wherein SEQ ID NO:200 is a clone designated herein as "DNA34431-1177".
  • Figure 74 shows the amino acid sequence (SEQ ID NO:201) derived from the coding sequence of SEQ ID NO:200 shown in Figure 73.
  • Figure 75 shows a nucleotide sequence (SEQ ID NO:206) of a native sequence PRO270 cDNA, wherein SEQ ID NO:206 is a clone designated herein as "DNA39510-1181 " .
  • Figure 76 shows the amino acid sequence (SEQ ID NO:207) derived from the coding sequence of SEQ ID NO: 206 shown in Figure 75.
  • Figure 77 shows a nucleotide sequence (SEQ ID NO : 212) of a native sequence PR0271 cDN A , wherein
  • SEQ ID NO:212 is a clone designated herein as "DNA39423-1182".
  • Figure 78 shows the amino acid sequence (SEQ ID NO:213) derived from the coding sequence of SEQ ID NO:212 shown in Figure 77.
  • Figure 79 shows a nucleotide sequence (SEQ ID NO : 220) of a native sequence PR0272 cDN A , wherein SEQ ID NO:220 is a clone designated herein as "DNA40620-1183".
  • Figure 80 shows the amino acid sequence (SEQ ID NO: 221) derived from the coding sequence of SEQ ID NO:220 shown in Figure 79.
  • Figure 81 shows a nucleotide sequence (SEQ ID NO : 226) of a native sequence PR0294 cDN A , wherein SEQ ID NO:226 is a clone designated herein as "DNA40604-1187".
  • Figure 82 shows the amino acid sequence (SEQ ID NO:227) derived from the coding sequence of SEQ
  • Figure 83 shows a nucleotide sequence (SEQ ID NO:235) of a native sequence PR0295 cDNA, wherein SEQ ID NO:235 is a clone designated herein as "DN A38268- 1188".
  • Figure 84 shows the amino acid sequence (SEQ ID NO: 236) derived from the coding sequence of SEQ ID NO: 235 shown in Figure 83.
  • Figure 85 shows a nucleotide sequence (SEQ ID NO:244) of a native sequence PR0293 cDNA, wherein SEQ ID NO:244 is a clone designated herein as "DNA37151-1193".
  • Figure 86 shows the amino acid sequence (SEQ ID NO:245) derived from the coding sequence of SEQ ID NO:244 shown in Figure 85.
  • Figure 87 shows a nucleotide sequence (SEQ ID NO : 249) of a native sequence PR0247 cDN A , wherein
  • SEQ ID NO:249 is a clone designated herein as "DNA35673-1201 ".
  • Figure 88 shows the amino acid sequence (SEQ ID NO:250) derived from the coding sequence of SEQ ID NO:249 shown in Figure 87.
  • Figure 89 shows a nucleotide sequence (SEQ ID NO:254) of a native sequence PRO302 cDNA, wherein SEQ ID NO:254 is a clone designated herein as "DNA40370-1217".
  • Figure 90 shows the amino acid sequence (SEQ ID NO:255) derived from the coding sequence of SEQ ID NO:254 shown in Figure 89.
  • Figure 91 shows a nucleotide sequence (SEQ IP NO:256) of a native sequence PRO303 cPNA, wherein SEQ IP NO:256 is a clone designated herein as "PNA42551-1217".
  • Figure 92 shows the amino acid sequence (SEQ IP NO:257) derived from the coding sequence of SEQ IP NO:256 shown in Figure 91.
  • Figure 93 shows a nucleotide sequence (SEQ ID NO: 258) of a native sequence PRO304 cDNA, wherein SEQ ID NO:258 is a clone designated herein as "DNA39520-1217" .
  • Figure 94 shows the amino acid sequence (SEQ ID NO:259) derived from the coding sequence of SEQ ID NO:258 shown in Figure 93.
  • Figure 95 shows a nucleotide sequence (SEQ ID NO:260) of a native sequence PRO307 cDNA, wherein SEQ ID NO:260 is a clone designated herein as "DNA41225-1217".
  • Figure 96 shows the amino acid sequence (SEQ ID NO: 261) derived from the coding sequence of SEQ
  • Figure 97 shows a nucleotide sequence (SEQ ID NO:262) of a native sequence PR0343 cDNA, wherein SEQ ID NO:262 is a clone designated herein as "DNA43318-1217".
  • Figure 98 shows the amino acid sequence (SEQ ID NO: 263) derived from the coding sequence of SEQ ID NO : 262 shown in Figure 97.
  • Figure 99 shows a nucleotide sequence (SEQ ID NO:284) of a native sequence PR0328 cDNA, wherein SEQ IP NO:284 is a clone designated herein as "PNA40587-1231 " .
  • Figure 100 shows the amino acid sequence (SEQ ID NO:285) derived from the coding sequence of SEQ ID NO: 284 shown in Figure 99.
  • Figure 101 shows a nucleotide sequence (SEQ ID NO:289) of a native sequence PR0335 cDNA, wherein SEQ ID NO:289 is a clone designated herein as "DNA41388-1234" .
  • Figure 102 shows the amino acid sequence (SEQ ID NO: 290) derived from the coding sequence of SEQ ID NO:289 shown in Figure 101.
  • Figure 103 shows a nucleotide sequence (SEQ ID NO:291) of a native sequence PR0331 cDNA, wherein SEQ ID NO:291 is a clone designated herein as "DNA40981-1234" .
  • Figure 104 shows the amino acid sequence (SEQ ID NO:292) derived from the coding sequence of SEQ ID NO:291 shown in Figure 103.
  • Figure 105 shows a nucleotide sequence (SEQ ID NO:293) of a native sequence PR0326 cDNA, wherein SEQ ID NO:293 is a clone designated herein as "DNA37140-1234".
  • Figure 106 shows the amino acid sequence (SEQ ID NO:294) derived from the coding sequence of SEQ
  • Figure 107 shows a nucleotide sequence (SEQ ID NO:309) of a native sequence PR0332 cDNA, wherein SEQ ID NO:309 is a clone designated herein as "DNA40982-1235".
  • Figure 108 shows the amino acid sequence (SEQ ID NO:310) derived from the coding sequence of SEQ ID NO:309 shown in Figure 107.
  • Figure 109 shows a nucleotide sequence (SEQ ID NO:314) of a native sequence PR0334 cDNA, wherein SEQ ID NO:314 is a clone designated herein as "DNA41379-1236".
  • Figure 110 shows the amino acid sequence (SEQ ID NO: 315) derived from the coding sequence of SEQ ID NO:314 shown in Figure 109.
  • Figure 111 shows a nucleotide sequence (SEQ ID NO:319) of a native sequence PR0346 cDNA, wherein SEQ ID NO:319 is a clone designated herein as "DNA44167- 1243".
  • Figure 112 shows the amino acid sequence (SEQ ID NO:320) derived from the coding sequence of SEQ ID NO:319 shown in Figure 111.
  • Figure 113 shows a nucleotide sequence (SEQ ID NO:324) of a native sequence PR0268 cDNA, wherein SEQ ID NO:324 is a clone designated herein as "DNA39427-1179".
  • Figure 114 shows the amino acid sequence (SEQ ID NO:325) derived from the coding sequence of SEQ ID NO:324 shown in Figure 113.
  • Figure 115 shows a nucleotide sequence (SEQ ID NO:331) of a native sequence PRO330 cDNA, wherein SEQ ID NO:331 is a clone designated herein as "DNA40603-1232".
  • Figure 116 shows the amino acid sequence (SEQ ID NO:332) derived from the coding sequence of SEQ ID NO: 331 shown in Figure 115.
  • Figure 117 shows a nucleotide sequence (SEQ ID NO:338) of a native sequence PR0339 cDNA, wherein SEQ ID NO:338 is a clone designated herein as "DNA43466-1225".
  • Figure 118 shows the amino acid sequence (SEQ ID NO:339) derived from the coding sequence of SEQ ID NO:338 shown in Figure 117.
  • Figure 119 shows a nucleotide sequence (SEQ ID NO: 340) of a native sequence PRO310 cDNA, wherein SEQ ID NO:340 is a clone designated herein as "DNA43046-1225".
  • Figure 120 shows the amino acid sequence (SEQ ID NO:341) derived from the coding sequence of SEQ
  • Figure 121 shows a nucleotide sequence (SEQ ID NO:376) of a native sequence PR0244 cDNA, wherein SEQ ID NO:376 is a clone designated herein as "DNA35668-1171".
  • Figure 122 shows the amino acid sequence (SEQ ID NO:377) derived from the coding sequence of SEQ ID NO : 376 shown in Figure 121.
  • Figure 123 shows a nucleotide sequence (SEQ ID NO:422) of a native sequence PR01868 cDNA, wherein SEQ ID NO:422 is a clone designated herein as "DNA77624-2515".
  • Figure 124 shows the amino acid sequence (SEQ ID NO:423) derived from the coding sequence of SEQ ID NO:422 shown in Figure 123.
  • PRO polypeptide and "PRO” as used herein and when immediately followed by a numerical designation refer to various polypeptides, wherein the complete designation (i.e. , PRO/number) refers to specific polypeptide sequences as described herein.
  • PRO/number polypeptide and “PRO/number” wherein the term “number” is provided as an actual numerical designation as used herein encompass native sequence polypeptides and polypeptide variants (which are further defined herein).
  • the PRO polypeptides described herein may be isolated from a variety of sources, such as from human tissue types or from another source, or prepared by recombinant or synthetic methods.
  • a “native sequence PRO polypeptide” comprises a polypeptide having the same amino acid sequence as the corresponding PRO polypeptide derived from nature. Such native sequence PRO polypeptides can be isolated from nature or can be produced by recombinant or synthetic means.
  • the term "native sequence PRO polypeptide” specifically encompasses naturally-occurring truncated or secreted forms of the specific PRO polypeptide (e.g., an extracellular domain sequence), naturally-occurring variant forms (e.g., alternatively spliced forms) and naturally-occurring allelic variants of the polypeptide.
  • the native sequence PRO polypeptides disclosed herein are mature or full-length native sequence polypeptides comprising the full-length amino acids sequences shown in the accompanying figures. Start and stop codons are shown in bold font and underlined in the figures. However, while the PRO polypeptide disclosed in the accompanying figures are shown to begin with methionine residues designated herein as amino acid position 1 in the figures, it is conceivable and possible that other methionine residues located either upstream or downstream from the amino acid position 1 in the figures may be employed as the starting amino acid residue for the PRO polypeptides.
  • the PRO polypeptide "extracellular domain” or “ECD” refers to a form of the PRO polypeptide which is essentially free of the transmembrane and cytoplasmic domains. Ordinarily, a PRO polypeptide ECD will have less than 1 % of such transmembrane and/or cytoplasmic domains and preferably, will have less than 0.5% of such domains. It will be understood that any transmembrane domains identified for the PRO polypeptides of the present invention are identified pursuant to criteria routinely employed in the art for identifying that type of hydrophobic domain. The exact boundaries of a transmembrane domain may vary but most likely by no more than about 5 amino acids at either end of the domain as initially identified herein.
  • an extracellular domain of a PRO polypeptide may contain from about 5 or fewer amino acids on either side of the transmembrane domain/extracellular domain boundary as identified in the Examples or specification and such polypeptides, with or without the associated signal peptide, and nucleic acid encoding them, are comtemplated by the present invention.
  • cleavage of a signal sequence from a secreted polypeptide is not entirely uniform, resulting in more than one secreted species.
  • These mature polypeptides, where the signal peptide is cleaved within no more than about 5 amino acids on either side of the C-terminal boundary of the signal peptide as identified herein, and the polynucleotides encoding them, are contemplated by the present invention.
  • PRO polypeptide variant means an active PRO polypeptide as defined above or below having at least about 80% amino acid sequence identity with a full-length native sequence PRO polypeptide sequence as disclosed herein, a PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO polypeptide, with or without the signal peptide, as disclosed herein or any other fragment of a full-length PRO polypeptide sequence as disclosed herein.
  • Such PRO polypeptide variants include, for instance, PRO polypeptides wherein one or more amino acid residues are added, or deleted, at the N- or C- terminus of the full-length native amino acid sequence.
  • a PRO polypeptide variant will have at least about 80% amino acid sequence identity, preferably at least about 81 % amino acid sequence identity, more preferably at least about 82% amino acid sequence identity, more preferably at least about 83% amino acid sequence identity, more preferably at least about 84% amino acid sequence identity, more preferably at least about 85 % amino acid sequence identity, more preferably at least about 86% amino acid sequence identity, more preferably at least about 87% amino acid sequence identity, more preferably at least about 88% amino acid sequence identity, more preferably at least about 89% amino acid sequence identity, more preferably at least about 90% amino acid sequence identity, more preferably at least about 91 % amino acid sequence identity, more preferably at least about 92% amino acid sequence identity, more preferably at least about 93% amino acid sequence identity, more preferably at least about 94% amino acid sequence identity, more preferably at least about 95 % amino acid sequence identity, more preferably at least about 96 % amino acid sequence identity, more preferably at least about 97% amino acid sequence identity, more preferably at least at least
  • PRO variant polypeptides are at least about 10 amino acids in length, often at least about 20 amino acids in length, more often at least about 30 amino acids in length, more often at least about 40 amino acids in length, more often at least about 50 amino acids in length, more often at least about 60 amino acids in length, more often at least about 70 amino acids in length, more often at least about 80 amino acids in length, more often at least about 90 amino acids in length, more often at least about 100 amino acids in length, more often at least about 150 amino acids in length, more often at least about 200 amino acids in length, more often at least about 300 amino acids in length, or more.
  • Percent (%) amino acid sequence identity with respect to the PRO polypeptide sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific PRO polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
  • % amino acid sequence identity values are generated using the sequence comparison computer program ALIGN-2, wherein the complete source code for the ALIGN-2 program is provided in Table 1 below.
  • the ALIGN-2 sequence comparison computer program was authored by Genentech, Inc. and the source code shown in Table 1 below has been filed with user documentation in the U.S. Copyright Office, Washington D.C. , 20559, where it is registered under U.S. Copyright Registration No. TXU510087.
  • the ALIGN-2 program is publicly available through Genentech, Inc., South San Francisco, California or may be compiled from the source code provided in Table 1 below.
  • the ALIGN-2 program should be compiled for use on a UNIX operating system, preferably digital UNIX V4.0D.
  • % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B is calculated as follows:
  • Tables 2 and 3 demonstrate how to calculate the % amino acid sequence identity of the amino acid sequence designated "Comparison Protein” to the amino acid sequence designated "PRO” , wherein “PRO” represents the amino acid sequence of a hypothetical PRO polypeptide of interest, “Comparison Protein” represents the amino acid sequence of a polypeptide against which the "PRO” polypeptide of interest is being compared, and "X, "Y” and “Z” each represent different hypothetical amino acid residues.
  • a % amino acid sequence identity value is determined by dividing (a) the number of matching identical amino acid residues between the amino acid sequence of the PRO polypeptide of interest having a sequence derived from the native PRO polypeptide and the comparison amino acid sequence of interest (i . e . , the sequence against which the PRO polypeptide of interest is being compared which may be a PRO variant polypeptide) as determined by WU-BLAST-2 by (b) the total number of amino acid residues of the PRO polypeptide of interest.
  • amino acid sequence A is the comparison amino acid sequence of interest and the amino acid sequence B is the amino acid sequence of the PRO polypeptide of interest.
  • Percent amino acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST2 (Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)).
  • NCBI-BLAST2 sequence comparison program may be downloaded from http://www.ncbi.nlm.nih.gov.
  • % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B is calculated as follows:
  • PRO variant polynucleotide or "PRO variant nucleic acid sequence” means a nucleic acid molecule which encodes an active PRO polypeptide as defined below and which has at least about 80% nucleic acid sequence identity with a nucleotide acid sequence encoding a full-length native sequence PRO polypeptide sequence as disclosed herein, a full-length native sequence PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO polypeptide, with or without the signal peptide, as disclosed herein or any other fragment of a full-length PRO polypeptide sequence as disclosed herein.
  • a PRO variant polynucleotide will have at least about 80% nucleic acid sequence identity, more preferably at least about 81 % nucleic acid sequence identity, more preferably at least about 82% nucleic acid sequence identity, more preferably at least about 83% nucleic acid sequence identity, more preferably at least about 84% nucleic acid sequence identity, more preferably at least about 85% nucleic acid sequence identity, more preferably at least about 86% nucleic acid sequence identity, more preferably at least about 87% nucleic acid sequence identity, more preferably at least about 88% nucleic acid sequence identity, more preferably at least about 89% nucleic acid sequence identity, more preferably at least about 90% nucleic acid sequence identity, more preferably at least about 91 % nucleic acid sequence identity, more preferably at least about 92% nucleic acid sequence identity, more preferably at least about 93% nucleic acid sequence identity, more preferably at least about 94% nucleic acid sequence identity, more preferably at least about 95% nucleic acid sequence
  • PRO variant polynucleotides are at least about 30 nucleotides in length, often at least about 60 nucleotides in length, more often at least about 90 nucleotides in length, more often at least about 120 nucleotides in length, more often at least about 150 nucleotides in length, more often at least about 180 nucleotides in length, more often at least about 210 nucleotides in length, more often at least about 240 nucleotides in length, more often at least about 270 nucleotides in length, more often at least about 300 nucleotides in length, more often at least about 450 nucleotides in length, more often at least about 600 nucleotides in length, more often at least about 900 nucleotides in length, or more.
  • Percent (%) nucleic acid sequence identity with respect to PRO-encoding nucleic acid sequences identified herein is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in the PRO nucleic acid sequence of interest, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software.
  • % nucleic acid sequence identity values are generated using the sequence comparison computer program ALIGN-2, wherein the complete source code for the ALIGN-2 program is provided in Table 1 below.
  • the ALIGN-2 sequence comparison computer program was authored by Genentech, Inc. and the source code shown in Table 1 below has been filed with user documentation in the U.S. Copyright Office, Washington D.C, 20559, where it is registered under U.S. Copyright Registration No. TXU510087.
  • the ALIGN-2 program is publicly available through Genentech, Inc., South San Francisco, California or may be compiled from the source code provided in Table 1 below.
  • the ALIGN-2 program should be compiled for use on a UNIX operating system, preferably digital UNIX V4.0D.
  • % nucleic acid sequence identity of a given nucleic acid sequence C to, with, or against a given nucleic acid sequence D is calculated as follows:
  • Tables 4 and 5 demonstrate how to calculate the % nucleic acid sequence identity of the nucleic acid sequence designated "Comparison DNA” to the nucleic acid sequence designated "PRO-DNA” , wherein "PRO-DNA” represents a hypothetical PRO-encoding nucleic acid sequence of interest, “Comparison DNA” represents the nucleotide sequence of a nucleic acid molecule against which the "PRO-DNA” nucleic acid molecule of interest is being compared, and "N", “L” and “V” each represent different hypothetical nucleotides.
  • a % nucleic acid sequence identity value is determined by dividing (a) the number of matching identical nucleotides between the nucleic acid sequence of the PRO polypeptide-encoding nucleic acid molecule of interest having a sequence derived from the native sequence PRO polypeptide-encoding nucleic acid and the comparison nucleic acid molecule of interest (i.e. , the sequence against which the PRO polypeptide-encoding nucleic acid molecule of interest is being compared which may be a variant PRO polynucleotide) as determined by WU-BLAST-2 by (b) the total number of nucleotides of the PRO polypeptide-encoding nucleic acid molecule of interest.
  • nucleic acid sequence A is the comparison nucleic acid molecule of interest and the nucleic acid sequence B is the nucleic acid sequence of the PRO polypeptide- encoding nucleic acid molecule of interest.
  • Percent nucleic acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST2 (Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)).
  • NCBI-BLAST2 sequence comparison program may be downloaded from http://www.ncbi.nlm.nih.gov.
  • % nucleic acid sequence identity of a given nucleic acid sequence C to, with, or against a given nucleic acid sequence D is calculated as follows:
  • PRO variant polynucleotides are nucleic acid molecules that encode an active PRO polypeptide and which are capable of hybridizing, preferably under stringent hybridization and wash conditions, to nucleotide sequences encoding a full-length PRO polypeptide as disclosed herein.
  • PRO variant polypeptides may be those that are encoded by a PRO variant polynucleotide.
  • the term "positives”, in the context of sequence comparison performed as described above, includes residues in the sequences compared that are not identical but have similar properties (e.g. as a result of conservative substitutions, see Table 6 below).
  • the % value of positives is determined by dividing (a) the number of amino acid residues scoring a positive value between the PRO polypeptide amino acid sequence of interest having a sequence derived from the native PRO polypeptide sequence and the comparison amino acid sequence of interest (i.e., the amino acid sequence against which the PRO polypeptide sequence is being compared) as determined in the BLOSUM62 matrix of WU-BLAST-2 by (b) the total number of amino acid residues of the PRO polypeptide of interest.
  • % value of positives is calculated as described in the immediately preceding paragraph.
  • amino acid sequence identity comparisons performed as described for ALIGN-2 and NCBI-BLAST-2 above includes amino acid residues in the sequences compared that are not only identical, but also those that have similar properties.
  • Amino acid residues that score a positive value to an amino acid residue of interest are those that are either identical to the amino acid residue of interest or are a preferred substitution (as defined in Table 6 below) of the amino acid residue of interest.
  • % value of positives of a given amino acid sequence A to, with, or against a given amino acid sequence B is calculated as follows:
  • X is the number of amino acid residues scoring a positive value as defined above by the sequence alignment program ALIGN-2 or NCBI-BLAST2 in that program's alignment of A and B
  • Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % positives of A to B will not equal the % positives of B to A.
  • Isolated, when used to describe the various polypeptides disclosed herein, means polypeptide that has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes.
  • the polypeptide will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain.
  • Isolated polypeptide includes polypeptide in situ within recombinant cells, since at least one component of the PRO polypeptide natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step.
  • An "isolated" PRO polypeptide-encoding nucleic acid or other polypeptide-encoding nucleic acid is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the polypeptide-encoding nucleic acid.
  • An isolated polypeptide-encoding nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated polypeptide-encoding nucleic acid molecules therefore are distinguished from the specific polypeptide- encoding nucleic acid molecule as it exists in natural cells.
  • an isolated polypeptide-encoding nucleic acid molecule includes polypeptide-encoding nucleic acid molecules contained in cells that ordinarily express the polypeptide where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
  • control sequences refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism.
  • the control sequences that are suitable for prokaryotes include a promoter, optionally an operator sequence, and a ribosome binding site.
  • Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
  • Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence.
  • DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide;
  • a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or
  • a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.
  • "operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
  • antibody is used in the broadest sense and specifically covers, for example, single anti-PRO monoclonal antibodies (including agonist, antagonist, and neutralizing antibodies), anti-PRO antibody compositions with polyepitopic specificity, single chain anti-PRO antibodies, and fragments of anti-PRO antibodies (see below).
  • monoclonal antibody refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e. , the individual antibodies comprising the population are identical except for possible naturally-occurring mutations that may be present in minor amounts.
  • “Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology. Wiley Interscience Publishers, (1995).
  • “Stringent conditions” or “high stringency conditions”, as defined herein, may be identified by those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1 % sodium dodecyl sulfate at 50°C; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1 % bovine serum albumin 0.1 % Ficoll/0.1 % polyvinylpyrrolidone/50mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42°C; or (3) employ 50% formamide, 5 x SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1 % sodium pyrophosphate, 5 x Denhardt's solution, sonicated salmon sperm DNA (50 ⁇ g/ml), 0.1 % SDS
  • Modely stringent conditions may be identified as described by Sambrook et al., Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and %SDS) less stringent that those described above.
  • washing solution and hybridization conditions e.g., temperature, ionic strength and %SDS
  • moderately stringent conditions is overnight incubation at 37°C in a solution comprising: 20% formamide, 5 x SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5 x Denhardt's solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1 x SSC at about 37-50 °C
  • the skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.
  • epitope tagged when used herein refers to a chimeric polypeptide comprising a PRO polypeptide fused to a "tag polypeptide" .
  • the tag polypeptide has enough residues to provide an epitope against which an antibody can be made, yet is short enough such that it does not interfere with activity of the polypeptide to which it is fused.
  • the tag polypeptide preferably also is fairly unique so that the antibody does not substantially cross-react with other epitopes.
  • Suitable tag polypeptides generally have at least six amino acid residues and usually between about 8 and 50 amino acid residues (preferably, between about 10 and 20 amino acid residues).
  • immunoadhesin designates antibody-like molecules which combine the binding specificity of a heterologous protein (an “adhesin”) with the effector functions of immunoglobulin constant domains.
  • the immunoadhesins comprise a fusion of an amino acid sequence with the desired binding specificity which is other than the antigen recognition and binding site of an antibody (i.e., is “heterologous"), and an immunoglobulin constant domain sequence.
  • the adhesin part of an immunoadhesin molecule typically is a contiguous amino acid sequence comprising at least the binding site of a receptor or a ligand.
  • the immunoglobulin constant domain sequence in the immunoadhesin may be obtained from any immunoglobulin, such as IgG-1, IgG-2, IgG-3, or IgG-4 subtypes, IgA (including IgA-1 and IgA-2), IgE, IgD or IgM.
  • immunoglobulin such as IgG-1, IgG-2, IgG-3, or IgG-4 subtypes, IgA (including IgA-1 and IgA-2), IgE, IgD or IgM.
  • Active or “activity” for the purposes herein refers to form(s) of a PRO polypeptide which retain a biological and/or an immunological activity of native or naturally-occurring PRO, wherein "biological” activity refers to a biological function (either inhibitory or stimulatory) caused by a native or naturally-occurring PRO other than the ability to induce the production of an antibody against an antigenic epitope possessed by a native or naturally-occurring PRO and an "immunological” activity refers to the ability to induce the production of an antibody against an antigenic epitope possessed by a native or naturally-occurring PRO.
  • antagonist is used in the broadest sense, and includes any molecule that partially or fully blocks, inhibits, or neutralizes a biological activity of a native PRO polypeptide disclosed herein.
  • agonist is used in the broadest sense and includes any molecule that mimics a biological activity of a native PRO polypeptide disclosed herein.
  • Suitable agonist or antagonist molecules specifically include agonist or antagonist antibodies or antibody fragments, fragments or amino acid sequence variants of native PRO polypeptides, peptides, antisense oligonucleotides, small organic molecules, etc.
  • Methods for identifying agonists or antagonists of a PRO polypeptide may comprise contacting a PRO polypeptide with a candidate agonist or antagonist molecule and measuring a detectable change in one or more biological activities normally associated with the PRO polypeptide.
  • Treatment refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathologic condition or disorder.
  • Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented.
  • Chronic administration refers to administration of the agent(s) in a continuous mode as opposed to an acute mode, so as to maintain the initial therapeutic effect (activity) for an extended period of time.
  • Intermittent administration is treatment that is not consecutively done without interruption, but rather is cyclic in nature.
  • “Mammal” for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, cats, cattle, horses, sheep, pigs, goats, rabbits, etc. Preferably, the mammal is human.
  • Carriers as used herein include pharmaceutically acceptable carriers, excipients, or stabilizers which are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Often the physiologically acceptable carrier is an aqueous pH buffered solution.
  • physiologically acceptable carriers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt- forming counterions such as sodium; and/or nonionic surfactants such as TWEENTM, polyethylene glycol (PEG), and PLURONICSTM.
  • buffers such as phosphate, citrate, and other organic acids
  • antioxidants including ascorbic acid
  • proteins such as serum albumin
  • Antibody fragments comprise a portion of an intact antibody, preferably the antigen binding or variable region of the intact antibody.
  • antibody fragments include Fab, Fab' , F(ab') 2 , and Fv fragments; diabodies; linear antibodies (Zapata et al., Protein Eng. 8(10): 1057-1062 [1995]); single-chain antibody molecules; and multispecific antibodies formed from antibody fragments.
  • Papain digestion of antibodies produces two identical antigen-binding fragments, called “Fab” fragments, each with a single antigen-binding site, and a residual "Fc” fragment, a designation reflecting the ability to crystallize readily.
  • Pepsin treatment yields an F(ab') 2 fragment that has two antigen-combining sites and is still capable of cross-linking antigen.
  • Fv is the minimum antibody fragment which contains a complete antigen-recognition and -binding site. This region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association. It is in this configuration that the three CDRs of each variable domain interact to define an antigen- binding site on the surface of the V H -V L dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.
  • the Fab fragment also contains the constant domain of the light chain and the first constant domain
  • Fab fragments differ from Fab' fragments by the addition of a few residues at the carboxy terminus of the heavy chain CHI domain including one or more cysteines from the antibody hinge region.
  • Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group.
  • F(ab') 2 antibody fragments originally were produced as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
  • the "light chains" of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa and lambda, based on the amino acid sequences of their constant domains.
  • immunoglobulins can be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g. , IgGl , IgG2, IgG3, IgG4, IgA, and IgA2.
  • immunoglobulins There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g. , IgGl , IgG2, IgG3, IgG4, IgA, and IgA2.
  • Single-chain Fv or “sFv” antibody fragments comprise the V H and V L domains of antibody, wherein these domains are present in a single polypeptide chain.
  • the Fv polypeptide further comprises a polypeptide linker between the V H and V L domains which enables the sFv to form the desired structure for antigen binding.
  • a polypeptide linker between the V H and V L domains which enables the sFv to form the desired structure for antigen binding.
  • Diabodies are described more fully in, for example, EP 404,097; WO 93/11161 ; and Hollinger et al., Proc. Natl. Acad. Sci. USA. 90:6444-6448 (1993).
  • an “isolated” antibody is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes.
  • the antibody will be purified (1) to greater than 95 % by weight of antibody as determined by the Lowry method, and most preferably more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions using Coomassie blue or, preferably, silver stain.
  • Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
  • label when used herein refers to a detectable compound or composition which is conjugated directly or indirectly to the antibody so as to generate a "labeled” antibody.
  • the label may be detectable by itself (e.g. radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition which is detectable.
  • solid phase is meant a non-aqueous matrix to which the antibody of the present invention can adhere. Examples of solid phases encompassed herein include those formed partially or entirely of glass (e.g., controlled pore glass), polysaccharides (e.g., agarose), polyacrylamides, polystyrene, polyvinyl alcohol and silicones.
  • the solid phase can comprise the well of an assay plate; in others it is a purification column (e.g., an affinity chromatography column).
  • This term also includes a discontinuous solid phase of discrete particles, such as those described in U.S. Patent No. 4,275,149.
  • a “liposome” is a small vesicle composed of various types of lipids, phospholipids and/or surfactant which is useful for delivery of a drug (such as a PRO polypeptide or antibody thereto) to a mammal.
  • the components of the liposome are commonly arranged in a bilayer formation, similar to the lipid arrangement of biological membranes.
  • a “small molecule” is defined herein to have a molecular weight below about 500 Daltons.
  • PR0317-associated disorder refers to a pathological condition or disease wherein PR0317 is over- or underexpressed.
  • disorders include diseases of the female genital tract or of the endometrium of a mammal, including hyperplasia, endometritis, endometriosis, wherein the patient is at risk for infertility due to endometrial factor, endometrioma, and endometrial cancer, especially those diseases involving abnormal bleeding such as a gynecological disease.
  • diseases involving angiogenesis include diseases involving angiogenesis, wherein the angiogenesis results in a pathological condition, such as cancer involving solid tumors (the therapy for the disorder would result in decreased vascularization and a decline in growth and metastasis of a variety of tumors).
  • the angiogenesis may be beneficial, such as for ischemia, especially coronary ischemia.
  • these disorders include those found in patients whose hearts are functioning but who have a blocked blood supply due to atherosclerotic coronary artery disease, and those with a functioning but underperfused heart, including patients with coronary arterial disease who are not optimal candidates for angioplasty and coronary artery by-pass surgery.
  • the disorders also include diseases involving the kidney or originating from the kidney tissue, such as polycystic kidney disease and chronic and acute renal failure.
  • /* w*/ 6,-5 -8 -1, ,-1: , 0, ,-7, ,-3, ,-5. , . ,-3. ,-2,-4 ,-4, , M ,-6, ,-5,2,-2,-5,0,-6,17,0,0,-6 ⁇ ,
  • filel and file2 are two dna or two protein sequences.
  • Max file length is 65535 (limited by unsigned short x in the jmp struct)
  • a sequence with 1/3 or more of its elements ACGTU is assumed to be DNA
  • the program may create a tmp file in /tmp to hold info about traceback.
  • dumpblockO * putline() put out a line (name, [num], seq, [num]): dumpblockO
  • static nm matches in core — for checking */ static lmax; /* lengths of stripped file names */ static ij[2]; /* jmp index for a path */ static nc[2]; /* number at start of current line */ static nip]; /* current elem number - for gapping */ static siz[2]; static char *ps[2]; /* ptr to current element */ static char *po[2]; /* ptr to next output char slot */ static char oouutt[[22]][[IP_LINE]; /* output line */ static char starfP 1 2]; /* set by stars() *//
  • *ps[i] toupper(*ps[i]); po[i]++; ps[i] + +;
  • *py++ *px; else if (islower(*px))
  • *py++ toupper(*px); if (index( " ATGCU “ , *(py- 1 ))) natgc++;
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO polypeptides.
  • cDNAs encoding various PRO polypeptides have been identified and isolated, as disclosed in further detail in the Examples below. It is noted that proteins produced in separate expression rounds may be given different PRO numbers but the UNQ number is unique for any given DNA and the encoded protein, and will not be changed.
  • PRO/number the protein encoded by the full length native nucleic acid molecules disclosed herein as well as all further native homologues and variants included in the foregoing definition of PRO, will be referred to as "PRO/number", regardless of their origin or mode of preparation.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0211 and PR0217.
  • Applicants have identified and isolated cDNA encoding PR0211 and PR0217 polypeptides, as disclosed in further detail in the Examples below.
  • BLAST FastA format sequence alignment computer programs, Applicants found that cDNA sequences encoding full-length native sequence PR0211 and PR0217 have homologies to known proteins having EGF-like domains.
  • the cDNA sequence DNA32292-1131 ( Figure 1, SEQ ID NO:l) has certain identify and a Blast score of 209 with PAC6_RAT and certain identify and a Blast score of 206 with Fibulin- 1, isoform c precursor.
  • the cDNA sequence DNA33094-1131 ( Figure 3, SEQ ID NO:3) has 36% identity and a Blast score of 336 with eastern newt tenascin, and 37 % identity and a Blast score of 331 with human tenascin- X precursor. Accordingly, it- is presently believed that PR0211 and PR0217 polypeptides disclosed in the present application are newly identified members of the EGF-like family and possesses properties typical of the EGF-like protein family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO230.
  • Applicants have identified and isolated cDNA encoding a PRO230 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that a cDNA sequence encoding full-length native sequence PRO230 has 48% amino acid identity with the rabbit tubulointerstitial nephritis antigen precursor.
  • PRO230 polypeptide disclosed in the present application is a newly identified member of the tubulointerstitial nephritis antigen family and possesses the ability to be recognized by human autoantibodies in certain forms of tubulointerstitial nephritis.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0232.
  • PR0232 polypeptides referred to in the present application as PR0232.
  • Applicants have identified and isolated cDNA encoding a PR0232 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that a portion of the full-length native sequence PR0232 (shown in Figure 9 and SEQ ID NO: 18) has 35 % sequence identity with a stem cell surface antigen from Gallus gallus. Accordingly, it is presently believed that the PR0232 polypeptide disclosed in the present application may be a newly identified stem cell antigen.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0187.
  • PR0187 polypeptides referred to in the present application as PR0187.
  • Applicants have identified and isolated cDNA encoding a PRO 187 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that a full-length native sequence PR0187 (shown in Figure 15) has 74% amino acid sequence identity and BLAST score of 310 with various androgen-induced growth factors and FGF-8. Accordingly, it is presently believed that PRO 187 polypeptide disclosed in the present application is a newly identified member of the FGF-8 protein family and may possess identify activity or property typical of the FGF-8-like protein family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0265.
  • PR0265 polypeptides referred to in the present application as PR0265.
  • Applicants have identified and isolated cDNA encoding a PR0265 polypeptide, as disclosed in further detail in the Examples below.
  • programs such as BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0265 polypeptide have significant homology with the fibromodulin protein and fibromodulin precursor protein.
  • the DNA encoding the PR0265 polypeptide has significant homology with platelet glycoprotein V, a member of the leucine rich related protein family involved in skin and wound repair.
  • PR0265 polypeptide disclosed in the present application is a newly identified member of the leucine rich repeat family and possesses protein protein binding capabilities, as well as be involved in skin and wound repair as typical of this family.
  • PR0219 Full-length PRQ219 Polypeptides
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0219.
  • Applicants have identified and isolated cDNA encoding a PR0219 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0219 polypeptide have significant homology with the mouse and human matrilin-2 precursor polypeptides. Accordingly, it is presently believed that PR0219 polypeptide disclosed in the present application is related to the matrilin-2 precursor polypeptide.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0246.
  • PR0246 polypeptides referred to in the present application as PR0246.
  • Applicants have identified and isolated cDNA encoding a PR0246 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that a portion of the PR0246 polypeptide has significant homology with the human cell surface protein HCAR. Accordingly, it is presently believed that PR0246 polypeptide disclosed in the present application may be a newly identified membrane-bound virus receptor or tumor cell-specific antigen.
  • PR0228 nucleotide sequences encoding polypeptides referred to in the present application as PR0228.
  • Applicants have identified and isolated cDNA encoding a PR0228 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0228 polypeptide have significant homology with the EMRl protein.
  • Applicants have also found that the DNA encoding the PR0228 polypeptide has significant homology with latrophilin, macrophage-restricted cell surface glycoprotein, B0457.1 and leucocyte antigen CD97 precursor.
  • PR0228 polypeptide disclosed in the present application is a newly identified member of the seven transmembrane superfamily and possesses characteristics and functional properties typical of this family.
  • PR0228 is a new member of the subgroup within this family to which CD97 and EMRl belong.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0533.
  • Applicants have identified and isolated cDNA encoding a PR0533 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST-2 and FastA sequence alignment computer programs Applicants found that a full-length native sequence PR0533 (shown in Figure 22 and SEQ ID NO: 59) has a Blast score of 509 and 53% amino acid sequence identity with fibroblast growth factor (FGF). Accordingly, it is presently believed that PR0533 disclosed in the present application is a newly identified member of the fibroblast growth factor family and may possess activity typical of such polypeptides.
  • FGF fibroblast growth factor
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0245.
  • PR0245 polypeptides referred to in the present application as PR0245.
  • Applicants have identified and isolated cDNA encoding a PR0245 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that a portion of the amino acid sequence of the PR0245 polypeptide has 60% amino acid identity with the human c-myb protein. Accordingly, it is presently believed that the PR0245 polypeptide disclosed in the present application may be a newly identified member of the transmembrane protein tyrosine kinase family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO220, PR0221 and PR0227.
  • PRO220 has amino acid identity with the amino acid sequence of a leucine rich protein wherein the identity is 87 % .
  • PRO220 additionally has amino acid identity with the neuronal leucine rich protein wherein the identity is 55 % .
  • the neuronal leucine rich protein is further described in Taguchi, et al, Mol. Brain Res.. 35:31-40 (1996).
  • PR0221 has amino acid identity with the SLIT protein precursor, wherein different portions of these two proteins have the respective percent identities of 39%, 38%, 34%, 31 %, and 30% .
  • PR0227 has amino acid identity with the amino acid sequence of platelet glycoprotein V precursor. The same results were obtained for human glycoprotein V. Different portions of these two proteins show the following percent identities of 30%, 28%, 28%, 31 %, 35%, 39% and 27%. Accordingly, it is presently believed that PRO220, PR0221 and PR0227 polypeptides disclosed in the present application are newly identified members of the leucine rich repeat protein superfamily and that each possesses protein-protein binding capabilities typical of the leucine rich repeat protein superfamily. It is also believed that they have capabilities similar to those of SLIT, the leucine rich repeat protein and human glycoprotein V.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0258.
  • PR0258 polypeptides referred to in the present application as PR0258.
  • Applicants have identified and isolated cDNA encoding a PR0258 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0258 polypeptide have significant homology with the CRTAM and poliovirus receptors. Accordingly, it is presently believed that PR0258 polypeptide disclosed in the present application is a newly identified member of the Ig superfamily and possesses virus receptor capabilities or regulates immune function as typical of this family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0266.
  • PR0266 polypeptides referred to in the present application as PR0266.
  • Applicants have identified and isolated cDNA encoding a PR0266 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0266 polypeptide have significant homology with the SLIT protein from Drosophilia. Accordingly, it is presently believed that PR0266 polypeptide disclosed in the present application is a newly identified member of the leucine rich repeat family and possesses ligand-ligand binding activity and neuronal development typical of this family.
  • SLIT has been shown to be useful in the study and treatment of Alzheimer's disease, supra, and thus, PR0266 may have involvement in the study and cure of this disease.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0269.
  • PR0269 polypeptides referred to in the present application as PR0269.
  • Applicants have identified and isolated cDNA encoding a PR0269 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST Altschul et al.
  • FAST Altschul et al.
  • sequence alignment computer programs Applicants found that the amino acid sequence encoded by nucleotides 314 to 1783 of the full-length native sequence PR0269 (shown in Figure 35 and SEQ ID NO:95) has significant homology to human urinary thrombomodulin and various thrombomodulin analogues respectively, to which it was aligned. Accordingly, it is presently believed that PR0269 polypeptide disclosed in the present application is a newly identified member of the thrombomodulin family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0287.
  • PR0287 polypeptides referred to in the present application as PR0287.
  • Applicants have identified and isolated cDNA encoding a PR0287 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0287 polypeptide have significant homology with the type 1 procollagen C-proteinase enhancer protein precursor and type 1 procollagen C-proteinase enhancer protein. Accordingly, it is presently believed that PR0287 polypeptide disclosed in the present application is a newly identified member of the C-proteinase enhancer protein family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0214.
  • Applicants have identified and isolated cDNA encoding a PR0214 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that a full-length native sequence PR0214 polypeptide (shown in Figure 40 and SEQ ID NO: 109) has 49% amino acid sequence identity with HT protein, a known member of the EGF-family.
  • the comparison resulted in a BLAST score of 920, with 150 matching nucleotides.
  • PR0214 polypeptide disclosed in the present application is a newly identified member of the family comprising EGF domains and may possess activities or properties typical of the EGF-domain containing family. 17.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0317.
  • cDN A encoding a PR0317 polypeptide has been identified and isolated, as disclosed in further detail in the Examples below.
  • BLASTTM and FastATM sequence alignment computer programs it was found that a full-length native-sequence PR0317 (shown in Figure 42 and SEQ ID NO: 114) has 92% amino acid sequence identity with EBAF-1. Further, it is closely aligned with many other members of the TGF- superfamily.
  • PR0317 disclosed in the present application is a newly identified member of the TGF- superfamily and may possess properties that are therapeutically useful in conditions of uterine bleeding, etc.
  • PR0317 may be useful in diagnosing or treating abnormal bleeding involved in gynecological diseases, for example, to avoid or lessen the need for a hysterectomy.
  • PR0317 may also be useful as an agent that affects angiogenesis in general, so PR0317 may be useful in anti-tumor indications, or conversely, in treating coronary ischemic conditions.
  • PR0317 has shown up in several tissues as well, but it does look to have a greater concentration in uterus. Hence, PR0317 may have a broader use by the body than EBAF-1. It is contemplated that, at least for some indications, PR0317 may have opposite effects from EBAF-1.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO301.
  • Applicants have identified and isolated cDNA encoding a PRO301 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that a full-length native sequence PRO301 (shown in Figure 44 and SEQ ID NO: 119) has a Blast score of 246 corresponding to 30% amino acid sequence identity with human A33 antigen precursor.
  • PRO301 disclosed in the present application is a newly identified member of the A33 antigen protein family and may be expressed in human neoplastic diseases such as colorectal cancer.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0224.
  • Applicants have identified and isolated cDNA encoding a PR0224 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that full-length native PR0224 ( Figure 46, SEQ ID NO: 127) has amino acid identity with apolipoprotein E receptor 2906 from homo sapiens.
  • the alignments of different portions of these two polypeptides show amino acid identities of 37% , 36% , 30% , 44% , 44% and 28% respectively.
  • Full-length native PR0224 (Figure 46, SEQ ID NO: 127) also has amino acid identity with very low-density lipoprotein receptor precursor from gall. The alignments of different portions of these two polypeptides show amino acid identities of 38% , 37% , 42% , 33% , and 37% respectively. Additionally, full-length native PR0224 (Figure 46, SEQ ID NO: 127) has amino acid identity with the chicken oocyte receptor P95 from Gallus gallus. The alignments of different portions of these two polypeptides show amino acid identities of 38%, 37%, 42%, 33 % , and 37% respectively. Moreover, full-length native PR0224 (Figure 46, SEQ ID NO: 127) has amino acid identity with very low density lipoprotein receptor short form precursor from humans.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0222.
  • Applicants have identified and isolated cDNA encoding a PR0222 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that a sequence encoding full-length native sequence PR0222 (shown in Figure 48 and SEQ ID NO: 132) has 25-26% amino acid identity with mouse complement factor h precursor, has 27-29% amino acid identity with complement receptor, has 25-47% amino acid identity with mouse complement C3b receptor type 2 long form precursor, has 40% amino acid identity with human hypothetical protein kiaa0247.
  • PR0222 polypeptide disclosed in the present application is a newly identified member of the complement receptor family and possesses activity typical of the complement receptor family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0234.
  • Applicants have identified and isolated cDNA encoding a PR0234 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST FastA- format sequence alignment computer programs
  • Applicants found that a cDNA sequence encoding full-length native sequence PR0234 has 31 % identity and Blast score of 134 with E-selectin precursor. Accordingly, it is presently believed that the PR0234 polypeptides disclosed in the present application are newly identified members of the lectin selectin family and possess activity typical of the lectin/selectin family.
  • PR0231 Full-length PRQ231 Polypeptides
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0231.
  • Applicants have identified and isolated cDNA encoding a PR0231 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that the full-length native sequence PR0231 polypeptide (shown in Figure 52 and SEQ ID NO: 142) has 30 % and 31 % amino acid identity with human and rat prostatic acid phosphatase precursor proteins, respectively. Accordingly, it is presently believed that the PR0231 polypeptide disclosed in the present application may be a newly identified member of the acid phosphatase protein family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0229.
  • PR0229 polypeptides referred to in the present application as PR0229.
  • Applicants have identified and isolated cDNA encoding a PR0229 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0229 polypeptide have significant homology with antigen wcl. l, M130 antigen, T cell surface glycoprotein CD6 and CD6. It also is related to Sp-alpha.
  • PR0229 polypeptide disclosed in the present application is a newly identified member of the family containing scavenger receptor homology, a sequence motif found in a number of proteins involved in immune function and thus possesses immune function and /or segments which resist degradation, typical of this family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0238.
  • PR0238 polypeptides referred to in the present application as PR0238.
  • Applicants have identified and isolated cDNA encoding a PR0238 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0238 polypeptide have significant homology with reductases, including oxidoreductase and fatty acyl-CoA reductase. Accordingly, it is presently believed that PR0238 polypeptide disclosed in the present application is a newly identified member of the reductase family and possesses reducing activity typical of the reductase family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0233.
  • PR0233 polypeptides referred to in the present application as PR0233.
  • Applicants have identified and isolated cDNA encoding a PR0233 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0233 polypeptide have significant homology with the reductase protein.
  • the DNA encoding the PR0233 polypeptide has significant homology with proteins from Caenorhabditis elegans. Accordingly, it is presently believed that PR0233 polypeptide disclosed in the present application is a newly identified member of the reductase family and possesses the ability to effect the redox state of the cell typical of the reductase family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0223.
  • PR0223 polypeptides referred to in the present application as PR0223.
  • Applicants have identified and isolated cDNA encoding a PR0223 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that the PR0223 polypeptide has significant homology with various serine carboxypeptidase polypeptides. Accordingly, it is presently believed that PR0223 polypeptide disclosed in the present application is a newly identified serine carboxypeptidase.
  • PR0235 Full-length PRQ235 Polypeptides
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0235.
  • Applicants have identified and isolated cDNA encoding a PR0235 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0235 polypeptide have significant homology with the various plexin proteins. Accordingly, it is presently believed that PR0235 polypeptide disclosed in the present application is a newly identified member of the plexin family and possesses cell adhesion properties typical of the plexin family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0236 and PR0262.
  • Applicants have identified and isolated cDNA encoding PR0236 and PR0262 polypeptides, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0236 and PR0262 polypeptides have significant homology with various ⁇ -galactosidase and ⁇ - galactosidase precursor polypeptides. Accordingly, it is presently believed that the PR0236 and PR0262 polypeptides disclosed in the present application are newly identified ⁇ -galactosidase homologs.
  • PR0239 Full-length PRQ239 Polypeptides
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0239.
  • Applicants have identified and isolated cDNA encoding a PR0239 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0239 polypeptide have significant homology with densin proteins. Accordingly, it is presently believed that PR0239 polypeptide disclosed in the present application is a newly identified member of the densin family and possesses cell adhesion and the ability to effect synaptic processes as is typical of the densin family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0257.
  • PR0257 polypeptides referred to in the present application as PR0257.
  • Applicants have identified and isolated cDNA encoding a PR0257 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0257 polypeptide have significant homology with the ebnerin precursor and ebnerin protein. Accordingly, it is presently believed that PR0257 polypeptide disclosed in the present application is a newly identified protein member which is related to the ebnerin protein.
  • PRO260 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO260.
  • Applicants have identified and isolated cDNA encoding a PRO260 polypeptide, as disclosed in further detail in the Examples below.
  • programs such as BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PRO260 polypeptide have significant homology with the alpha-1-fucosidase precursor. Accordingly, it is presently believed that PRO260 polypeptide disclosed in the present application is a newly identified member of the fucosidase family and possesses enzymatic activity related to fucose residues typical of the fucosidase family.
  • PR0263 Full-length polypeptides
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0263.
  • Applicants have identified and isolated cDNA encoding a PR0263 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0263 polypeptide have significant homology with the CD44 antigen and related proteins.
  • PR0263 polypeptide disclosed in the present application is a newly identified member of the CD44 antigen family and possesses at least one of the properties associated with these antigens, i.e., cancer and HIV marker, cell-cell or cell-matrix interactions, regulating cell traffic, lymph node homing, transmission of growth signals, and presentation of chemokines and growth facors to traveling cells.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO270.
  • Applicants have identified and isolated cDNA encoding a PRO270 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST Altschul et al.
  • FastA sequence alignment computer programs
  • Applicants found that that various portions of the PRO270 polypeptide have significant homology with various thioredoxin proteins. Accordingly, it is presently believed that PRO270 polypeptide disclosed in the present application is a newly identified member of the thioredoxin family and possesses the ability to effect reduction-oxidation (redox) state typical of the thioredoxin family.
  • redox reduction-oxidation
  • PR0271 Full-length PRQ271 Polypeptides
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0271.
  • Applicants have identified and isolated cDNA encoding a PR0271 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that the PR0271 polypeptide has significant homology with various link proteins and precursors thereof. Accordingly, it is presently believed that PR0271 polypeptide disclosed in the present application is a newly identified link protein homolog.
  • PR0272 nucleotide sequences encoding polypeptides referred to in the present application as PR0272.
  • Applicants have identified and isolated cDNA encoding a PR0272 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0272 polypeptide have significant homology with the human reticulocalbin protein and its precursors.
  • Applicants have also found that the DNA encoding the PR0272 polypeptide has significant homology with the mouse reticulocalbin precursor protein. Accordingly, it is presently believed that PR0272 polypeptide disclosed in the present application is a newly identified member of the reticulocalbin family and possesses the ability to bind calcium typical of the reticulocalbin family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0294.
  • PR0294 polypeptides referred to in the present application as PR0294.
  • Applicants have identified and isolated cDNA encoding a PR0294 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0294 polypeptide have significant homology with the various portions of a number of collagen proteins. Accordingly, it is presently believed that PR0294 polypeptide disclosed in the present application is a newly identified member of the collagen family.
  • PR0295 nucleotide sequences encoding polypeptides referred to in the present application as PR0295.
  • Applicants have identified and isolated cDNA encoding a PR0295 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0295 polypeptide have significant homology with integrin proteins. Accordingly, it is presently believed that PR0295 polypeptide disclosed in the present application is a newly identified member of the integrin family and possesses cell adhesion typical of the integrin family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0293.
  • PR0293 nucleotide sequences encoding polypeptides referred to in the present application as PR0293.
  • Applicants have identified and isolated cDNA encoding a PR0293 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that portions of the PR0293 polypeptide have significant homology with the neuronal leucine rich repeat proteins 1 and 2, (NLRR-1 and NLRR-2), particularly NLRR-2.
  • PR0293 polypeptide disclosed in the present application is a newly identified member of the neuronal leucine rich repeat protein family and possesses ligand-ligand binding activity typical of the NRLL protein family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0247.
  • PR0247 polypeptides referred to in the present application as PR0247.
  • Applicants have identified and isolated cDNA encoding a PR0247 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0247 polypeptide have significant homology with densin.
  • the DNA encoding the PR0247 polypeptide has significant homology with a number of other proteins, including KIAA0231. Accordingly, it is presently believed that PR0247 polypeptide disclosed in the present application is a newly identified member of the leucine rich repeat family and possesses ligand binding abilities typical of this family.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO302, PRO303, PRO304, PRO307 and PR0343.
  • Applicants have identified and isolated cDNA encoding PRO302, PRO303, PRO304, PRO307 and PR0343 polypeptides, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PRO302, PRO303, PRO304, PRO307 and PR0343 polypeptides have significant homology with various protease proteins. Accordingly, it is presently believed that the PRO302, PRO303, PRO304, PRO307 and PR0343 polypeptides disclosed in the present application are newly identified protease proteins.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0328.
  • PR0328 polypeptides referred to in the present application as PR0328.
  • Applicants have identified and isolated cDNA encoding a PR0328 polypeptide, as disclosed in further detail in the Examples below.
  • GLIP human glioblastoma protein
  • Applicants found that various portions of the PR0328 polypeptide have significant homology with the cysteine rich secretory protein (“CRISP”) as identified by BLAST homology [ECCRISP3 1, S68683, and CRS3 HUMAN].
  • CRISP cysteine rich secretory protein
  • PR0328 polypeptide disclosed in the present application is a newly identified member of the GLIP or CRISP families and possesses transcriptional regulatory activity typical of the GLIP or CRISP families. 42. Full-length PRQ335. PRQ331 and PRQ326 Polypeptides
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0335, PR0331 or PR0326.
  • Applicants have identified and isolated cDNA encoding a PR0335, PR0331 or PR0326 polypeptide, as disclosed in further detail in the Examples below.
  • BLAST and FastA sequence alignment computer programs Applicants found that various portions of the PR0335, PR0331 or PR0326 polypeptide have significant homology with LIG-1, ALS and in the case of PR0331, additionally, decorin.
  • PR0335, PR0331 and PR0326 polypeptides disclosed in the present application are newly identified members of the leucine rich repeat superfamily, and particularly, are related to LIG-1 and possess the biological functions of this family as discussed and referenced herein.
  • the present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0332.
  • Applicants have identified and isolated cDNA encoding PR0332 polypeptides, as disclosed in further detail in the Examples below.
  • a full-length native sequence PR0332 (shown in Figure 108 and SEQ ID NO:310) has about 30-40% amino acid sequence identity with a series of known proteoglycan sequences, including, for example, fibromodulin and fibromodulin precursor sequences of various species (FMOD_BOVIN, FMOD_CHICK, FMOD_RAT, FMOD_MOUSE, FMOD.HUMAN, P_R36773), osteomodulin sequences (AB000114_1, AB007848 ), decorin sequences (CFU83141_1, OCU03394 , P R42266, P R42267, P.R42260, P R89439), keratan sulfate proteoglycans (BTU48360.1 , AF022890 .
  • fibromodulin and fibromodulin precursor sequences of various species FMOD_BOVIN, FMOD_CHICK, FMOD_RAT, FMOD_MOUSE, FMOD.HUMAN, P_R36773
  • PR0332 disclosed in the present application is a new proteoglycan-type molecule, and may play a role in regulating extracellular matrix, cartilage, and/or bone function.

Abstract

The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.

Description

SECRETED AND TRANSMEMBRANE POLYPEPTIDES AND NUCLEIC ACIDS ENCODING THE
SAME
FIELD OF THE INVENTION The present invention relates generally to the identification and isolation of novel DNA and to the recombinant production of novel polypeptides.
BACKGROUND OF THE INVENTION Extracellular proteins play important roles in, among other things, the formation, differentiation and maintenance of multicellular organisms. The fate of many individual cells, e.g. , proliferation, migration, differentiation, or interaction with other cells, is typically governed by information received from other cells and/or the immediate environment. This information is often transmitted by secreted polypeptides (for instance, mitogenic factors, survival factors, cytotoxic factors, differentiation factors, neuropeptides, and hormones) which are, in turn, received and interpreted by diverse cell receptors or membrane-bound proteins. These secreted polypeptides or signaling molecules normally pass through the cellular secretory pathway to reach their site of action in the extracellular environment.
Secreted proteins have various industrial applications, including as pharmaceuticals, diagnostics, biosensors and bioreactors. Most protein drugs available at present, such as thrombolytic agents, interferons, interleukins, erythropoietins, colony stimulating factors, and various other cytokines, are secretory proteins. Their receptors, which are membrane proteins, also have potential as therapeutic or diagnostic agents. Efforts are being undertaken by both industry and academia to identify new, native secreted proteins. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)].
Membrane-bound proteins and receptors can play important roles in, among other things, the formation, differentiation and maintenance of multicellular organisms. The fate of many individual cells, e.g. , proliferation, migration, differentiation, or interaction with other cells, is typically governed by information received from other cells and/or the immediate environment. This information is often transmitted by secreted polypeptides (for instance, mitogenic factors, survival factors, cytotoxic factors, differentiation factors, neuropeptides, and hormones) which are, in turn, received and interpreted by diverse cell receptors or membrane-bound proteins. Such membrane-bound proteins and cell receptors include, but are not limited to, cytokine receptors, receptor kinases, receptor phosphatases, receptors involved in cell-cell interactions, and cellular adhesin molecules like selectins and integrins. For instance, transduction of signals that regulate cell growth and differentiation is regulated in part by phosphorylation of various cellular proteins. Protein tyrosine kinases, enzymes that catalyze that process, can also act as growth factor receptors. Examples include fibroblast growth factor receptor and nerve growth factor receptor. Membrane-bound proteins and receptor molecules have various industrial applications, including as pharmaceutical and diagnostic agents. Receptor immunoadhesins, for instance, can be employed as therapeutic agents to block receptor-ligand interactions. The membrane-bound proteins can also be employed for screening of potential peptide or small molecule inhibitors of the relevant receptor/ligand interaction.
Efforts are being undertaken by both industry and academia to identify new, native receptor or membrane-bound proteins . Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel receptor or membrane-bound proteins.
1. PRQ211 and PRQ217
Epidermal growth factor (EGF) is a conventional mitogenic factor that stimulates the proliferation of various types of cells including epithelial cells and fibroblasts. EGF binds to and activates the EGF receptor (EGFR), which initiates intracellular signaling and subsequent effects. The EGFR is expressed in neurons of the cerebral cortex, cerebellum, and hippocampus in addition to other regions of the central nervous system, (CNS). In addition, EGF is also expressed in various regions of the CNS. Therefore, EGF acts not only on mitotic cells, but also on postmitotic neurons. In fact, many studies have indicated that EGF has neurotrophic or neuromodulatory effects on various types of neurons in the CNS. For example, EGF acts directly on cultured cerebral cortical and cerebellar neurons, enhancing neurite outgrowth and survival. On the other hand, EGF also acts on other cell types, including septal cholinergic and mesencephalic dopaminergic neurons, indirectly through glial cells. Evidence of the effects of EGF on neurons in the CNS is accumulating, but the mechanisms of action remain essentially unknown. EGF-induced signaling in mitotic cells is better understood than in postmitotic neurons. Studies of cloned pheochromocytoma PC 12 cells and cultured cerebral cortical neurons have suggested that the EGF-induced neurotrophic actions are mediated by sustained activation of the EGFR and mitogen-activated protein kinase (MAPK) in response to EGF. The sustained intracellular signaling correlates with the decreased rate of EGFR down-regulation, which might determine the response of neuronal cells to EGF. It is likely that EGF is a multi-potent growth factor that acts upon various types of cells including mitotic cells and postmitotic neurons.
EGF is produced by the salivary and Brunner's glands of the gastrointestinal system, kidney, pancreas, thyroid gland, pituitary gland, and the nervous system, and is found in body fluids such as saliva, blood, cerebrospinal fluid (CSF), urine, amniotic fluid, prostatic fluid, pancreatic juice, and breast milk, Plata-Salaman, Peptides 12: 653-663 (1991). EGF is mediated by its membrane specific receptor, which contains an intrinsic tyrosine kinase.
Stoscheck et al, J. Cell Biochem. 31 : 135-152 (1986). EGF is believed to function by binding to the extracellular portion of its receptor which induces a transmembrane signal that activates the intrinsic tyrosine kinase.
Purification and sequence analysis of the EGF-like domain has revealed the presence of six conserved cysteine residues which cross-bind to create three peptide loops, Savage et al, J. Biol. Chem. 248: 7669-7672 (1979). It is now generally known that several other peptides can react with the EGF receptor which share the same generalized motif XJ2X1CXiι5CXwCXCXiGX2CXn, where X represents any non-cysteine amino acid, and n is a variable repeat number. Non isolated peptides having this motif include TGF-α, amphiregulin, schwannoma-derived growth factor (SDGF), heparin-binding EGF-like growth factors and certain virally encoded peptides (e.g., Vaccinia virus, Reisner, Nature 313: 801-803 (1985), Shope fibroma virus, Chang et al., Mol Cell Biol. 7: 535-540 (1987), Molluscum contagiosum, Porter and Archard, J. Gen. Virol. 68: 673-682 (1987), and Myxoma virus, Upton et al., J. Virol. 6J.: 1271-1275 (1987), Prigent and Lemoine, Prog. Growth Factor Res. 4: 1-24 (1992).
EGF-like domains are not confined to growth factors but have been observed in a variety of cell-surface and extracellular proteins which have interesting properties in cell adhesion, protein-protein interaction and development, Laurence and Gusterson, Tumor Biol. IT : 229-261 (1990). These proteins include blood coagulation factors (factors VI, IX, X, XII, protein C, protein S, protein Z, tissue plasminogen activator, urokinase), extracellular matrix components (laminin, cytotactin, entactin), cell surface receptors (LDL receptor, thrombomodulin receptor) and immunity-related proteins (complement Clr, uromodulin).
Even more interesting, the general structure pattern of EGF-like precursors is preserved through lower organisms as well as in mammalian cells. A number of genes with developmental significance have been identified in invertebrates with EGF-like repeats. For example, the notch gene of Drosophila encodes 36 tandemly arranged 40 amino acid repeats which show homology to EGF, Wharton et al., Cell 43: 557-581 (1985). Hydropathy plots indicate a putative membrane spanning domain, with the EGF-related sequences being located on the extracellular side of the membrane. Other homeotic genes with EGF-like repeats include Delta, 95F and 5ZD which were identified using probes based on Notch, and the nematode gene Lin-12 which encodes a putative receptor for a developmental signal transmitted between two specified cells. Specifically, EGF has been shown to have potential in the preservation and maintenance of gastrointestinal mucosa and the repair of acute and chronic mucosal lesions, Konturek et al, Eur. J. Gastroenterol Hepatol. 7 (10), 933-37 (1995), including the treatment of necrotizing enterocolitis, Zollinger- Ellison syndrome, gastrointestinal ulceration gastrointestinal ulcerations and congenital microvillus atrophy, Guglietta and Sullivan, Eur. J. Gastroenterol Hepatol, 7(10), 945-50 (1995). Additionally, EGF has been implicated in hair follicle differentiation; du Cros, J. Invest. Dermatol. 101 (1 Suppl.), 106S-113S (1993), Hillier, Clin. Endocrinol. 33(4), 427-28 (1990); kidney function, Hamm et al, Semin. Nephrol. 13 (1): 109-15 (1993), Harris, Am. J. Kidney Dis. 17(6): 627-30 (1991); tear fluid, van Setten et al, Int. Ophthalmol 15(6); 359-62 (1991); vitamin K mediated blood coagulation, Stenflo etal, BloodTS(7): 1637-51 (1991). EGF is also implicated various skin disease characterized by abnormal keratinocyte differentiation, e.g. , psoriasis, epithelial cancers such as squamous cell carcinomas of the lung, epidermoid carcinoma of the vulva and gliomas. King et al, Am. J. Med. Sci. 296: 154-158 (1988).
Of great interest is mounting evidence that genetic alterations in growth factors signaling pathways are closely linked to developmental abnormalities and to chronic diseases including cancer. Aaronson, Science 254: 1146-1153 (1991). For example, c-erb-2 (also known as HER-2), a proto-oncogene with close structural similarity to EGF receptor protein, is overexpressed in human breast cancer. King et al. , Science 229: 974-976 (1985); Gullick, Hormones and their actions, Cooke et al , eds, Amsterdam, Elsevier, pp 349-360 (1986). We herein describe the identification and characterization of novel polypeptides having homology to EGF, wherein those polypeptides are herein designated PR0211 and PR0217.
2. PRO230
Nephritis is a condition characterized by inflammation of the kidney affecting the structure and normal function of the kidney. This condition can be chronic or acute and is generally caused by infection, degenerative process or vascular disease. In all cases, early detection is desirable so that the patient with nephritis can begin treatment of the condition.
An approach to detecting nephritis is to determine the antigens associated with nephritis and antibodies thereto. In rabbit, a tubulointerstitial nephritis antigen (TIN-ag) has been reported in Nelson, T. R., et al., Biol. Chem.. 270(27): 16265-70 (July 1995) (GENBANK/U24270). This study reports that the rabbit TIN-ag is a basement membrane glycoprotein having a predicted amino acid sequence which has a carboxyl-terminal region exhibiting 30% homology with human preprocathepsin B, a member of the cy stein proteinase family of proteins. It is also reported that the rabbit TIN-ag has a domain in the amino-terminal region containing an epidermal growth factor-like motif that shares homology with laminin A and S chains, alpha 1 chain of type I collagen, von Willebrand's factor and mucin, indicating structural and functional similarities. Studies have also been conducted in mice. However, it is desirable to identify tubulointerstitial nephritis antigens in humans to aid in the development of early detection methods and treatment of nephritis.
Proteins which have homology to tubulointerstitial nephritis antigens are of particular interest to the medical and industrial communities. Often, proteins having homology to each other have similar function. It is also of interest when proteins having homology do not have similar functions, indicating that certain structural motifs identify information other than function, such as locality of function. We herein describe the identification and characterization of a novel polypeptide, designated hgerein as PRO230, which has homology to tubulointerstitial nephritis antigens.
3. PRQ232
Stem cells are undifferentiated cells capable of (a) proliferation, (b) self maintenance, (c) the production of a large number of differentiated functional progeny, (d) regeneration of tissue after injury and/or (e) a flexibility in the use of these options. Stem cells often express cell surface antigens which are capable of serving as cell specific markers that can be exploited to identify stem cells, thereby providing a means for identifying and isolating specific stem cell populations.
Having possession of different stem cell populations will allow for a number of important applications. For example, possessing a specific stem cell population will allow for the identification of growth factors and other proteins which are involved in their proliferation and differentiation. In addition, there may be as yet undiscovered proteins which are associated with (1) the early steps of dedication of the stem cell to a particular lineage, (2) prevention of such dedication, and (3) negative control of stem cell proliferation, all of which may be identified if one has possession of the stem cell population. Moreover, stem cells are important and ideal targets for gene therapy where the inserted genes promote the health of the individual into whom the stem cells are transplanted. Finally, stem cells may play important roles in transplantation of organs or tissues, for example liver regeneration and skin grafting.
Given the importance of stem cells in various different applications, efforts are currently being undertaken by both industry and academia to identify new, native stem cell antigen proteins so as to provide specific cell surface markers for identifying stem cell populations as well as for providing insight into the functional roles played by stem cell antigens in cell proliferation and differentiation. We herein describe the identification and characterization of novel polypeptides having homology to a stem cell antigen, wherein those polypeptides are herein designated as PR0232 polypeptides..
4. PRQ187 Growth factors are molecular signals or mediators that enhance cell growth or proliferation, alone or in concert, by binding to specific cell surface receptors. However, there are other cellular reactions than only growth upon expression to growth factors. As a result, growth factors are better characterized as multifunctional and potent cellular regulators. Their biological effects include proliferation, chemotaxis and stimulation of extracellular matrix production. Growth factors can have both stimulatory and inhibitory effects. For example, transforming growth factor (TGF-β) is highly pleiotropic and can stimulate proliferation in some cells, especially connective tissue, while being a potent inhibitor of proliferation in others, such as lymphocytes and epithelial cells.
The physiological effect of growth stimulation or inhibition by growth factors depends upon the state of development and differentiation of the target tissue. The mechanism of local cellular regulation by classical endocrine molecules involves comprehends autocrine (same cell), juxtacrine (neighbor cell), and paracrine (adjacent cells) pathways. Peptide growth factors are elements of a complex biological language, providing the basis for intercellular communication. They permit cells to convey information between each other, mediate interaction between cells and change gene expression. The effect of these multifunctional and pluripotent factors is dependent on the presence or absence of other peptides. FGF-8 is a member of the fibroblast growth factors (FGFs) which are a family of heparin-binding, potent mitogens for both normal diploid fibroblasts and established cell lines, Gospodarowicz et al. ( 1984), Proc. Natl. Acad. Sci. USA 81:6963. The FGF family comprises acidic FGF (FGF-1), basic FGF (FGF-2), INT-2 (FGF-3), K-FGF/HST (FGF-4), FGF-5, FGF-6, KGF (FGF-7), AIGF (FGF-8) among others. All FGFs have two conserved cysteine residues and share 30-50% sequence homology at the amino acid level. These factors are mitogenic for a wide variety of normal diploid mesoderm-derived and neural crest-derived cells, including granulosa cells, adrenal cortical cells, chondrocytes, myoblasts, corneal and vascular endothelial cells (bovine or human), vascular smooth muscle cells, lens, retina and prostatic epithelial cells, oligodendrocytes, astrocytes, chrondocytes, myoblasts and osteoblasts.
Fibroblast growth factors can also stimulate a large number of cell types in a non-mitogenic manner. These activities include promotion of cell migration into wound area (chemotaxis), initiation of new blood vessel formulation (angiogenesis), modulation of nerve regeneration and survival (neurotrophism), modulation of endocrine functions, and stimulation or suppression of specific cellular protein expression, extracellular matrix production and cell survival. Baird & Bohlen, Handbook of Exp. Pharmacol. 95(1): 369-418, Springer, (1990). These properties provide a basis for using fibroblast growth factors in therapeutic approaches to accelerate wound healing, nerve repair, collateral blood vessel formation, and the like. For example, fibroblast growth factors have been suggested to minimize myocardium damage in heart disease and surgery (U.S. P. 4,378,347). FGF-8, also known as androgen-induced growth factor (AIGF), is a 215 amino acid protein which shares 30-40% sequence homology with the other members of the FGF family. FGF-8 has been proposed to be under androgenic regulation and induction in the mouse mammary carcinoma cell line SC3. Tanaka et al., Proc. Natl. Acad. Sci. USA 89: .8928-8932 (1992); Sato et al, J. Steroid Biochem. Molec. Biol. £7: 91-98 (1993). As a result, FGF-8 may have a local role in the prostate, which is known to be an androgen-responsive organ. FGF-8 can also be oncogenic, as it displays transforming activity when transfected into NIH-3T3 fibroblasts. Kouhara et al., Oncogene 9455-462 (1994). While FGF-8 has been detected in heart, brain, lung, kidney, testis, prostate and ovary, expression was also detected in the absence of exogenous androgens. Schmitt et al., J. Steroid Biochem. Mol. Biol. 57 (3-4): 173-78 (1996).
FGF-8 shares the property with several other FGFs of being expressed at a variety of stages of murine embryogenesis, which supports the theory that the various FGFs have multiple and perhaps coordinated roles in differentiation and embryogenesis. Moreover, FGF-8 has also been identified as a protooncogene that cooperates with Wnt-1 in the process of mammary tumorigenesis (Shackleford etα/., Proc. Natl. Acad. Sci. USA 90, 740-744 (1993); Heikinheimo et al, Mech. Dev. 48: 129-138 (1994)).
In contrast to the other FGFs, FGF-8 exists as three protein isoforms, as a result of alternative splicing of the primary transcript. Tanaka et al., supra. Normal adult expression of FGF-8 is weak and confined to gonadal tissue, however northern blot analysis has indicated that FGF-8 mRNA is present from day 10 through day 12 or murine gestation, which suggests that FGF-8 is important to normal development. Heikinheimo et al., Mech Dev. 48(2): 129-38 (1994). Further in situ hybridization assays between day 8 and 16 of gestation indicated initial expression in the surface ectoderm of the first bronchial arches, the frontonasal process, the forebrain and the midbrain-hindbrain junction. At days 10-12, FGF-8 was expressed in the surface ectoderm of the forelimb and hindlimb buds, the nasal its and nasopharynx, the infundibulum and in the telencephalon, diencephalon and metencephalon. Expression continues in the developing hindlimbs through day 13 of gestation, but is undetectable thereafter. The results suggest that FGF-8 has a unique temporal and spatial pattern in embryogenesis and suggests a role for this growth factor in multiple regions of ectodermal differentiation in the post-gastrulation embryo. We herein describe the identification of novel poypeptides having homology to FGF-8, wherein those polypeptides are heein designated PRO 187 polypeptides.
5. PRQ265
Protein-protein interactions include receptor and antigen complexes and signaling mechanisms. As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction.
Thus, the underlying mechanisms of protein-protein interactions are of interest to the scientific and medical community.
All proteins containing leucine-rich repeats are thought to be involved in protein-protein interactions. Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. The crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglubular shape. These two features have been indicated as responsible for the protein-binding functions of proteins containing leucine-rich repeats. See, Kobe and Deisenhofer, Trends Biochem. Sci.. 19(10):415-421 (Oct. 1994).
A study has been reported on leucine-rich proteoglycans which serve as tissue organizers, orienting and ordering collagen fibrils during ontogeny and are involved in pathological processes such as wound healing, tissue repair, and tumor stroma formation. Iozzo, R. V., Crit. Rev. Biochem. Mol. Biol.. 32(2): 141-174 (1997). Others studies implicating leucine rich proteins in wound healing and tissue repair are De La Salle, C. , et al.. Vouv. Rev. Fr. Hematol. (Germany), 37(4):215-222 (1995), reporting mutations in the leucine rich motif in a complex associated with the bleeding disorder Bernard-Soulier syndrome and Chlemetson, K. J., Thromb. Haemost. (Germany), 74(1): 111-1 16 (July 1995), reporting that platelets have leucine rich repeats. Another protein of particular interest which has been reported to have leucine-rich repeats is the SLIT protein which has been reported to be useful in treating neuro-degenerative diseases such as Alzheimer's disease, nerve damage such as in Parkinson's disease, and for diagnosis of cancer, see, Artavanistsakonas, S. and Rothberg, J. M., WO9210518-A1 by Yale University. Other studies reporting on the biological functions of proteins having leucine-rich repeats include: Tayar, N., et al., Mol. Cell Endocrinol.. (Ireland), 125(l-2):65-70 (Dec. 1996) (gonadotropin receptor involvement); Miura, Y., et al., Nippon Rinsho (Japan), 54(7): 1784-1789 (July 1996) (apoptosis involvement); Harris, P. C, et al., J. Am. Soc. Nephrol.. 6(4): 1125-1133 (Oct. 1995) (kidney disease involvement); and Ruoslahti, E. I., et al., WO9110727-A by La Jolla Cancer Research Foundation (decorin binding to transforming growth factor-β involvement for treatment for cancer, wound healing and scarring). Also of particular interest is fibromodulin and its use to prevent or reduce dermal scarring. A study of fibromodulin is found in U.S. Patent No. 5,654,270 to Ruoslahti, et al.
Efforts are therefore being undertaken by both industry and academia to identify new proteins having leucine rich repeats to better understand protein-protein interactions. Of particular interest are those proteins having leucine rich repeats and homology to known proteins having leucine rich repeats such as fibromodulin, the SLIT protein and platelet glycoprotein V.1 Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound proteins having leucine rich repeats. We herein describe the identification and characterization of novel polypeptides having homology to fibromodulin, herein designated as PR0265 polypeptides.
6. PRQ219 Human matrilin-2 polypeptide is a member of the von Willebrand factor type A-like module superfamily. von Willebrand factor is a protein which plays an important role in the maintenence of hemostasis. More specifically, von Willebrand factor is a protein which is known to participate in platelet-vessel wall interactions at the site of vascular injury via its ability to interact and form a complex with Factor VIII. The absence of von Willebrand factor in the blood causes an abnormality with the blood platelets that prevents platelet adhesion to the vascular wall at the site of the vascular injury. The result is the propensity for brusing, nose bleeds, intestinal bleeding, and the like comprising von Willebrand's disease.
Given the physiological importance of the blood clotting factors, efforts are currently being undertaken by both industry and academia to identify new, native proteins which may be involved in the coagulation process. We herein describe the identification of a novel full-length polypeptide which possesses homology to the human matrilin-2 precursor polypeptide.
7. PRQ246 The cell surface protein HCAR is a membrane-bound protein that acts as a receptor for subgroup C of the adenoviruses and subgroup B of the coxsackieviruses. Thus, HCAR may provide a means for mediating viral infection of cells in that the presence of the HCAR receptor on the cellular surface provides a binding site for viral particles, thereby facilitating viral infection.
In light of the physiological importance of membrane-bound proteins and specficially those which serve a cell surface receptor for viruses, efforts are currently being undertaken by both industry and academia to identify new, native membrane-bound receptor proteins. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel receptor proteins. We herein describe a novel membrane-bound polypeptide (designated herein as PR0246) having homology to the cell surface protein HCAR and to various tumor antigens including A33 and carcinoembryonic antigen, wherein this polypeptide may be a novel cell surface virus receptor or tumor antigen.
8. PRQ228
There are a number of known seven transmembrane proteins and within this family is a group which includes CD97 and EMRl . CD97 is a seven-span transmembrane receptor which has a cellular ligand, CD55, DAF. Hamann, et al., J. Exp. Med. (U.S.), 184(3): 1189 (1996). Additionally, CD97 has been reported as being a dedifferentiation marker in human thyroid carcinomas and as associated with inflammation. Aust, et al. , Cancer Res. (U.S.), 57(9): 1798 (1997); Gray, et al., J. Immunol. (U.S.), 157(12):5438 (1996). CD97 has also been reported as being related to the secretin receptor superfamily, but unlike known members of that family, CD97 and EMRl have extended extracellular regions that possess several EGF domains at the N-terminus. Hamann, et al. , Genomics. 32(1): 144 (1996); Harmann, et al., J. Immunol.. 155(4): 1942 (1995). EMRl is further described in Lin, et al., Genomics. 41(3):301 (1997) and Baud, et al., Genomics. 26(2):334 (1995). While CD97 and EMRl appear to be related to the secretin receptors, a known member of the secretin family of G protein-coupled receptors includes the alpha-latroxin receptor, latrophilin, which has been described as calcium independent and abundant among neuronal tissues. Lelianova, et al., J. Biol. Chem.. 272(34), 21504 (1997); Davletov, et al., J. Biol. Chem. (U.S.), 271(38):23239 (1996). Both members of the secretin receptor superfamily and non-members which are related to the secretin receptor superfamily, or CRF and calcitonin receptors are of interest. In particular, new members of these families, identified by their homology to known proteins, are of interest.
Efforts are being undertaken by both industry and academia to identify new membrane-bound receptor proteins, particularly transmembrane proteins with EGF repeats and large N-terminuses which may belong to the family of seven-transmembrane proteins of which CD97 and EMRl are members. We herein describe the identification and charactization of novel polypeptides having homology to CD97 and EMRl, designated herein as PR0228 polypeptides.
9. PRQ533
Growth factors are molecular signals or mediators that enhance cell growth or proliferation, alone or in concert, by binding to specific cell surface receptors, however, there are other cellular reactions than only growth upon expression to growth factors. As a result, growth factors are better characterized as multifunctional and potent cellular regulators. Their biological effects include proliferation, chemotaxis and stimulation of extracellular matrix production. Growth factors can have both stimulatory and inhibitory effects. For example, transforming growth factors (TGF-β) is highly pleiotropic and can stimulate proliferation in some cells, especially connective tissues, while being a potent inhibitor of proliferation in others, such as lymphocytes and epithelial cells.
The physiological effect of growth stimulation or inhibition by growth factors depends upon the state of development and differentiation of the target tissue. The mechanism of local cellular regulation by classical endocrine molecules comprehends autocrine (same cell), juxtacrine (neighbor cell), and paracrine (adjacent cell) pathways. Peptide growth factors are elements of a complex biological language, providing the basis for intercellular communication. They permit cells to convey information between each other, mediate interaction between cells and change gene expression, the effect of these multifunctional and pluripotent factors is dependent on the presence or absence of other peptides.
Fibroblast growth factors (FGFs) are a family of heparin-binding, potent mitogens for both normal diploid fibroblasts and established cell lines, Godpodarowicz, D. et al. (1984), Proc. Natl. Acad. Sci. USA 81: 6983. the FGF family comprises acidic FGF (FGF-1), basic FGF (FGF-2), INT-2 (FGF-3), K-FGF/HST (FGF- ' 4), FGF-5, FGF-6, KGF (FGF-7), AIGF (FGF-8) among others. All FGFs have two conserved cysteine residues and share 30-50% sequence homology at the amino acid level. These factors are mitogenic for a wide variety of normal diploid mesoderm-derived and neural crest-derived cells, inducing granulosa cells, adrenal cortical cells, chrondocytes, myoblasts, corneal and vascular endothelial cells (bovine or human), vascular smooth muscle cells, lens, retina and prostatic epithelial cells, oligodendrocytes, astrocytes, chrondocytes, myoblasts and osteoblasts.
Fibroblast growth factors can also stimulate a large number of cell types in a non-mitogenic manner. These activities include promotion of cell migration into a wound area (chemotaxis), initiation of new blood vessel formulation (angiogenesis), modulation of nerve regeneration and survival (neurotrophism), modulation of endocrine functions, and stimulation or suppression of specific cellular protein expression, extracellular matrix production and cell survival. Baird, A. & Bohlen, P., Handbook of Exp. Phrmacol. 95(1): 369-418 (1990). These properties provide a basis for using fibroblast growth factors in therapeutic approaches to accelerate wound healing, nerve repair, collateral blood vessel formation, and the like. For example, fibroblast growth factors, have been suggested to minimize myocardium damage in heart disease and surgery (U.S. P. 4,378,437). We herein describe the identification and characterization of novel polypeptides having homology to FGF, herein designated PR0533 polypeptides.
10. PRQ245
Some of the most important proteins involved in the above described regulation and modulation of cellular processes are the enzymes which regulate levels of protein phosphorylation in the cell. For example, it is known that the transduction of signals that regulate cell growth and differentiation is regulated at least in part by phosphorylation and dephosphorylation of various cellular proteins. The enzymes that catalyze these processes include the protein kinases, which function to phosphorylate various cellular proteins, and the protein phosphatases, which function to remove phosphate residues from various cellular proteins. The balance of the level of protein phosphorylation in the cell is thus mediated by the relative activities of these two types of enzymes.
Although many protein kinase enzymes have been identified, the physiological role played by many of these catalytic proteins has yet to be elucidated. It is well known, however, that a number of the known protein kinases function to phosphorylate tyrosine residues in proteins, thereby leading to a variety of different effects. Perhaps most importantly, there has been a great deal of interest in the protein tyrosine kinases since the discovery that many oncogene products and growth factors possess intrinsic protein tyrosine kinase activity. There is, therefore, a desire to identify new members of the protein tyrosine kinase family. Given the physiological importance of the protein kinases, efforts are being undertaken by both industry and academia to identify new, native kinase proteins. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel kinase proteins. We herein describe the identification and characterization of novel polypeptides having homology to tyrosine kinase proteins, designated herein as PR0245 polypeptides.
11. PRO220. PRQ221 and PRQ227
Protein-protein interactions include receptor and antigen complexes and signaling mechanisms. As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction. Thus, the underlying mechanisms of protein-protein interactions are of interest to the scientific and medical community.
All proteins containing leucine-rich repeats are thought to be involved in protein-protein interactions. Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. The crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglubular shape. These two features have been indicated as responsible for the protein-binding functions of proteins containing leucine-rich repeats. See, Kobe and Deisenhofer, Trends Biochem. Sci.. 19(10):415-421 (Oct. 1994).
A study has been reported on leucine-rich proteoglycans which serve as tissue organizers, orienting and ordering collagen fibrils during ontogeny and are involved in pathological processes such as wound healing, tissue repair, and tumor stroma formation. Iozzo, R. V., Crit. Rev. Biochem. Mol. Biol. , 32(2): 141-174 (1997). Others studies implicating leucine rich proteins in wound healing and tissue repair are De La Salle, C, et al.. Vouv. Rev. Fr. Hematol. (Germany), 37(4):215-222 (1995), reporting mutations in the leucine rich motif in a complex associated with the bleeding disorder Bernard-Soulier syndrome and Chlemetson, K. J., Thromb. Haemost. (Germany), 74(1): 111-116 (July 1995), reporting that platelets have leucine rich repeats. Another protein of particular interest which has been reported to have leucine-rich repeats is the SLIT protein which has been reported to be useful in treating neuro-degenerative diseases such as Alzheimer's disease, nerve damage such as in Parkinson's disease, and for diagnosis of cancer, see, Artavanistsakonas, S. and Rothberg, J. M., WO9210518-A1 by Yale University. Other studies reporting on the biological functions of proteins having leucine-rich repeats include: Tayar, N., et al. , Mol. Cell Endocrinol.. (Ireland), 125(l-2):65-70 (Dec. 1996) (gonadotropin receptor involvement); Miura, Y., et al., Nippon Rinsho (Japan), 54(7): 1784-1789 (July 1996) (apoptosis involvement); Harris, P. C, et al. , J. Am. Soc. Nephrol.. 6(4): 1125-1133 (Oct. 1995) (kidney disease involvement); and Ruoslahti, E. I., et al., WO9110727-A by La Jolla Cancer Research Foundation (decorin binding to transforming growth factorβ involvement for treatment for cancer, wound healing and scarring).
Efforts are therefore being undertaken by both industry and academia to identify new proteins having leucine rich repeats to better understand protein-protein interactions. Of particular interest are those proteins having leucine rich repeats and homology to known proteins having leucine rich repeats such as the SLIT protein and platelet glycoprotein V.
12. PRQ258
Immunoglobulins are antibody molecules, the proteins that function both as receptors for antigen on the B-cell membrane and as the secreted products of the plasma cell. Like all antibody molecules, immunoglobulins perform two major functions: they bind specifically to an antigen and they participate in a limited number of biological effector functions. Therefore, new members of the Ig superfamily are always of interest. Molecules which act as receptors by various viruses and those which act to regulate immune function are of particular interest. Also of particular interest are those molecules which have homology to known Ig family members which act as virus receptors or regulate immune function. Thus, molecules having homology to poliovirus receptors, CRTAM and CD166 (a ligand for lymphocyte antigen CD6) are of particular interest.
Extracellular and membrane-bound proteins play important roles in the formation, differentiation and maintenance of multicellular organisms. The fate of many individual cells, e.g., proliferation, migration, differentiation, or interaction with other cells, is typically governed by information received from other cells and/or the immediate environment. This information is often transmitted by secreted polypeptides (for instance, mitogenic factors, survival factors, cytotoxic factors, differentiation factors, neuropeptides, and hormones) which are, in turn, received and interpreted by diverse cell receptors or membrane-bound proteins. These secreted polypeptides or signaling molecules normally pass through the cellular secretory pathway to reach their site of action in the extracellular environment, usually at a membrane-bound receptor protein.
We herein describe the identification and characterization of novel polypeptides having homology to CRT AM, designated herein as PR0258 polypeptides.
13. PRQ266
Protein-protein interactions include receptor and antigen complexes and signaling mechanisms. As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction. Thus, the underlying mechanisms of protein-protein interactions are of interest to the scientific and medical community.
All proteins containing leucine-rich repeats are thought to be involved in protein-protein interactions. Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. The crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglobular shape. These two features have been indicated as responsible for the protein-binding functions of proteins containing leucine-rich repeats. See, Kobe and Deisenhofer, Trends Biochem. Sci.. 19(10):415-421 (Oct. 1994).
A study has been reported on leucine-rich proteoglycans which serve as tissue organizers, orienting and ordering collagen fibrils during ontogeny and are involved in pathological processes such as wound healing, tissue repair, and tumor stroma formation. Iozzo, R. V., Crit. Rev. Biochem. Mol. Biol.. 32(2): 141-174 (1997). Others studies implicating leucine rich proteins in wound healing and tissue repair are De La Salle, C, et al.. Vouv. Rev. Fr. Hematol. (Germany), 37(4):215-222 (1995), reporting mutations in the leucine rich motif in a complex associated with the bleeding disorder Bernard-Soulier syndrome and Chlemetson, K. J., Thromb. Haemost. (Germany), 74(1): 111-116 (July 1995), reporting that platelets have leucine rich repeats. Another protein of particular interest which has been reported to have leucine-rich repeats is the SLIT protein which has been reported to be useful in treating neuro-degenerative diseases such as Alzheimer's disease, nerve damage such as in Parkinson's disease, and for diagnosis of cancer, see, Artavanistsakonas, S. and Rothberg, J. M., WO9210518-A1 by Yale University. Other studies reporting on the biological functions of proteins having leucine-rich repeats include: Tayar, N., et al., Mol. Cell Endocrinol.. (Ireland), 125(l-2):65-70 (Dec. 1996) (gonadotropin receptor involvement); Miura, Y., et al., Nippon Rinsho (Japan), 54(7): 1784-1789 (July 1996) (apoptosis involvement); Harris, P. C, et al., J. Am. Soc. Nephrol.. 6(4): 1125-1133 (Oct. 1995) (kidney disease involvement); and Ruoslahti, E. I., et al., WO9110727-A by La Jolla Cancer Research Foundation (decorin binding to transforming growth factorβ involvement for treatment for cancer, wound healing and scarring). Efforts are therefore being undertaken by both industry and academia to identify new proteins having leucine rich repeats to better understand protein-protein interactions, neuronal development and adhesin molecules. Of particular interest are those proteins having leucine rich repeats and homology to known proteins having leucine rich repeats such as the SLIT protein. We herein describe novel polypeptides having homology to SLIT, designated herein as PR0266 polypeptides.
14. PRQ269
Thrombomodulin binds to and regulates the activity of thrombin. It is important in the control of blood coagulation. Thrombomodulin functions as a natural anticoagulant by accelerating the activation of protein C by thrombin. Soluble thrombomodulin may have therapeutic use as an antithrombotic agent with reduced risk for hemorrhage as compared with heparin. Thrombomodulin is a cell surface trans-membrane glycoprotein, present on endothelial cells and platelets. A smaller, functionally active form of thrombomodulin circulates in the plasma and is also found in urine. (In Haeberli, A., Human Protein Data, VCH Oub., N.Y., 1992). Peptides having homology to thrombomodulin are particularly desirable.
We herein describe the identification and characterization of novel polypeptides having homology to thrombomodulin, designated herein as PR0269 polypeptides.
15. PRQ287 Procollagen C-proteinase enhancer protein binds to and enhances the activity of bone morphogenic protein "BMP1 "/procollagen C-proteinase (PCP). It plays a role in extracellular matrix deposition. BMP1 proteins may be used to induce bone and/or cartilage formation and in wound healing and tissue repair. Therefore, procollagen C-proteinase enhancer protein, BMP1 and proteins having homology thereto, are of interest to the scientific and medical communities. We herein describe the identification and characterization of novel polypeptides having homology to procollagen C-proteinase enhancer protein precursor and procollagen C-proteinase enhancer protein, designated herein as PR0287 polypeptides.
16. PRQ214 Growth factors are molecular signals or mediators that enhances cell growth or proliferation, alone or in concert, by binding to specific cell surface receptors. However, there are other cellular reactions than only growth upon expression to growth factors. As a result, growth factors are better characterized as multifunctional and potent cellular regulators. Their biological effects include proliferation, chemotaxis and stimulation of extracellular matrix production. Growth factors can have both stimulatory and inhibitory effects. For example, transforming growth factor β (TGF-β) is highly pleiotropic and can stimulate proliferation in some cells, especially connective tissue, while being a potent inhibitor of proliferation in others, such as lymphocytes and epithelial cells.
The physiological effect of growth stimulation or inhibition by growth factors depends upon the state of development and differentiation of the target tissue. The mechanism of local cellular regulation by classical endocrine molecules involves comprehends autocrine (same cell), juxtacrine (neighbor cell), and paracrine (adjacent cells) pathways. Peptide growth factors are elements of a complex biological language, providing the basis for intercellular communication. They permit cells to convey information between each other, mediate interaction between cells and change gene expression. The effect of these multifunctional and pluripotent factors is dependent on the presence or absence of other peptides.
Epidermal growth factor (EGF) is a conventional mitogenic factor that stimulates the proliferation of various types of cells including epithelial cells and fibroblasts. EGF binds to and activates the EGF receptor (EGFR), which initiates intracellular signaling and subsequent effects. The EGFR is expressed in neurons of the cerebral cortex, cerebellum, and hippocampus in addition to other regions of the central nervous system (CNS). In addition, EGF is also expressed in various regions of the CNS. Therefore, EGF acts not only on mitotic cells, but also on postmitotic neurons. In fact, many studies have indicated that EGF has neurotrophic or neuromodulatory effects on various types of neurons in the CNS. For example, EGF acts directly on cultured cerebral cortical and cerebellar neurons, enhancing neurite outgrowth and survival. On the other hand, EGF also acts on other cell types, including septal cholinergic and mesencephalic dopaminergic neurons, indirectly through glial cells. Evidence of the effects of EGF on neurons in the CNS is accumulating, but the mechanisms of action remain essentially unknown. EGF-induced signaling in mitotic cells is better understood than in postmitotic neurons. Studies of cloned pheochromocytoma PC12 cells and cultured cerebral cortical neurons have suggested that the EGF-induced neurotrophic actions are mediated by sustained activation of the EGFR and mitogen-activated protein kinase (MAPK) in response to EGF. The sustained intracellular signaling correlates with the decreased rate of EGFR down-regulation, which might determine the response of neuronal cells to EGF. It is likely that EGF is a multi-potent growth factor that acts upon various types of cells including mitotic cells and postmitotic neurons.
EGF is produced by the salivary and Brunner's glands of the gastrointestinal system, kidney, pancreas, thyroid gland, pituitary gland, and the nervous system, and is found in body fluids such as saliva, blood, cerebrospinal fluid (CSF), urine, amniotic fluid, prostatic fluid, pancreatic juice, and breast milk, Plata-Salaman, CR Peptides 12: 653-663 (1991).
EGF is mediated by its membrane specific receptor, which contains an intrinsic tyrosine kinase. Stoscheck CM et al., J. Cell Biochem. 31: 135-152 (1986). EGF is believed to function by binding to the extracellular portion of its receptor which induces a transmembrane signal that activates the intrinsic tyrosine kinase.
Purification and sequence analysis of the EGF-like domain has revealed the presence of six conserved cysteine residues which cross-bind to create three peptide loops, Savage CR et al., J. Biol. Chem. 248: 7669- 7672 (1979). It is now generally known that several other peptides can react with the EGF receptor which share the same generalized motif XnCX7CX4/5CX10CXCX5GX2CXn, where X represents any non-cysteine amino acid, and n is a variable repeat number. Non isolated peptides having this motif include TGF-a, amphiregulin, schwannoma-derived growth factor (SDGF), heparin-binding EGF-like growth factors and certain virally encoded peptides (e.g., Vaccinia virus, Reisner AH, Nature 313: 801-803 (1985), Shope fibroma virus, Chang W. , et al. , Mol Cell Biol. 7: 535-540 (1987), Molluscum contagiosum, Porter CD & Archard LC, /. Gen. Virol. 68: 673-682 (1987), and Myxoma virus, Upton C e/α/., . Virol. 61 : 1271-1275 (1987). Prigent SA & Lemoine N.R., Prog. Growth Factor Res. 4: 1-24 (1992). EGF-like domains are not confined to growth factors but have been observed in a variety of cell-surface and extracellular proteins which have interesting properties in cell adhesion, protein-protein interaction and development, Laurence DJR & Gusterson BA, Tumor Biol. 11 : 229-261 (1990). These proteins include blood coagulation factors (factors VI, IX, X, XII, protein C, protein S, protein Z, tissue plasminogen activator, urokinase), extracellular matrix components (laminin, cytotactin, entactin), cell surface receptors (LDL receptor, thrombomodulin receptor) and immunity-related proteins (complement Clr, uromodulin).
Even more interesting, the general structure pattern of EGF-like precursors is preserved through lower organisms as well as in mammalian cells. A number of genes with developmental significance have been identified in invertebrates with EGF-like repeats. For example, the notch gene of Drosophila encodes 36 tandemly arranged 40 amino acid repeats which show homology to EGF, Wharton W et al., Cell 43: 557-581 (1985). Hydropathy plots indicate a putative membrane spanning domain, with the EGF-related sequences being located on the extracellular side of the membrane. Other homeotic genes with EGF-like repeats include Delta, 95F and 5ZD which were identified using probes based on Notch, and the nematode gene Lin-12 which encodes a putative receptor for a developmental signal transmitted between two specified cells.
Specifically, EGF has been shown to have potential in the preservation and maintenance of gastrointestinal mucosa and the repair of acute and chronic mucosal lesions, Konturek, PC et al, Eur. J. Gastroenterol Hepatol. 7 (10), 933-37 (1995), including the treatment of necrotizing enterocolitis, Zollinger- Ellison syndrome, gastrointestinal ulceration gastrointestinal ulcerations and congenital microvillus atrophy, A. Guglietta & PB Sullivan, Eur. J. Gastroenterol Hepatol, 7(10), 945-50 (1995). Additionally, EGF has been implicated in hair follicle differentiation; CL. du Cros, . Invest. Dermatol. J01 (1 Suppl.), 106S-113S (1993), SG Hillier, Clin. Endocrinol. 33(4), 427-28 (1990); kidney function, L.L. Ua m etal., Semin. Nephrol. 13 (1): 109-15 (1993), RC Harris, Am. J. Kidney Dis. 17(6): 627-30 (1991); tear fluid, GB van Setten et al., Int. Ophthalmol 15(6); 359-62 (1991); vitamin K mediated blood coagulation, J. Stenflo etal., BloodTS(l): 1637-51 ( 1991 ) . EGF is also implicated various skin disease characterized by abnormal keratinocyte differentiation, e.g., psoriasis, epithelial cancers such as squamous cell carcinomas of the lung, epidermoid carcinoma of the vulva and gliomas. King, LE et al., Am. J. Med. Sci. 296: 154-158 (1988).
Of great interest is mounting evidence that genetic alterations in growth factors signaling pathways are closely linked to developmental abnormalities and to chronic diseases including cancer. Aaronson SA, Science 254: 1146-1153 (1991). For example, c-erb-2 (also known as HER-2), a proto-oncogene with close structural similarity to EGF receptor protein, is overexpressed in human breast cancer. King et al. , Science 229: 974-976 (1985); Gullick, WJ, Hormones and their actions, Cooke BA et al. , eds, Amsterdam, Elsevier, pp 349-360 (1986).
17. PRQ317
The TGF-β supergene family, or simply TGF-β superfamily, a group of secreted proteins, includes a large number of related growth and differentiation factors expressed in virtually all phyla. Superfamily members bind to specific cell surface receptors that activate signal transduction mechanisms to elicit their multifunctional cytokine effects. Kolodziejczyk and Hall, Biochem. Cell. Biol.. 74: 299-314 (1996); Attisano and Wrana, Cytokine Growth Factor Rev.. 7: 327-339 (1996); and Hill, Cellular Signaling. 8: 533-544 (1996). Members of this family include five distinct forms of TGF-β (Sporn and Roberts, in Peptide Growth Factors and Their Receptors. Sporn and Roberts, eds. (Springer- Verlag: Berlin, 1990) pp. 419-472), as well as the differentiation factors vgl (Weeks and Melton, Cell, 5k 861-867 (1987)) and DPP-C polypeptide (Padgett etal. , Nature. 325: 81-84 (1987)), the hormones activin and inhibin (Mason etal. , Nature, 318: 659-663 (1985) Mason et al. , Growth Factors, 1: 77-88 (1987)), the Mullerian-inhibiting substance (MIS) (Cate et al. , Cell, 45 685-698 (1986)), the bone morphogenetic proteins (BMPs) (Wozney et al., Science. 242: 1528-1534 (1988) PCT WO 88/00205 published January 14, 1988; U.S. 4,877,864 issued October 31 , 1989), the developmentally regulated proteins Vgr-1 (Lyons et al, Proc. Natl. Acad. Sci. USA. 86: 4554-4558 (1989)) and Vgr-2 (Jones etal. , Molec. Endocrinol.. 6: 1961-1968 (1992)), the mouse growth differentiation factor (GDF), such as GDF- 3 and GDF-9 (Kingsley, Genes Dev.. 8: 133-146 (1994); McPherron and Lee, J. Biol. Chem.. 268: 3444-3449 (1993)), the mouse lefty/Stral (Meno etal. , Nature. 381: 151-155 (1996); Bouillet etal. Dev. Biol.. 170: 420- 433 (1995)), glial cell line-derived neurotrophic factor (GDNF) (Lin et al., Science. 260: 1130-1132 (1993), neurturin (Kotzbauer et al. , Nature. 384: 467-470 (1996)), and endometrial bleeding-associated factor (EBAF) (Kothapalli et al. , J. Clin. Invest.. 99: 2342-2350 (1997)). The subset BMP-2A and BMP-2B is approximately 75% homologous in sequence to DPP-C and may represent the mammalian equivalent of that protein.
The proteins of the TGF-β superfamily are disulfide-linked homo- or heterodimers encoded by larger precursor polypeptide chains containing a hydrophobic signal sequence, a long and relatively poorly conserved N-terminal pro region of several hundred amino acids, a cleavage site (usually polybasic), and a shorter and more highly conserved C-terminal region. This C-terminal region corresponds to the processed mature protein and contains approximately 100 amino acids with a characteristic cysteine motif, i. e. , the conservation of seven of the nine cysteine residues of TGF-β among all known family members. Although the position of the cleavage site between the mature and pro regions varies among the family members, the C-terminus of all of the proteins is in the identical position, ending in the sequence Cys-X-Cys-X, but differing in every case from the TGF-β consensus C-terminus of Cys-Lys-Cys-Ser. Sporn and Roberts, 1990, supra. There are at least five forms of TGF-β currently identified, TGF-βl, TGF-β2, TGF-β3, TGF-β4, and
TGF-β5. The activated form of TGF-βl is a homodimer formed by dimerization of the carboxy-terminal 112 amino acids of a 390 amino acid precursor. Recombinant TGF-βl has been cloned (Derynck et al, Nature. 316:701-705 (1985)) and expressed in Chinese hamster ovary cells (Gentry etal., Mol. Cell. Biol..7: 3418-3427 (1987)). Additionally, recombinant human TGF-β2 (deMartin et al , EMBO J.. 6: 3673 (1987)), as well as human and porcine TGF-β3 (Derynck etal. , EMBOJ.. 7: 3737-3743 (1988); ten Dijke etal. , Proc. Natl. Acad. Sci. USA. 85: 4715 (1988)) have been cloned. TGF-β2 has a precursor form of 414 amino acids and is also processed to a homodimer from the carboxy-terminal 112 amino acids that shares approximately 70% homology with the active form of TGF-βl (Marquardt et al. , J. Biol. Chem.. 262: 12127 (1987)). See also EP 200,341; 169,016; 268,561; and 267,463; U.S. Pat. No. 4,774,322; Cheifetz etal. , Cell, 48: 409-415 (1987); Jakowlew et al., Molecular Endocrin.. 2: 747-755 (1988); Derynck et al, J. Biol. Chem.. 261: 4377-4379 (1986); Sharpies et al. , DNA. 6: 239-244 (1987); Derynck et al. , Nucl. Acids. Res.. 15: 3188-3189 (1987); Derynck e /.. Nucl. Acids. Res.. 15: 3187 (1987); Seyedin et al. , J. Biol. Chem.. 261: 5693-5695 (1986); Madisen et al, DNA. 7: 1-8 (1988); and Hanks et al , Proc. Natl. Acad. Sci. (U.S.A.). 85: 79-82 (1988).
TGF-β4 and TGF-β5 were cloned from a chicken chondrocyte cDNA library (Jakowlew et al. , Molec. Endocrinol.. 2: 1186-1195 (1988)) and from a frog oocyte cDNA library, respectively.
The pro region of TGF-β associates non-covalently with the mature TGF-β dimer (Wakefield et al. , J. Biol. Chem.. 263: 7646-7654 (1988); Wakefield et al , Growth Factors. 1: 203-218 (1989)), and the pro regions are found to be necessary for proper folding and secretion of the active mature dimers of both TGF-β and activin (Gray and Mason, Science. 247: 1328-1330 (1990)). The association between the mature and pro regions of TGF-β masks the biological activity of the mature dimer, resulting in formation of an inactive latent form. Latency is not a constant of the TGF-β superfamily, since the presence of the pro region has no effect on activin or inhibin biological activity. A unifying feature of the biology of the proteins from the TGF-β superfamily is their ability to regulate developmental processes. TGF-β has been shown to have numerous regulatory actions on a wide variety of both normal and neoplastic cells. TGF-β is multifunctional, as it can either stimulate or inhibit cell proliferation, differentiation, and other critical processes in cell function (Sporn and Roberts, supra).
One member of the TGF-β superfamily, EBAF, is expressed in endometrium only in the late secretory phase and during abnormal endometrial bleeding. Kothapalli et al , J. Clin. Invest.. 99: 2342-2350 (1997). Human endometrium is unique in that it is the only tissue in the body that bleeds at regular intervals. In addition, abnormal endometrial bleeding is one of the most common manifestations of gynecological diseases, and is a prime indication for hysterectomy. In situ hybridization showed that the mRNA of EBAF was expressed in the stroma without any significant mRNA expression in the endometrial glands or endothelial cells. The predicted protein sequence of EBAF showed a strong homology to the protein encoded by mouse lefty IstraS of the TGF-β superfamily. A motif search revealed that the predicted EBAF protein contains most of the cysteine residues which are conserved among the TGF-β-related proteins and which are necessary for the formation of the cysteine knot structure. The EBAF sequence contains an additional cysteine residue, 12 amino acids upstream from the first conserved cysteine residue. The only other family members known to contain an additional cysteine residue are TGF-βs, inhibins, and GDF-3. EBAF, similar to LEFTY, GDF-3/Vgr2, and GDF-9, lacks the cysteine residue that is known to form the intermolecular disulfide bond. Therefore, EBAF appears to be an additional member of the TGF-β superfamily with an unpaired cysteine residue that may not exist as a dimer. However, hydrophobic contacts between the two monomer subunits may promote dimer formation. Fluorescence in situ hybridization showed that the ebaf gene is located on human chromosome 1 at band q42.1.
Additional members of the TGF-β superfamily, such as those related to EBAF, are being searched for by industry and academics. We herein describe the identification and characterization of novel polypeptides having homology to EBAF, designated herein as PR0317 polypeptides.
18. PRQ301
The widespread occurrence of cancer has prompted the devotion of considerable resources and discovering new treatments of treatment. One particular method involves the creation of tumor or cancer specific monoclonal antibodies (mAbs) which are specific to tumor antigens. Such mAbs, which can distinguish between normal and cancerous cells are useful in the diagnosis, prognosis and treatment of the disease. Particular antigens are known to be associated with neoplastic diseases, such as colorectal cancer.
One particular antigen, the A33 antigen is expressed in more than 90% of primary or metastatic colon cancers as well as normal colon epithelium. Since colon cancer is a widespread disease, early diagnosis and treatment is an important medical goal. Diagnosis and treatment of colon cancer can be implemented using monoclonal antibodies (mAbs) specific therefore having fluorescent, nuclear magnetic or radioactive tags. Radioactive gene, toxins and/or drug tagged mAbs can be used for treatment in situ with minimal patient description. mAbs can also be used to diagnose during the diagnosis and treatment of colon cancers. For example, when the serum levels of the A33 antigen are elevated in a patient, a drop of the levels after surgery would indicate the mmor resection was successful. On the other hand, a subsequent rise in serum A33 antigen levels after surgery would indicate that metastases of the original tumor may have formed or that new primary tumors may have appeared. Such monoclonal antibodies can be used in lieu of, or in conjunction with surgery and/or other chemotherapies. For example, U.S. P. 4,579,827 and U.S.S.N. 424,991 (E.P. 199,141) are directed to therapeutic administration of monoclonal antibodies, the latter of which relates to the application of anti-A33 mAb.
Many cancers of epithelial origin have adenovirus receptors. In fact, adenovirus-derived vectors have been proposed as a means of inserting antisense nucleic acids into tumors (U.S. P. 5,518,885). Thus, the association of viral receptors with neoplastic tumors is not unexpected.
We herein describe the identification and characterization of novel polypeptides having homology to certain cancer-associated antigens, designated herein as PRO301 polypeptides.
19. PRQ224
Cholesterol uptake can have serious implications on one's health. Cholesterol uptake provides cells with most of the cholesterol they require for membrane synthesis. If this uptake is blocked, cholesterol accumulates in the blood and can contribute to the formation of atherosclerotic plaques in blood vessel walls. Most cholesterol is transported in the blood bound to protein in the form of complexes known as low-density lipoproteins (LDLs). LDLs are endocytosed into cells via LDL receptor proteins. Therefore, LDL receptor proteins, and proteins having homology thereto, are of interest to the scientific and medical communities.
Membrane-bound proteins and receptors can play an important role in the formation, differentiation and maintenance of multicellular organisms. The LDL receptors are an example of membrane-bound proteins which are involved in the synthesis and formation of cell membranes, wherein the health of an individual is affected directly and indirectly by its function. Many membrane-bound proteins act as receptors such as the LDL receptor. These receptors can function to endocytose substrates or they can function as a receptor for a channel. Other membrane-bound proteins function as signals or antigens. Membrane-bound proteins and receptor molecules have various industrial applications, including as pharmaceutical and diagnostic agents. The membrane-bound proteins can also be employed for screening of potential peptide or small molecule regulators of the relevant receptor/ligand interaction. In the case of the LDL receptor, it is desirable to find molecules which enhance endocytosis so as to lower blood cholesterol levels and plaque formation. It is also desirable to identify molecules which inhibit endocytosis so that these molecules can be avoided or regulated by individuals having high blood cholesterol. Polypeptides which are homologous to lipoprotein receptors but which do not function as lipoprotein receptors are also of interest in the determination of the function of the fragments which show homology. The following studies report on previously known low density lipoprotein receptors and related proteins including apolipoproteins: Sawamura, etal., Nippon Chemiphar Co, Japan patent application J09098787; Novak, S., et al., J. Biol. Chem.. 271 :(20)11732-6 (1996); Blaas, D., J. Virol.. 69(11)7244-7 (Nov. 1995); Scott, J., J. Inherit. Metab. Pis. (UK), 9/Supp. 1 (3-16) (1986); Yamamoto, et al., Cell, 39:27-38 (1984); Rebece, et al., Neurobiol. Aging. 15:5117 (1994): Novak. S.. etal.. J. Biol. Chemistry.271:11732-11736 (1996): and Sestavel and Fruchart, Cell Mol. Biol.. 40(4):461-81 (June 1994). These publications and others published prior to the filing of this application provide further background to peptides already known in the art.
Efforts are being undertaken by both industry and academia to identify new, native membrane-bound receptor proteins, particularly those having homology to lipoprotein receptors. We herein describe the identification and characterization of novel polypeptides having homology to lipoprotein receptors, designated herein as PR0224 polypeptides.
20. PRQ222
Complement is a group of proteins found in the blood that are important in humoral immunity and inflammation. Complement proteins are sequentially activated by antigen-antibody complexes or by proteolytic enzymes. When activated, complement proteins kill bacteria and other microorganisms, affect vascular permeability, release histamine and attract white blood cells. Complement also enhances phagocytosis when bound to target cells. In order to prevent harm to autologous cells, the complement activation pathway is tightly regulated.
Deficiencies in the regulation of complement activation or in the complement proteins themselves may lead to immune-complex diseases, such as systemic lupus erythematosus, and may result in increased susceptibility to bacterial infection. In all cases, early detection of complement deficiency is desirable so that the patient can begin treatment. Thus, research efforts are currently directed toward identification of soluble and membrane proteins that regulate complement activation.
Proteins known to be important in regulating complement activation in humans include Factor H and Complement receptor type 1 (CRl). Factor H is a 150 kD soluble serum protein that interacts with complement protein C3b to accelerate the decay of C3 convertase and acts as a cofactor for Factor I-mediated cleavage of complement protein C4b. Complement receptor type 1 is a 190-280 kD membrane bound protein found in mast cells and most blood cells. CRl interacts with complement proteins C3b, C4b, and iC3b to accelerate dissociation of C3 convertases, acts as a cofactor for Factor I-mediated cleavage of C3b and C4b, and binds immune complexes and promotes their dissolution and phagocytosis.
Proteins which have homology to complement proteins are of particular interest to the medical and industrial communities. Often, proteins having homology to each other have similar function. It is also of interest when proteins having homology do not have similar functions, indicating that certain structural motifs identify information other than function, such as locality of function.
Efforts are being undertaken by both industry and academia to identify new, native secreted and membrane-bound proteins, particularly those having homology to known proteins involved in the complement pathway. Proteins involved in the complement pathway were reviewed in Birmingham DJ (1995), Critical Reviews in Immunology. 15(2): 133-154 and in Abbas AK, et al. (1994) Cellular and Molecular Immunology,
2nd Ed. W.B. Saunders Company, Philadelphia, pp 295-315.
We herein describe the identification and characterization of novel polypeptides having homology to complement receptors, designated herein as PR0222 polypeptides.
21. PRQ234
The successful function of many systems within multicellular organisms is dependent on cell-cell interactions. Such interactions are affected by the alignment of particular ligands with particular receptors in a manner which allows for ligand-receptor binding and thus a cell-cell adhesion. While protein-protein interactions in cell recognition have been recognized for some time, only recently has the role of carbohydrates in physiologically relevant recognition been widely considered (see B.K. Brandley et al, J. Leuk. Biol. 40: 97 (1986) and N. Sharon etal, Science 246: 227 (1989). Oligosaccharides are well positioned to act as recognition novel lectins due to their cell surface location and structural diversity. Many oligosaccharide structures can be created through the differential activities of a smaller number of glycosyltransferases. The diverse structures of oligosaccharides can be generated by transcription of relatively few gene products, which suggests that the oligosaccharides are a plausible mechanism by which is directed a wide range of cell-cell interactions. Examples of differential expression of cell surface carbohydrates and putative carbohydrate binding proteins (lectins) on interacting cells have been described (J. Dodd & T.M. Jessel, /. Neurosci. 5: 3278 (1985); L.J. Regan et al, Proc. Natl. Acad. Sci. USA 83: 2248 (1986); M. Constantine-Paton et al, Nature 2A: 459 (1986); and M. Tiemeyer et al, J. Biol. Chem. 263: 1671 (1989). One interesting member of the lectin family are selectins. The migration of leukocytes to sites of acute or chronic inflammation involves adhesive interactions between these cells and the endothelium. This specific adhesion is the initial event in the cascade that is initiated by inflammatory insults, and it is, therefore, of paramount importance to the regulated defense of the organism.
The types of cell adhesion molecules that are involved in the interaction between leukocytes and the endothelium during an inflammatory response currently stands at four: (1) selectins; (2) (carbohydrate and glycoprotein) ligands for selectins; (3) integrins; and (4) integrin ligands, which are members of the immunoglobulin gene superfamily.
The selectins are cell adhesion molecules that are unified both structurally and functionally. Structurally, selectins are characterized by the inclusion of a domain with homology to a calcium-dependent lectin (C -lectins), an epidermal growth factor (egf)-like domain and several complement binding-like domains, Bevilacqua, M.P. et al, Science 243: 1160-1165 (1989); Johnston et al., Cell 56: 1033-1044 (1989); Lasky et al, Cell 56: 1045-1055 (1989); Siegalman, M. et al, Science 243: 1165-1172 (1989); Stoolman, L.M., Ce// 56: 907-910 (1989). Functionally, selectins share the common property of their ability to mediate cell binding through interactions between their lectin domains and cell surface carbohydrate ligands (Brandley , B, et al. , Cell 63, 861-863 (1990); Springer, T. and Lasky, L.A. , Nature 349. 19-197 (1991); Bevilacqua, M.P. and Nelson, R.M., /. Clin. Invest. 91 379-387 (1993) and Tedder et al, J. Exp. Med. 170: 123-133 (1989).
There are three members identified so far in the selectin family of cell adhesion molecules: L-selectin (also called peripheral lymph node homing receptor (pnHR), LEC-CAM-1 , LAM-1, gp90MEL, gpl00MEL, gpl 10MEL, MEL-14 antigen, Leu-8 antigen, TQ-1 antigen, DREG antigen), E-selectin (LEC-CAM-2, LECAM-2, ELAM-1) and P-selectin (LEC-CAM-3, LECAM-3, GMP-140, PADGEM).
The identification of the C-lectin domain has led to an intense effort to define carbohydrate binding ligands for proteins containing such domains. E-selectin is believed to recognize the carbohydrate sequence NeuNAc 2-3Galβl-4(Fucαl-3)GlcNAc (sialyl-Lewis x, or sLex) and related oligosaccharides, Berg et al, J. Biol. Chem. 265: 14869-14872 (1991); Lowe etal, CellξΛ: 475-484 (1990); Phillips etal, Science 250: 1130- 1132 (1990); Tiemeyer et al, Proc. Natl. Acad. Sci. USA SS: 1138-1142 (1991).
L-selectin, which comprises a lectin domain, performs its adhesive function by recognizing carbohydrate-containing ligands on endothelial cells. L-selectin is expressed on the surface of leukocytes, such as lymphocytes, neutrophils, monocytes and eosinophils, and is involved with the trafficking of lymphocytes to peripheral lymphoid tissues (Gallatin et al, Nature 303: 30-34 (1983)) and with acute neutrophil-medicated inflammatory responses (Watson, S.R., Nature 349: 164-167 (1991)). The amino acid sequence of L-selectin and the encoding nucleic acid sequence are, for example, disclosed in U.S. patent No. 5,098,833 issued 24 March 1992.
L-selectin (LECAM-1) is particularly interesting because of its ability to block neutrophil influx (Watson et al, Nature 349: 164-167 (1991). It is expressed in chronic lymphocytic leukemia cells which bind to HEV (Spertini et al, Nature 349: 691-694 (1991). It is also believed that HEV structures at sites of chronic inflammation are associated with the symptoms of diseases such as rheumatoid arthritis, psoriasis and multiple sclerosis.
E-selectin (ELAM-1), is particularly interesting because of its transient expression on endothelial cells in response to IL-1 or TNF. Bevilacqua et al., Science 243: 1160 (1989). The time course of this induced expression (2-8 h) suggests a role for this receptor in initial neutrophil induced extravasation in response to infection and injury. It has further been reported that anti-ELAM-1 antibody blocks the influx of neutrophils in a primate asthma model and thus is beneficial for preventing airway obstruction resulting from the inflammatory response. Gundel et al, J. Clin. Invest. 88: 1407 (1991). The adhesion of circulating neutrophils to stimulated vascular endothelium is a primary event of the inflammatory response. P-selectin has been reported to recognize the Lewis x structure (Galβl-4(Fucαl-3) GlcNAc), Larsen et al, Cell 63: 467-474(1990). Others report that an additional terminal linked sialic acid is required for high affinity binding, Moore et al, J. Cell. Biol. \ 2: 491-499 (1991). P-selectin has been shown to be significant in acute lung injury. Anti-P-selectin antibody has been shown to have strong protective effects in a rodent lung injury model. M.S. Mulligan et al, J. Clin. Invest. 90: 1600 (1991).
We herein describe the identification and characterization of novel polypeptides having homology to lectin proteins, herein designated as PR0234 polypeptides. 22. PRQ231
Some of the most important proteins involved in the above described regulation and modulation of cellular processes are the enzymes which regulate levels of protein phosphorylation in the cell. For example, it is known that the transduction of signals that regulate cell growth and differentiation is regulated at least in part by phosphorylation and dephosphorylation of various cellular proteins. The enzymes that catalyze these processes include the protein kinases, which function to phosphorylate various cellular proteins, and the protein phosphatases, which function to remove phosphate residues from various cellular proteins. The balance of the level of protein phosphorylation in the cell is thus mediated by the relative activities of these two types of enzymes.
Protein phosphatases represent a growing family of enzymes that are found in many diverse forms, including both membrane-bound and soluble forms. While many protein phosphatases have been described, the functions of only a very few are beginning to be understood (Tonks, Semin. Cell Biol. 4:373-453 (1993) and Dixon, Recent Prog. Horm. Res. 51 :405-414 (1996)). However, in general, it appears that many of the protein phosphatases function to modulate the positive or negative signals induced by various protein kinases. Therefore, it is likely that protein phosphatases play critical roles in numerous and diverse cellular processes. Given the physiological importance of the protein phosphatases, efforts are being undertaken by both industry and academia to identify new, native phosphatase proteins. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel phosphatase proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)]. We herein describe the identification and characterization of novel polypeptides having homology to acid phosphatases, designated herein as PR0231 polypeptides.
23. PRQ229
Scavenger receptors are known to protect IgG molecules from catabolic degradation. Riechmann and Hollinger, Nature Biotechnology. 15:617 (1997). In particular, studies of the CH2 and CH3 domains have shown that specific sequences of these domains are important in determining the half-lives of antibodies. Ellerson, et al., J. Immunol.. 116: 510 (1976); Yasmeen, et al., J. Immunol. 116: 518 (1976; Pollock, et al., Eur. J. Immunol .. 20: 2021 (1990). Scavenger receptor proteins and antibodies thereto are further reported in U.S. Patent No. 5,510,466 to Krieger, et al. Due to the ability of scavenger receptors to increase the half-life of polypeptides and their involvement in immune function, molecules having homology to scavenger receptors are of importance to the scientific and medical community.
Efforts are being undertaken by both industry and academia to identify new, native secreted and membrane-bound receptor proteins, particularly those having homology to scavenger receptors. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound receptor proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)]. We herein describe the identification and characterization of novel polypeptides having homology to scavenger receptors, designated herein as PR0229 polypeptides.
24. PRQ238
Oxygen free radicals and antioxidants appear to play an important role in the central nervous system after cerebral ischemia and reperfusion. Moreover, cardiac injury, related to ischaemia and reperfusion has been reported to be caused by the action of free radicals. Additionally, studies have reported that the redox state of the cell is a pivotal determinant of the fate of the cells. Furthermore, reactive oxygen species have been reported to be cytotoxic, causing inflammatory disease, including tissue necrosis, organ failure, atherosclerosis, infertility, birth defects, premature aging, mutations and malignancy. Thus, the control of oxidation and reduction is important for a number of reasons including for control and prevention of strokes, heart attacks, oxidative stress and hypertension. In this regard, reductases, and particularly, oxidoreductases, are of interest. Publications further describing this subject matter include Kelsey, et al., Br. J. Cancer. 76(7):852-4 (1997); Friedrich and Weiss, J. Theor. Biol.. 187(4):529-40 (1997) and Pieulle, et al., J. Bacteriol.. 179(18):5684-92 (1997).
Efforts are being undertaken by both industry and academia to identify new, native secreted and membrane-bound receptor proteins, particularly secreted proteins which have homology to reductase. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound receptor proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)]. We herein describe the identification and characterization of novel polypeptides having homology to reductase, designated herein as PR0238 polypeptides.
25. PRQ233
Studies have reported that the redox state of the cell is an important determinant of the fate of the cell. Furthermore, reactive oxygen species have been reported to be cytotoxic, causing inflammatory disease, including tissue necrosis, organ failure, atherosclerosis, infertility, birth defects, premature aging, mutations and malignancy. Thus, the control of oxidation and reduction is important for a number of reasons, including the control and prevention of strokes, heart attacks, oxidative stress and hypertension. Oxygen free radicals and antioxidants appear to play an important role in the central nervous system after cerebral ischemia and reperfusion. Moreover, cardiac injury, related to ischaemia and reperfusion has been reported to be caused by the action of free radicals. In this regard, reductases, and particularly, oxidoreductases, are of interest. In addition, the transcription factors, NF-kappa B and AP-1 , are known to be regulated by redox state and to affect the expression of a large variety of genes thought to be involved in the pathogenesis of AIDS, cancer, atherosclerosis and diabetic complications. Publications further describing this subject matter include Kelsey, et al. , Br. J. Cancer. 76(7):852-4 (1997); Friedrich and Weiss, J. Theor. Biol.. 187(4):529-40 (1997) and Pieulle, et al., J. Bacteriol.. 179(18): 5684-92 (1997). Given the physiological importance of redox reactions in vivo, efforts are currently being under taken to identify new, native proteins which are involved in redox reactions. We describe herein the identification of novel polypeptides which have homology to reductase, designated herein as PR0233 polypeptides.
26. PRQ223
The carboxypeptidase family of exopeptidases constitutes a diverse group of enzymes that hydrolyze carboxyl-terminal amide bonds in polypeptides, wherein a large number of mammalian tissues produce these enzymes. Many of the carboxypeptidase enzymes that have been identified to date exhibit rather strong cleavage specificities for certain amino acids in polypeptides. For example, carboxypeptidase enzymes have been identified which prefer lysine, arginine, serine or amino acids with either aromatic or branched aliphatic side chains as substrates at the carboxyl terminus of the polypeptide. With regard to the serine carboxypeptidases, such amino acid specific enzymes have been identified from a variety of different mammalian and non-mammalian organisms. The mammalian serine carboxypeptidase enzymes play important roles in many different biological processes including, for example, protein digestion, activation, inactivation, or modulation of peptide hormone activity, and alteration of the physical properties of proteins and enzymes. In light of the physiological importance of the serine carboxypeptidases, efforts are being undertaken by both industry and academia to identify new, native secreted and membrane-bound receptor proteins and specifically novel carboxypeptidases. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound receptor proteins. We describe herein novel polypeptides having homology to one or more serine carboxypeptidase polypeptides, designated herein as PR0223 polypeptides.
27. PRQ235
Plexin was first identified in Xenopus tadpole nervous system as a membrane glycoprotein which was shown to mediate cell adhesion via a homophilic binding mechanism in the presence of calcium ions. Strong evolutionary conservation between Xenopus, mouse and human homologs of plexin has been observed. [Kaneyama et al., Biochem. And Biophys. Res. Comm. 226: 524-529 (1996)]. Given the physiological importance of cell adhesion mechanisms in vivo, efforts are currently being under taken to identify new, native proteins which are involved in cell adhesion. We describe herein the identification of a novel polypeptide which has homology to plexin, designated herein as PR0235.
28. PRQ236 and PRQ262 β-galactosidase is a well known enzymatic protein which functions to hydrolyze β-galactoside molecules, β-galactosidase has been employed for a variety of different applications, both in vitro and in vivo and has proven to be an extremely useful research tool. As such, there is an interest in obtaining novel polypeptides which exhibit homology to the β-galactosidase polypeptide.
Given the strong interest in obtaining novel polypeptides having homology to β-galactosidase, efforts are currently being undertaken by both industry and academia to identify new, native β-galactosidase homolog proteins. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel β-galactosidase-like proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)]. We herein describe novel poylpeptides having siginificant homology to the β-galactosidase enzyme, designated herein as PR0236 and PR0262 polypeptides.
29. PRQ239
Densin is a glycoprotein which has been isolated from the brain which has all the hallmarks of an adhesion molecule. It is highly concentrated at synaptic sites in the brain and is expressed prominently in dendritic processes in developing neurons. Densin has been characterized as a member of the O-linked sialoglycoproteins. Densin has relevance to medically important processes such as regeneration. Given the physiological importance of synaptic processes and cell adhesion mechanisms in vivo, efforts are currently being under taken to identify new, native proteins which are involved in synaptic machinery and cell adhesion. We describe herein the identification of novel polypeptides which have homology to densin, designated herein as PR0239 polypeptides.
30. PRQ257
Ebnerin is a cell surface protein associated with von Ebner glands in mammals. Efforts are being undertaken by both industry and academia to identify new, native cell surface receptor proteins and specifically those which possess sequence homology to cell surface proteins such as ebnerin. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel receptor proteins. We herein describe the identification of novel polypeptides having significant homology to the von Ebner's gland-associated protein ebnerin, designated herein as PR0257 polypeptides.
31. PRO260 Fucosidases are enzymes that remove fucose residues from fucose containing proteoglycans. In some pathological conditions, such as cancer, rheumatoid arthritis, and diabetes, there is an abnormal fucosylation of serum proteins. Therefore, fucosidases, and proteins having homology to fucosidase, are of importance to the study and abrogation of these conditions. In particular, proteins having homology to the alρha-1-fucosidase precursor are of interest. Fucosidases and fucosidase inhibitors are further described in U.S. Patent Nos. 5,637,490, 5,382,709, 5,240,707, 5, 153,325, 5,100,797, 5,096,909 and 5,017,704. Smdies are also reported in Valk, et al.. J. Virol.. 71(9): 6796 (1997), Aktogu, et al.. Monaldi. Arch. Chest Pis. (Italy), 52(2): 118 (1997) and Focarelli, et al., Biochem. Biophys. Res. Commun. (U.S.), 234(1):54 (1997).
Efforts are being undertaken by both industry and academia to identify new, native secreted and membrane-bound receptor proteins . Of particular interest are proteins having homology to the alpha-1-fucosidase precursor. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound receptor proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108- 7113 (1996); U.S. Patent No. 5,536,637)].
We herein describe the identification and characterization of novel polypeptides having homology to fucosidases, designated herein as PRO260 polypeptides.
32. PRQ263 CD44 is a cell surface adhesion molecule involved in cell-cell and cell-matrix interactions. Hyaluronic acid, a component of the extracellular matrix is a major ligand. Other ligands include collagen, fibronectin, laminin, chrondroitin sulfate, mucosal addressin, serglycin and osteoponin. CD44 is also important in regulating cell traffic, lymph node homing, transmission of growth signals, and presentation of chemokines and growth factors to traveling cells. CD44 surface proteins are associated with metastatic tumors and CD44 has been used as a marker for HIV infection. Certain splice variants are associated with metastasis and poor prognosis of cancer patients. Therefore, molecules having homology with CD44 are of particular interest, as their homology indicates that they may have functions related to those functions of CD44. CD44 is further described in U.S. Patent Nos. 5,506, 119, 5,504,194 and 5, 108,904; Gerberick, et al. , Toxicol. Appl. Pharmacol.. 146(1): 1 (1997); Wittig, et al.. Immunol. Letters (Netherlands), 57(1-3):217 (1997); and Oliveira and Odell, Oral Oncol. (England), 33(4):260 (1997).
Efforts are being undertaken by both industry and academia to identify new, native secreted and membrane-bound receptor proteins, particularly transmembrane proteins with homology to CD44 antigen. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound receptor proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)].
We herein describe the identification and characterization of novel polypeptides having homology to CD44 antigen, designated herein as PR0263 polypeptides.
33. PRO270
Thioredoxins effect reduction-oxidation (redox) state. Many diseases are potentially related to redox state and reactive oxygen species may play a role in many important biological processes. The transcription factors, NF-kappa B and AP-1, are regulated by redox state and are known to affect the expression of a large variety of genes thought to be involved in the pathogenesis of AIDS, cancer, atherosclerosis and diabetic complications. Such proteins may also play a role in cellular antioxidant defense, and in pathological conditions involving oxidative stress such as stroke and inflammation in addition to having a role in apoptosis. Therefore, thioredoxins, and proteins having homology thereto, are of interest to the scientific and medical communities. We herein describe the identification and characterization of novel polypeptides having homology to thioredoxin, designated herein as PRO270 polypeptides.
34. PRQ271
The proteoglycan link protein is a protein which is intimately associated with various extracellular matrix proteins and more specifically with proteins such as collagen. For example, one primary component of collagen is a large proteoglycan called aggrecan. This molecule is retained by binding to the glycosaminoglycan hyaluronan through the amino terminal Gl globular domain of the core protein. This binding is stabilized by the proteoglycan link protein which is a protein that is also associated with other tissues containing hyaluronan binding proteoglycans such as versican.
Link protein has been identified as a potential target for autoimmune antibodies in individuals who suffer from juvenile rheumatoid arthritis (see Guerassimov et al., J. Rheumatology 24(5):959-964 (1997)). As such, there is strong interest in identifying novel proteins having homology to link protein. We herein describe the identification and characterization of novel polypeptides having such homology, designated herein as PR0271 polypeptides.
35. PRQ272
Reticulocalbin is an endoplasmic reticular protein which may be involved in protein transport and luminal protein processing. Reticulocalbin resides in the lumen of the endopladsmic rerticulum, is known to bind calcium, and may be involved in a luminal retention mechanism of the endoplasmic reticulum. It contains six domains of the EF-hand motif associated with high affinity calcium binding. We describe herein the identification and characterization of a novel polypeptide which has homology to the reticulocalbin protein, designated herein as PR0272.
36. PRQ294 Collagen, a naturally occurring protein, finds wide application in industry. Chemically hydrolyzed natural collagen can be denatured and renatured by heating and cooling to produce gelatin, which is used in photographic and medical, among other applications. Collagen has important properties such as the ability to form interchain aggregates having a conformation designated as a triple helix. We herein describe the identification and characterization of a novel polypeptide which has homology to portions of the collagen molecule, designated herein as PR0294.
37. PRQ295
The integrins comprise a supergene family of cell-surface glycoprotein receptors that promote cellular adhesion. Each cell has numerous receptors that define its cell adhesive capabilities. Integrins are involved in a wide variety of interaction between cells and other cells or matrix components . The integrins are of particular importance in regulating movement and function of immune system cells The platelet Hb/IIIA integrin complex is of particular importance in regulating platelet aggregation. A member of the integrin family, integrin β-6, is expressed on epithelial cells and modulates epithelial inflammation. Another integrin, leucocyte-associated antigen- 1 (LFA-1) is important in the adhesion of lymphocytes during an immune response. The integrins are expressed as heterodimers of non-covalently associated alpha and beta subunits. Given the physiological importance of cell adhesion mechanisms in vivo, efforts are currently being under taken to identify new, native proteins which are involved in cell adhesion. We describe herein the identification and characterization of a novel polypeptide which has homology to integrin, designated herein as PR0295.
38. PRQ293
Protein-protein interactions include receptor and antigen complexes and signaling mechanisms. As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction.
Thus, the underlying mechanisms of protein-protein interactions are of interest to the scientific and medical community.
All proteins containing leucine-rich repeats are thought to be involved in protein-protein interactions. Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. The crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglubular shape. These two features have been indicated as responsible for the protein-binding functions of proteins containing leucine-rich repeats. See, Kobe and Deisenhofer, Trends Biochem. Sci.. 19(10):415-421 (Oct. 1994). A study has been reported on leucine-rich proteoglycans which serve as tissue organizers, orienting and ordering collagen fibrils during ontogeny and are involved in pathological processes such as wound healing, tissue repair, and tumor stroma formation. Iozzo, R. V., Crit. Rev. Biochem. Mol. Biol.. 32(2): 141-174 (1997). Others smdies implicating leucine rich proteins in wound healing and tissue repair are De La Salle, C, et al. , Vouv. Rev. Fr. Hematol. (Germany), 37(4):215-222 (1995), reporting mutations in the leucine rich motif in a complex associated with the bleeding disorder Bernard-Soulier syndrome and Chlemetson, K. J. , Thromb. Haemost. (Germany), 74(1): 111-116 (July 1995), reporting that platelets have leucine rich repeats. Another protein of particular interest which has been reported to have leucine-rich repeats is the SLIT protein which has been reported to be useful in treating neuro-degenerative diseases such as Alzheimer's disease, nerve damage such as in Parkinson's disease, and for diagnosis of cancer, see, Artavanistsakonas, S. and Rothberg, J. M., WO9210518-A1 by Yale University. Other smdies reporting on the biological functions of proteins having leucine-rich repeats include: Tayar, N., et al., Mol. Cell Endocrinol.. (Ireland), 125(l-2):65-70 (Dec. 1996) (gonadotropin receptor involvement); Miura, Y., et al., Nippon Rinsho (Japan), 54(7): 1784-1789 (July 1996) (apoptosis involvement); Harris, P. C, et al., J. Am. Soc. Nephrol.. 6(4): 1125-1133 (Oct. 1995) (kidney disease involvement); and Ruoslahti, E. I., et al., WO9110727-A by La Jolla Cancer Research Foundation (decorin binding to transforming growth factorβ involvement for treatment for cancer, wound healing and scarring).
Efforts are therefore being undertaken by both industry and academia to identify new proteins having leucine rich repeats to better understand protein-protein interactions. Of particular interest are those proteins having leucine rich repeats and homology to known neuronal leucine rich repeat proteins. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound proteins having leucine rich repeats. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)].
We describe herein the identification and characterization of a novel polypeptide which has homology to leucine rich repeat proteins, designated herein as PR0293.
39. PRQ247 Protein-protein interactions include receptor and antigen complexes and signaling mechanisms . As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction. Thus, the underlying mechanisms of protein-protein interactions are of interest to the scientific and medical community. All proteins containing leucine-rich repeats are thought to be involved in protein-protein interactions.
Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. The crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglubular shape. These two features have been indicated as responsible for the protein-binding functions of proteins containing leucine-rich repeats. See, Kobe and Deisenhofer, Trends Biochem. Sci.. 19(10):415-421 (Oct. 1994).
A study has been reported on leucine-rich proteoglycans which serve as tissue organizers, orienting and ordering collagen fibrils during ontogeny and are involved in pathological processes such as wound healing, tissue repair, and tumor stroma formation. Iozzo, R. V., Crit. Rev. Biochem. Mol. Biol.. 32(2): 141-174 (1997). Others studies implicating leucine rich proteins in wound healing and tissue repair are De La Salle, C. , et al. , Vouv. Rev. Fr. Hematol. (Germany), 37(4):215-222 (1995), reporting mutations in the leucine rich motif in a complex associated with the bleeding disorder Bernard-Soulier syndrome and Chlemetson, K. J., Thromb. Haemost. (Germany), 74(1): 1 11-116 (July 1995), reporting that platelets have leucine rich repeats. Another protein of particular interest which has been reported to have leucine-rich repeats is the SLIT protein which has been reported to be useful in treating neuro-degenerative diseases such as Alzheimer's disease, nerve damage such as in Parkinson's disease, and for diagnosis of cancer, see, Artavanistsakonas, S. and Rothberg, J. M., WO9210518-A1 by Yale University. Other studies reporting on the biological functions of proteins having leucine-rich repeats include: Tayar, N., et al., Mol. Cell Endocrinol.. (Ireland), 125(l-2):65-70 (Dec. 1996) (gonadotropin receptor involvement); Miura, Y., et al., Nippon Rinsho (Japan), 54(7): 1784-1789 (July 1996) (apoptosis involvement); Harris, P. C, et al., J. Am. Soc. NephroL. 6(4): 1125-1133 (Oct. 1995) (kidney disease involvement); and Ruoslahti, E. I., et al., WO9110727-A by La Jolla Cancer Research Foundation (decorin binding to transforming growth factorβ involvement for treatment for cancer, wound healing and scarring).
Densin is a glycoprotein which has been isolated from the brain which has all the hallmarks of an adhesion molecule. It is highly concentrated at synaptic sites in the brain and is expressed prominently in dendritic processes in developing neurons. Densin has been characterized as a member of the O-linked sialoglycoproteins. Densin has relevance to medically important processes such as regeneration. Given the physiological importance of synaptic processes and cell adhesion mechanisms in vivo, efforts are currently being under taken to identify new, native proteins which are involved in synaptic machinery and cell adhesion. Densin is further described in Kennedy, M.B, Trends Neurosci. (England), 20(6):264 (1997) and Apperson, et al., L Neurosci.. 16(21):6839 (1996).
Efforts are therefore being undertaken by both industry and academia to identify new proteins having leucine rich repeats to better understand protein-protein interactions. Of particular interest are those proteins having leucine rich repeats and homology to known proteins having leucine rich repeats such as KIA A0231 and densin. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound proteins having leucine rich repeats. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)].
We describe herein the identification and characterization of a novel polypeptide which has homology to leucine rich repeat proteins, designated herein as PR0247.
40. PRO302. PRO303. PRO304. PRO307 and PRQ343 Proteases are enzymatic proteins which are involved in a large number of very important biological processes in mammalian and non-mammalian organisms. Numerous different protease enzymes from a variety of different mammalian and non-mammalian organisms have been both identified and characterized. The mammalian protease enzymes play important roles in many different biological processes including, for example, protein digestion, activation, inactivation, or modulation of peptide hormone activity, and alteration of the physical properties of proteins and enzymes.
In light of the important physiological roles played by protease enzymes, efforts are currently being undertaken by both industry and academia to identify new, native protease homologs. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound receptor proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al. , Proc. Natl. Acad. Sci.. 93:7108-7113 (1996); U.S. Patent No. 5 ,536,637)] . We herein describe the identification of novel polypeptides having homology to various protease enzymes, designated herein as PRO302, PRO303, PRO304, PRO307 and PR0343 polypeptides.
41. PRQ328 The GLIP protein family has been characterized as comprising zinc-finger proteins which play important roles in embryogenesis. These proteins may function as transcriptional regulatory proteins and are known to be amplified in a subset of human tumors. Glioma pathogenesis protein is structurally related to a group of plant pathogenesis-related proteins. It is highly expressed in glioblastoma. See US Pat. Nos. 5,582,981 (issued Dec. 10, 1996) and 5,322,801 (issued June 21 , 1996), Ellington, A.D. et al., Nature. 346:818 (1990), Grindley, J.C. et al., Dev. Biol.. 188(2): 337 (1997), Marine, J.C. et al., Mech. Dev.. 63(2):2U (1997), The CRISP or cysteine rich secretory protein family are a group of proteins which are also structurally related to a group of plant pathogenesis proteins. [Schwidetzky, U., Biochem. J.. 321:325 (1997), Pfisterer, P., Mol. Cell Biol.. 16(11):6160 (1996), Kratzschmar, J., Eur. J. Biochem.. 236(3): 827 (1996)]. We describe herein the identification of a novel polypeptide which has homology to GLIP and CRISP, designated herein as PR0328 polypeptides.
42. PRQ335. PRQ331 and PRQ326 Protein-protein interactions include receptor and antigen complexes and signal ing mechanisms . As more is known about the structural and functional mechanisms underlying protein-protein interactions, protein-protein interactions can be more easily manipulated to regulate the particular result of the protein-protein interaction. Thus, the underlying mechanisms of protein-protein interactions are of interest to the scientific and medical community. All proteins containing leucine-rich repeats are thought to be involved in protein-protein interactions.
Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. The crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to beta-alpha structural units. These units are arranged so that they form a parallel beta-sheet with one surface exposed to solvent, so that the protein acquires an unusual, nonglubular shape. These two features have been indicated as responsible for the protein-binding functions of proteins containing leucine-rich repeats. See, Kobe and Deisenhofer, Trends Biochem. Sci.. 19(10):415-421 (Oct. 1994).
A study has been reported on leucine-rich proteoglycans which serve as tissue organizers, orienting and ordering collagen fibrils during ontogeny and are involved in pathological processes such as wound healing, tissue repair, and mmor stroma formation. Iozzo, R. V., Crit. Rev. Biochem. Mol. Biol.. 32(2): 141-174 (1997). Others smdies implicating leucine rich proteins in wound healing and tissue repair are De La Salle, C, et al., Vouv. Rev. Fr. Hematol. (Germany), 37(4):215-222 (1995), reporting mutations in the leucine rich motif in a complex associated with the bleeding disorder Bernard-Soulier syndrome, Chlemetson, K. J., Thromb. Haemost. (Germany), 74(l): l l l-116 (July 1995), reporting that platelets have leucine rich repeats and Ruoslahti, E. I., et al., WO9110727-A by La Jolla Cancer Research Foundation reporting that decorin binding to transforming growth factorβ has involvement in a treatment for cancer, wound healing and scarring. Related by function to this group of proteins is the insulin like growth factor (IGF), in that it is useful in wound-healing and associated therapies concerned with re-growth of tissue, such as connective tissue, skin and bone; in promoting body growth in humans and animals; and in stimulating other growth-related processes. The acid labile subunit of IGF (ALS) is also of interest in that it increases the half-life of IGF and is part of the IGF complex in vivo. Another protein which has been reported to have leucine-rich repeats is the SLIT protein which has been reported to be useful in treating neuro-degenerative diseases such as Alzheimer's disease, nerve damage such as in Parkinson's disease, and for diagnosis of cancer, see, Artavanistsakonas, S. and Rothberg, J. M., W09210518- A 1 by Yale University . Of particular interest is LIG- 1 , a membrane glycoprotein that is expressed specifically in glial cells in the mouse brain, and has leucine rich repeats and immunoglobulin-like domains. Suzuki, et al., J. Biol. Chem. (U.S.), 271(37):22522 (1996). Other smdies reporting on the biological functions of proteins having leucine rich repeats include: Tayar, N. , et al., Mol. Cell Endocrinol. , (Ireland), 125(l-2):65- 70 (Dec. 1996) (gonadotropin receptor involvement); Miura, Y., et al.. Nippon Rinsho (Japan). 54(7): 1784-1789 (July 1996) (apoptosis involvement); Harris, P. C, et al., J. Am. Soc. NephroL. 6(4): 1125-1133 (Oct. 1995) (kidney disease involvement).
Efforts are therefore being undertaken by both industry and academia to identify new proteins having leucine rich repeats to better understand protein-protein interactions. Of particular interest are those proteins having leucine rich repeats and homology to known proteins having leucine rich repeats such as LIG- 1 , ALS and decorin. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound proteins having leucine rich repeats. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)].
We describe herein the identification and characterization of novel polypeptides which have homology to proteins of the leucine rich repeat superfamily, designated herein as PR0335, PR0331 and PR0326 polypeptides.
43. PRQ332
Secreted proteins comprising a repeat characterized by an arrangement of conserved leucine residues (leucine-rich repeat motif) have diverse biological roles. Certain proteoglycans, such as biglycan, fibromodulin and decorin, are, for example, characterized by the presence of a leucine-rich repeat of about 24 amino acids [Ruoslahti, Ann. Rev. Cell. Biol. 4 229-255 (1988); Oldberg et al , EMBO J. 8, 2601-2604 (1989)]. In general, proteoglycans are believed to play a role in regulating extracellular matrix, cartilage or bone function. The proteoglycan decorin binds to collagen type I and II and affects the rate of fibril formation. Fibromodulin also binds collagen and delays fibril formation. Both fibromodulin and decorin inhibit the activity of transforming growth factor beta (TGF-β) (U.S. Patent No. 5,583, 103 issued December 10, 1996). TGF-β is known to play a key role in the induction of extracellular matrix and has been implicated in the development of fibrotic diseases, such as cancer and glomerulonephritis. Accordingly, proteoglycans have been proposed for the treatment of fibrotic cancer, based upon their ability to inhibit TGF-β's growth stimulating activity on the cancer cell. Proteoglycans have also been described as potentially useful in the treatment of other proliferative pathologies, including rheumatoid arthritis, arteriosclerosis, adult respiratory distress syndrome, cirrhosis of the liver, fibrosis of the lungs, post-myocardial infarction, cardiac fibrosis, post-angioplasty restenosis, renal interstitial fibrosis and certain dermal fibrotic conditions, such as keloids and scarring, which might result from burn injuries, other invasive skin injuries, or cosmetic or reconstructive surgery (U.S. Patent No. 5,654,270, issued August 5, 1997).
We describe herein the identification and characterization of novel polypeptides which have homology to proteins of the leucine rich repeat superfamily, designated herein as PR0332 polypeptides.
44. PRQ334 Microfibril bundles and proteins found in association with these bundles, particularly attachment molecules, are of interest in the field of dermatology, particularly in the study of skin which has been damaged from aging, injuries or the sun. Fibrillin microfibrils define the continuous elastic network of skin, and are present in dermis as microfibril bundles devoid of measurable elastin extending from the dermal-epithelial junction and as components of the thick elastic fibres present in the deep reticular dermis. Moreover, Marfan syndrome has been linked to mutations which interfere with multimerization of fibrillin monomers or other connective tissue elements.
Fibulin-1 is a modular glycoprotein with amino-terminal anaphlatoxin-like modules followed by nine epidermal growth factor (EGF)-like modules and, depending on alternative splicing, four possible carboxyl termini. Fibulin-2 is a novel extracellular matrix protein frequently found in close association with microfibrils containing either fibronectin or fibrillin. Thus, fibrillin, fibulin, and molecules related thereto are of interest, particularly for the use of preventing skin from being damaged from aging, injuries or the sun, or for restoring skin damaged from same. Moreover, these molecules are generally of interest in the study of connective tissue and attachment molecules and related mechanisms. Fibrillin, fibulin and related molecules are further described in Adams, et al.. J. Mol. Biol., 272(2): 226-36 (1997): Kielty and Shuttleworth. Microsc. Res. Tech.. 38(4):413- 27 (1997); and Child. J. Card. Surg.. 12(2Supp.): 131-5 (1997).
Currently, efforts are being undertaken by both industry and academia to identify new, native secreted and membrane-bound receptor proteins, particularly secreted proteins which have homology to fibulin and fibrillin. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound receptor proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108- 7113 (1996); U.S. Patent No. 5,536,637)].
We herein describe the identification and characterization of novel polypeptides having homology to fibulin and fibrillin, designated herein as PR0334 polypeptides.
45. PRQ346
The widespread occurrence of cancer has prompted the devotion of considerable resources and discovering new treatments of treatment. One particular method involves the creation of tumor or cancer specific monoclonal antibodies (mAbs) which are specific to tumor antigens. Such mAbs, which can distinguish between normal and cancerous cells are useful in the diagnosis, prognosis and treatment of the disease. Particular antigens are known to be associated with neoplastic diseases, such as colorectal and breast cancer. Since colon cancer is a widespread disease, early diagnosis and treatment is an important medical goal. Diagnosis and treatment of cancer can be implemented using monoclonal antibodies (mAbs) specific therefore having fluorescent, nuclear magnetic or radioactive tags. Radioactive genes, toxins and/or drug tagged mAbs can be used for treatment in situ with minimal patient description.
Carcinoembryonic antigen (CEA) is a glycoprotein found in human colon cancer and the digestive organs of a 2-6 month human embryos. CEA is a known human mmor marker and is widely used in the diagnosis of neoplastic diseases, such as colon cancer. For example, when the serum levels of CEA are elevated in a patient, a drop of CEA levels after surgery would indicate the mmor resection was successful. On the other hand, a subsequent rise in serum CEA levels after surgery would indicate that metastases of the original mmor may have formed or that new primary tumors may have appeared. CEA may also be a target for mAb, antisense nucleotides
46. PRQ268
Protein disulfide isomerase is an enzymatic protein which is involved in the promotion of correct refolding of proteins through the establishment of correct disulfide bond formation. Protein disulfide isomerase was initially identified based upon its ability to catalyze the renaturation of reduced denatured RNAse (Goldberger et al., J. Biol. Chem. 239: 1406-1410 (1964) and Epstein et al. , Cold Spring Harbor Symp. Quant. Biol. 28:439-449 (1963)). Protein disulfide isomerase has been shown to be a resident enzyme of the endoplasmic reticulum which is retained in the endoplasmic reticulum via a -KDEL or -HDEL amino acid sequence at its C-terminus. Given the importance of disulfide bond-forming enzymes and their potential uses in a number of different applications, for example in increasing the yield of correct refolding of recombinantly produced proteins, efforts are currently being undertaken by both industry and academia to identify new, native proteins having homology to protein disulfide isomerase. Many of these efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel protein disulfide isomerase homologs. We herein describe a novel polypeptide having homology to protein disulfide isomerase, designated herein as PR0268.
47. PRO330
Prolyl 4-hydroxylase is an enzyme which functions to post-translationally hydroxylate proline residues at the Y position of the amino acid sequence Gly-X-Y, which is a repeating three amino acid sequence found in both collagen and procollagen. Hydroxylation of proline residues at the Y position of the Gly-X-Y amino acid triplet to form 4-hydroxyproline residues at those positions is required before newly synthesized collagen polypeptide chains may fold into their proper three-dimensional triple-helical conformation. If hydroxylation does not occur, synthesized collagen polypeptides remain non-helical, are poorly secreted by cells and cannot assemble into stable functional collagen fibrils. Vuorio et al. , Proc. Natl. Acad. Sci. USA 89:7467-7470 (1992). Prolyl 4-hydroxylase is comprised of at least two different polypeptide subunits, alpha and beta.
Efforts are being undertaken by both industry and academia to identify new, native secreted and membrane-bound receptor proteins. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound receptor proteins. Examples of screening methods and techniques are described in the literature [see, for example, Klein et al., Proc. Natl. Acad. Sci.. 93:7108-7113 (1996); U.S. Patent No. 5,536,637)]. Based upon these efforts, Applicants have herein identified and describe a novel polypeptide having homology to the alpha subunit of prolyl 4-hydroxylase, designated herein as PRO330.
48. PRQ339 and PRO310
Fringe is a protein which specifically blocks serrate-mediated activation of notch in the dorsal compartment of the Drosophila wing imaginal disc. Fleming, et al., Development. 124(15):2973-81 (1997). Therefore, fringe is of interest for both its role in development as well as its ability to regulate serrate, particularly serrate's signaling abilities. Also of interest are novel polypeptides which may have a role in development and/or the regulation of serrate-like molecules. Of particular interest are novel polypeptides having homology to fringe as identified and described herein, designated herein as PR0339 and PRO310 polypeptides.
49. PRQ244
Lectins are a class of proteins comprising a region that binds carbohydrates specifically and non- covalently. Numerous lectins have been identified in higher animals, both membrane-bound and soluble, and have been implicated in a variety of cell-recognition phenomena and mmor metastasis.
Most lectins can be classified as either C-type (calcium-dependent) or S-type (thiol -dependent). Lectins are thought to play a role in regulating cellular events that are initiated at the level of the plasma membrane. For example, plasma membrane associated molecules are involved in the activation of various subsets of lymphoid cells, e.g. T-lymphocytes, and it is known that cell surface molecules are responsible for activation of these cells and consequently their response during an immune reaction.
A particular group of cell adhesion molecules, selectins, belong in the superfamily of C-type lectins. This group includes L-selectin (peripheral lymph node homing receptor (pnHR), LEC-CAM-1 , LAM-1, gp90MEL, gpl00MEL, gpl lOME , MEL-14 antigen, Leu-8 antigen, TQ-1 antigen, DREG antigen), E-selectin (LEC-CAM-2, LECAM-2, ELAM-1), and P-selectin (LEC-CAM-3, LECAM-3, GMP-140, PADGEM). The structure of selectins consists of a C-type lectin (carbohydrate binding) domain, an epidermal growth factor-like (EGF-like) motif, and variable numbers of complement regulatory (CR) motifs. Selectins are associated with leukocyte adhesion, e.g. the attachment of neutrophils to venular endothelial cells adjacent to inflammation (E- selectin), or with the trafficking of lymphocytes from blood to secondary lymphoid organs, e.g. lymph nodes and Peyer's patches (L-selectin).
Another exemplary lectin is the cell-associated macrophage antigen, Mac-2 that is believed to be involved in cell adhesion and immune responses. Macrophages also express a lectin that recognizes Tn Ag, a human carcinoma-associated epitope.
Another C-type lectin is CD95 (Fas antigen/APO-1) that is an important mediator of immunologically relevant regulated or programmed cell death (apoptosis). "Apoptosis" is a non-necrotic cell death that takes place in metazoan animal cells following activation of an intrinsic cell suicide program. The cloning of Fas antigen is described in PCT publication WO 91/10448, and European patent application EP510691. The mature Fas molecule consists of 319 amino acids of which 157 are extracellular, 17 constimte the transmembrane domain, and 145 are intracellular. Increased levels of Fas expression at T cell surface have been associated with mmor cells and HIV-infected cells. Ligation of CD95 triggers apoptosis in the presence of interleukin-1 (IL-2).
C-type lectins also include receptors for oxidized low-density lipoprotein (LDL). This suggests a possible role in the pathogenesis of atherosclerosis. We herein describe the identification and characterization of novel polypeptides having homology to C- type lectins, designated herein as PR0244 polypeptides. SUMMARY OF THE INVENTION 1. PRQ211 and PRQ217
Applicants have identified cDNA clones that encode novel polypeptides having homology to EGF, designated in the present application as "PR021 1 " and "PR0217" polypeptides.
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0211 or PR0217 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding EGF-like homologue PR0211 and PR0217 polypeptides of Fig. 2 (SEQ ID NO:2) and/or 4 (SEQ ID NO:4) indicated in Fig. 1 (SEQ ID NOl) and/or Fig. 3 (SEQ ID NO:3), respectively, or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0211 and PR0217 EGF-like homologue
PR0211 and PR0217 polypeptides. In particular, the invention provides isolated native sequence PR0211 and PR0217 EGF-like homologue polypeptides, which in one embodiment, includes an amino acid sequence comprising residues: 1 to 353 of Fig. 2 (SEQ ID NO:2) or (2) 1 to 379 of Fig. 4 (SEQ ID NO: 4).
2. PRO230
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PRO230".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO230 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PRO230 polypeptide having amino acid residues 1 through 467 of Figure 6 (SEQ ID NO : 12) , or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PRO230 polypeptide. In particular, the invention provides isolated native sequence PRO230 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 through 467 of Figure 6 (SEQ ID NO: 12).
In another embodiment, the invention provides an expressed sequence tag (EST) comprising the nucleotide sequence of SEQ ID NO: 13 (Figure 7) which is herein designated as DNA20088.
3. PRQ232 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0232" .
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0232 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0232 polypeptide having amino acid residues 1 to 114 of Figure 9 (SEQ ID NO: 18), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0232 polypeptide. In particular, the invention provides isolated native sequence PR0232 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 114 of Figure 9 (SEQ ID NO: 18).
4. PRQ187 Applicants have identified a cDNA clone that encodes a novel polypeptide, designated in the present application as "PRO 187".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0187 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0187 polypeptide of Figure 11 (SEQ ID NO:23), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another aspect, the invention provides a nucleic acid comprising the coding sequence of Figure 10 (SEQ ID NO: 22) or its complement. In another aspect, the invention provides a nucleic acid of the full length protein of clone DNA27864-1155, deposited with the ATCC under accession number ATCC 209375, alternatively the coding sequence of clone DNA27864-1155, deposited under accession number ATCC 209375. In yet another embodiment, the invention provides isolated PR0187 polypeptide. In particular, the invention provides isolated native sequence PRO 187 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 205 of Figure 11 (SEQ ID NO:23). Alternatively, the invention provides a polypeptide encoded by the nucleic acid deposited under accession number ATCC 209375.
5. PRQ265
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0265".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0265 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0265 polypeptide having amino acid residues 1 to 660 of Figure 13 (SEQ ID NO: 28), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0265 polypeptide. In particular, the invention provides isolated native sequence PR0265 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 660 of Figure 13 (SEQ ID NO:28). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0265 polypeptide.
6. PRQ219
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0219".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0219 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0219 polypeptide having amino acid residues 1 to 915 of Figure 15 (SEQ ID NO:34), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0219 polypeptide. In particular, the invention provides isolated native sequence PR0219 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 915 of Figure 15 (SEQ ID NO:34).
7. PRQ246
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0246". In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0246 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0246 polypeptide having amino acid residues 1 to 390 of Figure 17 (SEQ ID NO:39), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0246 polypeptide. In particular, the invention provides isolated native sequence PR0246 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 390 of Figure 17 (SEQ ID NO: 39). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0246 polypeptide.
8. PRQ228
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to CD97, EMRl and latrophilin, wherein the polypeptide is designated in the present application as "PR0228" .
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0228 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0228 polypeptide having amino acid residues 1 to 690 of Figure 19 (SEQ ID NO:49), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0228 polypeptide. In particular, the invention provides isolated native sequence PR0228 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 690 of Figure 19 (SEQ ID NO: 49). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0228 polypeptide.
In another embodiment, the invention provides an expressed sequence tag (EST) comprising the nucleotide sequence of SEQ ID NO:50, designated herein as DNA21951.
9. PRQ533
Applicants have identified a cDNA clone (DNA49435-1219) that encodes a novel polypeptide, designated in the present application as PR0533. In one embodiment, the invention provides an isolated nucleic acid molecule having at least about 80% sequence identity to (a) a DNA molecule encoding a PR0533 polypeptide comprising the sequence of amino acids 23 to 216 of Figure 22 (SEQ ID NO:59), or (b) the complement of the DNA molecule of (a). The sequence identity preferably is about 85 % , more preferably about 90% , most preferably about 95 % . In one aspect, the isolated nucleic acid has at least about 80%, preferably at least about 85 % , more preferably at least about 90% , and most preferably at least about 95% sequence identity with a polypeptide having amino acid residues 23 to 216 of Figure 22 (SEQ ID NO:59). Preferably, the highest degree of sequence identity occurs within the secreted portion (amino acids 23 to 216 of Figure 22, SEQ ID NO:59). In a further embodiment, the isolated nucleic acid molecule comprises DNA encoding a PR0533 polypeptide having amino acid residues 1 to 216 of Figure 22 (SEQ ID NO:59), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another aspect, the invention provides a nucleic acid of the full length protein of clone DNA49435-1219, deposited with the ATCC under accession number ATCC 209480.
In yet another embodiment, the invention provides isolated PR0533 polypeptide. In particular, the invention provides isolated native sequence PR0533 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 23 to 216 of Figure 22 (SEQ ID NO:59). Native PR0533 polypeptides with or without the native signal sequence (amino acids 1 to 22 in Figure 22 (SEQ ID NO:59)), and with or without the initiating methionine are specifically included. Alternatively, the invention provides a PR0533 polypeptide encoded by the nucleic acid deposited under accession number ATCC 209480.
10. PRQ245
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0245".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0245 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0245 polypeptide having amino acid residues 1 to 312 of Fig. 24 (SEQ ID NO:64), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0245 polypeptide. In particular, the invention provides isolated native sequence PR0245 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 312 of Figure 24 (SEQ ID NO:64).
11. PRO220. PRQ221 and PRQ227
Applicants have identified cDNA clones that each encode novel polypeptides, all having leucine rich repeats. These polypeptides are designated in the present application as PRO220, PR0221 and PR0227. In one embodiment, the invention provides isolated nucleic acid molecules comprising DNA respectively encoding PRO220, PR0221 and PR0227, respectively. In one aspect, provided herein is an isolated nucleic acid comprises DNA encoding the PRO220 polypeptide having amino acid residues 1 through 708 of Figure 26 (SEQ ID NO: 69), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. Also provided herein is an isolated nucleic acid comprises DNA encoding the PR0221 polypeptide having amino acid residues 1 through 259 of Figure 28 (SEQ ID NO:71), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. Moreover, also provided herein is an isolated nucleic acid comprises DNA encoding the PR0227 polypeptide having amino acid residues 1 through 620 of Figure 30 (SEQ ID NO:73), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PRO220, PR0221 and PR0227 polypeptides. In particular, provided herein is the isolated native sequence for the PRO220 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 708 of Figure 26 (SEQ ID NO:69). Additionally provided herein is the isolated native sequence for the PR0221 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 259 of Figure 28 (SEQ ID NO:71). Moreover, provided herein is the isolated native sequence for the PR0227 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 620 of Figure 30 (SEQ ID NO:73).
12. PRQ258
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to CRTAM and poliovirus receptor precursors, wherein the polypeptide is designated in the present application as "PR0258" . In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0258 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0258 polypeptide having amino acid residues 1 to 398 of Figure 32 (SEQ ID NO:84), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0258 polypeptide. In particular, the invention provides isolated native sequence PR0258 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 398 of Figure 32 (SEQ ID N0:84). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0258 polypeptide.
13. PRQ266
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0266".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0266 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0266 polypeptide having amino acid residues 1 to 696 of Figure 34 (SEQ ID NO:91), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0266 polypeptide. In particular, the invention provides isolated native sequence PR0266 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 696 of Figure 34 (SEQ ID NO:91).
14. PRQ269 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as PR0269.
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0269 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0269 polypeptide having amino acid residues 1 to 490 of Fig. 36 (SEQ ID NO:96), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0269 polypeptide. In particular, the invention provides isolated native sequence PR0269 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 490 of Figure 36 (SEQ ID NO:96). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0269 polypeptide.
15. PRQ287
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0287". In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0287 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0287 polypeptide having amino acid residues 1 to 415 of Fig. 38 (SEQ ID NO: 104), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0287 polypeptide. In particular, the invention provides isolated native sequence PR0287 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 415 of Figure 38 (SEQ ID NO: 104).
16. PRQ214 Applicants have identified a cDNA clone that encodes a novel polypeptide, designated in the present application as "PR0214" .
In one embodiment , the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0214 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0214 polypeptide of Fig. 40 (SEQ ID NO: 109), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another aspect, the invention provides a nucleic acid comprising the coding sequence of Fig. 39 (SEQ ID NO: 108) or its complement. In another aspect, the invention provides a nucleic acid of the full length protein of clone DNA32286-1191 , deposited with ATCC under accession number ATCC 209385.
In yet another embodiment, the invention provides isolated PR0214 polypeptide. In particular, the invention provides isolated native sequence PR0214 polypeptide, which in one embodiment, includes an amino acid sequence comprising the residues of Figure 40 (SEQ ID NO: 109). Alternatively, the invention provides a polypeptide encoded by the nucleic acid deposited under accession number ATCC 209385.
17. PRQ317
Applicants have identified a cDNA clone that encodes a novel polypeptide, designated in the present application as "PR0317".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding PR0317 polypeptide. In one aspect, the isolated nucleic acid comprises DNA (SEQ ID NO: 113) encoding
PR0317 polypeptide having amino acid residues 1 to 366 of Fig. 42, or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0317 polypeptide. In particular, the invention provides isolated native-sequence PR0317 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 366 of Figure 42 (SEQ ID NO: 114).
In yet another embodiment, the invention supplies a method of detecting the presence of PR0317 in a sample, the method comprising: a) contacting a detectable anti-PR0317 antibody with a sample suspected of containing PR0317; and b) detecting binding of the antibody to the sample; wherein the sample is selected from the group consisting of a body fluid, a tissue sample, a cell extract, and a cell culture medium.
In a still further embodiment a method is provided for determining the presence of PR0317 mRNA in a sample, the method comprising: a) contacting a sample suspected of containing PR0317 mRNA with a detectable nucleic acid probe that hybridizes under moderate to stringent conditions to PR0317 mRNA; and b) detecting hybridization of the probe to the sample.
Preferably, in this method the sample is a tissue sample and the detecting step is by in situ hybridization, or the sample is a cell extract and detection is by Northern analysis.
Further, the invention provides a method for treating a PR0317-associated disorder comprising administering to a mammal an effective amount of the PR0317 polypeptide or a composition thereof containing a carrier, or with an effective amount of a PR0317 agonist or PR0317 antagonist, such as an antibody which binds specifically to PR0317.
18. PRQ301 Applicants have identified a cDNA clone (DNA40628-1216) that encodes a novel polypeptide, designated in the present application as "PRO301 ". In one embodiment, the invention provides an isolated nucleic acid molecule having at least about 80% sequence identity to (a) a DNA molecule encoding a PRO301 polypeptide comprising the sequence of amino acids 28 to 258 of Fig. 44 (SEQ ID NO: 119), or (b) the complement of the DNA molecule of (a). The sequence identity preferably is about 85% , more preferably about 90% , most preferably about 95 % . In one aspect, the isolated nucleic acid has at least about 80 % , preferably at least about 85 % , more preferably at least about 90 % , and most preferably at least about 95 % sequence identity with a polypeptide having amino acid residues 28 to 258 of Fig. 44 (SEQ ID NO: 119). Preferably, the highest degree of sequence identity occurs within the extracellular domains (amino acids 28 to 258 of Fig. 44, SEQ ID NO: 119). In a further embodiment, the isolated nucleic acid molecule comprises DNA encoding a PRO301 polypeptide having amino acid residues 28 to 299 of Fig. 44 (SEQ ID NO: 119), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another aspect, the invention provides a nucleic acid of the full length protein of clone DNA40628-1216, deposited with the ATCC under accession number ATCC 209432, alternatively the coding sequence of clone DNA40628-1216, deposited under accession number ATCC 209432.
In yet another embodiment, the invention provides isolated PRO301 polypeptide. In particular, the invention provides isolated native sequence PRO301 polypeptide, which in one embodiment, includes an amino acid sequence comprising the extracellular domain residues 28 to 258 of Figure 44 (SEQ ID NO: 119). Native PRO301 polypeptides with or without the native signal sequence (amino acids 1 to 27 in Figure 44 (SEQ ID NO: 119), and with or without the initiating methionine are specifically included. Additionally, the sequences of the invention may also comprise the transmembrane domain (residues 236 to about 258 in Figure 44; SEQ ID NO: 119) and/or the intracellular domain (about residue 259 to 299 in Figure 44; SEQ ID NO: 119). Alternatively, the invention provides a PRO301 polypeptide encoded by the nucleic acid deposited under accession number ATCC 209432.
19. PRQ224 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0224" .
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0224 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0224 polypeptide having amino acid residues 1 to 282 of Figure 46 (SEQ ID NO: 127), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0224 polypeptide. In particular, the invention provides isolated native sequence PR0224 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 282 of Figure 46 (SEQ ID NO: 127). 20. PRQ222
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0222".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0222 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0222 polypeptide having amino acid residues 1 to 490 of Fig. 48 (SEQ ID NO: 132), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0222 polypeptide. In particular, the invention provides isolated native sequence PR0222 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 490 of Figure 48 (SEQ ID NO: 132).
21. PRQ234
Applicants have identified a cDNA clone that encodes a novel lectin polypeptide molecule, designated in the present application as "PR0234" . In one embodiment, the invention provides an isolated nucleic acid encoding a novel lectin comprising
DNA encoding a PR0234 polypeptide. In one aspect, the isolated nucleic acid comprises the DNA encoding PR0234 polypeptides having amino acid residues 1 to 382 of Fig. 50 (SEQ ID NO: 137), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another aspect, the invention provides an isolated nucleic acid molecule comprising the nucleotide sequence of Fig. 49 (SEQ ID NO: 136).
In another embodiment, the invention provides isolated novel PR0234 polypeptides. In particular, the invention provides isolated native sequence PR0234 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 382 of Figure 50 (SEQ ID NO: 137).
In yet another embodiment, the invention provides oligonucleotide probes useful for isolating genomic and cDNA nucleotide sequences.
22. PRQ231
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to a putative acid phosphatase, wherein the polypeptide is designated in the present application as "PR0231 ". In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0231 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0231 polypeptide having amino acid residues 1 to 428 of Fig. 52 (SEQ ID NO: 142), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0231 polypeptide. In particular, the invention provides isolated native sequence PR0231 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 428 of Figure 52 (SEQ ID NO: 142). 23. PRQ229
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to scavenger receptors wherein the polypeptide is designated in the present application as "PR0229".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0229 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0229 polypeptide having amino acid residues 1 to 347 of Figure 54 (SEQ ID NO: 148), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0229 polypeptide. In particular, the invention provides isolated native sequence PR0229 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 347 of Figure 54 (SEQ ID NO: 148).
24. PRQ238
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to reductase, wherein the polypeptide is designated in the present application as "PR0238". In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0238 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0238 polypeptide having amino acid residues 1 to 310 of Figure 56 (SEQ ID NO: 153), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0238 polypeptide. In particular, the invention provides isolated native sequence PR0238 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 310 of Figure 56 (SEQ ID NO: 153).
25. PRQ233 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0233".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0233 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0233 polypeptide having amino acid residues 1 to 300 of Figure 58 (SEQ ID NO: 159), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0233 polypeptide. In particular, the invention provides isolated native sequence PR0233 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 300 of Figure 58 (SEQ ID NO: 159). 26. PRQ223
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to serine carboxypeptidase polypeptides, wherein the polypeptide is designated in the present application as "PR0223".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0223 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0223 polypeptide having amino acid residues 1 to 476 of Figure 60 (SEQ ID NO: 164), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0223 polypeptide. In particular, the invention provides isolated native sequence PR0223 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 476 of Figure 60 (SEQ ID NO: 164).
27. PRQ235
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0235". In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0235 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0235 polypeptide having amino acid residues 1 to 552 of Figure 62 (SEQ ID NO: 170), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0235 polypeptide. In particular, the invention provides isolated native sequence PR0235 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 552 of Figure 62 (SEQ ID NO: 170).
28. PRQ236 and PRQ262 Applicants have identified cDNA clones that encode novel polypeptides having homology to β- galactosidase, wherein those polypeptides are designated in the present application as "PR0236" and "PR0262".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0236 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0236 polypeptide having amino acid residues 1 to 636 of Figure 64 (SEQ ID NO: 175), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0262 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0262 polypeptide having amino acid residues 1 to 654 of Figure 66 (SEQ ID NO: 177), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0236 polypeptide. In particular, the invention provides isolated native sequence PR0236 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 636 of Figure 64 (SEQ ID NO: 175).
In another embodiment, the invention provides isolated PR0262 polypeptide. In particular, the invention provides isolated native sequence PR0262 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 654 of Figure 66 (SEQ ID NO: 177).
29. PRQ239
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0239". In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0239 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0239 polypeptide having amino acid residues 1 to 501 of Figure 68 (SEQ ID NO: 185), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0239 polypeptide. In particular, the invention provides isolated native sequence PR0239 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 501 of Figure 68 (SEQ ID NO: 185).
30. PRQ257 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0257".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0257 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0257 polypeptide having amino acid residues 1 to 607 of Figure 70 (SEQ ID NO: 190), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0257 polypeptide. In particular, the invention provides isolated native sequence PR0257 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 607 of Figure 70 (SEQ ID NO: 190). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0257 polypeptide.
31. PRO260
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PRO260" . In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO260 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PRO260 polypeptide having amino acid residues 1 to 467 of Figure 72 (SEQ ID NO: 195), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PRO260 polypeptide. In particular, the invention provides isolated native sequence PRO260 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 467 of Figure 72 (SEQ ID NO: 195).
32. PRQ263
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to CD44 antigen, wherein the polypeptide is designated in the present application as "PR0263".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0263 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0263 polypeptide having amino acid residues 1 to 322 of Figure 74 (SEQ ID NO:201), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0263 polypeptide. In particular, the invention provides isolated native sequence PR0263 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 322 of Figure 74 (SEQ ID NO: 201). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0263 polypeptide.
33. PRO270 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PRO270".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO270 polypeptide. In one aspect, the isolated nucleic acid comprises DNA whivch includes the sequence encoding the PRO270 polypeptide having amino acid residues 1 to 296 of Fig. 76 (SEQ ID NO: 207), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PRO270 polypeptide. In particular, the invention provides isolated native sequence PRO270 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 296 of Figure 76 (SEQ ID NO: 207).
34. PRQ271
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to the proteoglycan link protein, wherein the polypeptide is designated in the present application as "PR0271".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0271 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0271 polypeptide having amino acid residues 1 to 360 of Figure 78 (SEQ ID N0:213), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0271 polypeptide. In particular, the invention provides isolated native sequence PR0271 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 360 of Figure 78 (SEQ ID NO:213).
35. PRQ272
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0272".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0272 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0272 polypeptide having amino acid residues 1 to 328 of Figure 80 (SEQ ID NO:221), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0272 polypeptide. In particular, the invention provides isolated native sequence PR0272 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 328 of Figure 80 (SEQ ID NO:211).
36. PRQ294
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0294". In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0294 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0294 polypeptide having amino acid residues 1 to 550 of Figure 82 (SEQ ID NO:227), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0294 polypeptide. In particular, the invention provides isolated native sequence PR0294 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 550 of Figure 82 (SEQ ID NO: 227).
37. PRQ295 Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0295" .
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0295 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0295 polypeptide having amino acid residues 1 to 350 of Figure 84 (SEQ ID NO:236), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0295 polypeptide. In particular, the invention provides isolated native sequence PR0295 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 350 of Figure 84 (SEQ ID NO: 236).
38. PRQ293 Applicants have identified a cDNA clone that encodes a novel human neuronal leucine rich repeat polypeptide, wherein the polypeptide is designated in the present application as "PR0293" .
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0293 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0293 polypeptide having amino acid residues 1 to 713 of Figure 86 (SEQ ID NO: 245), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0293 polypeptide. In particular, the invention provides isolated native sequence PR0293 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 713 of Figure 86 (SEQ ID NO: 245). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0293 polypeptide.
39. PRQ247
Applicants have identified a cDNA clone that encodes a novel polypeptide having leucine rich repeats wherein the polypeptide is designated in the present application as "PR0247". In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0247 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0247 polypeptide having amino acid residues 1 to 546 of Figure 88 (SEQ ID NO:250), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0247 polypeptide. In particular, the invention provides isolated native sequence PR0247 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 546 of Figure 88 (SEQ ID NO:250). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0247 polypeptide.
40. PRO302. PRO303. PRQ304. PRO307 and PRQ343
Applicants have identified cDNA clones that encode novel polypeptides having homology to various proteases, wherein those polypeptide are designated in the present application as "PRO302", "PRO303", "PRO304", "PRO307" and "PR0343" polypeptides.
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO302 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PRO302 polypeptide having amino acid residues 1 to 452 of Figure 90 (SEQ ID NO:255), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO303 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PRO303 polypeptide having amino acid residues 1 to 314 of Figure 92 (SEQ ID NO:257), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In yet another embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO304 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PRO304 polypeptide having amino acid residues 1 to 556 of Figure 94 (SEQ ID NO:259), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO307 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PRO307 polypeptide having amino acid residues 1 to 383 of Figure 96 (SEQ ID NO:261), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0343 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0343 polypeptide having amino acid residues 1 to 317 of Figure 98 (SEQ ID NO:263), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PRO302 polypeptide. In particular, the invention provides isolated native sequence PRO302 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 452 of Figure 90 (SEQ ID NO:255).
In another embodiment, the invention provides isolated PRO303 polypeptide. In particular, the invention provides isolated native sequence PRO303 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 314 of Figure 92 (SEQ ID NO:257).
In another embodiment, the invention provides isolated PRO304 polypeptide. In particular, the invention provides isolated native sequence PRO304 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 556 of Figure 94 (SEQ ID NO:259). In another embodiment, the invention provides isolated PRO307 polypeptide. In particular, the invention provides isolated native sequence PRO307 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 383 of Figure 96 (SEQ ID NO:261).
In another embodiment, the invention provides isolated PR0343 polypeptide. In particular, the invention provides isolated native sequence PR0343 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 317 of Figure 98 (SEQ ID NO: 263). 41. PRQ328
Applicants have identified a cDNA clone that encodes a novel polypeptide, wherein the polypeptide is designated in the present application as "PR0328" .
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0328 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0328 polypeptide having amino acid residues 1 to 463 of Figure 100 (SEQ ID NO: 285), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0328 polypeptide. In particular, the invention provides isolated native sequence PR0328 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 463 of Figure 100 (SEQ ID NO:285). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PRO306 polypeptide.
42. PRQ335. PRQ331 and PRQ326
Applicants have identified three cDNA clones that respectively encode three novel polypeptides, each having leucine rich repeats and homology to LIG-1 and ALS. These polypeptides are designated in the present application as PR0335, PR0331 and PR0326, respectively.
In one embodiment, the invention provides three isolated nucleic acid molecules comprising DNA respectively encoding PR0335, PR0331 and PR0326, respectively. In one aspect, herein is provided an isolated nucleic acid comprising DNA encoding the PR0335 polypeptide having amino acid residues 1 through 1059 of Figure 102 (SEQ ID NO:290), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate , and optionally , under high stringency conditions . Also provided herein is an isolated nucleic acid comprises DNA encoding the PR0331 polypeptide having amino acid residues 1 through 640 of Figure 104 (SEQ ID NO:292), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. Additionally provided herein is an isolated nucleic acid comprises DNA encoding the PR0326 polypeptide having amino acid residues 1 through 1119 of Figure 106 (SEQ ID NO:294), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0335, PR0331 and PR0326 polypeptides or extracellular domains thereof. In particular, the invention provides isolated native sequence for the PR0335 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 through 1059 of Figure 102 (SEQ ID NO:290). Also provided herein is the isolated native sequence for the PR0331 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 through 640 of Figure 104 (SEQ ID NO:292). Also provided herein is the isolated native sequence for the PR0326 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 through 1119 of Figure 106 (SEQ ID NO:294). 43. PRQ332
Applicants have identified a cDNA clone (DNA40982-1235) that encodes a novel polypeptide, designated in the present application as "PR0332. "
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA having at least about 80% sequence identity to (a) a DNA molecule encoding a PR0358 polypeptide comprising the sequence of amino acids 49 to 642 of Fig. 108 (SEQ ID NO:310), or (b) the complement of the DNA molecule of (a). The sequence identity preferably is about 85 % , more preferably about 90% , most preferably about 95 % . In one aspect, the isolated nucleic acid has at least about 80%, preferably at least about 85% , more preferably at least about 90% , and most preferably at least about 95% sequence identity with a polypeptide having amino acid residues 1 to 642 of Fig. 108 (SEQ ID NO: 310). Preferably, the highest degree of sequence identity occurs within the leucine-rich repeat domains (amino acids 116 to 624 of Fig. 108, SEQ ID NO:310). In a further embodiment, the isolated nucleic acid molecule comprises DNA encoding a PR0332 polypeptide having amino acid residues 49 to 642 of Fig. 108 (SEQ ID NO:310), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0332 polypeptides. In particular, the invention provides isolated native sequence PR0332 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 49 to 624 of Figure 108 (SEQ ID NO:310). Native PR0332 polypeptides with or without the native signal sequence (amino acids 1 to 48 in Figure 108, SEQ ID NO:310), and with or without the initiating methionine are specifically included.
44. PRQ334
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to fibulin and fibrillin, wherein the polypeptide is designated in the present application as "PR0334".
In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0334 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0334 polypeptide having amino acid residues 1 to 509 of Figure 110 (SEQ ID NO:315), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0334 polypeptide. In particular, the invention provides isolated native sequence PR0334 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 509 of Figure 110 (SEQ ID NO:315).
45. PRQ346
Applicants have identified a cDNA clone (DNA44167-1243) that encodes a novel polypeptide, designated in the present application as "PR0346. "
In one embodiment, the invention provides an isolated nucleic acid molecule having at least about 80% sequence identity to (a) a DNA molecule encoding a PR0346 polypeptide comprising the sequence of amino acids 19 to 339 of Fig. 112 (SEQ ID NO: 320), or (b) the complement of the DNA molecule of (a). The sequence identity preferably is about 85%, more preferably about 90%, most preferably about 95 % . In one aspect, the isolated nucleic acid has at least about 80% , preferably at least about 85% , more preferably at least about 90% , and most preferably at least about 95% sequence identity with a polypeptide having amino acid residues 19 to 339 of Fig. 112 (SEQ ID NO:320). Preferably, the highest degree of sequence identity occurs within the extracellular domains (amino acids 19 to 339 of Fig. 112, SEQ IP NO:320). In alternative embodiments, the polypeptide by which the homology is measured comprises the residues 1-339, 19-360 or 19- 450 of Fig. 112, SEQ IP NO:320). In a further embodiment, the isolated nucleic acid molecule comprises PNA encoding a PR0346 polypeptide having amino acid residues 19 to 339 of Fig. 112 (SEQ IP NO:320), alternatively residues 1-339, 19-360 or 19-450 of Fig. 112 (SEQ IP NO:320) or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another aspect, the invention provides a nucleic acid of the full length protein of clone PNA44167-1243, deposited with the ATCC under accession number ATCC 209434, alternatively the coding sequence of clone DNA44167- 1243, deposited under accession number ATCC 209434.
In yet another embodiment, the invention provides isolated PR0346 polypeptide. In particular, the invention provides isolated native sequence PR0346 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 19 to 339 of Figure 112 (SEQ ID NO:320). Native PR0346 polypeptides with or without the native signal sequence (residues 1 to 18 in Figure 112 (SEQ ID NO:320), with or without the initiating methionine, with or without the transmembrane domain (residues 340 to 360) and with or without the intracellular domain (residues 361 to 450) are specifically included. Alternatively, the invention provides a PR0346 polypeptide encoded by the nucleic acid deposited under accession number ATCC 209434.
46. PRQ268
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to protein disulfide isomerase, wherein the polypeptide is designated in the present application as "PR0268". In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PR0268 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0268 polypeptide having amino acid residues 1 to 280 of Figure 114 (SEQ ID NO:325), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0268 polypeptide. In particular, the invention provides isolated native sequence PR0268 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 280 of Figure 114 (SEQ ID NO:325). An additional embodiment of the present invention is directed to an isolated extracellular domain of a PR0268 polypeptide.
47. PRO330
Applicants have identified a cDNA clone that encodes a novel polypeptide having homology to the alpha subunit of prolyl 4-hydroxylase, wherein the polypeptide is designated in the present application as "PRO330" . In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding a PRO330 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PRO330 polypeptide having amino acid residues 1 to 533 of Figure 116 (SEQ ID NO:332), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PRO330 polypeptide. In particular, the invention provides isolated native sequence PRO330 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 533 of Figure 116 (SEQ ID NO:332).
48. PRQ339 and PRO310 Applicants have identified two cDNA clones wherein each clone encodes a novel polypeptide having homology to fringe, wherein the polypeptides are designated in the present application as "PR0339" and "PRO310" .
In one embodiment, the invention provides isolated nucleic acid molecules comprising DNA encoding a PR0339 and/or a PR0310 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding the PR0339 polypeptide having amino acid residues 1 to 772 of Figure 118 (SEQ ID NO:339), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another aspect, the isolated nucleic acid comprises DNA encoding the PR0310 polypeptide having amino acid residues 1 to 318 of Figure 120 (SEQ ID NO : 341 ) , or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions.
In another embodiment, the invention provides isolated PR0339 as well as isolated PRO310 polypeptides. In particular, the invention provides isolated native sequence PR0339 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 772 of Figure 118 (SEQ ID NO:339). The invention further provides isolated native sequence PR0310 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 318 of Figure 120 (SEQ ID NO:341).
49. PRQ244
Applicants have identified a cDNA clone that encodes a novel polypeptide, designated in the present application as "PR0244". In one embodiment, the invention provides an isolated nucleic acid molecule comprising DNA encoding
PR0244 polypeptide. In one aspect, the isolated nucleic acid comprises DNA encoding PR0244 polypeptide having amino acid residues 1 to 219 of Fig. 122 (SEQ ID NO:377), or is complementary to such encoding nucleic acid sequence, and remains stably bound to it under at least moderate, and optionally, under high stringency conditions. In another embodiment, the invention provides isolated PR0244 polypeptide. In particular, the invention provides isolated native sequence PR0244 polypeptide, which in one embodiment, includes an amino acid sequence comprising residues 1 to 219 of Figure 122 (SEQ ID NO: 377). 50. Additional Embodiments
In other embodiments of the present invention, the invention provides vectors comprising DNA encoding any of the herein described polypeptides. Host cell comprising any such vector are also provided. By way of example, the host cells may be CHO cells, E. coli, or yeast. A process for producing any of the herein described polypeptides is further provided and comprises culturing host cells under conditions suitable for expression of the desired polypeptide and recovering the desired polypeptide from the cell culture.
In other embodiments, the invention provides chimeric molecules comprising any of the herein described polypeptides fused to a heterologous polypeptide or amino acid sequence. Example of such chimeric molecules comprise any of the herein described polypeptides fused to an epitope tag sequence or a Fc region of an immunoglobulin. In another embodiment, the invention provides an antibody which specifically binds to any of the above or below described polypeptides. Optionally, the antibody is a monoclonal antibody, humanized antibody, antibody fragment or single-chain antibody.
In yet other embodiments, the invention provides oligonucleotide probes useful for isolating genomic and cDNA nucleotide sequences, wherein those probes may be derived from any of the above or below described nucleotide sequences.
In other embodiments, the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence that encodes a PRO polypeptide.
In one aspect, the isolated nucleic acid molecule comprises a nucleotide sequence having at least about
80% sequence identity, preferably at least about 81 % sequence identity, more preferably at least about 82% sequence identity, yet more preferably at least about 83% sequence identity, yet more preferably at least about
84% sequence identity, yet more preferably at least about 85% sequence identity, yet more preferably at least about 86% sequence identity, yet more preferably at least about 87% sequence identity, yet more preferably at least about 88 % sequence identity, yet more preferably at least about 89 % sequence identity, yet more preferably at least about 90% sequence identity, yet more preferably at least about 91 % sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93% sequence identity, yet more preferably at least about 94 % sequence identity, yet more preferably at least about 95 % sequence identity, yet more preferably at least about 96% sequence identity, yet more preferably at least about 97% sequence identity, yet more preferably at least about 98% sequence identity and yet more preferably at least about 99% sequence identity to (a) a DNA molecule encoding a PRO polypeptide having a full-length amino acid sequence as disclosed herein, an amino acid sequence lacking the signal peptide as disclosed herein or an extracellular domain of a transmembrane protein, with or without the signal peptide, as disclosed herein, or (b) the complement of the DNA molecule of (a).
In other aspects, the isolated nucleic acid molecule comprises a nucleotide sequence having at least about
80% sequence identity, preferably at least about 81 % sequence identity, more preferably at least about 82% sequence identity, yet more preferably at least about 83% sequence identity, yet more preferably at least about
84% sequence identity, yet more preferably at least about 85% sequence identity, yet more preferably at least about 86% sequence identity, yet more preferably at least about 87% sequence identity, yet more preferably at least about 88% sequence identity, yet more preferably at least about 89% sequence identity, yet more preferably at least about 90% sequence identity, yet more preferably at least about 91 % sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93 % sequence identity, yet more preferably at least about 94% sequence identity, yet more preferably at least about 95% sequence identity, yet more preferably at least about 96% sequence identity, yet more preferably at least about 97% sequence identity, yet more preferably at least about 98% sequence identity and yet more preferably at least about 99% sequence identity to (a) a DNA molecule comprising the coding sequence of a full-length PRO polypeptide cDNA as disclosed herein, the coding sequence of a PRO polypeptide lacking the signal peptide as disclosed herein or the coding sequence of an extracellular domain of a transmembrane PRO polypeptide, with or without the signal peptide, as disclosed herein, or (b) the complement of the DNA molecule of (a). In a further aspect, the invention concerns an isolated nucleic acid molecule comprising a nucleotide sequence having at least about 80% sequence identity, preferably at least about 81 % sequence identity, more preferably at least about 82% sequence identity, yet more preferably at least about 83 % sequence identity, yet more preferably at least about 84% sequence identity, yet more preferably at least about 85 % sequence identity, yet more preferably at least about 86% sequence identity, yet more preferably at least about 87% sequence identity, yet more preferably at least about 88% sequence identity, yet more preferably at least about 89% sequence identity, yet more preferably at least about 90% sequence identity, yet more preferably at least about 91 % sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93% sequence identity, yet more preferably at least about 94% sequence identity, yet more preferably at least about 95 % sequence identity, yet more preferably at least about 96 % sequence identity, yet more preferably at least about 97% sequence identity, yet more preferably at least about 98% sequence identity and yet more preferably at least about 99% sequence identity to (a) a DNA molecule that encodes the same mature polypeptide encoded by any of the human protein cDNAs deposited with the ATCC as disclosed herein, or (b) the complement of the DNA molecule of (a).
Another aspect the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence encoding a PRO polypeptide which is either transmembrane domain-deleted or transmembrane domain- inactivated, or is complementary to such encoding nucleotide sequence, wherein the transmembrane domain(s) of such polypeptide are disclosed herein. Therefore, soluble extracellular domains of the herein described PRO polypeptides are contemplated.
Another embodiment is directed to fragments of a PRO polypeptide coding sequence, or the complement thereof, that may find use as, for example, hybridization probes or for encoding fragments of a PRO polypeptide that may optionally encode a polypeptide comprising a binding site for an anti-PRO antibody. Such nucleic acid fragments are usually at least about 20 nucleotides in length, preferably at least about 30 nucleotides in length, more preferably at least about 40 nucleotides in length, yet more preferably at least about 50 nucleotides in length, yet more preferably at least about 60 nucleotides in length, yet more preferably at least about 70 nucleotides in length, yet more preferably at least about 80 nucleotides in length, yet more preferably at least about 90 nucleotides in length, yet more preferably at least about 100 nucleotides in length, yet more preferably at least about 110 nucleotides in length, yet more preferably at least about 120 nucleotides in length, yet more preferably at least about 130 nucleotides in length, yet more preferably at least about 140 nucleotides in length, yet more preferably at least about 150 nucleotides in length, yet more preferably at least about 160 nucleotides in length, yet more preferably at least about 170 nucleotides in length, yet more preferably at least about 180 nucleotides in length, yet more preferably at least about 190 nucleotides in length, yet more preferably at least about 200 nucleotides in length, yet more preferably at least about 250 nucleotides in length, yet more preferably at least about 300 nucleotides in length, yet more preferably at least about 350 nucleotides in length, yet more preferably at least about 400 nucleotides in length, yet more preferably at least about 450 nucleotides in length, yet more preferably at least about 500 nucleotides in length, yet more preferably at least about 600 nucleotides in length, yet more preferably at least about 700 nucleotides in length, yet more preferably at least about 800 nucleotides in length, yet more preferably at least about 900 nucleotides in length and yet more preferably at least about 1000 nucleotides in length, wherein in this context the term "about" means the referenced nucleotide sequence length plus or minus 10% of that referenced length. It is noted that novel fragments of a PRO polypeptide-encoding nucleotide sequence may be determined in a routine manner by aligning the PRO polypeptide-encoding nucleotide sequence with other known nucleotide sequences using any of a number of well known sequence alignment programs and determining which PRO polypeptide-encoding nucleotide sequence fragment(s) are novel. All of such PRO polypeptide-encoding nucleotide sequences are contemplated herein. Also contemplated are the PRO polypeptide fragments encoded by these nucleotide molecule fragments, preferably those PRO polypeptide fragments that comprise a binding site for an anti-PRO antibody.
In another embodiment, the invention provides isolated PRO polypeptide encoded by any of the isolated nucleic acid sequences hereinabove identified. In a certain aspect, the invention concerns an isolated PRO polypeptide, comprising an amino acid sequence having at least about 80% sequence identity, preferably at least about 81 % sequence identity, more preferably at least about 82% sequence identity, yet more preferably at least about 83% sequence identity, yet more preferably at least about 84% sequence identity, yet more preferably at least about 85% sequence identity, yet more preferably at least about 86% sequence identity, yet more preferably at least about 87% sequence identity, yet more preferably at least about 88% sequence identity, yet more preferably at least about 89% sequence identity, yet more preferably at least about 90% sequence identity, yet more preferably at least about 91 % sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93% sequence identity, yet more preferably at least about 94% sequence identity, yet more preferably at least about 95 % sequence identity, yet more preferably at least about 96 % sequence identity, yet more preferably at least about 97% sequence identity, yet more preferably at least about 98% sequence identity and yet more preferably at least about 99% sequence identity to a PRO polypeptide having a full-length amino acid sequence as disclosed herein, an amino acid sequence lacking the signal peptide as disclosed herein or an extracellular domain of a transmembrane protein, with or without the signal peptide, as disclosed herein.
In a further aspect, the invention concerns an isolated PRO polypeptide comprising an amino acid sequence having at least about 80% sequence identity, preferably at least about 81 % sequence identity, more preferably at least about 82% sequence identity, yet more preferably at least about 83% sequence identity, yet more preferably at least about 84 % sequence identity, yet more preferably at least about 85 % sequence identity, yet more preferably at least about 86% sequence identity, yet more preferably at least about 87% sequence identity, yet more preferably at least about 88% sequence identity, yet more preferably at least about 89% sequence identity, yet more preferably at least about 90% sequence identity, yet more preferably at least about 91 % sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93% sequence identity, yet more preferably at least about 94% sequence identity, yet more preferably at least about 95 % sequence identity , yet more preferably at least about 96 % sequence identity , yet more preferably at least about 97% sequence identity, yet more preferably at least about 98% sequence identity and yet more preferably at least about 99% sequence identity to an amino acid sequence encoded by any of the human protein cDNAs deposited with the ATCC as disclosed herein.
In a further aspect, the invention concerns an isolated PRO polypeptide comprising an amino acid sequence scoring at least about 80% positives, preferably at least about 81 % positives, more preferably at least about 82% positives, yet more preferably at least about 83% positives, yet more preferably at least about 84% positives, yet more preferably at least about 85% positives, yet more preferably at least about 86% positives, yet more preferably at least about 87% positives, yet more preferably at least about 88% positives, yet more preferably at least about 89% positives, yet more preferably at least about 90% positives, yet more preferably at least about 91 % positives, yet more preferably at least about 92% positives, yet more preferably at least about 93% positives, yet more preferably at least about 94% positives, yet more preferably at least about 95% positives, yet more preferably at least about 96% positives, yet more preferably at least about 97% positives, yet more preferably at least about 98% positives and yet more preferably at least about 99% positives when compared with the amino acid sequence of a PRO polypeptide having a full-length amino acid sequence as disclosed herein, an amino acid sequence lacking the signal peptide as disclosed herein or an extracellular domain of a transmembrane protein, with or without the signal peptide, as disclosed herein.
In a specific aspect, the invention provides an isolated PRO polypeptide without the N-terminal signal sequence and/or the initiating methionine and is encoded by a nucleotide sequence that encodes such an amino acid sequence as hereinbefore described. Processes for producing the same are also herein described, wherein those processes comprise culmring a host cell comprising a vector which comprises the appropriate encoding nucleic acid molecule under conditions suitable for expression of the PRO polypeptide and recovering the PRO polypeptide from the cell culture.
Another aspect the invention provides an isolated PRO polypeptide which is either transmembrane domain-deleted or transmembrane domain-inactivated. Processes for producing the same are also herein described, wherein those processes comprise culmring a host cell comprising a vector which comprises the appropriate encoding nucleic acid molecule under conditions suitable for expression of the PRO polypeptide and recovering the PRO polypeptide from the cell culture.
In yet another embodiment, the invention concerns agonists and antagonists of a native PRO polypeptide as defined herein. In a particular embodiment, the agonist or antagonist is an anti-PRO antibody or a small molecule.
In a further embodiment, the invention concerns a method of identifying agonists or antagonists to a PRO polypeptide which comprise contacting the PRO polypeptide with a candidate molecule and monitoring a biological activity mediated by said PRO polypeptide. Preferably, the PRO polypeptide is a native PRO polypeptide.
In a still further embodiment, the invention concerns a composition of matter comprising a PRO polypeptide, or an agonist or antagonist of a PRO polypeptide as herein described, or an anti-PRO antibody, in combination with a carrier. Optionally, the carrier is a pharmaceutically acceptable carrier. Another embodiment of the present invention is directed to the use of a PRO polypeptide, or an agonist or antagonist thereof as hereinbefore described, or an anti-PRO antibody, for the preparation of a medicament useful in the treatment of a condition which is responsive to the PRO polypeptide, an agonist or antagonist thereof or an anti-PRO antibody.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 shows a nucleotide sequence (SEQ ID NO: l) of a native sequence PR0211 cDNA, wherein SEQ ID NO: l is a clone designated herein as "DNA32292-1131 ".
Figure 2 shows the amino acid sequence (SEQ ID NO: 2) derived from the coding sequence of SEQ ID NO: l shown in Figure 1. Figure 3 shows a nucleotide sequence (SEQ ID NO:3) of a native sequence PR0217 cDNA, wherein
SEQ ID NO:3 is a clone designated herein as "DNA33094-1131 ".
Figure 4 shows the amino acid sequence (SEQ ID NO: 4) derived from the coding sequence of SEQ ID NO: 3 shown in Figure 3.
Figure 5 shows a nucleotide sequence (SEQ ID NO: 11) of a native sequence PRO230 cDNA, wherein SEQ ID NO: 11 is a clone designated herein as "DNA33223-1136" .
Figure 6 shows the amino acid sequence (SEQ ID NO: 12) derived from the coding sequence of SEQ ID NO: 11 shown in Figure 5.
Figure 7 shows a nucleotide sequence designated herein as DNA20088 (SEQ ID NO: 13). Figure 8 shows a nucleotide sequence (SEQ ID NO: 17) of a native sequence PR0232 cDNA, wherein SEQ ID NO: 17 is a clone designated herein as "PNA34435-1140" .
Figure 9 shows the amino acid sequence (SEQ IP NO: 18) derived from the coding sequence of SEQ ID NO: 17 shown in Figure 8.
Figure 10 shows a nucleotide sequence (SEQ ID NO: 22) of a native sequence PRO 187 cDNA, wherein SEQ ID NO:22 is a clone designated herein as "DNA27864-1155" . Figure 11 shows the amino acid sequence (SEQ ID NO:23) derived from the coding sequence of SEQ
ID NO:22 shown in Figure 10.
Figure 12 shows a nucleotide sequence (SEQ ID NO: 27) of a native sequence PR0265 cDNA, wherein SEQ ID NO:27 is a clone designated herein as "DNA36350-1158" .
Figure 13 shows the amino acid sequence (SEQ ID NO: 28) derived from the coding sequence of SEQ ID NO:27 shown in Figure 12.
Figure 14 shows a nucleotide sequence (SEQ ID NO:33) of a native sequence PR0219 cDNA, wherein SEQ ID NO:33 is a clone designated herein as "DNA32290-1164" . Figure 15 shows the amino acid sequence (SEQ ID NO: 34) derived from the coding sequence of SEQ ID NO: 33 shown in Figure 14.
Figure 16 shows a nucleotide sequence (SEQ ID NO:38) of a native sequence PR0246 cDNA, wherein SEQ ID NO:38 is a clone designated herein as "DNA35639-1172".
Figure 17 shows the amino acid sequence (SEQ ID NO:39) derived from the coding sequence of SEQ ID NO:38 shown in Figure 16.
Figure 18 shows a nucleotide sequence (SEQ ID NO:48) of a native sequence PR0228 cDNA, wherein SEQ ID NO:48 is a clone designated herein as "DNA33092-1202".
Figure 19 shows the amino acid sequence (SEQ ID NO:49) derived from the coding sequence of SEQ ID NO:48 shown in Figure 18. Figure 20 shows a nucleotide sequence designated herein as DNA21951 (SEQ ID NO:50).
Figure 21 shows a nucleotide sequence (SEQ ID NO:58) of a native sequence PR0533 cDNA, wherein SEQ ID N0:58 is a clone designated herein as "DNA49435-1219".
Figure 22 shows the amino acid sequence (SEQ ID NO:59) derived from the coding sequence of SEQ ID NO:58 shown in Figure 21. Figure 23 shows a nucleotide sequence (SEQ ID NO:63) of a native sequence PR0245 cDNA, wherein
SEQ ID NO:63 is a clone designated herein as "DNA35638-1141".
Figure 24 shows the amino acid sequence (SEQ ID NO: 64) derived from the coding sequence of SEQ ID NO:63 shown in Figure 23.
Figure 25 shows a nucleotide sequence (SEQ ID NO:68) of a native sequence PRO220 cDNA, wherein SEQ ID NO:68 is a clone designated herein as "DNA32298-1132" .
Figure 26 shows the amino acid sequence (SEQ ID NO: 69) derived from the coding sequence of SEQ ID NO:68 shown in Figure 25.
Figure 27 shows a nucleotide sequence (SEQ ID NO:70) of a native sequence PR0221 cDNA, wherein SEQ ID NO:70 is a clone designated herein as "DNA33089-1132". Figure 28 shows the amino acid sequence (SEQ ID NO:71) derived from the coding sequence of SEQ
ID NO: 70 shown in Figure 27.
Figure 29 shows a nucleotide sequence (SEQ ID NO:72) of a native sequence PR0227 cDNA, wherein SEQ ID NO:72 is a clone designated herein as "DNA33786-1132".
Figure 30 shows the amino acid sequence (SEQ ID NO:73) derived from the coding sequence of SEQ ID NO:72 shown in Figure 29.
Figure 31 shows a nucleotide sequence (SEQ ID NO:83) of a native sequence PR0258 cDNA, wherein SEQ ID NO:83 is a clone designated herein as "DNA35918-1174".
Figure 32 shows the amino acid sequence (SEQ ID NO: 84) derived from the coding sequence of SEQ ID NO:83 shown in Figure 31. Figure 33 shows a nucleotide sequence (SEQ ID NO:90) of a native sequence PR0266 cDNA, wherein
SEQ ID NO:90 is a clone designated herein as "DNA37150-1178". Figure 34 shows the amino acid sequence (SEQ ID NO:91) derived from the coding sequence of SEQ ID NO: 90 shown in Figure 33.
Figure 35 shows a nucleotide sequence (SEQ ID NO:95) of a native sequence PR0269 cDNA, wherein SEQ ID NO:95 is a clone designated herein as "DNA38260-1180".
Figure 36 shows the amino acid sequence (SEQ ID NO:96) derived from the coding sequence of SEQ ID NO:95 shown in Figure 35.
Figure 37 shows a nucleotide sequence (SEQ ID NO: 103) of a native sequence PR0287 cDNA, wherein SEQ ID NO: 103 is a clone designated herein as "DNA39969-1185".
Figure 38 shows the amino acid sequence (SEQ ID NO: 104) derived from the coding sequence of SEQ ID NO: 103 shown in Figure 37. Figure 39 shows a nucleotide sequence (SEQ ID NO: 108) of a native sequence PR0214 cDNA, wherein
SEQ ID NO: 108 is a clone designated herein as "DNA32286-1191".
Figure 40 shows the amino acid sequence (SEQ ID NO: 109) derived from the coding sequence of SEQ ID NO: 108 shown in Figure 39.
Figure 41 shows a nucleotide sequence (SEQ ID NO: 113) of a native sequence PR0317 cDNA, wherein SEQ ID NO: 113 is a clone designated herein as "DNA33461-1199" .
Figure 42 shows the amino acid sequence (SEQ ID NO: 114) derived from the coding sequence of SEQ ID NO: 113 shown in Figure 41.
Figure 43 shows a nucleotide sequence (SEQ ID NO: 118) of a native sequence PRO301 cDNA, wherein SEQ ID NO: 118 is a clone designated herein as "DNA40628-1216". Figure 44 shows the amino acid sequence (SEQ ID NO: 119) derived from the coding sequence of SEQ
ID NO: 118 shown in Figure 43.
Figure 45 shows a nucleotide sequence (SEQ ID NO: 126) of a native sequence PR0224 cDNA, wherein SEQ ID NO: 126 is a clone designated herein as "DNA33221-1133".
Figure 46 shows the amino acid sequence (SEQ ID NO: 127) derived from the coding sequence of SEQ ID NO : 126 shown in Figure 45.
Figure 47 shows a nucleotide sequence (SEQ ID NO: 131) of a native sequence PR0222 cDNA, wherein SEQ ID NO:131 is a clone designated herein as "DNA33107-1135".
Figure 48 shows the amino acid sequence (SEQ ID NO: 132) derived from the coding sequence of SEQ ID NO: 131 shown in Figure 47. Figure 49 shows a nucleotide sequence (SEQ ID NO: 136) of a native sequence PR0234 cDNA, wherein
SEQ ID NO:136 is a clone designated herein as "DNA35557-1137".
Figure 50 shows the amino acid sequence (SEQ ID NO: 137) derived from the coding sequence of SEQ ID NO: 136 shown in Figure 49.
Figure 51 shows a nucleotide sequence (SEQID NO: 141) ofa native sequence PR0231 cDN A , wherein SEQ ID NO: 141 is a clone designated herein as "DNA34434-1139" .
Figure 52 shows the amino acid sequence (SEQ ID NO: 142) derived from the coding sequence of SEQ ID NO: 141 shown in Figure 51. Figure 53 shows a nucleotide sequence (SEQ ID NO: 147) of a native sequence PR0229 cDNA, wherein SEQ ID NO:147 is a clone designated herein as "DNA33100-1159".
Figure 54 shows the amino acid sequence (SEQ ID NO: 148) derived from the coding sequence of SEQ ID NO: 147 shown in Figure 53.
Figure 55 shows a nucleotide sequence (SEQ ID NO: 152) of a native sequence PR0238 cDNA, wherein SEQ ID NO:152 is a clone designated herein as "DNA35600-1162".
Figure 56 shows the amino acid sequence (SEQ ID NO: 153) derived from the coding sequence of SEQ ID NO: 152 shown in Figure 55.
Figure 57 shows a nucleotide sequence (SEQ ID NO: 158) of a native sequence PR0233 cDNA, wherein SEQ ID NO: 158 is a clone designated herein as "DNA34436-1238". Figure 58 shows the amino acid sequence (SEQ ID NO: 159) derived from the coding sequence of SEQ
ID NO: 158 shown in Figure 57.
Figure 59 shows a nucleotide sequence (SEQ ID NO: 163) of a native sequence PR0223 cDNA, wherein SEQ ID NO:163 is a clone designated herein as "DNA33206-1165".
Figure 60 shows the amino acid sequence (SEQ ID NO: 164) derived from the coding sequence of SEQ ID NO: 163 shown in Figure 59.
Figure 61 shows a nucleotide sequence (SEQ ID NO: 169) of a native sequence PR0235 cDNA, wherein SEQ ID NO:169 is a clone designated herein as "DNA35558-1167".
Figure 62 shows the amino acid sequence (SEQ ID NO: 170) derived from the coding sequence of SEQ ID NO: 169 shown in Figure 61. Figure 63 shows a nucleotide sequence (SEQ ID NO: 174) of a native sequence PR0236 cDNA, wherein
SEQ ID NO: 174 is a clone designated herein as "DNA35599-1168".
Figure 64 shows the amino acid sequence (SEQ ID NO: 175) derived from the coding sequence of SEQ ID NO: 174 shown in Figure 63.
Figure 65 shows a nucleotide sequence (SEQ ID NO: 176) of a native sequence PR0262 cDNA, wherein SEQ ID NO: 176 is a clone designated herein as "DNA36992-1168" .
Figure 66 shows the amino acid sequence (SEQ ID NO: 177) derived from the coding sequence of SEQ ID NO: 176 shown in Figure 65.
Figure 67 shows a nucleotide sequence (SEQ ID NO: 184) of a native sequence PR0239 cDNA, wherein SEQ ID NO: 184 is a clone designated herein as "DNA34407-1169". Figure 68 shows the amino acid sequence (SEQ ID NO: 185) derived from the coding sequence of SEQ
ID NO: 184 shown in Figure 67.
Figure 69 shows a nucleotide sequence (SEQ ID NO: 189) of a native sequence PR0257 cDNA, wherein SEQ ID NO: 189 is a clone designated herein as "DNA35841-1173".
Figure 70 shows the amino acid sequence (SEQ ID NO: 190) derived from the coding sequence of SEQ ID NO: 189 shown in Figure 69.
Figure 71 shows a nucleotide sequence (SEQ ID NO: 194) of a native sequence PRO260 cDNA, wherein SEQ ID NO: 194 is a clone designated herein as "DNA33470-1175". Figure 72 shows the amino acid sequence (SEQ ID NO: 195) derived from the coding sequence of SEQ ID NO: 194 shown in Figure 71.
Figure 73 shows a nucleotide sequence (SEQ ID NO: 200) of a native sequence PR0263 cDNA, wherein SEQ ID NO:200 is a clone designated herein as "DNA34431-1177".
Figure 74 shows the amino acid sequence (SEQ ID NO:201) derived from the coding sequence of SEQ ID NO:200 shown in Figure 73.
Figure 75 shows a nucleotide sequence (SEQ ID NO:206) of a native sequence PRO270 cDNA, wherein SEQ ID NO:206 is a clone designated herein as "DNA39510-1181 " .
Figure 76 shows the amino acid sequence (SEQ ID NO:207) derived from the coding sequence of SEQ ID NO: 206 shown in Figure 75. Figure 77 shows a nucleotide sequence (SEQ ID NO : 212) of a native sequence PR0271 cDN A , wherein
SEQ ID NO:212 is a clone designated herein as "DNA39423-1182".
Figure 78 shows the amino acid sequence (SEQ ID NO:213) derived from the coding sequence of SEQ ID NO:212 shown in Figure 77.
Figure 79 shows a nucleotide sequence (SEQ ID NO : 220) of a native sequence PR0272 cDN A , wherein SEQ ID NO:220 is a clone designated herein as "DNA40620-1183".
Figure 80 shows the amino acid sequence (SEQ ID NO: 221) derived from the coding sequence of SEQ ID NO:220 shown in Figure 79.
Figure 81 shows a nucleotide sequence (SEQ ID NO : 226) of a native sequence PR0294 cDN A , wherein SEQ ID NO:226 is a clone designated herein as "DNA40604-1187". Figure 82 shows the amino acid sequence (SEQ ID NO:227) derived from the coding sequence of SEQ
ID NO:226 shown in Figure 81.
Figure 83 shows a nucleotide sequence (SEQ ID NO:235) of a native sequence PR0295 cDNA, wherein SEQ ID NO:235 is a clone designated herein as "DN A38268- 1188".
Figure 84 shows the amino acid sequence (SEQ ID NO: 236) derived from the coding sequence of SEQ ID NO: 235 shown in Figure 83.
Figure 85 shows a nucleotide sequence (SEQ ID NO:244) of a native sequence PR0293 cDNA, wherein SEQ ID NO:244 is a clone designated herein as "DNA37151-1193".
Figure 86 shows the amino acid sequence (SEQ ID NO:245) derived from the coding sequence of SEQ ID NO:244 shown in Figure 85. Figure 87 shows a nucleotide sequence (SEQ ID NO : 249) of a native sequence PR0247 cDN A , wherein
SEQ ID NO:249 is a clone designated herein as "DNA35673-1201 ".
Figure 88 shows the amino acid sequence (SEQ ID NO:250) derived from the coding sequence of SEQ ID NO:249 shown in Figure 87.
Figure 89 shows a nucleotide sequence (SEQ ID NO:254) of a native sequence PRO302 cDNA, wherein SEQ ID NO:254 is a clone designated herein as "DNA40370-1217".
Figure 90 shows the amino acid sequence (SEQ ID NO:255) derived from the coding sequence of SEQ ID NO:254 shown in Figure 89. Figure 91 shows a nucleotide sequence (SEQ IP NO:256) of a native sequence PRO303 cPNA, wherein SEQ IP NO:256 is a clone designated herein as "PNA42551-1217".
Figure 92 shows the amino acid sequence (SEQ IP NO:257) derived from the coding sequence of SEQ IP NO:256 shown in Figure 91.
Figure 93 shows a nucleotide sequence (SEQ ID NO: 258) of a native sequence PRO304 cDNA, wherein SEQ ID NO:258 is a clone designated herein as "DNA39520-1217" .
Figure 94 shows the amino acid sequence (SEQ ID NO:259) derived from the coding sequence of SEQ ID NO:258 shown in Figure 93.
Figure 95 shows a nucleotide sequence (SEQ ID NO:260) of a native sequence PRO307 cDNA, wherein SEQ ID NO:260 is a clone designated herein as "DNA41225-1217". Figure 96 shows the amino acid sequence (SEQ ID NO: 261) derived from the coding sequence of SEQ
ID NO:260 shown in Figure 95.
Figure 97 shows a nucleotide sequence (SEQ ID NO:262) of a native sequence PR0343 cDNA, wherein SEQ ID NO:262 is a clone designated herein as "DNA43318-1217".
Figure 98 shows the amino acid sequence (SEQ ID NO: 263) derived from the coding sequence of SEQ ID NO : 262 shown in Figure 97.
Figure 99 shows a nucleotide sequence (SEQ ID NO:284) of a native sequence PR0328 cDNA, wherein SEQ IP NO:284 is a clone designated herein as "PNA40587-1231 " .
Figure 100 shows the amino acid sequence (SEQ ID NO:285) derived from the coding sequence of SEQ ID NO: 284 shown in Figure 99. Figure 101 shows a nucleotide sequence (SEQ ID NO:289) of a native sequence PR0335 cDNA, wherein SEQ ID NO:289 is a clone designated herein as "DNA41388-1234" .
Figure 102 shows the amino acid sequence (SEQ ID NO: 290) derived from the coding sequence of SEQ ID NO:289 shown in Figure 101.
Figure 103 shows a nucleotide sequence (SEQ ID NO:291) of a native sequence PR0331 cDNA, wherein SEQ ID NO:291 is a clone designated herein as "DNA40981-1234" .
Figure 104 shows the amino acid sequence (SEQ ID NO:292) derived from the coding sequence of SEQ ID NO:291 shown in Figure 103.
Figure 105 shows a nucleotide sequence (SEQ ID NO:293) of a native sequence PR0326 cDNA, wherein SEQ ID NO:293 is a clone designated herein as "DNA37140-1234". Figure 106 shows the amino acid sequence (SEQ ID NO:294) derived from the coding sequence of SEQ
ID NO:293 shown in Figure 105.
Figure 107 shows a nucleotide sequence (SEQ ID NO:309) of a native sequence PR0332 cDNA, wherein SEQ ID NO:309 is a clone designated herein as "DNA40982-1235".
Figure 108 shows the amino acid sequence (SEQ ID NO:310) derived from the coding sequence of SEQ ID NO:309 shown in Figure 107.
Figure 109 shows a nucleotide sequence (SEQ ID NO:314) of a native sequence PR0334 cDNA, wherein SEQ ID NO:314 is a clone designated herein as "DNA41379-1236". Figure 110 shows the amino acid sequence (SEQ ID NO: 315) derived from the coding sequence of SEQ ID NO:314 shown in Figure 109.
Figure 111 shows a nucleotide sequence (SEQ ID NO:319) of a native sequence PR0346 cDNA, wherein SEQ ID NO:319 is a clone designated herein as "DNA44167- 1243".
Figure 112 shows the amino acid sequence (SEQ ID NO:320) derived from the coding sequence of SEQ ID NO:319 shown in Figure 111.
Figure 113 shows a nucleotide sequence (SEQ ID NO:324) of a native sequence PR0268 cDNA, wherein SEQ ID NO:324 is a clone designated herein as "DNA39427-1179".
Figure 114 shows the amino acid sequence (SEQ ID NO:325) derived from the coding sequence of SEQ ID NO:324 shown in Figure 113. Figure 115 shows a nucleotide sequence (SEQ ID NO:331) of a native sequence PRO330 cDNA, wherein SEQ ID NO:331 is a clone designated herein as "DNA40603-1232".
Figure 116 shows the amino acid sequence (SEQ ID NO:332) derived from the coding sequence of SEQ ID NO: 331 shown in Figure 115.
Figure 117 shows a nucleotide sequence (SEQ ID NO:338) of a native sequence PR0339 cDNA, wherein SEQ ID NO:338 is a clone designated herein as "DNA43466-1225".
Figure 118 shows the amino acid sequence (SEQ ID NO:339) derived from the coding sequence of SEQ ID NO:338 shown in Figure 117.
Figure 119 shows a nucleotide sequence (SEQ ID NO: 340) of a native sequence PRO310 cDNA, wherein SEQ ID NO:340 is a clone designated herein as "DNA43046-1225". Figure 120 shows the amino acid sequence (SEQ ID NO:341) derived from the coding sequence of SEQ
ID NO:340 shown in Figure 119.
Figure 121 shows a nucleotide sequence (SEQ ID NO:376) of a native sequence PR0244 cDNA, wherein SEQ ID NO:376 is a clone designated herein as "DNA35668-1171".
Figure 122 shows the amino acid sequence (SEQ ID NO:377) derived from the coding sequence of SEQ ID NO : 376 shown in Figure 121.
Figure 123 shows a nucleotide sequence (SEQ ID NO:422) of a native sequence PR01868 cDNA, wherein SEQ ID NO:422 is a clone designated herein as "DNA77624-2515".
Figure 124 shows the amino acid sequence (SEQ ID NO:423) derived from the coding sequence of SEQ ID NO:422 shown in Figure 123. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS I. Definitions
The terms "PRO polypeptide" and "PRO" as used herein and when immediately followed by a numerical designation refer to various polypeptides, wherein the complete designation (i.e. , PRO/number) refers to specific polypeptide sequences as described herein. The terms "PRO/number polypeptide" and "PRO/number" wherein the term "number" is provided as an actual numerical designation as used herein encompass native sequence polypeptides and polypeptide variants (which are further defined herein). The PRO polypeptides described herein may be isolated from a variety of sources, such as from human tissue types or from another source, or prepared by recombinant or synthetic methods.
A "native sequence PRO polypeptide" comprises a polypeptide having the same amino acid sequence as the corresponding PRO polypeptide derived from nature. Such native sequence PRO polypeptides can be isolated from nature or can be produced by recombinant or synthetic means. The term "native sequence PRO polypeptide" specifically encompasses naturally-occurring truncated or secreted forms of the specific PRO polypeptide (e.g., an extracellular domain sequence), naturally-occurring variant forms (e.g., alternatively spliced forms) and naturally-occurring allelic variants of the polypeptide. In various embodiments of the invention, the native sequence PRO polypeptides disclosed herein are mature or full-length native sequence polypeptides comprising the full-length amino acids sequences shown in the accompanying figures. Start and stop codons are shown in bold font and underlined in the figures. However, while the PRO polypeptide disclosed in the accompanying figures are shown to begin with methionine residues designated herein as amino acid position 1 in the figures, it is conceivable and possible that other methionine residues located either upstream or downstream from the amino acid position 1 in the figures may be employed as the starting amino acid residue for the PRO polypeptides.
The PRO polypeptide "extracellular domain" or "ECD" refers to a form of the PRO polypeptide which is essentially free of the transmembrane and cytoplasmic domains. Ordinarily, a PRO polypeptide ECD will have less than 1 % of such transmembrane and/or cytoplasmic domains and preferably, will have less than 0.5% of such domains. It will be understood that any transmembrane domains identified for the PRO polypeptides of the present invention are identified pursuant to criteria routinely employed in the art for identifying that type of hydrophobic domain. The exact boundaries of a transmembrane domain may vary but most likely by no more than about 5 amino acids at either end of the domain as initially identified herein. Optionally, therefore, an extracellular domain of a PRO polypeptide may contain from about 5 or fewer amino acids on either side of the transmembrane domain/extracellular domain boundary as identified in the Examples or specification and such polypeptides, with or without the associated signal peptide, and nucleic acid encoding them, are comtemplated by the present invention.
The approximate location of the "signal peptides" of the various PRO polypeptides disclosed herein are shown in the present specification and/or the accompanying figures. It is noted, however, that the C-terminal boundary of a signal peptide may vary, but most likely by no more than about 5 amino acids on either side of the signal peptide C-terminal boundary as initially identified herein, wherein the C-terminal boundary of the signal peptide may be identified pursuant to criteria routinely employed in the art for identifying that type of amino acid sequence element (e.g. , Nielsen et al. , Prot. Eng. 10:1-6 (1997) and von Heinje et al. , Nucl. Acids. Res. 14:4683-4690 (1986)). Moreover, it is also recognized that, in some cases, cleavage of a signal sequence from a secreted polypeptide is not entirely uniform, resulting in more than one secreted species. These mature polypeptides, where the signal peptide is cleaved within no more than about 5 amino acids on either side of the C-terminal boundary of the signal peptide as identified herein, and the polynucleotides encoding them, are contemplated by the present invention.
"PRO polypeptide variant" means an active PRO polypeptide as defined above or below having at least about 80% amino acid sequence identity with a full-length native sequence PRO polypeptide sequence as disclosed herein, a PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO polypeptide, with or without the signal peptide, as disclosed herein or any other fragment of a full-length PRO polypeptide sequence as disclosed herein. Such PRO polypeptide variants include, for instance, PRO polypeptides wherein one or more amino acid residues are added, or deleted, at the N- or C- terminus of the full-length native amino acid sequence. Ordinarily, a PRO polypeptide variant will have at least about 80% amino acid sequence identity, preferably at least about 81 % amino acid sequence identity, more preferably at least about 82% amino acid sequence identity, more preferably at least about 83% amino acid sequence identity, more preferably at least about 84% amino acid sequence identity, more preferably at least about 85 % amino acid sequence identity, more preferably at least about 86% amino acid sequence identity, more preferably at least about 87% amino acid sequence identity, more preferably at least about 88% amino acid sequence identity, more preferably at least about 89% amino acid sequence identity, more preferably at least about 90% amino acid sequence identity, more preferably at least about 91 % amino acid sequence identity, more preferably at least about 92% amino acid sequence identity, more preferably at least about 93% amino acid sequence identity, more preferably at least about 94% amino acid sequence identity, more preferably at least about 95 % amino acid sequence identity, more preferably at least about 96 % amino acid sequence identity, more preferably at least about 97% amino acid sequence identity, more preferably at least about 98% amino acid sequence identity and most preferably at least about 99% amino acid sequence identity with a full-length native sequence PRO polypeptide sequence as disclosed herein, a PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO polypeptide, with or without the signal peptide, as disclosed herein or any other specifically defined fragment of a full-length PRO polypeptide sequence as disclosed herein. Ordinarily, PRO variant polypeptides are at least about 10 amino acids in length, often at least about 20 amino acids in length, more often at least about 30 amino acids in length, more often at least about 40 amino acids in length, more often at least about 50 amino acids in length, more often at least about 60 amino acids in length, more often at least about 70 amino acids in length, more often at least about 80 amino acids in length, more often at least about 90 amino acids in length, more often at least about 100 amino acids in length, more often at least about 150 amino acids in length, more often at least about 200 amino acids in length, more often at least about 300 amino acids in length, or more. "Percent (%) amino acid sequence identity" with respect to the PRO polypeptide sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific PRO polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For purposes herein, however, % amino acid sequence identity values are generated using the sequence comparison computer program ALIGN-2, wherein the complete source code for the ALIGN-2 program is provided in Table 1 below. The ALIGN-2 sequence comparison computer program was authored by Genentech, Inc. and the source code shown in Table 1 below has been filed with user documentation in the U.S. Copyright Office, Washington D.C. , 20559, where it is registered under U.S. Copyright Registration No. TXU510087. The ALIGN-2 program is publicly available through Genentech, Inc., South San Francisco, California or may be compiled from the source code provided in Table 1 below. The ALIGN-2 program should be compiled for use on a UNIX operating system, preferably digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary. In situations where ALIGN-2 is employed for amino acid sequence comparisons, the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) is calculated as follows:
100 times the fraction X/Y
where X is the number of amino acid residues scored as identical matches by the sequence alignment program ALIGN-2 in that program's alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A. As examples of % amino acid sequence identity calculations using this method, Tables 2 and 3 demonstrate how to calculate the % amino acid sequence identity of the amino acid sequence designated "Comparison Protein" to the amino acid sequence designated "PRO" , wherein "PRO" represents the amino acid sequence of a hypothetical PRO polypeptide of interest, "Comparison Protein" represents the amino acid sequence of a polypeptide against which the "PRO" polypeptide of interest is being compared, and "X, "Y" and "Z" each represent different hypothetical amino acid residues.
Unless specifically stated otherwise, all % amino acid sequence identity values used herein are obtained as described in the immediately preceding paragraph using the ALIGN-2 computer program. However, % amino acid sequence identity values may also be obtained as described below by using the WU-BLAST-2 computer program (Altschul et al., Methods in Enzymology 266:460-480 (1996)). Most of the WU-BLAST-2 search parameters are set to the default values. Those not set to default values, i.e., the adjustable parameters, are set with the following values: overlap span = 1, overlap fraction = 0.125, word threshold (T) = 11, and scoring matrix = BLOSUM62. When WU-BLAST-2 is employed, a % amino acid sequence identity value is determined by dividing (a) the number of matching identical amino acid residues between the amino acid sequence of the PRO polypeptide of interest having a sequence derived from the native PRO polypeptide and the comparison amino acid sequence of interest (i . e . , the sequence against which the PRO polypeptide of interest is being compared which may be a PRO variant polypeptide) as determined by WU-BLAST-2 by (b) the total number of amino acid residues of the PRO polypeptide of interest. For example, in the statement "a polypeptide comprising an the amino acid sequence A which has or having at least 80% amino acid sequence identity to the amino acid sequence B", the amino acid sequence A is the comparison amino acid sequence of interest and the amino acid sequence B is the amino acid sequence of the PRO polypeptide of interest.
Percent amino acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST2 (Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)). The NCBI-BLAST2 sequence comparison program may be downloaded from http://www.ncbi.nlm.nih.gov. NCBI-BLAST2 uses several search parameters, wherein all of those search parameters are set to default values including, for example, unmask = yes, strand = all, expected occurrences = 10, minimum low complexity length = 15/5, multi-pass e- value = 0.01, constant for multi-pass = 25, dropoff for final gapped alignment = 25 and scoring matrix = BLOSUM62.
In situations where NCBI-BLAST2 is employed for amino acid sequence comparisons, the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) is calculated as follows:
100 times the fraction X/Y
where X is the number of amino acid residues scored as identical matches by the sequence alignment program NCBI-BLAST2 in that program's alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A.
"PRO variant polynucleotide" or "PRO variant nucleic acid sequence" means a nucleic acid molecule which encodes an active PRO polypeptide as defined below and which has at least about 80% nucleic acid sequence identity with a nucleotide acid sequence encoding a full-length native sequence PRO polypeptide sequence as disclosed herein, a full-length native sequence PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO polypeptide, with or without the signal peptide, as disclosed herein or any other fragment of a full-length PRO polypeptide sequence as disclosed herein. Ordinarily, a PRO variant polynucleotide will have at least about 80% nucleic acid sequence identity, more preferably at least about 81 % nucleic acid sequence identity, more preferably at least about 82% nucleic acid sequence identity, more preferably at least about 83% nucleic acid sequence identity, more preferably at least about 84% nucleic acid sequence identity, more preferably at least about 85% nucleic acid sequence identity, more preferably at least about 86% nucleic acid sequence identity, more preferably at least about 87% nucleic acid sequence identity, more preferably at least about 88% nucleic acid sequence identity, more preferably at least about 89% nucleic acid sequence identity, more preferably at least about 90% nucleic acid sequence identity, more preferably at least about 91 % nucleic acid sequence identity, more preferably at least about 92% nucleic acid sequence identity, more preferably at least about 93% nucleic acid sequence identity, more preferably at least about 94% nucleic acid sequence identity, more preferably at least about 95% nucleic acid sequence identity, more preferably at least about 96% nucleic acid sequence identity, more preferably at least about 97% nucleic acid sequence identity, more preferably at least about 98% nucleic acid sequence identity and yet more preferably at least about 99% nucleic acid sequence identity with a nucleic acid sequence encoding a full-length native sequence PRO polypeptide sequence as disclosed herein, a full-length native sequence PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO polypeptide, with or without the signal sequence, as disclosed herein or any other fragment of a full-length PRO polypeptide sequence as disclosed herein. Variants do not encompass the native nucleotide sequence.
Ordinarily, PRO variant polynucleotides are at least about 30 nucleotides in length, often at least about 60 nucleotides in length, more often at least about 90 nucleotides in length, more often at least about 120 nucleotides in length, more often at least about 150 nucleotides in length, more often at least about 180 nucleotides in length, more often at least about 210 nucleotides in length, more often at least about 240 nucleotides in length, more often at least about 270 nucleotides in length, more often at least about 300 nucleotides in length, more often at least about 450 nucleotides in length, more often at least about 600 nucleotides in length, more often at least about 900 nucleotides in length, or more. "Percent (%) nucleic acid sequence identity" with respect to PRO-encoding nucleic acid sequences identified herein is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in the PRO nucleic acid sequence of interest, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. For purposes herein, however, % nucleic acid sequence identity values are generated using the sequence comparison computer program ALIGN-2, wherein the complete source code for the ALIGN-2 program is provided in Table 1 below. The ALIGN-2 sequence comparison computer program was authored by Genentech, Inc. and the source code shown in Table 1 below has been filed with user documentation in the U.S. Copyright Office, Washington D.C, 20559, where it is registered under U.S. Copyright Registration No. TXU510087. The ALIGN-2 program is publicly available through Genentech, Inc., South San Francisco, California or may be compiled from the source code provided in Table 1 below. The ALIGN-2 program should be compiled for use on a UNIX operating system, preferably digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary. In situations where ALIGN-2 is employed for nucleic acid sequence comparisons, the % nucleic acid sequence identity of a given nucleic acid sequence C to, with, or against a given nucleic acid sequence D (which can alternatively be phrased as a given nucleic acid sequence C that has or comprises a certain % nucleic acid sequence identity to, with, or against a given nucleic acid sequence D) is calculated as follows:
100 times the fraction W/Z
where W is the number of nucleotides scored as identical matches by the sequence alignment program ALIGN-2 in that program's alignment of C and D, and where Z is the total number of nucleotides in D. It will be appreciated that where the length of nucleic acid sequence C is not equal to the length of nucleic acid sequence D, the % nucleic acid sequence identity of C to D will not equal the % nucleic acid sequence identity of D to C. As examples of % nucleic acid sequence identity calculations, Tables 4 and 5, demonstrate how to calculate the % nucleic acid sequence identity of the nucleic acid sequence designated "Comparison DNA" to the nucleic acid sequence designated "PRO-DNA" , wherein "PRO-DNA" represents a hypothetical PRO-encoding nucleic acid sequence of interest, "Comparison DNA" represents the nucleotide sequence of a nucleic acid molecule against which the "PRO-DNA" nucleic acid molecule of interest is being compared, and "N", "L" and "V" each represent different hypothetical nucleotides.
Unless specifically stated otherwise, all % nucleic acid sequence identity values used herein are obtained as described in the immediately preceding paragraph using the ALIGN-2 computer program. However, % nucleic acid sequence identity values may also be obtained as described below by using the WU-BLAST-2 computer program (Altschul et al. , Methods in Enzymology 266:460-480 (1996)). Most of the WU-BLAST-2 search parameters are set to the default values. Those not set to default values, i.e., the adjustable parameters, are set with the following values: overlap span = 1, overlap fraction = 0.125, word threshold (T) = 11, and scoring matrix = BLOSUM62. When WU-BLAST-2 is employed, a % nucleic acid sequence identity value is determined by dividing (a) the number of matching identical nucleotides between the nucleic acid sequence of the PRO polypeptide-encoding nucleic acid molecule of interest having a sequence derived from the native sequence PRO polypeptide-encoding nucleic acid and the comparison nucleic acid molecule of interest (i.e. , the sequence against which the PRO polypeptide-encoding nucleic acid molecule of interest is being compared which may be a variant PRO polynucleotide) as determined by WU-BLAST-2 by (b) the total number of nucleotides of the PRO polypeptide-encoding nucleic acid molecule of interest. For example, in the statement "an isolated nucleic acid molecule comprising a nucleic acid sequence A which has or having at least 80% nucleic acid sequence identity to the nucleic acid sequence B", the nucleic acid sequence A is the comparison nucleic acid molecule of interest and the nucleic acid sequence B is the nucleic acid sequence of the PRO polypeptide- encoding nucleic acid molecule of interest.
Percent nucleic acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST2 (Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)). The NCBI-BLAST2 sequence comparison program may be downloaded from http://www.ncbi.nlm.nih.gov. NCBI-BLAST2 uses several search parameters, wherein all of those search parameters are set to default values including, for example, unmask = yes, strand = all, expected occurrences = 10, minimum low complexity length = 15/5, multi-pass e-value = 0.01, constant for multi-pass = 25, dropoff for final gapped alignment = 25 and scoring matrix = BLOSUM62. In situations where NCBI-BLAST2 is employed for sequence comparisons, the % nucleic acid sequence identity of a given nucleic acid sequence C to, with, or against a given nucleic acid sequence D (which can alternatively be phrased as a given nucleic acid sequence C that has or comprises a certain % nucleic acid sequence identity to, with, or against a given nucleic acid sequence D) is calculated as follows:
100 times the fraction W/Z
where W is the number of nucleotides scored as identical matches by the sequence alignment program NCBI- BLAST2 in that program's alignment of C and D, and where Z is the total number of nucleotides in D. It will be appreciated that where the length of nucleic acid sequence C is not equal to the length of nucleic acid sequence D, the % nucleic acid sequence identity of C to D will not equal the % nucleic acid sequence identity of D to C
In other embodiments, PRO variant polynucleotides are nucleic acid molecules that encode an active PRO polypeptide and which are capable of hybridizing, preferably under stringent hybridization and wash conditions, to nucleotide sequences encoding a full-length PRO polypeptide as disclosed herein. PRO variant polypeptides may be those that are encoded by a PRO variant polynucleotide.
The term "positives", in the context of sequence comparison performed as described above, includes residues in the sequences compared that are not identical but have similar properties (e.g. as a result of conservative substitutions, see Table 6 below). For purposes herein, the % value of positives is determined by dividing (a) the number of amino acid residues scoring a positive value between the PRO polypeptide amino acid sequence of interest having a sequence derived from the native PRO polypeptide sequence and the comparison amino acid sequence of interest (i.e., the amino acid sequence against which the PRO polypeptide sequence is being compared) as determined in the BLOSUM62 matrix of WU-BLAST-2 by (b) the total number of amino acid residues of the PRO polypeptide of interest.
Unless specifically stated otherwise, the % value of positives is calculated as described in the immediately preceding paragraph. However, in the context of the amino acid sequence identity comparisons performed as described for ALIGN-2 and NCBI-BLAST-2 above, includes amino acid residues in the sequences compared that are not only identical, but also those that have similar properties. Amino acid residues that score a positive value to an amino acid residue of interest are those that are either identical to the amino acid residue of interest or are a preferred substitution (as defined in Table 6 below) of the amino acid residue of interest. For amino acid sequence comparisons using ALIGN-2 or NCBI-BLAST2, the % value of positives of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % positives to, with, or against a given amino acid sequence B) is calculated as follows:
100 times the fraction X/Y
where X is the number of amino acid residues scoring a positive value as defined above by the sequence alignment program ALIGN-2 or NCBI-BLAST2 in that program's alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % positives of A to B will not equal the % positives of B to A.
"Isolated, " when used to describe the various polypeptides disclosed herein, means polypeptide that has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In preferred embodiments, the polypeptide will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain. Isolated polypeptide includes polypeptide in situ within recombinant cells, since at least one component of the PRO polypeptide natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step.
An "isolated" PRO polypeptide-encoding nucleic acid or other polypeptide-encoding nucleic acid is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the polypeptide-encoding nucleic acid. An isolated polypeptide-encoding nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated polypeptide-encoding nucleic acid molecules therefore are distinguished from the specific polypeptide- encoding nucleic acid molecule as it exists in natural cells. However, an isolated polypeptide-encoding nucleic acid molecule includes polypeptide-encoding nucleic acid molecules contained in cells that ordinarily express the polypeptide where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
The term "control sequences" refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, "operably linked" means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
The term "antibody" is used in the broadest sense and specifically covers, for example, single anti-PRO monoclonal antibodies (including agonist, antagonist, and neutralizing antibodies), anti-PRO antibody compositions with polyepitopic specificity, single chain anti-PRO antibodies, and fragments of anti-PRO antibodies (see below). The term "monoclonal antibody" as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e. , the individual antibodies comprising the population are identical except for possible naturally-occurring mutations that may be present in minor amounts.
"Stringency" of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology. Wiley Interscience Publishers, (1995).
"Stringent conditions" or "high stringency conditions", as defined herein, may be identified by those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1 % sodium dodecyl sulfate at 50°C; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1 % bovine serum albumin 0.1 % Ficoll/0.1 % polyvinylpyrrolidone/50mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42°C; or (3) employ 50% formamide, 5 x SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1 % sodium pyrophosphate, 5 x Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1 % SDS, and 10% dextran sulfate at 42°C, with washes at 42°C in 0.2 x SSC (sodium chloride/sodium citrate) and 50% formamide at 55 °C, followed by a high-stringency wash consisting of 0.1 x SSC containing EDTA at 55 °C.
"Moderately stringent conditions" may be identified as described by Sambrook et al., Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and %SDS) less stringent that those described above. An example of moderately stringent conditions is overnight incubation at 37°C in a solution comprising: 20% formamide, 5 x SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5 x Denhardt's solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1 x SSC at about 37-50 °C The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.
The term "epitope tagged" when used herein refers to a chimeric polypeptide comprising a PRO polypeptide fused to a "tag polypeptide" . The tag polypeptide has enough residues to provide an epitope against which an antibody can be made, yet is short enough such that it does not interfere with activity of the polypeptide to which it is fused. The tag polypeptide preferably also is fairly unique so that the antibody does not substantially cross-react with other epitopes. Suitable tag polypeptides generally have at least six amino acid residues and usually between about 8 and 50 amino acid residues (preferably, between about 10 and 20 amino acid residues).
As used herein, the term "immunoadhesin" designates antibody-like molecules which combine the binding specificity of a heterologous protein (an "adhesin") with the effector functions of immunoglobulin constant domains. Structurally, the immunoadhesins comprise a fusion of an amino acid sequence with the desired binding specificity which is other than the antigen recognition and binding site of an antibody (i.e., is "heterologous"), and an immunoglobulin constant domain sequence. The adhesin part of an immunoadhesin molecule typically is a contiguous amino acid sequence comprising at least the binding site of a receptor or a ligand. The immunoglobulin constant domain sequence in the immunoadhesin may be obtained from any immunoglobulin, such as IgG-1, IgG-2, IgG-3, or IgG-4 subtypes, IgA (including IgA-1 and IgA-2), IgE, IgD or IgM. "Active" or "activity" for the purposes herein refers to form(s) of a PRO polypeptide which retain a biological and/or an immunological activity of native or naturally-occurring PRO, wherein "biological" activity refers to a biological function (either inhibitory or stimulatory) caused by a native or naturally-occurring PRO other than the ability to induce the production of an antibody against an antigenic epitope possessed by a native or naturally-occurring PRO and an "immunological" activity refers to the ability to induce the production of an antibody against an antigenic epitope possessed by a native or naturally-occurring PRO.
The term "antagonist" is used in the broadest sense, and includes any molecule that partially or fully blocks, inhibits, or neutralizes a biological activity of a native PRO polypeptide disclosed herein. In a similar manner, the term "agonist" is used in the broadest sense and includes any molecule that mimics a biological activity of a native PRO polypeptide disclosed herein. Suitable agonist or antagonist molecules specifically include agonist or antagonist antibodies or antibody fragments, fragments or amino acid sequence variants of native PRO polypeptides, peptides, antisense oligonucleotides, small organic molecules, etc. Methods for identifying agonists or antagonists of a PRO polypeptide may comprise contacting a PRO polypeptide with a candidate agonist or antagonist molecule and measuring a detectable change in one or more biological activities normally associated with the PRO polypeptide. "Treatment" refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathologic condition or disorder. Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented.
"Chronic" administration refers to administration of the agent(s) in a continuous mode as opposed to an acute mode, so as to maintain the initial therapeutic effect (activity) for an extended period of time. "Intermittent" administration is treatment that is not consecutively done without interruption, but rather is cyclic in nature.
"Mammal" for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, cats, cattle, horses, sheep, pigs, goats, rabbits, etc. Preferably, the mammal is human.
Administration "in combination with" one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order. "Carriers" as used herein include pharmaceutically acceptable carriers, excipients, or stabilizers which are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Often the physiologically acceptable carrier is an aqueous pH buffered solution. Examples of physiologically acceptable carriers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt- forming counterions such as sodium; and/or nonionic surfactants such as TWEEN™, polyethylene glycol (PEG), and PLURONICS™. "Antibody fragments" comprise a portion of an intact antibody, preferably the antigen binding or variable region of the intact antibody. Examples of antibody fragments include Fab, Fab' , F(ab')2, and Fv fragments; diabodies; linear antibodies (Zapata et al., Protein Eng. 8(10): 1057-1062 [1995]); single-chain antibody molecules; and multispecific antibodies formed from antibody fragments.
Papain digestion of antibodies produces two identical antigen-binding fragments, called "Fab" fragments, each with a single antigen-binding site, and a residual "Fc" fragment, a designation reflecting the ability to crystallize readily. Pepsin treatment yields an F(ab')2 fragment that has two antigen-combining sites and is still capable of cross-linking antigen.
"Fv" is the minimum antibody fragment which contains a complete antigen-recognition and -binding site. This region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association. It is in this configuration that the three CDRs of each variable domain interact to define an antigen- binding site on the surface of the VH-VL dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site. The Fab fragment also contains the constant domain of the light chain and the first constant domain
(CHI) of the heavy chain. Fab fragments differ from Fab' fragments by the addition of a few residues at the carboxy terminus of the heavy chain CHI domain including one or more cysteines from the antibody hinge region. Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab')2 antibody fragments originally were produced as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
The "light chains" of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa and lambda, based on the amino acid sequences of their constant domains.
Depending on the amino acid sequence of the constant domain of their heavy chains, immunoglobulins can be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g. , IgGl , IgG2, IgG3, IgG4, IgA, and IgA2. "Single-chain Fv" or "sFv" antibody fragments comprise the VH and VL domains of antibody, wherein these domains are present in a single polypeptide chain. Preferably, the Fv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the sFv to form the desired structure for antigen binding. For a review of sFv, see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer- Verlag, New York, pp. 269-315 (1994). The term "diabodies" refers to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VJ in the same polypeptide chain (VH-VL). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites. Diabodies are described more fully in, for example, EP 404,097; WO 93/11161 ; and Hollinger et al., Proc. Natl. Acad. Sci. USA. 90:6444-6448 (1993).
An "isolated" antibody is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes. In preferred embodiments, the antibody will be purified (1) to greater than 95 % by weight of antibody as determined by the Lowry method, and most preferably more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions using Coomassie blue or, preferably, silver stain. Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
The word " label " when used herein refers to a detectable compound or composition which is conjugated directly or indirectly to the antibody so as to generate a "labeled" antibody. The label may be detectable by itself (e.g. radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition which is detectable. By "solid phase" is meant a non-aqueous matrix to which the antibody of the present invention can adhere. Examples of solid phases encompassed herein include those formed partially or entirely of glass (e.g., controlled pore glass), polysaccharides (e.g., agarose), polyacrylamides, polystyrene, polyvinyl alcohol and silicones. In certain embodiments, depending on the context, the solid phase can comprise the well of an assay plate; in others it is a purification column (e.g., an affinity chromatography column). This term also includes a discontinuous solid phase of discrete particles, such as those described in U.S. Patent No. 4,275,149.
A "liposome" is a small vesicle composed of various types of lipids, phospholipids and/or surfactant which is useful for delivery of a drug (such as a PRO polypeptide or antibody thereto) to a mammal. The components of the liposome are commonly arranged in a bilayer formation, similar to the lipid arrangement of biological membranes. A "small molecule" is defined herein to have a molecular weight below about 500 Daltons.
"PR0317-associated disorder" refers to a pathological condition or disease wherein PR0317 is over- or underexpressed. Such disorders include diseases of the female genital tract or of the endometrium of a mammal, including hyperplasia, endometritis, endometriosis, wherein the patient is at risk for infertility due to endometrial factor, endometrioma, and endometrial cancer, especially those diseases involving abnormal bleeding such as a gynecological disease. They also include diseases involving angiogenesis, wherein the angiogenesis results in a pathological condition, such as cancer involving solid tumors (the therapy for the disorder would result in decreased vascularization and a decline in growth and metastasis of a variety of tumors). Alternatively, the angiogenesis may be beneficial, such as for ischemia, especially coronary ischemia. Hence, these disorders include those found in patients whose hearts are functioning but who have a blocked blood supply due to atherosclerotic coronary artery disease, and those with a functioning but underperfused heart, including patients with coronary arterial disease who are not optimal candidates for angioplasty and coronary artery by-pass surgery. The disorders also include diseases involving the kidney or originating from the kidney tissue, such as polycystic kidney disease and chronic and acute renal failure.
Table 1
/* *
* C-C increased from 12 to 15
* Z is average of EQ
* B is average of ND
* match with stop is _M; stop-stop = 0; J (joker) match = 0
*/
^define M /* value of a match with a stop */ int day[26][26] = {
/* A B C D E F G H I J K L M N O P Q R S T U V W X Y Z*/
/* A*/ 2, 0,-2, 0, 0,-4, 1,-1,-1, 0,-1,-2,-1, 0,_M, 1, 0,-2, 1, 1, 0, 0,-6, 0,-3, 0},
/* B */ 0, 3,-4, 3, 2,-5, 0, 1,-2, 0, 0,-3,-2, 2,_M,-1, 1, 0, 0, 0, 0,-2,-5, 0,-3, 1},
/* C*/ ■2,-4,15,-5,-5,-4,-3,-3,-2, 0,-5,-6,-5,-4 ,_M,-3,-5,-4, 0,-2, 0,-2,-8, 0, 0,-5},
/* D*/ 0, 3,-5, 4, 3,-6, 1, 1,-2, 0, 0,-4,-3, 2,_M,-1, 2,-1, 0, 0, 0,-2,-7, 0,-4, 2},
/* E*/ 0, 2,-5, 3, 4,-5, 0, 1,-2, 0, 0,-3,-2, 1,_M,-1, 2,-1, 0, 0, 0,-2,-7, 0,-4, 3},
/* F*/ -4,-5,-4,-6,-5, 9,-5,-2, 1, 0,-5, 2, 0,-4,_M,-5,-5,-4,-3,-3, 0,-1, 0, 0, 7,-5},
/* G*/ 1, 0,-3, 1, 0,-5, 5,-2,-3, 0,-2,-4,-3, 0,_M,-l,-l,-3, 1, 0, 0,-1,-7, 0,-5, 0},
/* H*/ -1, 1,-3, 1, 1,-2,-2, 6,-2, 0, 0,-2,-2, 2,_M, 0, 3, 2,-1,-1, 0,-2,-3, 0, 0, 2},
/* I*/ -1,-2,-2,-2,-2, 1,-3,-2, 5, 0,-2, 2, 2,-2,_M,-2,-2,-2,-l, 0, 0, 4,-5, 0,-1,-2},
/* J*/ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,_M, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
/* K*/ -1, 0,-5, 0, 0,-5,-2, 0,-2, 0, 5,-3, 0, 1,_M,-1, 1, 3, 0, 0, 0,-2,-3, 0,-4, 0},
/* L*/ -2,-3,-6,-4,-3, 2,-4,-2, 2, 0,-3, 6, 4,-3,_M,-3,-2,-3,-3,-l, 0, 2,-2, 0,-1,-2},
/* M*/ -1,-2,-5,-3,-2, 0,-3,-2, 2, 0, 0, 4, 6,-2,_M,-2,-l, 0,-2,-1, 0, 2,-4, 0,-2,-1},
/* N*/ 0, 2,-4, 2, 1,-4, 0, 2,-2, 0, 1,-3,-2, 2,_M,-1, 1, 0, 1, 0, 0,-2,-4, 0,-2, 1},
/* O*/ M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M, 0,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M},
/* P*/ ι,-ι ■3, -1, -L ,-5, ,-1, , , ,-2. , 0, .-L ,-3: ,-2, ,-L , M ,6, , 0, 0, 1, 0, 0,-1,-6, 0,-5, 0},
/* Q*/ 0, 1 ■5, 2, 2, -5, -1, 3, -2, 0, 1, -2, -1, 1, M, 0, 4, 1,-1,-1,0,-2,-5,0,-4,3},
/* R*/ ■2,0 ■4, -1, -L ,-4, ,-3, ,2, ,-2: , 0, ,3, ,-3, .0, 0, M, 0, 1,6,0,-1,0,-2,2,0,-4,0},
/* S*/ 1,0. 0, 0, 0, -3, 1, -1, -1, 0, 0, -3, -2, 1, M, 1,- -1,0,2, 1,0,-1,-2,0,-3,0},
/* T*/ 1,0 2, 0, 0, -3, 0, -1, 0, 0, 0, -1, -1, 0, M, 0,- -1,-1, 1, 3, 0, 0,-5, 0,-3, 0},
/* TJ*/ 0,0 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, M, 0,1 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
/* V*/ 0,-2 ■2, -2, -2, -1, ,-1, ,-2, ,4, , 0, .-2.. ,2, ,2, -2~ M, ,-1, ,-2,-2,-1, 0, 0, 4,-6, 0,-2,-2},
/* w*/ 6,-5 -8, -1, ,-1: , 0, ,-7, ,-3, ,-5. , . ,-3. ,-2,-4 ,-4, , M ,-6, ,-5,2,-2,-5,0,-6,17,0,0,-6},
/* x*/ 0,0 0, o, o, o, 0, 0, 0, 0, 0, 0, 0, 0, M, 0,1 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
/* Y*/ ■3,-3 0, -4, -4, 7, -5, o, -1, 0, -4, ,-L .-2, -2, ' M. ,-5, ,-4,-4,-3,-3,0,-2,0,0,10,-4},
/* z*/ 0, 1 ■5, 2, 3, -5, 0, 2, -2, 0, 0, -2, -1, 1, M, 0, 3, 0, 0, 0, 0,-2,-6, 0,-4, 4}
};
Page 1 of day. h Table 1 (cont')
/* */
#include < stdio.h> ^include < ctype.h>
#define MAXJMP 16 /* max jumps in a diag */
#define MAXGAP 24 /* don't continue to penalize gaps larger than this */
#define JMPS 1024 /* max jmps in an path */
#define MX ■4 /* save if there's at least MX-1 bases since last jmp */
#define DMAT 3 /* value of matching bases */
#define DMIS 0 /* penalty for mismatched bases */
#define DINSO 8 /* penalty for a gap */
#define DINS1 1 /* penalty per base */
#define PINSO 8 /* penalty for a gap */
#defϊne PINS1 4 /* penalty per residue */ struct jmp { short n[MAXJMP]; /* size of jmp (neg for dely) */ unsigned short x[MAXJMP]; /* base no. of jmp in seq x */
}; /* limits seq to 2Λ16 -1 */ struct diag { int score; /* score at last jmp */ long offset; /* offset of prev block */ short ijmp; /* current jmp index */ struct jmp jp; /* list of jmps */
}; struct path { int spc; /* number of leading spaces */ short n[JMPS]; /* size of jmp (gap) */ int x[JMPS]; /* loc of jmp (last elem before gap) */
}; char *ofile; /* output file name */ char *namex[2]; /* seq names: getseqs() */ char *prog; /* prog name for err msgs */ char *seqx[2]; /* seqs: getseqs() */ int dmax; /* best diag: nw() */ int dmaxO; /* final diag */ int dna; /* set if dna: main() */ int endgaps; /* set if penalizing end gaps */ int gapx, gapy; /* total gaps in seqs */ int lenO, lenl; /* seq lens */ int ngapx, ngapy; /* total size of gaps */ int smax; /* max score: nw() */ int *xbm; /* bitmap for matching */ long offset; /* current offset in jmp file */ struct diag *dx; /* holds diagonals */ struct path pp[2]; /* holds path for seqs */ char *calloc(), *malloc(), *index(), *strcpy(); char *getseq(), *g_calloc();
Page 1 of nw.h Table 1 (cont')
/* Needleman-Wunsch alignment program
* usage: progs filel file2
* where filel and file2 are two dna or two protein sequences.
* The sequences can be in upper- or lower-case an may contain ambiguity
* Any lines beginning with ';', ' > ' or ' < ' are ignored
* Max file length is 65535 (limited by unsigned short x in the jmp struct)
* A sequence with 1/3 or more of its elements ACGTU is assumed to be DNA
* Output is in the file "align. out" *
* The program may create a tmp file in /tmp to hold info about traceback.
* Original version developed under BSD 4.3 on a vax 8650 */
^include "nw.h" ^include "day.h" static _dbval[26] = {
1 , 14,2, 13,0,0,4, 11,0,0, 12,0,3, 15,0,0,0,5,6,8,8,7,9,0, 10,0
}; static _pbval[26] = {
1, 2|(1< <('D'-'A'))|(1< <(,N'-'A')), 4, 8, 16, 32, 64,
128, 256, OxFFFFFFF, 1< < 10, 1< < 11, 1< < 12, 1< < 13, 1< < 14,
1< < 15, 1< < 16, 1< < 17, 1< < 18, 1< < 19, 1< <20, 1< <21, 1< <22,
1<<23, 1<<24, K^SKK^'E'-'A'^KK-ζCQ'-Α'))
};
Figure imgf000084_0001
int ac; char *av[] prog = av[0]; if(ac ! = 3){ fprintf(stderr, "usage: %s filel file2\n", prog); fprintf(stderr, "where filel and file2 are two dna or two protein sequences. \n"); fprintf(stderr,"The sequences can be in upper- or lower-case\n"); fprintf(stderr, " Any lines beginning with ';' or ' < ' are ignored\n"); fprintf(stderr, "Output is in the file \"align.out\"\n"); exit(l);
} namexfO] = av[l]; namex[l] = av[2]; seqx[0] = getseq(namex[0], &len0); seqx[l] = getseq(namex[l], &lenl); xbm = (dna)? .dbval : _pbval; endgaps = 0; /* 1 to penalize endgaps */ ofile = "align.out"; /* output file */ nw(); /* fill in the matrix, get the possible jmps */ readjmpsO; /* get the actual jmps */ print(); /* print stats, alignment */ cleaπup(O); /* unlink any tmp files */ }
Page 1 of nw.c Table 1 (cont')
/* do the alignment, return best score: main()
* dna: values in Fitch and Smith, PNAS, 80, 1382-1386, 1983
* pro: PAM 250 values
* When scores are equal, we prefer mismatches to any gap, prefer
* a new gap to extending an ongoing gap, and prefer a gap in seqx
* to a gap in seq y.
*/ nw() nw
{ char *px, *py; /* seqs and ptrs */ int *ndely, *dely; /* keep track of dely */ int ndelx, delx; /* keep track of delx */ int *tmp; /* for swapping rowO, rowl */ int mis; /* score for each type */ int insO, insl; /* insertion penalties */ register id; /* diagonal index */ register ϋ; /* jmp index */ register *col0, *coll; /* score for curr, last row */ register xx, yy; /* index into seqs */ dx = (struct diag *)g_calloc("to get diags", len0+lenl + l , sizeof(struct diag)); ndely = (int *)g_calloc("to get ndely", lenl + 1, sizeof(int)); dely = (int *)g_calloc("to get dely", lenl + 1, sizeof(int)); colO = (int *)g_calloc("to get colO", lenl + 1, sizeof(int)); coll = (int *)g_calloc("to get coll ", lenl + 1, sizeof(int)); insO = (dna)? DINS0 : PINS0; insl = (dna)? DINS1 : PINS1; smax = -10000; if (endgaps) { for (col0[0] = dely[0] = -insO, yy = 1; yy < = lenl; yy+ +) { col0[yy] = delyfyy] = col0[yy-l] - insl ; ndely[yy] = yy;
} col0[0] = 0; /* Waterman Bull Math Biol 84 */
} else for (yy = 1 ; yy < = lenl; yy+ +) dely[yy] = -insO;
/* fill in match matrix */ for (px = seqx[0], xx = 1; xx < = lenO; px+ + , xx+ +) { /* initialize first entry in col */ if (endgaps) { if (xx = = 1) coll[0] = delx = -(insO+insl); else coll[0] = delx = col0[0] - insl ; ndelx = xx;
} else { col l [0] = 0; delx = -insO; ndelx = 0;
Page 2 of nw.c Table 1 (conn
...nw seqx[l], yy = 1; yy < = lenl; py+ + , yy+ +) { mis = col0[yy-l]; if (dna) mis + = (xbm[*px-'A-']&xbm[*py-'A'])? DMAT : DMIS; else mis + = _day[*px-'A'][*py-'A'];
/* update penalty for del in x seq; * favor new del over ongong del
* ignore MAXGAP if weighting endgaps */ if (endgaps 1 1 ndelytyy] < MAXGAP) { if (coIOfyy] - insO > = dely[yy]) { dely[yy] = colOfyy] - (insO + insl); ndely [yy] = 1; } else { dely[yy] -= insl; ndely[yy] + + ; }
} else { if (col0[yy] - (insO+insl) > = dely[yy]) { dely[yy] = col0[yy] - (insO+insl); ndelyfyy] = L } else ndelyfyy] + + ; }
/* update penalty for del in y seq; * favor new del over ongong del
*/ if (endgaps 1 1 ndelx < MAXGAP) { if (coll[yy-l] - insO > = delx) { delx = coll[yy-l] - (insO+insl); ndelx = 1;
} else { delx -= insl; ndelx + + ;
} } else { if (coll[yy-l] - (insO+insl) > = delx) { delx = coll[yy-l] - (insO+insl); ndelx = 1; } else ndelx+ +;
}
/* pick the maximum score; we're favoring
* mis over any del and delx over dely */
Page 3 of nw.c Table 1 (cont')
...nw id = xx - yy + lenl - 1; if (mis > = delx && mis > = delyfyy]) collfyy] = mis; else if (delx > = delyfyy]) { collfyy] = delx; ij = dx[id].ijmp; if (dx[id].jp.n[0] && (!dna 1 1 (ndelx > = MAXJMP && xx > dx[id].jp.x[ij] +MX) | | mis > dxfid]. score +DINS0)) { dxfid]. ijmp+ + ; if (+ +ij > = MAXJMP) { writejmps(id); ij = dxfid]. ijmp = 0; dxfid]. offset = offset; offset + = sizeof(struct jmp) + sizeof(offset);
}
} dx[id].jp.n[ij] = ndelx dx[id].jp.x[ij] = xx; dx[id]. score = delx;
} else { collfyy] = delyfyy]; ij = dxfid], ijmp; if (dx[id].jp.n[0] && (!dna | | (ndelyfyy] > = MAXJMP
&& xx > dx[id].jp.x[ij] +MX) | | mis > dxfid]. score +DINS0)) { dxfid]. ijmp + + ; if (+ +ij > = MAXJMP) { writejmps(id); ij = dxfid]. ijmp = 0; dxfid]. offset = offset; offset + = sizeof(struct jmp) + sizeof(offset); } } dx[id].jp.n[ij] = -ndelyfyy]; dx[id].jp.x[ij] = xx; dxfid]. score = delyfyy];
} if (xx = = lenO && yy < lenl) { /* last col
*/ if (endgaps) collfyy] -= ins0+insl*(lenl-yy); if (collfyy] > smax) { smax = collfyy]; dmax = id; } } } if (endgaps && xx < lenO) coll[yy-l] -= ins0+insl*(len0-xx); if (collfyy- 1] > smax) { smax = coll[yy-l]; dmax = id; } tmp = colO; colO = coll; coll = tmp;
}
(void) free((char *)ndely); (void) free((char *)dely) (void) free((char *)col0)
(void) free((char *)coll) } Page 4 of nw.c Table 1 (cont')
/*
* print() - only routine visible outside this module * * static:
* getmatO — trace back best path, count matches: print()
* pr_align() — print alignment of described in array pfj: print()
* dumpblockO — dump a block of lines with numbers, stars: pr_align()
* nums() — put out a number line: dumpblockO * putline() — put out a line (name, [num], seq, [num]): dumpblockO
* stars() - -put a line of stars: dumpblockO
* stripnameO — strip any path and prefix from a seqname */ ^include "nw.h"
^define SPC 3 #define P LINE 256 /* maximum output line */ #define P SPC 3 /* space between name or num and seq */ extern _day[26][26]; int olen; /* set output line length */
FILE *fx; /* output file */ pprriinntt(o) print { int I Ixx,, 1ly, firstgap, lastgap; /* overlap */ if ((fx = ffooppeen(ofile, "w")) = = 0) { fprintf(stderr," %s: can't write %s\n" , prog, ofile); cleanup(l);
} fprintf(fx, " < first sequence: %s (length = %d)\n", namexfO], lenO); fprintf(fx, " < second sequence: %s (length = %d)\n", namexfl], lenl); olen = 60; lx = lenO; ly = lenl; firstgap = lastgap = 0; if (dmax < lenl - 1) { /* leading gap in x */ pp[0].spc = firstgap = lenl - dmax - 1 ; ly -= pp[0].spc;
} else if (dmax > lenl - 1) { /* leading gap in y */ pp[l].spc = firstgap = dmax - (lenl - 1); lx -= pp[l].spc;
} if (dmaxO < lenO - 1) { /* trailing gap in x */ lastgap = lenO - dmaxO -1; lx - = lastgap; } else if (dmaxO > lenO - 1) { /* trailing gap in y */ lastgap = dmaxO - (lenO - 1); ly - = lastgap; getmat(lx, ly, firstgap, lastgap); pr_align();
Page 1 of nwprint.c Table 1 (cont')
/*
* trace back the best path, count matches
*/ static getmat(lx, ly, firstgap, lastgap) getmat int lx, ly; /* "core" (minus endgaps) */ int firstgap, lastgap; /* leading trailing overlap */
{ int nm, iO, il, sizO, sizl; char outx[32]; double pet; register nO, nl; register char *p0, *pl;
/* get total matches, score
*/ iO = = il = sizO : = sizl = 0; pO = seqx[0] + pp[l].spc; pi = seqxfl] + pp[0].spc; nO = pp[l].spc + l; nl = pp[0].spc + l; nm = 0; whUe ( *p0 && *pl ) { if (sizO) { pl + +; nl + + ; sizO-;
} else if (sizl) { p0+ +; n0+ + ; sizl—;
} else { if (xbm[*pO-'A']&xbm[*pl-'A']) nm+ +; if (nO+ + = = pp[0].x[iO]) sizO = pp[0].n[i0+ +]; if (nl + + = = pp[l].x[il]) sizl = pp[l].n[il + +]; p0+ + ; pl + + ; } }
/* pet homology:
* if penalizing endgaps, base is the shorter seq
* else, knock off overhangs and take shorter core */ if (endgaps) lx = (lenO < lenl)? lenO : lenl ; else lx = (lx < ly)? lx : ly; pet = 100.*(double)nm/(double)lx; fprintf(fx, "\n"); fprintf(fx, " < %d match%s in an overlap of %d: % .2f percent similarity\n" nm, (nm = = 1)? " " : "es", lx, pet);
Page 2 of nwprint.c Table 1 (cont') fprintf(fx, " < gaps in first sequence: %d", gapx); ...getmat if (gapx) {
(void) sprintf(outx, " (%d s%s)\ ngapx, (dna)? "base": "residue", (ngapx 1)7 "" : "s"); fprintf(fx," %s", outx); fjprintf(fx, ", gaps in second sequence: %d", gapy); if (gapy) {
(void) sprintf(outx, " (%d %s%s)", ngapy, (dna)? "base": "residue", (ngapy = = 1)? " " : "s"); fprintf(fx," %s", outx);
} if (dna) fprintf(fx,
"\n < score: %d (match = %d, mismatch = %d, gap penalty = %d + d per base)\n" smax, DMAT, DMIS, DINS0, DINS1); else fprintf(fx,
"\n< score: %d (Dayhoff PAM 250 matrix, gap penalty = %d + %d per residue)\n" smax, PINS0, PINS1); if (endgaps) fprintf(fx,
" < endgaps penalized, left endgap: %d %s s, right endgap: %d %s%s\n", firstgap, (dna)? "base" : "residue", (firstgap = = 1)? " " : "s", lastgap, (dna)? "base" : "residue", (lastgap = = 1)? "" : "s"); else fprintf(fx, " < endgaps not penalized\n");
static nm; /* matches in core — for checking */ static lmax; /* lengths of stripped file names */ static ij[2]; /* jmp index for a path */ static nc[2]; /* number at start of current line */ static nip]; /* current elem number - for gapping */ static siz[2]; static char *ps[2]; /* ptr to current element */ static char *po[2]; /* ptr to next output char slot */ static char oouutt[[22]][[IP_LINE]; /* output line */ static char starfP 1 2]; /* set by stars() */
/*
* print alignment of described in struct path pp[] */ static pr align() pr align
{ int nn; /* char count */ int more; register i; for (i = 0, lmax = 0; i < 2; i+ +) { nn = stripname(namex[i]); if (nn > lmax) lmax = nn; ncfi] = 1; ni[i] = 1 ; sizfi] = ijfi] = 0; psfi] = seqxfi]; pofi] = outfi];
Page 3 of nwprint.c Table 1 (cont') for (nn = nm = 0, more = 1 ; more; ) { .pralign for (i = more = 0; i < 2; i+ +) { /*
* do we have more of this sequence? */ if (!*ps[i]) continue; more++; if (pp[i].spc) { /* leading space */ *po[i] + + = ' '; pp[i].spc-;
} else if (sizfi]) { /* in a gap */
*po[i] + + = '-'; sizfi]—;
} else { /* we're putting a seq element */ *po[i] = *ps[i]; if (islower(*ps[i]))
*ps[i] = toupper(*ps[i]); po[i]++; ps[i] + +;
/*
* are we at next gap for this seq? */ if(ni[i] ==pp[i].x[ij[i]]){ /*
* we need to merge all gaps
* at this location */ sizfi] =pp[i].n[ij[i] + +]; while (nifi] == pp[i].x[ij[i]]) sizfi] +=pp[i].n[ij[i]++]
} ni[i] + + ;
} if (+ +nn = = olen | | !more && nn) { dumpblockO; for(i = 0; i < 2; i++) pofi] = outfi]; nn = 0; } } }
/*
* dump a block of lines, including numbers, stars: pr_align()
*/ static dumpblockO dumpblock
{ register i; for(i = 0; i < 2; i++) ♦pofi]- = '\0';
Page 4 of nwprint.c Table 1 (cont')
.dumpblock
(void) putc('\n', fx); for (i = 0; i < 2; i++){ if (*out[i] && (*out[i] != ' ' || *(po[i]) != ' ')){ if(i==0) nums(i); if(i ==0&&*out[l]) stars(); putline(i); if (i = = 0 && *out[l]) tprintf(fx, star); if(i == 1) nums(i);
}
}
/*
* put out a number line: dumpblockO */ static nums(ix) nums int ix; /* index in out[] holding seq line */ { char nline[P_LINE]; register i.j; register char for (pn = nline, 0; i < lmax+P_SPC; i++, pn++) for (i = πc[ix], py = out[ix]; *py; py+ +, pn+ +) { if(*py == " II *py == '-') else { if(i%10 ==0 || (i == 1 &&nc[ix] != 1)) { j = (i < 0)? -i : i; for (px = pn; j; j / = 10, px-)
*px = j%10 + '0'; if (i < 0)
*px = '-';
} else
*pn = i++;
}
*pn = '\0'; ncfix] = i; for (pn = nline; *pn; pn+ +) (void) putc(*pn, fx); (void) putc('\n', fx);
} /*
* put out a line (name, [num], seq, [num]): dumpblockO
*/ static putline(ix) putline int ix;
{ Page 5 of nwprint.c Table 1 (cont')
...putline int i; register char *px; for (px = namex[ix], i = 0; *px && *px != ':'; px+ + , i++)
(void) putc(*px, fx); for (; i < lmax+P_SPC; i+ +)
(void) putc(' ', fx);
/* these count from 1 :
* ni[] is current element (from 1)
* nc[] is number at start of current line */ for (px = out[ix]; *px; px+ +)
(void) putc(*px&0x7F, fx); (void)putc('\n\ fx);
* put a line of stars (seqs always in out[0], out[l]): dumpblockO */ static starso stars
{ int i; register char *p0, *pl, ex, *px; if (!*out[0] 11 (*out[0] == ' '&& *(po[0]) == ' ') | |
!*out[l] I I (*out[l] == ' •&& *(po[l]) == " ')) return; px = star; for (i = lmax+P SPC; i; i~) *px++ = ' '; for (pO = out[0], pi = out[l]; *p0 && *pl; p0+ + , pl + +) { if (isalpha(*p0) && isalpha(*pl)) { if (xbm[*pO-'A']&xbm[*pl-'A']) { ex = '*'; nm+ +;
} else if (!dna && day[*p0-'A'][*pl-' A'] > 0) ex = '.'; else ex = ' ';
} else ex = ' ';
*px+ + = ex;
}
*px++ = '\n'; *px = '\0'; }
Page 6 of nwprint.c Table 1 (cont')
/*
* strip path or prefix from pn, return len: pr_align() */ static stripname(pn) stripname char *pn; /* file name (may be path) */
{ register char *px, *py; py = 0; for (px = pn; *px; px+ +) if (*pχ = = '/') py = px + 1; if (ρy) (void) strcpy(pn, py); return(strlen(pn));
}
Page 7 of nwprint.c Table 1 (conf)
/*
* cleanupO ~ cleanup any tmp file
* getseqO - read in seq, set dna, len, maxlen
* g_calloc() — calloc() with error checkin
* readjmpsO - get the good jmps, from tmp file if necessary
* writejmpsO — write a filled array of jmps to a tmp file: nw() */
^include "nw.h" ^include < sys/file.h> char *jname = "/tmp/homgXXXXXX"; /* tmp file for jmps */
FILE *fj; int cleanupO; /* cleanup tmp file */ long lseek();
/*
* remove any tmp file if we blow cleanup(i) cleanup int i;
{ if (fj)
(void) unlink(jname); exit(i); }
/*
* read, return ptr to seq, set dna, len, maxlen
* skip lines starting with ' ;' , ' < ', or ' > '
* seq in upper or lower case */ char * getseq(file, len) getseq char ♦file; /* file name */ int *len; /* seq len */
{ char line[1024], *pseq: register char *px, *py; int natgc, tlen;
FILE *fp; if ((φ = fopen(file,"r")) = = 0) { φrintf(stderr," %s: can't read %s\n", prog, file); exit(l);
} tlen = natgc = 0; while (fgets(line, 1024, φ)) { if (*line = = ' ;' | | *line = = ' < ' 1 1 *line = = ' > ') continue; for (px = line; *px ! = '\n'; px+ +) if (isupper(*px) | | islower(*px)) tlen+ + ;
} if ((pseq = malloc((unsigned)(tlen+6))) = = 0) { φrintf(stderr, " %s: malloc() failed to get %d bytes for %s\n", prog, tlen+6, file); exit(l);
} pseq[0] = pseq[l] = pseq[2] = pseq[3] = '\0' ;
Page 1 of nwsubr.c Table 1 (cont')
.getseq py = pseq + 4; *len = tlen; rewind(φ); while (fgets(line, 1024, φ)) { if (*line == ';' | | *line == '<' 11 *line == '>') continue; for (px = line; *px != '\n'; px++) { if (isupper(*px))
*py++ = *px; else if (islower(*px))
*py++ = toupper(*px); if (index( " ATGCU " , *(py- 1 ))) natgc++;
} }
*py++ = '\0';
*py = '\0'; (void) fclose(φ); dna = natgc > (tlen/3); return(pseq+4); } char * g_calloc(msg, nx, sz) g_CallθC char *msg; /* program, calling routine */ int nx, sz; /* number and size of elements */
{ char *px, *calloc(); if ((px = calloc((unsigned)nx, (unsigned)sz)) = = 0) { if (*msg) { φrintf(stderr, "%s: g_calloc() failed %s (n=%d, sz=%d)\n", prog, msg, nx, sz); exit(l);
} } return(px);
}
/* * get final jmps from dx[] or tmp file, set pp[], reset dmax: main()
*/ readjmpsO readjmps { int fd = -1; int siz, iO, il; register i, j, xx; if(fj){
(void) fclose(fj); if ((fd = open(jname, O RDONLY, 0)) < 0) { φrintf(stderr, "%s: can't open() %s\n", prog, jname); cleanupO ); }
} for (i = iO = il = 0, dmaxO = dmax, xx = lenO; ; i+ +) { while (1){ for (j = dx[dmax].ijmp; j > = 0 && dx[dmax].jp.x[j] > = xx; j-)
Page 2 of nwsubr.c Table 1 (conf)
...readjmps if (j < 0 && dx[dmax]. offset && fj) {
(void) lseek(fd, dx[dmax]. offset, 0); (void) read(fd, (char *)&dx[dmax].jp, sizeof(struct jmp)); (void) read(fd, (char *)&dx[dmax]. offset, sizeof(dx[dmax]. offset)); dx[dmax].ijmp = MAXJMP-1 ;
} else break; } if (i > = JMPS) { φrintf(stderr, " %s: too many gaps in alignmenΛn", prog); cleanup(l); } if (j > = 0) { siz = dx[dmax].jp.n[j]; xx = dx[dmax].jp.x[j]; dmax + = siz; if (siz < 0) { /* gap in second seq */ pp[l].n[il] = -siz; xx + = siz;
/* id = xx - yy + lenl - 1 */ pp[l].x[il] = xx - dmax + lenl - 1; gapy+ + ; ngapy -= siz; /* ignore MAXGAP when doing endgaps */ siz = (-siz < MAXGAP | | endgaps)? -siz : MAXGAP; il + + ; } else if (siz > 0) { /* gap in first seq */ pp[0].n[i0] = siz; pp[0].x[i0] = xx; gapx+ + ; ngapx + = siz;
/* ignore MAXGAP when doing endgaps */ siz = (siz < MAXGAP 1 1 endgaps)? siz : MAXGAP; i0+ + ; } } else break; } /* reverse the order of jmps
*/ for (j = 0, i0~; j < iO; j + + , i0~) { i = pp[0].n[j]; pprθ].n[j] = pp[0].n[i0]; pp[0].n[i0] = i; i = pp[0].x[j]; pp[0].x[j] = pp[0].x[i0]; pp[0].x[i0] = i; } for (j = 0, il-; j < il ; j + + , il-) { i = pp[l].n[j]; pp[l].n[j] = pp[l].n[il]; pp[l].n[il] = i; i = pp[i].χϋl; ppfU-xlj] = pp[i].χ[iU; PP H-XPU = i;
} if (fd > = 0)
(void) close(fd); if (fj) {
(void) unlink(jname); fj = 0; offset = 0;
}
Page 3 of nwsubr.c Table 1 (conf)
/*
* write a filled jmp struct offset of the prev one (if any): nw()
*/ writejmps(iχ) writejmps int ix;
{ char *mktemp(); if (!fj) { if (mktemp(jname) < 0) { φrintf(stderr, "%s: can't mktempO %s\n", prog, jname); cleanup(l);
} if ((fj = fopen(jname, "w")) = = 0) { φrintf(stderr, " %s: can't write %s\n", prog, jname); exit(l); } } (void) f rite((char *)&dx[ix].jp, sizeof(struct jmp), 1, fi);
(void) fwrite((char *)&dx[ix]. offset, sizeof(dx[ix] . offset), 1, fj);
Page 4 of nwsubr.c Table 2
PRO xxxxxxxxxxxxxxx (Length = 15 amino acids)
Comparison Protein XXXXXYYYYYYY (Length = 12 amino acids)
% amino acid sequence identity =
(the number of identically matching amino acid residues between the two polypeptide sequences as determined by ALIGN-2) divided by (the total number of amino acid residues of the PRO polypeptide) =
5 divided by 15 = 33.3%
Table 3
PRO xxxxxxxxxx (Length = 10 amino acids)
Comparison Protein XXXXXYYYYYYZZYZ (Length = 15 amino acids)
% amino acid sequence identity =
(the number of identically matching amino acid residues between the two polypeptide sequences as determined by ALIGN-2) divided by (the total number of amino acid residues of the PRO polypeptide) =
5 divided by 10 = 50%
Table 4
PRO-DNA NNNNNNNNNNNNNN (Length = 14 nucleotides) Comparison DNA NNNNNNLLLLLLLLLL (Length = 16 nucleotides)
% nucleic acid sequence identity =
(the number of identically matching nucleotides between the two nucleic acid sequences as determined by ALIGN-2) divided by (the total number of nucleotides of the PRO-DNA nucleic acid sequence) =
6 divided by 14 = 42.9%
Table 5
PRO-DNA NNNNNNNNNNNN (Length = 12 nucleotides) Comparison DNA NNNNLLLVV (Length = 9 nucleotides)
% nucleic acid sequence identity =
(the number of identically matching nucleotides between the two nucleic acid sequences as determined by ALIGN-2) divided by (the total number of nucleotides of the PRO-DNA nucleic acid sequence) =
4 divided by 12 = 33.3 %
II. Compositions and Methods of the Invention
A. Full-Length PRO Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO polypeptides. In particular, cDNAs encoding various PRO polypeptides have been identified and isolated, as disclosed in further detail in the Examples below. It is noted that proteins produced in separate expression rounds may be given different PRO numbers but the UNQ number is unique for any given DNA and the encoded protein, and will not be changed. However, for sake of simplicity, in the present specification the protein encoded by the full length native nucleic acid molecules disclosed herein as well as all further native homologues and variants included in the foregoing definition of PRO, will be referred to as "PRO/number", regardless of their origin or mode of preparation. As disclosed in the Examples below, various cDNA clones have been deposited with the ATCC. The actual nucleotide sequences of those clones can readily be determined by the skilled artisan by sequencing of the deposited clone using routine methods in the art. The predicted amino acid sequence can be determined from the nucleotide sequence using routine skill. For the PRO polypeptides and encoding nucleic acids described herein, Applicants have identified what is believed to be the reading frame best identifiable with the sequence information available at the time.
1. Full-length PRQ211 and PRQ217 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0211 and PR0217. In particular, Applicants have identified and isolated cDNA encoding PR0211 and PR0217 polypeptides, as disclosed in further detail in the Examples below. Using BLAST (FastA format) sequence alignment computer programs, Applicants found that cDNA sequences encoding full-length native sequence PR0211 and PR0217 have homologies to known proteins having EGF-like domains. Specifically, the cDNA sequence DNA32292-1131 (Figure 1, SEQ ID NO:l) has certain identify and a Blast score of 209 with PAC6_RAT and certain identify and a Blast score of 206 with Fibulin- 1, isoform c precursor. The cDNA sequence DNA33094-1131 (Figure 3, SEQ ID NO:3) has 36% identity and a Blast score of 336 with eastern newt tenascin, and 37 % identity and a Blast score of 331 with human tenascin- X precursor. Accordingly, it- is presently believed that PR0211 and PR0217 polypeptides disclosed in the present application are newly identified members of the EGF-like family and possesses properties typical of the EGF-like protein family.
2. Full-length PRO230 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO230. In particular, Applicants have identified and isolated cDNA encoding a PRO230 polypeptide, as disclosed in further detail in the Examples below. Using known programs such as BLAST and FastA sequence alignment computer programs, Applicants found that a cDNA sequence encoding full-length native sequence PRO230 has 48% amino acid identity with the rabbit tubulointerstitial nephritis antigen precursor. Accordingly, it is presently believed that PRO230 polypeptide disclosed in the present application is a newly identified member of the tubulointerstitial nephritis antigen family and possesses the ability to be recognized by human autoantibodies in certain forms of tubulointerstitial nephritis.
3. Full-length PRQ232 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0232. In particular, Applicants have identified and isolated cDNA encoding a PR0232 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that a portion of the full-length native sequence PR0232 (shown in Figure 9 and SEQ ID NO: 18) has 35 % sequence identity with a stem cell surface antigen from Gallus gallus. Accordingly, it is presently believed that the PR0232 polypeptide disclosed in the present application may be a newly identified stem cell antigen.
4. Full-length PRQ187 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0187. In particular, Applicants have identified and isolated cDNA encoding a PRO 187 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that a full-length native sequence PR0187 (shown in Figure 15) has 74% amino acid sequence identity and BLAST score of 310 with various androgen-induced growth factors and FGF-8. Accordingly, it is presently believed that PRO 187 polypeptide disclosed in the present application is a newly identified member of the FGF-8 protein family and may possess identify activity or property typical of the FGF-8-like protein family.
5. Full-length PRQ265 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0265. In particular, Applicants have identified and isolated cDNA encoding a PR0265 polypeptide, as disclosed in further detail in the Examples below. Using programs such as BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0265 polypeptide have significant homology with the fibromodulin protein and fibromodulin precursor protein. Applicants have also found that the DNA encoding the PR0265 polypeptide has significant homology with platelet glycoprotein V, a member of the leucine rich related protein family involved in skin and wound repair. Accordingly, it is presently believed that PR0265 polypeptide disclosed in the present application is a newly identified member of the leucine rich repeat family and possesses protein protein binding capabilities, as well as be involved in skin and wound repair as typical of this family.
6. Full-length PRQ219 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0219. In particular, Applicants have identified and isolated cDNA encoding a PR0219 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0219 polypeptide have significant homology with the mouse and human matrilin-2 precursor polypeptides. Accordingly, it is presently believed that PR0219 polypeptide disclosed in the present application is related to the matrilin-2 precursor polypeptide.
7. Full-length PRQ246 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0246. In particular, Applicants have identified and isolated cDNA encoding a PR0246 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that a portion of the PR0246 polypeptide has significant homology with the human cell surface protein HCAR. Accordingly, it is presently believed that PR0246 polypeptide disclosed in the present application may be a newly identified membrane-bound virus receptor or tumor cell-specific antigen.
8. Full-length PRQ228 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0228. In particular, Applicants have identified and isolated cDNA encoding a PR0228 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0228 polypeptide have significant homology with the EMRl protein. Applicants have also found that the DNA encoding the PR0228 polypeptide has significant homology with latrophilin, macrophage-restricted cell surface glycoprotein, B0457.1 and leucocyte antigen CD97 precursor. Accordingly, it is presently believed that PR0228 polypeptide disclosed in the present application is a newly identified member of the seven transmembrane superfamily and possesses characteristics and functional properties typical of this family. In particular, it is believed that PR0228 is a new member of the subgroup within this family to which CD97 and EMRl belong.
9. Full-length PRQ533 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0533. In particular, Applicants have identified and isolated cDNA encoding a PR0533 polypeptide, as disclosed in further detail in the Examples below. Using BLAST-2 and FastA sequence alignment computer programs, Applicants found that a full-length native sequence PR0533 (shown in Figure 22 and SEQ ID NO: 59) has a Blast score of 509 and 53% amino acid sequence identity with fibroblast growth factor (FGF). Accordingly, it is presently believed that PR0533 disclosed in the present application is a newly identified member of the fibroblast growth factor family and may possess activity typical of such polypeptides.
10. Full-length PRQ245 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0245. In particular, Applicants have identified and isolated cDNA encoding a PR0245 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that a portion of the amino acid sequence of the PR0245 polypeptide has 60% amino acid identity with the human c-myb protein. Accordingly, it is presently believed that the PR0245 polypeptide disclosed in the present application may be a newly identified member of the transmembrane protein tyrosine kinase family.
11. Full-length PRO220. PRQ221 and PRQ227 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO220, PR0221 and PR0227. In particular, Applicants have identified and isolated cDN As encoding a PRO220, PR0221 and PR0227 polypeptide, respectively, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, PRO220 has amino acid identity with the amino acid sequence of a leucine rich protein wherein the identity is 87 % . PRO220 additionally has amino acid identity with the neuronal leucine rich protein wherein the identity is 55 % . The neuronal leucine rich protein is further described in Taguchi, et al, Mol. Brain Res.. 35:31-40 (1996). PR0221 has amino acid identity with the SLIT protein precursor, wherein different portions of these two proteins have the respective percent identities of 39%, 38%, 34%, 31 %, and 30% .
PR0227 has amino acid identity with the amino acid sequence of platelet glycoprotein V precursor. The same results were obtained for human glycoprotein V. Different portions of these two proteins show the following percent identities of 30%, 28%, 28%, 31 %, 35%, 39% and 27%. Accordingly, it is presently believed that PRO220, PR0221 and PR0227 polypeptides disclosed in the present application are newly identified members of the leucine rich repeat protein superfamily and that each possesses protein-protein binding capabilities typical of the leucine rich repeat protein superfamily. It is also believed that they have capabilities similar to those of SLIT, the leucine rich repeat protein and human glycoprotein V.
12. Full-length PRQ258 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0258. In particular, Applicants have identified and isolated cDNA encoding a PR0258 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0258 polypeptide have significant homology with the CRTAM and poliovirus receptors. Accordingly, it is presently believed that PR0258 polypeptide disclosed in the present application is a newly identified member of the Ig superfamily and possesses virus receptor capabilities or regulates immune function as typical of this family.
13. Full-length PRQ266 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0266. In particular, Applicants have identified and isolated cDNA encoding a PR0266 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0266 polypeptide have significant homology with the SLIT protein from Drosophilia. Accordingly, it is presently believed that PR0266 polypeptide disclosed in the present application is a newly identified member of the leucine rich repeat family and possesses ligand-ligand binding activity and neuronal development typical of this family. SLIT has been shown to be useful in the study and treatment of Alzheimer's disease, supra, and thus, PR0266 may have involvement in the study and cure of this disease.
14. Full-length PRQ269 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0269. In particular, Applicants have identified and isolated cDNA encoding a PR0269 polypeptide, as disclosed in further detail in the Examples below. Using BLAST, FastA and sequence alignment computer programs, Applicants found that the amino acid sequence encoded by nucleotides 314 to 1783 of the full-length native sequence PR0269 (shown in Figure 35 and SEQ ID NO:95) has significant homology to human urinary thrombomodulin and various thrombomodulin analogues respectively, to which it was aligned. Accordingly, it is presently believed that PR0269 polypeptide disclosed in the present application is a newly identified member of the thrombomodulin family.
15. Full-length PRQ287 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0287. In particular, Applicants have identified and isolated cDNA encoding a PR0287 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0287 polypeptide have significant homology with the type 1 procollagen C-proteinase enhancer protein precursor and type 1 procollagen C-proteinase enhancer protein. Accordingly, it is presently believed that PR0287 polypeptide disclosed in the present application is a newly identified member of the C-proteinase enhancer protein family.
16. Full-length PRQ214 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0214. In particular, Applicants have identified and isolated cDNA encoding a PR0214 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that a full-length native sequence PR0214 polypeptide (shown in Figure 40 and SEQ ID NO: 109) has 49% amino acid sequence identity with HT protein, a known member of the EGF-family. The comparison resulted in a BLAST score of 920, with 150 matching nucleotides. Accordingly, it is presently believed that the PR0214 polypeptide disclosed in the present application is a newly identified member of the family comprising EGF domains and may possess activities or properties typical of the EGF-domain containing family. 17. Full-length PR0317 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0317. In particular, cDN A encoding a PR0317 polypeptide has been identified and isolated, as disclosed in further detail in the Examples below. Using BLAST™ and FastA™ sequence alignment computer programs, it was found that a full-length native-sequence PR0317 (shown in Figure 42 and SEQ ID NO: 114) has 92% amino acid sequence identity with EBAF-1. Further, it is closely aligned with many other members of the TGF- superfamily.
Accordingly, it is presently believed that PR0317 disclosed in the present application is a newly identified member of the TGF- superfamily and may possess properties that are therapeutically useful in conditions of uterine bleeding, etc. Hence, PR0317 may be useful in diagnosing or treating abnormal bleeding involved in gynecological diseases, for example, to avoid or lessen the need for a hysterectomy. PR0317 may also be useful as an agent that affects angiogenesis in general, so PR0317 may be useful in anti-tumor indications, or conversely, in treating coronary ischemic conditions.
Library sources reveal that ESTs used to obtain the consensus DNA for generating PR0317 primers and probes were found in normal tissues (uterus, prostate, colon, and pancreas), in several tumors (colon, brain (twice), pancreas, and mullerian cell), and in a heart with ischemia. PR0317 has shown up in several tissues as well, but it does look to have a greater concentration in uterus. Hence, PR0317 may have a broader use by the body than EBAF-1. It is contemplated that, at least for some indications, PR0317 may have opposite effects from EBAF-1.
18. Full-length PRQ301 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO301. In particular, Applicants have identified and isolated cDNA encoding a PRO301 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that a full-length native sequence PRO301 (shown in Figure 44 and SEQ ID NO: 119) has a Blast score of 246 corresponding to 30% amino acid sequence identity with human A33 antigen precursor. Accordingly, it is presently believed that PRO301 disclosed in the present application is a newly identified member of the A33 antigen protein family and may be expressed in human neoplastic diseases such as colorectal cancer.
19. Full-length PRQ224 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0224. In particular, Applicants have identified and isolated cDNA encoding a PR0224 polypeptide, as disclosed in further detail in the Examples below. Using known programs such as BLAST and FastA sequence alignment computer programs, Applicants found that full-length native PR0224 (Figure 46, SEQ ID NO: 127) has amino acid identity with apolipoprotein E receptor 2906 from homo sapiens. The alignments of different portions of these two polypeptides show amino acid identities of 37% , 36% , 30% , 44% , 44% and 28% respectively. Full-length native PR0224 (Figure 46, SEQ ID NO: 127) also has amino acid identity with very low-density lipoprotein receptor precursor from gall. The alignments of different portions of these two polypeptides show amino acid identities of 38% , 37% , 42% , 33% , and 37% respectively. Additionally, full-length native PR0224 (Figure 46, SEQ ID NO: 127) has amino acid identity with the chicken oocyte receptor P95 from Gallus gallus. The alignments of different portions of these two polypeptides show amino acid identities of 38%, 37%, 42%, 33 % , and 37% respectively. Moreover, full-length native PR0224 (Figure 46, SEQ ID NO: 127) has amino acid identity with very low density lipoprotein receptor short form precursor from humans. The alignments of different portions of these two polypeptides show amino acid identities of 32%, 38% , 34%, 45 % , and 31 % , respectively. Accordingly, it is presently believed that PR0224 polypeptide disclosed in the present application is a newly identified member of the low density lipoprotein receptor family and possesses the structural characteristics required to have the functional ability to recognize and endocytose low density lipoproteins typical of the low density lipoprotein receptor family. (The alignments described above used the following scoring parameters: T=7, S+65, S2=36, Matrix: BLOSUM62.)
20. Full-length PRQ222 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0222. In particular, Applicants have identified and isolated cDNA encoding a PR0222 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that a sequence encoding full-length native sequence PR0222 (shown in Figure 48 and SEQ ID NO: 132) has 25-26% amino acid identity with mouse complement factor h precursor, has 27-29% amino acid identity with complement receptor, has 25-47% amino acid identity with mouse complement C3b receptor type 2 long form precursor, has 40% amino acid identity with human hypothetical protein kiaa0247. Accordingly, it is presently believed that PR0222 polypeptide disclosed in the present application is a newly identified member of the complement receptor family and possesses activity typical of the complement receptor family.
21. Full-length PRQ234 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0234. In particular, Applicants have identified and isolated cDNA encoding a PR0234 polypeptide, as disclosed in further detail in the Examples below. Using BLAST (FastA- format) sequence alignment computer programs, Applicants found that a cDNA sequence encoding full-length native sequence PR0234 has 31 % identity and Blast score of 134 with E-selectin precursor. Accordingly, it is presently believed that the PR0234 polypeptides disclosed in the present application are newly identified members of the lectin selectin family and possess activity typical of the lectin/selectin family.
22. Full-length PRQ231 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0231. In particular, Applicants have identified and isolated cDNA encoding a PR0231 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that the full-length native sequence PR0231 polypeptide (shown in Figure 52 and SEQ ID NO: 142) has 30 % and 31 % amino acid identity with human and rat prostatic acid phosphatase precursor proteins, respectively. Accordingly, it is presently believed that the PR0231 polypeptide disclosed in the present application may be a newly identified member of the acid phosphatase protein family.
23. Full-length PRQ229 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0229. In particular, Applicants have identified and isolated cDNA encoding a PR0229 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0229 polypeptide have significant homology with antigen wcl. l, M130 antigen, T cell surface glycoprotein CD6 and CD6. It also is related to Sp-alpha. Accordingly, it is presently believed that PR0229 polypeptide disclosed in the present application is a newly identified member of the family containing scavenger receptor homology, a sequence motif found in a number of proteins involved in immune function and thus possesses immune function and /or segments which resist degradation, typical of this family.
24. Full-length PRQ238 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0238. In particular, Applicants have identified and isolated cDNA encoding a PR0238 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0238 polypeptide have significant homology with reductases, including oxidoreductase and fatty acyl-CoA reductase. Accordingly, it is presently believed that PR0238 polypeptide disclosed in the present application is a newly identified member of the reductase family and possesses reducing activity typical of the reductase family.
25. Full-length PRQ233 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0233. In particular, Applicants have identified and isolated cDNA encoding a PR0233 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0233 polypeptide have significant homology with the reductase protein. Applicants have also found that the DNA encoding the PR0233 polypeptide has significant homology with proteins from Caenorhabditis elegans. Accordingly, it is presently believed that PR0233 polypeptide disclosed in the present application is a newly identified member of the reductase family and possesses the ability to effect the redox state of the cell typical of the reductase family.
26. Full-length PRQ223 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0223. In particular, Applicants have identified and isolated cDNA encoding a PR0223 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that the PR0223 polypeptide has significant homology with various serine carboxypeptidase polypeptides. Accordingly, it is presently believed that PR0223 polypeptide disclosed in the present application is a newly identified serine carboxypeptidase.
27. Full-length PRQ235 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0235. In particular, Applicants have identified and isolated cDNA encoding a PR0235 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0235 polypeptide have significant homology with the various plexin proteins. Accordingly, it is presently believed that PR0235 polypeptide disclosed in the present application is a newly identified member of the plexin family and possesses cell adhesion properties typical of the plexin family.
28. Full-length PRQ236 and PRQ262 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0236 and PR0262. In particular, Applicants have identified and isolated cDNA encoding PR0236 and PR0262 polypeptides, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0236 and PR0262 polypeptides have significant homology with various β-galactosidase and β- galactosidase precursor polypeptides. Accordingly, it is presently believed that the PR0236 and PR0262 polypeptides disclosed in the present application are newly identified β-galactosidase homologs.
29. Full-length PRQ239 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0239. In particular, Applicants have identified and isolated cDNA encoding a PR0239 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0239 polypeptide have significant homology with densin proteins. Accordingly, it is presently believed that PR0239 polypeptide disclosed in the present application is a newly identified member of the densin family and possesses cell adhesion and the ability to effect synaptic processes as is typical of the densin family.
30. Full-length PRQ257 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0257. In particular, Applicants have identified and isolated cDNA encoding a PR0257 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0257 polypeptide have significant homology with the ebnerin precursor and ebnerin protein. Accordingly, it is presently believed that PR0257 polypeptide disclosed in the present application is a newly identified protein member which is related to the ebnerin protein.
31. Full-length PRO260 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO260. In particular, Applicants have identified and isolated cDNA encoding a PRO260 polypeptide, as disclosed in further detail in the Examples below. Using programs such as BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PRO260 polypeptide have significant homology with the alpha-1-fucosidase precursor. Accordingly, it is presently believed that PRO260 polypeptide disclosed in the present application is a newly identified member of the fucosidase family and possesses enzymatic activity related to fucose residues typical of the fucosidase family.
32. Full-length PRQ263 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0263. In particular, Applicants have identified and isolated cDNA encoding a PR0263 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0263 polypeptide have significant homology with the CD44 antigen and related proteins. Accordingly, it is presently believed that PR0263 polypeptide disclosed in the present application is a newly identified member of the CD44 antigen family and possesses at least one of the properties associated with these antigens, i.e., cancer and HIV marker, cell-cell or cell-matrix interactions, regulating cell traffic, lymph node homing, transmission of growth signals, and presentation of chemokines and growth facors to traveling cells.
33. Full-length PRO270 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO270. In particular, Applicants have identified and isolated cDNA encoding a PRO270 polypeptide, as disclosed in further detail in the Examples below. Using BLAST, FastA and sequence alignment computer programs, Applicants found that that various portions of the PRO270 polypeptide have significant homology with various thioredoxin proteins. Accordingly, it is presently believed that PRO270 polypeptide disclosed in the present application is a newly identified member of the thioredoxin family and possesses the ability to effect reduction-oxidation (redox) state typical of the thioredoxin family.
34. Full-length PRQ271 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0271. In particular, Applicants have identified and isolated cDNA encoding a PR0271 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that the PR0271 polypeptide has significant homology with various link proteins and precursors thereof. Accordingly, it is presently believed that PR0271 polypeptide disclosed in the present application is a newly identified link protein homolog.
35. Full-length PRQ272 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0272. In particular, Applicants have identified and isolated cDNA encoding a PR0272 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0272 polypeptide have significant homology with the human reticulocalbin protein and its precursors. Applicants have also found that the DNA encoding the PR0272 polypeptide has significant homology with the mouse reticulocalbin precursor protein. Accordingly, it is presently believed that PR0272 polypeptide disclosed in the present application is a newly identified member of the reticulocalbin family and possesses the ability to bind calcium typical of the reticulocalbin family.
36. Full-length PRQ294 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0294. In particular, Applicants have identified and isolated cDNA encoding a PR0294 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0294 polypeptide have significant homology with the various portions of a number of collagen proteins. Accordingly, it is presently believed that PR0294 polypeptide disclosed in the present application is a newly identified member of the collagen family.
37. Full-length PRQ295 Polypeptides The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0295. In particular, Applicants have identified and isolated cDNA encoding a PR0295 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0295 polypeptide have significant homology with integrin proteins. Accordingly, it is presently believed that PR0295 polypeptide disclosed in the present application is a newly identified member of the integrin family and possesses cell adhesion typical of the integrin family.
38. Full-length PRQ293 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0293. In particular, Applicants have identified and isolated cDNA encoding a PR0293 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that portions of the PR0293 polypeptide have significant homology with the neuronal leucine rich repeat proteins 1 and 2, (NLRR-1 and NLRR-2), particularly NLRR-2. Accordingly, it is presently believed that PR0293 polypeptide disclosed in the present application is a newly identified member of the neuronal leucine rich repeat protein family and possesses ligand-ligand binding activity typical of the NRLL protein family.
39. Full-length PRQ247 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0247. In particular, Applicants have identified and isolated cDNA encoding a PR0247 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0247 polypeptide have significant homology with densin. Applicants have also found that the DNA encoding the PR0247 polypeptide has significant homology with a number of other proteins, including KIAA0231. Accordingly, it is presently believed that PR0247 polypeptide disclosed in the present application is a newly identified member of the leucine rich repeat family and possesses ligand binding abilities typical of this family.
40. Full-length PRO302. PRO303. PRO304. PRO307 and PRQ343 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO302, PRO303, PRO304, PRO307 and PR0343. In particular, Applicants have identified and isolated cDNA encoding PRO302, PRO303, PRO304, PRO307 and PR0343 polypeptides, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PRO302, PRO303, PRO304, PRO307 and PR0343 polypeptides have significant homology with various protease proteins. Accordingly, it is presently believed that the PRO302, PRO303, PRO304, PRO307 and PR0343 polypeptides disclosed in the present application are newly identified protease proteins.
41. Full-length PRQ328 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0328. In particular, Applicants have identified and isolated cDNA encoding a PR0328 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0328 polypeptide have significant homology with the human glioblastoma protein ("GLIP"). Further, Applicants found that various portions of the PR0328 polypeptide have significant homology with the cysteine rich secretory protein ("CRISP") as identified by BLAST homology [ECCRISP3 1, S68683, and CRS3 HUMAN]. Accordingly, it is presently believed that PR0328 polypeptide disclosed in the present application is a newly identified member of the GLIP or CRISP families and possesses transcriptional regulatory activity typical of the GLIP or CRISP families. 42. Full-length PRQ335. PRQ331 and PRQ326 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0335, PR0331 or PR0326. In particular, Applicants have identified and isolated cDNA encoding a PR0335, PR0331 or PR0326 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0335, PR0331 or PR0326 polypeptide have significant homology with LIG-1, ALS and in the case of PR0331, additionally, decorin. Accordingly, it is presently believed that the PR0335, PR0331 and PR0326 polypeptides disclosed in the present application are newly identified members of the leucine rich repeat superfamily, and particularly, are related to LIG-1 and possess the biological functions of this family as discussed and referenced herein.
43. Full-length PRQ332 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0332. In particular, Applicants have identified and isolated cDNA encoding PR0332 polypeptides, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that a full-length native sequence PR0332 (shown in Figure 108 and SEQ ID NO:310) has about 30-40% amino acid sequence identity with a series of known proteoglycan sequences, including, for example, fibromodulin and fibromodulin precursor sequences of various species (FMOD_BOVIN, FMOD_CHICK, FMOD_RAT, FMOD_MOUSE, FMOD.HUMAN, P_R36773), osteomodulin sequences (AB000114_1, AB007848 ), decorin sequences (CFU83141_1, OCU03394 , P R42266, P R42267, P.R42260, P R89439), keratan sulfate proteoglycans (BTU48360.1 , AF022890.1), corneal proteoglycan (AF022256_1), and bone/cartilage proteoglycans and proteoglycane precursors (PGSl_BOVIN, PGS2. MOUSE, PGS2_HUMAN). Accordingly, it is presently believed that PR0332 disclosed in the present application is a new proteoglycan-type molecule, and may play a role in regulating extracellular matrix, cartilage, and/or bone function.
44. Full-length PRQ334 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0334. In particular, Applicants have identified and isolated cDNA encoding a PR0334 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0334 polypeptide have significant homology with fibulin and fibrillin. Accordingly, it is presently believed that PR0334 polypeptide disclosed in the present application is a newly identified member of the epidermal growth factor family and possesses properties and activities typical of this family.
45. Full-length PRQ346 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0346. In particular, Applicants have identified and isolated cDNA encoding a PR0346 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that a full-length native sequence PR0346 (shown in Figure 112 and SEQ ID NO: 320) has 28 % amino acid sequence identity with carcinoembryonic antigen. Accordingly, it is presently believed that PR0346 disclosed in the present application is a newly identified member of the carcinoembryonic protein family and may be expressed in association with neoplastic tissue disorders.
46. Full-length PRQ268 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0268. In particular, Applicants have identified and isolated cDNA encoding a PR0268 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that portions of the PR0268 polypeptide have significant homology with the various protein disulfide isomerase proteins. Accordingly, it is presently believed that PR0268 polypeptide disclosed in the present application is a homolog of the protein disulfide isomerase ρ5 protein.
47. Full-length PRO330 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO330. In particular, Applicants have identified and isolated cDNA encoding a PRO330 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PRO330 polypeptide have significant homology with the murine prolyl 4-hydroxylase alpha-II subunit protein. Accordingly, it is presently believed that PRO330 polypeptide disclosed in the present application is a novel prolyl 4-hydroxylase subunit polypeptide.
48. Full-length PRQ339 and PRO310 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PR0339 and PRO310. In particular, Applicants have identified and isolated cDNA encoding a PR0339 polypeptide, as disclosed in further detail in the Examples below. Applicants have also identified and isolated cDNA encoding a PRO310 polypeptide, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that various portions of the PR0339 and PRO310 polypeptides have significant homology with small secreted proteins from C. elegans and are distantly related to fringe. PR0339 also shows homology to collagen-like polymers. Sequences which were used to identify PRO310, designated herein as DNA40533 and DNA42267, also show homology to proteins from C. elegans. Accordingly, it is presently believed that the PR0339 and PR0310 polypeptides disclosed in the present application are newly identified member of the family of proteins involved in development, and which may have regulatory abilities similar to the capability of fringe to regulate serrate. 49. Full Length PR0244 Polypeptides
The present invention provides newly identified and isolated nucleotide sequences encoding C-type lectins referred to in the present application as PR0244. In particular, applicants have identified and isolated cDNA encoding PR0244 polypeptides, as disclosed in further detail in the Examples below. Using BLAST and FastA sequence alignment computer programs, Applicants found that a full-length native sequence PR0244 (shown in Figure 122 and SEQ ID NO:377) has 43 % amino acid sequence identity with the hepatic lectin gallus gallus (LECH-CHICK), and 42% amino acid sequence identity with an HIV gpl20 binding C-type lectin (A46274). Accordingly, it is presently believed that PR0244 disclosed in the present application is a newly identified member of the C-lectin superfamily and may play a role in immune function, apoptosis, or in the pathogenesis of atherosclerosis. In addition, PR0244 may be useful in identifying tumor-associated epitopes.
B. PRO Polypeptide Variants
In addition to the full-length native sequence PRO polypeptides described herein, it is contemplated that PRO variants can be prepared. PRO variants can be prepared by introducing appropriate nucleotide changes into the PRO DNA, and/or by synthesis of the desired PRO polypeptide. Those skilled in the art will appreciate that amino acid changes may alter post-translational processes of the PRO, such as changing the number or position of glycosylation sites or altering the membrane anchoring characteristics.
Variations in the native full-length sequence PRO or in various domains of the PRO described herein, can be made, for example, using any of the techniques and guidelines for conservative and non-conservative mutations set forth, for instance, in U.S. Patent No. 5,364,934. Variations may be a substitution, deletion or insertion of one or more codons encoding the PRO that results in a change in the amino acid sequence of the PRO as compared with the native sequence PRO. Optionally the variation is by substitution of at least one amino acid with any other amino acid in one or more of the domains of the PRO. Guidance in determining which amino acid residue may be inserted, substituted or deleted without adversely affecting the desired activity may be found by comparing the sequence of the PRO with that of homologous known protein molecules and minimizing the number of amino acid sequence changes made in regions of high homology. Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements. Insertions or deletions may optionally be in the range of about 1 to 5 amino acids. The variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting variants for activity exhibited by the full-length or mature native sequence.
PRO polypeptide fragments are provided herein. Such fragments may be truncated at the N-terminus or C-terminus, or may lack internal residues, for example, when compared with a full length native protein.
Certain fragments lack amino acid residues that are not essential for a desired biological activity of the PRO polypeptide. PRO fragments may be prepared by any of a number of conventional techniques. Desired peptide fragments may be chemically synthesized. An alternative approach involves generating PRO fragments by enzymatic digestion, e.g., by treating the protein with an enzyme known to cleave proteins at sites defined by particular amino acid residues, or by digesting the DNA with suitable restriction enzymes and isolating the desired fragment. Yet another suitable technique involves isolating and amplifying a DNA fragment encoding a desired polypeptide fragment, by polymerase chain reaction (PCR). Oligonucleotides that define the desired termini of the DNA fragment are employed at the 5' and 3' primers in the PCR. Preferably, PRO polypeptide fragments share at least one biological and/or immunological activity with the native PRO polypeptide disclosed herein.
In particular embodiments, conservative substitutions of interest are shown in Table 6 under the heading of preferred substitutions. If such substitutions result in a change in biological activity, then more substantial changes, denominated exemplary substitutions in Table 6, or as further described below in reference to amino acid classes, are introduced and the products screened.
Table 6
Original Exemplary Preferred
Residue Substimtions Substimtions
Ala (A) val; leu; ile val
Arg (R) lys; gin; asn lys
Asn (N) gin; his; lys; arg gin
Asp (D) glu glu
Cys (C) ser ser
Gin (Q) asn asn
Glu (E) asp asp
Gly (G) pro; ala ala
His (H) asn; gin; lys; arg arg
He (I) leu; val; met; ala; phe; norleucine leu
Leu (L) norleucine; ile; val; met; ala; phe ile
Lys (K) arg; gin; asn arg
Met (M) leu; phe; ile leu
Phe (F) leu; val; ile; ala; tyr leu
Pro (P) ala ala
Ser (S) thr thr
Thr (T) ser ser
Trp (W) tyr; phe tyr
Tyr (Y) tip; phe; thr; ser phe
Val (V) ile; leu; met; phe; ala; norleucine leu
Substantial modifications in function or immunological identity of the PRO polypeptide are accomplished by selecting substimtions that differ significantly in their effect on maintaining (a) the strucmre of the polypeptide backbone in the area of the substimtion, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. Naturally occurring residues are divided into groups based on common side-chain properties:
(1) hydrophobic: norleucine, met, ala, val, leu, ile; (2) neutral hydrophilic: cys, ser, thr;
(3) acidic: asp, glu;
(4) basic: asn, gin, his, lys, arg;
(5) residues that influence chain orientation: gly, pro; and
(6) aromatic: trp, tyr, phe. Non-conservative substitutions will entail exchanging a member of one of these classes for another class .
Such substituted residues also may be introduced into the conservative substitution sites or, more preferably, into the remaining (non-conserved) sites.
The variations can be made using methods known in the art such as oligonucleotide-mediated (site- directed) mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis [Carter et al., Nucl. Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res.. 10:6487 (1987)], cassette mutagenesis [Wells et al., Gene. 34:315 (1985)], restriction selection mutagenesis [Wells et al., Philos. Trans. R. Soc. London Ser A. 317:415 (1986)] or other known techniques can be performed on the cloned DNA to produce the PRO variant DNA.
Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main- chain conformation of the variant [Cunningham and Wells, Science. 244: 1081-1085 (1989)]. Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions [Creighton, The Proteins. (W.H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol.. 150: 1 ( 1976)] . If alanine substimtion does not yield adequate amounts of variant, an isoteric amino acid can be used.
C. Modifications of PRO
Covalent modifications of PRO are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a PRO polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C- terminal residues of the PRO. Derivatization with bifunctional agents is useful, for instance, for crosslinking PRO to a water-insoluble support matrix or surface for use in the method for purifying anti-PRO antibodies, and vice-versa. Commonly used crosslinking agents include, e.g., l, l-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3'-dithiobis(succinimidylproρionate), bifunctional maleimides such as bis-N-maleimido-1,8- octane and agents such as methyl-3-[(ρ-azidophenyl)dithio]propioimidate. Other modifications include deamidation of glutaminyl and asparaginyl residues to the corresponding glutamyl and aspartyl residues, respectively, hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the α-amino groups of lysine, arginine, and histidine side chains [T.E. Creighton, Proteins: Strucmre and Molecular Properties. W.H. Freeman & Co., San Francisco, pp. 79-86 (1983)], acetylation of the N-terminal amine, and amidation of any C-terminal carboxyl group. Another type of covalent modification of the PRO polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of the polypeptide. "Altering the native glycosylation pattern" is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence PRO (either by removing the underlying glycosylation site or by deleting the glycosylation by chemical and/or enzymatic means), and/or adding one or more glycosylation sites that are not present in the native sequence PRO. In addition, the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present.
Addition of glycosylation sites to the PRO polypeptide may be accomplished by altering the amino acid sequence. The alteration may be made, for example, by the addition of, or substitution by, one or more serine or threonine residues to the native sequence PRO (for O-linked glycosylation sites). The PRO amino acid sequence may optionally be altered through changes at the DNA level, particularly by mutating the DNA encoding the PRO polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids. Another means of increasing the number of carbohydrate moieties on the PRO polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Such methods are described in the art, e.g., in WO 87/05330 published 11 September 1987, and in Aplin and Wriston, CRC Crit. Rev. Biochem.. pp. 259- 306 (1981).
Removal of carbohydrate moieties present on the PRO polypeptide may be accomplished chemically or enzymatically or by mutational substimtion of codons encoding for amino acid residues that serve as targets for glycosylation. Chemical deglycosylation techniques are known in the art and described, for instance, by Hakimuddin, et al., Arch. Biochem. Biophys.. 259:52 (1987) and by Edge et al., Anal. Biochem.. 118: 131 (1981). Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of endo- and exo-glycosidases as described by Thotakura et al., Meth. EnzvmoL. 138:350 (1987). Another type of covalent modification of PRO comprises linking the PRO polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Patent Nos. 4,640,835; 4,496,689; 4,301, 144; 4,670,417; 4,791, 192 or 4, 179,337.
The PRO of the present invention may also be modified in a way to form a chimeric molecule comprising PRO fused to another, heterologous polypeptide or amino acid sequence. In one embodiment, such a chimeric molecule comprises a fusion of the PRO with a tag polypeptide which provides an epitope to which an anti-tag antibody can selectively bind. The epitope tag is generally placed at the amino- or carboxyl- terminus of the PRO. The presence of such epitope-tagged forms of the PRO can be detected using an antibody against the tag polypeptide. Also, provision of the epitope tag enables the PRO to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag. Various tag polypeptides and their respective antibodies are well known in the art. Examples include poly-histidine (poly-his) or poly-histidine-glycine (poly-his-gly) tags; the flu HA tag polypeptide and its antibody 12CA5 [Field et al., Mol. Cell. Biol.. 8:2159-2165 (1988)]; the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto [Evan et al., Molecular and Cellular Biology. 5:3610-3616 (1985)]; and the Herpes Simplex virus glycoprotein D (gD) tag and its antibody [Paborsky et al.. Protein Engineering. 3(6):547- 553 (1990)]. Other tag polypeptides include the Flag-peptide [Hopp et al., BioTechnology. 6: 1204-1210 (1988)]; the KT3 epitope peptide [Martin et al., Science. 255:192-194 (1992)]; an α-tubulin epitope peptide [Skinner et al., J. Biol. Chem.. 266:15163-15166 (1991)]; and the T7 gene 10 protein peptide tag [Lutz- Freyermuth et al., Proc. Natl. Acad. Sci. USA. 87:6393-6397 (1990)].
In an alternative embodiment, the chimeric molecule may comprise a fusion of the PRO with an immunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule (also referred to as an "immunoadhesin"), such a fusion could be to the Fc region of an IgG molecule. The Ig fusions preferably include the substimtion of a soluble (transmembrane domain deleted or inactivated) form of a PRO polypeptide in place of at least one variable region within an Ig molecule. In a particularly preferred embodiment, the immunoglobulin fusion includes the hinge, CH2 and CH3, or the hinge, CHI, CH2 and CH3 regions of an IgGl molecule. For the production of immunoglobulin fusions see also US Patent No. 5,428,130 issued June 27, 1995. D. Preparation of PRO
The description below relates primarily to production of PRO by culturing cells transformed or transfected with a vector containing PRO nucleic acid. It is, of course, contemplated that alternative methods, which are well known in the art, may be employed to prepare PRO. For instance, the PRO sequence, or portions thereof, may be produced by direct peptide synthesis using solid-phase techniques [see, e.g., Stewart et al.. Solid-Phase Peptide Synthesis. W.H. Freeman Co., San Francisco, CA (1969); Merrifield. J. Am. Chem.
Soc, 85:2149-2154 (1963)]. In vitro protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be accomplished, for instance, using an Applied Biosystems Peptide
Synthesizer (Foster City, CA) using manufacturer's instructions. Various portions of the PRO may be chemically synthesized separately and combined using chemical or enzymatic methods to produce the full-length PRO.
1. Isolation of DNA Encoding PRO
DNA encoding PRO may be obtained from a cDNA library prepared from tissue believed to possess the PRO mRNA and to express it at a detectable level. Accordingly, human PRO DNA can be conveniently obtained from a cDNA library prepared from human tissue, such as described in the Examples. The PRO- encoding gene may also be obtained from a genomic library or by known synthetic procedures (e.g. , automated nucleic acid synthesis).
Libraries can be screened with probes (such as antibodies to the PRO or oligonucleotides of at least about 20-80 bases) designed to identify the gene of interest or the protein encoded by it. Screening the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in
Sambrooket al.. Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press,
1989). An alternative means to isolate the gene encoding PRO is to use PCR methodology [Sambrook et al., supra: Dieffenbach et al., PCR Primer: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995)].
The Examples below describe techniques for screening a cDNA library. The oligonucleotide sequences selected as probes should be of sufficient length and sufficiently unambiguous that false positives are minimized. The oligonucleotide is preferably labeled such that it can be detected upon hybridization to DNA in the library being screened. Methods of labeling are well known in the art, and include the use of radiolabels like 32P-labeled ATP, biotinylation or enzyme labeling. Hybridization conditions, including moderate stringency and high stringency, are provided in Sambrook et al., supra. Sequences identified in such library screening methods can be compared and aligned to other known sequences deposited and available in public databases such as GenBank or other private sequence databases. Sequence identity (at either the amino acid or nucleotide level) within defined regions of the molecule or across the full-length sequence can be determined using methods known in the art and as described herein.
Nucleic acid having protein coding sequence may be obtained by screening selected cDNA or genomic libraries using the deduced amino acid sequence disclosed herein for the first time, and, if necessary, using conventional primer extension procedures as described in Sambrook et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA. 2. Selection and Transformation of Host Cells
Host cells are transfected or transformed with expression or cloning vectors described herein for PRO production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences. The culture conditions, such as media, temperature, pH and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in Mammalian Cell Biotechnology: a Practical Approach. M. Butler, ed. (IRL Press, 1991) and Sambrooket al., supra.
Methods of eukaryotic cell transfection and prokaryotic cell transformation are known to the ordinarily skilled artisan, for example, CaCl2, CaP04, liposome-mediated and electroporation. Depending on the host cell used, transformation is performed using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride, as described in Sambrook et al., supra, or electroporation is generally used for prokaryotes. Infection with Agrobacterium tumefaciens is used for transformation of certain plant cells, as described by Shaw et al. , Gene. 23:315 (1983) and WO 89/05859 published 29 June 1989. For mammalian cells without such cell walls, the calcium phosphate precipitation method of Graham and van der Eb, Virology. 52:456-457 (1978) can be employed. General aspects of mammalian cell host system transfections have been described in U.S. Patent No. 4,399,216. Transformations into yeast are typically carried out according to the method of Van Solingen et al., J. Bact..130:946 (1977) and Hsiao et al., Proc. Natl. Acad. Sci. (USA). 76:3829 (1979). However, other methods for introducing DNA into cells, such as by nuclear microinjection, electroporation, bacterial protoplast fusion with intact cells, or polycations, e.g. , polybrene, polyorni thine, may also be used. For various techniques for transforming mammalian cells, see Keown et al., Methods in Enzymology. 185:527-537 (1990) and Mansour et al., Nature, 336:348-352 (1988).
Suitable host cells for cloning or expressing the DNA in the vectors herein include prokaryote, yeast, or higher eukaryote cells. Suitable prokaryotes include but are not limited to eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as E. coli. Various E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC 31,446); E. coli X1776 (ATCC 31,537); E. coli strain W3110 (ATCC 27,325) and K5 772 (ATCC 53,635). Other suitable prokaryotic host cells include Enterobacteriaceae such as Escherichia, e.g., E. coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e.g., Salmonella typhimurium, Serratia, e.g., Serratia marcescans, and Shigella, as well as Bacilli such as B. subtilis and B. licheniformis (e.g., B. licheniformis 41P disclosed in DD 266,710 published 12 April 1989), Pseudomonas such as P. aeruginosa, and Streptomyces . These examples are illustrative rather than limiting. Strain W3110 is one particularly preferred host or parent host because it is a common host strain for recombinant DNA product fermentations. Preferably, the host cell secretes minimal amounts of proteolytic enzymes. For example, strain W3110 may be modified to effect a genetic mutation in the genes encoding proteins endogenous to the host, with examples of such hosts including E. coli W3110 strain 1A2, which has the complete genotype tonA ; E. coli W3110 strain 9E4, which has the complete genotype tonA ptr3; E. coli W3110 strain 27C7 (ATCC 55,244), which has the complete genotype tonA ptr3 phoA El 5 (argF-lac)I69 degP ompTkanr; E. coli W3110 strain 37D6, which has the complete genotype tonA ptr3 phoA El 5 (argF-lac)169 degP ompT rbs7 ilvG kanr; E. coli W3110 strain 40B4, which is strain 37D6 with a non-kanamycin resistant degP deletion mutation; and an£. coli strain having mutant periplasmic protease disclosed in U.S. Patent No.4,946,783 issued 7 August 1990. Alternatively, in vitro methods of cloning, e.g., PCR or other nucleic acid polymerase reactions, are suitable.
In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for PRO-encoding vectors. Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism. Others include Schizosaccharomyces pombe (Beach and Nurse, Nature. 290: 140 [1981]; EP 139,383 published 2 May 1985); Kluyveromyces hosts (U.S. Patent No. 4,943,529; Fleer et al., Bio/Technology. 9:968-975 (1991)) such as, e.g., K. lactis (MW98-8C, CBS683, CBS4574; Louvencourt et al.. J. Bacteriol..737 [1983]), K.fragilis (ATCC 12,424), K. bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178), K. waltii (ATCC 56,500), K. drosophilarum (ATCC 36,906; Van den Berg et al., Bio/Technology. 8:135 (1990)), K. thermotolerans, and K. marxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070; Sreekrishna et al., J. Basic MicrobioL. 28:265-278 [1988]); Candida; Trichoderma reesia (EP 244,234); Neurospora crassa (Case et al., Proc. Natl. Acad. Sci. USA. 76:5259-5263 [1979]); Schwanniomyces such as Schwanniomyces occidentalis (EP 394,538 published 31 October 1990); and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium (WO 91/00357 published lOJanuary 1991), and Aspergillus hosts such as A. nidulans (Ballance et al., Biochem. Biophys. Res. Comrnun.. 112:284-289 [1983]; Tilburn et al., Gene. 26:205-221 [1983]; Yelton et al., Proc. Natl. Acad. Sci. USA. 81: 1470-1474 [1984]) and . niger (Kelly and Hynes, EMBO J.. 4:475-479 [1985]). Methylotropic yeasts are suitable herein and include, but are not limited to, yeast capable of growth on methanol selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula. A list of specific species that are exemplary of this class of yeasts may be found in C. Anthony, The Biochemistry of Methylotrophs. 269 (1982).
Suitable host cells for the expression of glycosylated PRO are derived from multicellular organisms. Examples of invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells. Examples of useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al., L Gen Virol .. 36:59 (1977)); Chinese hamster ovary cells/-DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci. USA. 77:4216 (1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod.. 23:243-251 (1980)); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); and mouse mammary mmor (MMT 060562, ATCC CCL51). The selection of the appropriate host cell is deemed to be within the skill in the art.
3. Selection and Use of a Replicable Vector
The nucleic acid (e.g. , cDNA or genomic DNA) encoding PRO may be inserted into a replicable vector for cloning (amplification of the DNA) or for expression. Various vectors are publicly available. The vector may, for example, be in the form of a plasmid, cosmid, viral particle, or phage. The appropriate nucleic acid sequence may be inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site(s) using techniques known in the art. Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniques which are known to the skilled artisan.
The PRO may be produced recombinantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide, which may be a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide. In general, the signal sequence may be a component of the vector, or it may be a part of the PRO-encoding DNA that is inserted into the vector. The signal sequence may be a prokaryotic signal sequence selected, for example, from the group of the alkaline phosphatase, penicillinase, lpp, or heat-stable enterotoxin II leaders. For yeast secretion the signal sequence may be, e.g., the yeast invertase leader, alpha factor leader (including Saccharomyces and Kluyveromyces α-factor leaders, the latter described in U.S. Patent No. 5,010, 182), or acid phosphatase leader, the C. albicans glucoamylase leader (EP 362, 179 published 4 April 1990), or the signal described in WO 90/13646 published 15 November 1990. In mammalian cell expression, mammalian signal sequences may be used to direct secretion of the protein, such as signal sequences from secreted polypeptides of the same or related species, as well as viral secretory leaders.
Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses. The origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2μ plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells.
Expression and cloning vectors will typically contain a selection gene, also termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli. An example of suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the PRO-encoding nucleic acid, such as DHFR or thymidine kinase. An appropriate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described by Urlaub et al . , Proc. Natl. Acad. Sci. USA. 77:4216 (1980) . A suitable selection gene for use in yeast is the trpl gene present in the yeast plasmid YRp7 [Stinchcomb et al., Nature. 282:39 (1979); Kingsman et al., Gene. 7: 141 (1979); Tschemper et al., Gene. 10: 157 (1980)]. The trpl gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1 [Jones, Genetics. 85: 12 (1977)].
Expression and cloning vectors usually contain a promoter operably linked to the PRO-encoding nucleic acid sequence to direct mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the β-lactamase and lactose promoter systems [Chang et al., Nature. 275:615 (1978); Goeddel et al. , Nature. 281:544 (1979)], alkaline phosphatase, a tryptophan (trp) promoter system [Goeddel, Nucleic Acids Res.. 8:4057 (1980); EP 36,776], and hybrid promoters such as the tac promoter [deBoer et al., Proc. Natl. Acad. Sci. USA. 80:21-25 (1983)]. Promoters for use in bacterial systems also will contain a Shine-Dalgarno (S.D.) sequence operably linked to the DNA encoding PRO.
Examples of suitable promoting sequences for use with yeast hosts include the promoters for 3- phosphoglycerate kinase [Hitzeman et al., J. Biol. Chem.. 255:2073 (1980)] or other glycolytic enzymes [Hess et al., J. Adv. Enzyme Reg.. 7: 149 (1968); Holland, Biochemistry. 17:4900 (1978)], such as enolase, glyceraldehyde-3 -phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose- 6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase.
Other yeast promoters, which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3- phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73,657.
PRO transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published 5 July 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, and from heat-shock promoters, provided such promoters are compatible with the host cell systems. Transcription of a DNA encoding the PRO by higher eukaryotes may be increased by inserting an enhancer sequence into the vector. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription. Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, α-fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. The enhancer may be spliced into the vector at a position 5' or 3' to the PRO coding sequence, but is preferably located at a site 5' from the promoter.
Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant, animal, human, or nucleated cells from other multicellular organisms) will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding PRO.
Still other methods, vectors, and host cells suitable for adaptation to the synthesis of PRO in recombinant vertebrate cell culture are described in Gething et al., Nature. 293:620-625 (1981); Mantei et al., Nature, 281:40-46 (1979); EP 117,060; and EP 117,058. 4. Detecting Gene Amplification/Expression
Gene amplification and/or expression may be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA [Thomas, Proc. Natl. Acad. Sci. USA. 77:5201-5205 (1980)], dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn may be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.
Gene expression, alternatively, may be measured by immunological methods, such as immunohistochemical staining of cells or tissue sections and assay of cell culture or body fluids, to quantitate directly the expression of gene product. Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native sequence PRO polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence fused to PRO DNA and encoding a specific antibody epitope.
5. Purification of Polypeptide
Forms of PRO may be recovered from culture medium or from host cell lysates. If membrane-bound, it can be released from the membrane using a suitable detergent solution (e.g. Triton-X 100) or by enzymatic cleavage. Cells employed in expression of PRO can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or cell lysing agents.
It may be desired to purify PRO from recombinant cell proteins or polypeptides. The following procedures are exemplary of suitable purification procedures: by fractionation on an ion-exchange column; ethanol precipitation; reverse phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration using, for example, Sephadex G-75; protein A Sepharose columns to remove contaminants such as IgG; and metal chelating columns to bind epitope-tagged forms of the PRO. Various methods of protein purification may be employed and such methods are known in the art and described for example in Deutscher, Methods in Enzymology. 182 (1990); Scopes, Protein Purification: Principles and Practice. Springer- Verlag, New York (1982). The purification steρ(s) selected will depend, for example, on the namre of the production process used and the particular PRO produced.
E. Uses for PRO Nucleotide sequences (or their complement) encoding PRO have various applications in the art of molecular biology, including uses as hybridization probes, in chromosome and gene mapping and in the generation of anti-sense RNA and DNA. PRO nucleic acid will also be useful for the preparation of PRO polypeptides by the recombinant techniques described herein. The full-length native sequence PRO gene, or portions thereof, may be used as hybridization probes for a cDNA library to isolate the full-length PRO cDNA or to isolate still other cDNAs (for instance, those encoding naturally-occurring variants of PRO or PRO from other species) which have a desired sequence identity to the native PRO sequence disclosed herein. Optionally, the length of the probes will be about 20 to about 50 bases. The hybridization probes may be derived from at least partially novel regions of the full length native nucleotide sequence wherein those regions may be determined without undue experimentation or from genomic sequences including promoters, enhancer elements and introns of native sequence PRO. By way of example, a screening method will comprise isolating the coding region of the PRO gene using the known DNA sequence to synthesize a selected probe of about 40 bases. Hybridization probes may be labeled by a variety of labels, including radionucleotides such as 32P or 35S, or enzymatic labels such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems. Labeled probes having a sequence complementary to that of the PRO gene of the present invention can be used to screen libraries of human cDNA, genomic DNA or mRNA to determine which members of such libraries the probe hybridizes to. Hybridization techniques are described in further detail in the Examples below.
Any EST sequences disclosed in the present application may similarly be employed as probes, using the methods disclosed herein.
Other useful fragments of the PRO nucleic acids include antisense or sense oligonucleotides comprising a singe-stranded nucleic acid sequence (either RNA or DNA) capable of binding to target PRO mRNA (sense) or PRO DNA (antisense) sequences. Antisense or sense oligonucleotides, according to the present invention, comprise a fragment of the coding region of PRO DNA. Such a fragment generally comprises at least about 14 nucleotides, preferably from about 14 to 30 nucleotides. The ability to derive an antisense or a sense oligonucleotide, based upon a cDNA sequence encoding a given protein is described in, for example, Stein and Cohen (Cancer Res. 48:2659, 1988) and van der Krol et al. (BioTechniques 6:958, 1988).
Binding of antisense or sense oligonucleotides to target nucleic acid sequences results in the formation of duplexes that block transcription or translation of the target sequence by one of several means, including enhanced degradation of the duplexes, premature termination of transcription or translation, or by other means. The antisense oligonucleotides thus may be used to block expression of PRO proteins. Antisense or sense oligonucleotides further comprise oligonucleotides having modified sugar-phosphodiester backbones (or other sugar linkages, such as those described in WO 91/06629) and wherein such sugar linkages are resistant to endogenous nucleases. Such oligonucleotides with resistant sugar linkages are stable in vivo (i.e., capable of resisting enzymatic degradation) but retain sequence specificity to be able to bind to target nucleotide sequences.
Other examples of sense or antisense oligonucleotides include those oligonucleotides which are covalently linked to organic moieties, such as those described in WO 90/10048, and other moieties that increases affinity of the oligonucleotide for a target nucleic acid sequence, such as poly-(L-lysine). Further still, intercalating agents, such as ellipticine, and alkylating agents or metal complexes may be attached to sense or antisense oligonucleotides to modify binding specificities of the antisense or sense oligonucleotide for the target nucleotide sequence. Antisense or sense oligonucleotides may be introduced into a cell containing the target nucleic acid sequence by any gene transfer method, including, for example, CaP04-mediated DNA transfection, electroporation, or by using gene transfer vectors such as Epstein-Barr virus. In a preferred procedure, an antisense or sense oligonucleotide is inserted into a suitable retroviral vector. A cell containing the target nucleic acid sequence is contacted with the recombinant retroviral vector, either in vivo or ex vivo. Suitable retroviral vectors include, but are not limited to, those derived from the murine retrovirus M-MuLV, N2 (a retrovirus derived from M-MuLV), or the double copy vectors designated DCT5A, DCT5B and DCT5C (see WO 90/13641).
Sense or antisense oligonucleotides also may be introduced into a cell containing the target nucleotide sequence by formation of a conjugate with a ligand binding molecule, as described in WO 91/04753. Suitable ligand binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to cell surface receptors. Preferably, conjugation of the ligand binding molecule does not substantially interfere with the ability of the ligand binding molecule to bind to its corresponding molecule or receptor, or block entry of the sense or antisense oligonucleotide or its conjugated version into the cell.
Alternatively, a sense or an antisense oligonucleotide may be introduced into a cell containing the target nucleic acid sequence by formation of an oligonucleotide-lipid complex, as described in WO 90/10448. The sense or antisense oligonucleotide-lipid complex is preferably dissociated within the cell by an endogenous lipase.
Antisense RNA or DNA molecules are generally at least about 5 bases in length, about 10 bases in length, about 15 bases in length, about 20 bases in length, about 25 bases in length, about 30 bases in length, about 35 bases in length, about 40 bases in length, about 45 bases in length, about 50 bases in length, about 55 bases in length, about 60 bases in length, about 65 bases in length, about 70 bases in length, about 75 bases in length, about 80 bases in length, about 85 bases in length, about 90 bases in length, about 95 bases in length, about 100 bases in length, or more.
The probes may also be employed in PCR techniques to generate a pool of sequences for identification of closely related PRO coding sequences. Nucleotide sequences encoding a PRO can also be used to construct hybridization probes for mapping the gene which encodes that PRO and for the genetic analysis of individuals with genetic disorders. The nucleotide sequences provided herein may be mapped to a chromosome and specific regions of a chromosome using known techniques, such as in situ hybridization, linkage analysis against known chromosomal markers, and hybridization screening with libraries. When the coding sequences for PRO encode a protein which binds to another protein (example, where the PRO is a receptor), the PRO can be used in assays to identify the other proteins or molecules involved in the binding interaction. By such methods, inhibitors of the receptor/ligand binding interaction can be identified.
Proteins involved in such binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction. Also, the receptor PRO can be used to isolate correlative ligand(s). Screening assays can be designed to find lead compounds that mimic the biological activity of a native PRO or a receptor for PRO. Such screening assays will include assays amenable to high-throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates. Small molecules contemplated include synthetic organic or inorganic compounds. The assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays and cell based assays, which are well characterized in the art.
Nucleic acids which encode PRO or its modified forms can also be used to generate either transgenic animals or "knock out" animals which, in turn, are useful in the development and screening of therapeutically useful reagents. A transgenic animal (e.g., a mouse or rat) is an animal having cells that contain a transgene, which transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage. A transgene is a DNA which is integrated into the genome of a cell from which a transgenic animal develops. In one embodiment, cDNA encoding PRO can be used to clone genomic DNA encoding PRO in accordance with established techniques and the genomic sequences used to generate transgenic animals that contain cells which express DNA encoding PRO. Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Patent Nos. 4,736,866 and 4,870,009. Typically, particular cells would be targeted for PRO transgene incorporation with tissue-specific enhancers. Transgenic animals that include a copy of a transgene encoding PRO introduced into the germ line of the animal at an embryonic stage can be used to examine the effect of increased expression of DNA encoding PRO. Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression. In accordance with this facet of the invention, an animal is treated with the reagent and a reduced incidence of the pathological condition, compared to untreated animals bearing the transgene, would indicate a potential therapeutic intervention for the pathological condition. Alternatively, non-human homologues of PRO can be used to construct a PRO "knock out" animal which has a defective or altered gene encoding PRO as a result of homologous recombination between the endogenous gene encoding PRO and altered genomic DNA encoding PRO introduced into an embryonic stem cell of the animal. For example, cDNA encoding PRO can be used to clone genomic DNA encoding PRO in accordance with established techniques. A portion of the genomic DNA encoding PRO can be deleted or replaced with another gene, such as a gene encoding a selectable marker which can be used to monitor integration. Typically, several kilobases of unaltered flanking DNA (both at the 5' and 3' ends) are included in the vector [see e.g., Thomas and Capecchi, Cell. 51:503 (1987) for a description of homologous recombination vectors]. The vector is introduced into an embryonic stem cell line (e.g. , by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected [see e.g., Li et al., Cell. 69:915 (1992)]. The selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras [see e.g. , Bradley, in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152]. A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term to create a "knock out" animal. Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knockout animals can be characterized for instance, for their ability to defend against certain pathological conditions and for their development of pathological conditions due to absence of the PRO polypeptide.
Nucleic acid encoding the PRO polypeptides may also be used in gene therapy. In gene therapy applications, genes are introduced into cells in order to achieve in vivo synthesis of a therapeutically effective genetic product, for example for replacement of a defective gene. "Gene therapy" includes both conventional gene therapy where a lasting effect is achieved by a single treatment, and the administration of gene therapeutic agents, which involves the one time or repeated administration of a therapeutically effective DNA or mRNA. Antisense RNAs and DNAs can be used as therapeutic agents for blocking the expression of certain genes in vivo. It has already been shown that short antisense oligonucleotides can be imported into cells where they act as inhibitors, despite their low intracellular concentrations caused by their restricted uptake by the cell membrane. (Zamecnik et al. , Proc. Natl. Acad. Sci. USA 83:4143-4146 [1986]). The oligonucleotides can be modified to enhance their uptake, e.g. by substituting their negatively charged phosphodiester groups by uncharged groups.
There are a variety of techniques available for introducing nucleic acids into viable cells. The techniques vary depending upon whether the nucleic acid is transferred into cultured cells in vitro, or in vivo in the cells of the intended host. Techniques suitable for the transfer of nucleic acid into mammalian cells in vitro include the use of liposomes, electroporation, microiηjection, cell fusion, DEAE-dextran, the calcium phosphate precipitation method, etc. The currently preferred in vivo gene transfer techniques include transfection with viral (typically retroviral) vectors and viral coat protein-liposome mediated transfection (Dzau et al., Trends in Biotechnology 11 , 205-210 [1993]). In some situations it is desirable to provide the nucleic acid source with an agent that targets the target cells, such as an antibody specific for a cell surface membrane protein or the target cell, a ligand for a receptor on the target cell, etc. Where liposomes are employed, proteins which bind to a cell surface membrane protein associated with endocytosis may be used for targeting and/or to facilitate uptake, e.g. capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo intemalization in cycling, proteins that target intracellular localization and enhance intracellular half-life. The technique of receptor-mediated endocytosis is described, for example, by Wu et al., J. Biol. Chem. 262, 4429-4432 (1987); and Wagner et al., Proc. Natl. Acad. Sci. USA 87, 3410-3414 (1990). For review of gene marking and gene therapy protocols see Anderson et al., Science 256, 808-813 (1992).
The PRO polypeptides described herein may also be employed as molecular weight markers for protein electrophoresis purposes and the isolated nucleic acid sequences may be used for recombinantly expressing those markers. The nucleic acid molecules encoding the PRO polypeptides or fragments thereof described herein are useful for chromosome identification. In this regard, there exists an ongoing need to identify new chromosome markers, since relatively few chromosome marking reagents, based upon actual sequence data are presently available. Each PRO nucleic acid molecule of the present invention can be used as a chromosome marker.
The PRO polypeptides and nucleic acid molecules of the present invention may also be used for tissue typing, wherein the PRO polypeptides of the present invention may be differentially expressed in one tissue as compared to another. PRO nucleic acid molecules will find use for generating probes for PCR, Northern analysis, Southern analysis and Western analysis. The PRO polypeptides described herein may also be employed as therapeutic agents. The PRO polypeptides of the present invention can be formulated according to known methods to prepare pharmaceutically useful compositions, whereby the PRO product hereof is combined in admixture with a pharmaceutically acceptable carrier vehicle. Therapeutic formulations are prepared for storage by mixing the active ingredient having the desired degree of purity with optional physiologically acceptable carriers, excipients or stabilizers (Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980)), in the form of lyophilized formulations or aqueous solutions. Acceptable carriers, excipients or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone, amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN™, PLURONICS™ or PEG.
The formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes, prior to or following lyophilization and reconstitution.
Therapeutic compositions herein generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.
The route of administration is in accord with known methods, e.g. injection or infusion by intravenous, intraperitoneal, intracerebral, intramuscular, intraocular, intraarterial or intralesional routes, topical administration, or by sustained release systems.
Dosages and desired drug concentrations of pharmaceutical compositions of the present invention may vary depending on the particular use envisioned. The determination of the appropriate dosage or route of administration is well within the skill of an ordinary physician. Animal experiments provide reliable guidance for the determination of effective doses for human therapy. Interspecies scaling of effective doses can be performed following the principles laid down by Mordenti, J. and Chappell, W. "The use of interspecies scaling in toxicokinetics" In Toxicokinetics and New Drug Development, Yacobi et al., Eds., Pergamon Press, New York 1989, pp. 42-96.
When in vivo administration of a PRO polypeptide or agonist or antagonist thereof is employed, normal dosage amounts may vary from about 10 ng/kg to up to 100 mg/kg of mammal body weight or more per day, preferably about 1 μg/kg/day to 10 mg/kg/day, depending upon the route of administration. Guidance as to particular dosages and methods of delivery is provided in the literature; see, for example, U.S. Pat. Nos. 4,657,760; 5,206,344; or 5,225,212. It is anticipated that different formulations will be effective for different treatment compounds and different disorders, that administration targeting one organ or tissue, for example, may necessitate delivery in a manner different from that to another organ or tissue. Where sustained-release administration of a PRO polypeptide is desired in a formulation with release characteristics suitable for the treatment of any disease or disorder requiring administration of the PRO polypeptide, microencapsulation of the PRO polypeptide is contemplated. Microencapsulation of recombinant proteins for sustained release has been successfully performed with human growth hormone (rhGH), interferon- (rhlFN- ), interleukin-2, and MN rgpl20. Johnson et al., Nat. Med.. 2:795-799 (1996); Yasuda, Biomed. Ther. , 27: 1221-1223 (1993); Hora et al.. Bio/Technology. 8:755-758 (1990); Cleland, "Design and Production of Single Immunization Vaccines Using Polylactide Polyglycolide Microsphere Systems," in Vaccine Design: The Subunit and Adjuvant Approach. Powell and Newman, eds, (Plenum Press: New York, 1995), pp. 439-462; WO 97/03692, WO 96/40072, WO 96/07399; and U.S. Pat. No. 5,654,010.
The sustained-release formulations of these proteins were developed using poly-lactic-coglycolic acid (PLGA) polymer due to its biocompatibility and wide range of biodegradable properties. The degradation products of PLGA, lactic and glycolic acids, can be cleared quickly within the human body. Moreover, the degradability of this polymer can be adjusted from months to years depending on its molecular weight and composition. Lewis, "Controlled release of bioactive agents from lactide/glycolide polymer," in: M. Chasin and R. Langer (Eds.), Biodegradable Polymers as Drug Delivery Systems (Marcel Dekker: New York, 1990), pp. 1-41.
This invention encompasses methods of screening compounds to identify those that mimic the PRO polypeptide (agonists) or prevent the effect of the PRO polypeptide (antagonists). Screening assays for antagonist drug candidates are designed to identify compounds that bind or complex with the PRO polypeptides encoded by the genes identified herein, or otherwise interfere with the interaction of the encoded polypeptides with other cellular proteins. Such screening assays will include assays amenable to high-throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates.
The assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays, and cell-based assays, which are well characterized in the art.
All assays for antagonists are common in that they call for contacting the drug candidate with a PRO polypeptide encoded by a nucleic acid identified herein under conditions and for a time sufficient to allow these two components to interact.
In binding assays, the interaction is binding and the complex formed can be isolated or detected in the reaction mixmre . In a particular embodiment, the PRO polypeptide encoded by the gene identified herein or the drug candidate is immobilized on a solid phase, e.g., on a microtiter plate, by covalent or non-covalent attachments. Non-covalent attachment generally is accomplished by coating the solid surface with a solution of the PRO polypeptide and drying. Alternatively, an immobilized antibody, e.g. , a monoclonal antibody, specific for the PRO polypeptide to be immobilized can be used to anchor it to a solid surface. The assay is performed by adding the non-immobilized component, which may be labeled by a detectable label, to the immobilized component, e.g., the coated surface containing the anchored component. When the reaction is complete, the non-reacted components are removed, e.g., by washing, and complexes anchored on the solid surface are detected. When the originally non-immobilized component carries a detectable label, the detection of label immobilized on the surface indicates that complexing occurred. Where the originally non-immobilized component does not carry a label, complexing can be detected, for example, by using a labeled antibody specifically binding the immobilized complex. If the candidate compound interacts with but does not bind to a particular PRO polypeptide encoded by a gene identified herein, its interaction with that polypeptide can be assayed by methods well known for detecting protein-protein interactions. Such assays include traditional approaches, such as, e.g., cross-linking, co- immunoprecipitation, and co-purification through gradients or chromatographic columns. In addition, protein- protein interactions can be monitored by using a yeast-based genetic system described by Fields and co-workers (Fields and Song, Nature (London), 340:245-246 (1989); Chien et al. , Proc. Natl. Acad. Sci. USA. 88:9578- 9582 (1991)) as disclosed by Chevray and Nathans, Proc. Natl. Acad. Sci. USA. 89: 5789-5793 (1991). Many transcriptional activators, such as yeast GAL4, consist of two physically discrete modular domains, one acting as the DNA-binding domain, the other one functioning as the transcription-activation domain. The yeast expression system described in the foregoing publications (generally referred to as the "two-hybrid system") takes advantage of this property, and employs two hybrid proteins, one in which the target protein is fused to the DNA-binding domain of GAL4, and another, in which candidate activating proteins are fused to the activation domain. The expression of a GALl-ZαcZ reporter gene under control of a GAL4-activated promoter depends on reconstitution of GAL4 activity via protein-protein interaction. Colonies containing interacting polypeptides are detected with a chromogenic substrate for β-galactosidase. A complete kit (MATCHMAKER™) for identifying protein-protein interactions between two specific proteins using the two- hybrid technique is commercially available from Clontech. This system can also be extended to map protein domains involved in specific protein interactions as well as to pinpoint amino acid residues that are crucial for these interactions.
Compounds that interfere with the interaction of a gene encoding a PRO polypeptide identified herein and other intra- or extracellular components can be tested as follows: usually a reaction mixmre is prepared containing the product of the gene and the intra- or extracellular component under conditions and for a time allowing for the interaction and binding of the two products. To test the ability of a candidate compound to inhibit binding, the reaction is run in the absence and in the presence of the test compound. In addition, a placebo may be added to a third reaction mixture, to serve as positive control. The binding (complex formation) between the test compound and the intra- or extracellular component present in the mixmre is monitored as described hereinabove. The formation of a complex in the control reaction(s) but not in the reaction mixmre containing the test compound indicates that the test compound interferes with the interaction of the test compound and its reaction partner.
To assay for antagonists, the PRO polypeptide may be added to a cell along with the compound to be screened for a particular activity and the ability of the compound to inhibit the activity of interest in the presence of the PRO polypeptide indicates that the compound is an antagonist to the PRO polypeptide. Alternatively, antagonists may be detected by combining the PRO polypeptide and a potential antagonist with membrane-bound PRO polypeptide receptors or recombinant receptors under appropriate conditions for a competitive inhibition assay. The PRO polypeptide can be labeled, such as by radioactivity, such that the number of PRO polypeptide molecules bound to the receptor can be used to determine the effectiveness of the potential antagonist. The gene encoding the receptor can be identified by numerous methods known to those of skill in the art, for example, ligand panning and FACS sorting. Coligan et al., Current Protocols in Immun.. 1(2): Chapter 5 (1991). Preferably, expression cloning is employed wherein polyadenylated RNA is prepared from a cell responsive to the PRO polypeptide and a cDNA library created from this RNA is divided into pools and used to transfect COS cells or other cells that are not responsive to the PRO polypeptide. Transfected cells that are grown on glass slides are exposed to labeled PRO polypeptide. The PRO polypeptide can be labeled by a variety of means including iodination or inclusion of a recognition site for a site-specific protein kinase. Following fixation and incubation, the slides are subjected to autoradiographic analysis. Positive pools are identified and sub-pools are prepared and re-transfected using an interactive sub-pooling and re-screening process, eventually yielding a single clone that encodes the putative receptor.
As an alternative approach for receptor identification, labeled PRO polypeptide can be photoaffinity- linked with cell membrane or extract preparations that express the receptor molecule. Cross-linked material is resolved by PAGE and exposed to X-ray film. The labeled complex containing the receptor can be excised, resolved into peptide fragments, and subjected to protein micro-sequencing. The amino acid sequence obtained from micro- sequencing would be used to design a set of degenerate oligonucleotide probes to screen a cDNA library to identify the gene encoding the putative receptor.
In another assay for antagonists, mammalian cells or a membrane preparation expressing the receptor would be incubated with labeled PRO polypeptide in the presence of the candidate compound. The ability of the compound to enhance or block this interaction could then be measured.
More specific examples of potential antagonists include an oligonucleotide that binds to the fusions of immunoglobulin with PRO polypeptide, and, in particular, antibodies including, without limitation, poly- and monoclonal antibodies and antibody fragments, single-chain antibodies, anti-idiotypic antibodies, and chimeric or humanized versions of such antibodies or fragments, as well as human antibodies and antibody fragments. Alternatively, a potential antagonist may be a closely related protein, for example, a mutated form of the PRO polypeptide that recognizes the receptor but imparts no effect, thereby competitively inhibiting the action of the PRO polypeptide.
Another potential PRO polypeptide antagonist is an antisense RNA or DNA construct prepared using antisense technology, where, e.g., an antisense RNA or DNA molecule acts to block directly the translation of mRNA by hybridizing to targeted mRNA and preventing protein translation. Antisense technology can be used to control gene expression through triple-helix formation or antisense DNA or RNA, both of which methods are based on binding of a polynucleotide to DNA or RNA. For example, the 5' coding portion of the polynucleotide sequence, which encodes the mature PRO polypeptides herein, is used to design an antisense RNA oligonucleotide of from about 10 to 40 base pairs in length. A DNA oligonucleotide is designed to be complementary to a region of the gene involved in transcription (triple helix - see Lee et al., Nucl. Acids Res.. 6:3073 (1979); Cooney et al., Science. 241 : 456 (1988); Dervan et al. , Science. 251 : 1360 (1991)), thereby preventing transcription and the production of the PRO polypeptide. The antisense RNA oligonucleotide hybridizes to the mRNA in vivo and blocks translation of the mRNA molecule into the PRO polypeptide (antisense - Okano, Neurochem.. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression (CRC Press: Boca Raton, FL, 1988). The oligonucleotides described above can also be delivered to cells such that the antisense RNA or DNA may be expressed in vivo to inhibit production of the PRO polypeptide. When antisense DNA is used, oligodeoxyribonucleotides derived from the translation-initiation site, e.g., between about -10 and + 10 positions of the target gene nucleotide sequence, are preferred.
Potential antagonists include small molecules that bind to the active site, the receptor binding site, or growth factor or other relevant binding site of the PRO polypeptide, thereby blocking the normal biological activity of the PRO polypeptide. Examples of small molecules include, but are not limited to, small peptides or peptide-like molecules, preferably soluble peptides, and synthetic non-peptidyl organic or inorganic compounds.
Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA.
Ribozymes act by sequence-specific hybridization to the complementary target RNA, followed by endonucleolytic cleavage. Specific ribozyme cleavage sites within a potential RNA target can be identified by known techniques. For further details see, e.g., Rossi, Current Biology.4:469-471 (1994), and PCT publication
No. WO 97/33551 (published September 18, 1997).
Nucleic acid molecules in triple-helix formation used to inhibit transcription should be single-stranded and composed of deoxynucleotides. The base composition of these oligonucleotides is designed such that it promotes triple-helix formation via Hoogsteen base-pairing rules, which generally require sizeable stretches of purines or pyrimidines on one strand of a duplex. For further details see, e.g., PCT publication No. WO
97/33551, supra.
These small molecules can be identified by any one or more of the screening assays discussed hereinabove and/or by any other screening techniques well known for those skilled in the art.
With regard to the PR0211 and PR0217 polypeptide, therapeutic indications include disorders associated with the preservation and maintenance of gastrointestinal mucosa and the repair of acute and chronic mucosal lesions (e.g., enterocolitis, Zollinger-Ellison syndrome, gastrointestinal ulceration and congenital microvillus atrophy), skin diseases associated with abnormal keratinocyte differentiation (e.g., psoriasis, epithelial cancers such as lung squamous cell carcinoma, epidermoid carcinoma of the vulva and gliomas.
Since the PR0232 polypeptide and nucleic acid encoding it possess sequence homology to a cell surface stem cell antigen and its encoding nucleic acid, probes based upon the PR0232 nucleotide sequence may be employed to identify other novel stem cell surface antigen proteins. Soluble forms of the PR0232 polypeptide may be employed as antagonists of membrane bound PR0232 activity both in vitro and in vivo. PR0232 polypeptides may be employed in screening assays designed to identify agonists or antagonists of the native PR0232 polypeptide, wherein such assays may take the form of any conventional cell-type or biochemical binding assay. Moreover, the PR0232 polypeptide may serve as a molecular marker for the tissues in which the polypeptide is specifically expressed.
With regard to the PRO 187 polypeptides disclosed herein, FGF-8 has been implicated in cellular differentiation and embryogenesis, including the patterning which appears during limb formation. FGF-8 and the PRO 187 molecules of the invention therefore are likely to have potent effects on cell growth and development. Diseases which relate to cellular growth and differentiation are therefore suitable targets for therapeutics based on functionality similar to FGF-8. For example, diseases related to growth or survival of nerve cells including Parkinson's disease, Alzheimer's disease, ALS, neuropathies. Additionally, disease related to uncontrolled cell growth, e.g., cancer, would also be expected therapeutic targets.
With regard to the PR0265 polypeptides disclosed herein, other methods for use with PR0265 are described in U.S. Patent 5,654,270 to Ruoslahti et al. In particular, PR0265 can be used in comparison with the fibromodulin disclosed therein to compare its effects on reducing dermal scarring and other properties of the fibromodulin described therein including where it is located and with what it binds and does not. The PR0219 polypeptides of the present invention which play a regulatory role in the blood coagulation cascade may be employed in vivo for therapeutic purposes as well as for in vitro purposes. Those of ordinary skill in the art will well know how to employ PR0219 polypeptides for such uses.
The PR0246 polypeptides of the present invention which serve as cell surface receptors for one or more viruses will find other uses. For example, extracellular domains derived from these PR0246 polypeptides may be employed therapeutically in vivo for lessening the effects of viral infection. Those PR0246 polypeptides which serves as mmor specific antigens may be exploited as therapeutic targets for anti-tumor drugs, and the like. Those of ordinary skill in the art will well know how to employ PR0246 polypeptides for such uses.
Assays in which connective growth factor and other growth factors are usually used should be performed with PR0261. An assay to determine whether TGF beta induces PR0261 , indicating a role in cancer is performed as known in the art. Wound repair and tissue growth assays are also performed with PR0261. The results are applied accordingly.
PR0228 polypeptides should be used in assays in which EMRl, CD97 and latrophilin would be used in to determine their relative activities. The results can be applied accordingly. For example, a competitive binding assay with PR0228 and CD97 can be performed with the ligand for CD97, CD55. Native PR0533 is a 216 amino acid polypeptide of which residues 1-22 are the signal sequence.
Residues 3 to 216 have a Blast score of 509, corresponding to 53% homology to fibroblast growth factor. At the nucleotide level, DNA47412, the EST from which PCR oligos were generated to isolate the full length DNA49435-1219, has been observed to map to 1 lρl5. Sequence homology to the 1 lpl5 locus would indicate that PR0533 may have utility in the treatment of Usher Syndrome or Atrophia areata. As mentioned previously, fibroblast growth factors can act upon cells in both a mitogenic and non- mitogenic manner. These factors are mitogenic for a wide variety of normal diploid mesoderm-derived and neural crest-derived cells, inducing granulosa cells, adrenal cortical cells, chrondrocytes, myoblasts, corneal and vascular endothelial cells (bovine or human), vascular smooth muscle cells, lens, retina and prostatic epithelial cells, oligodendrocytes, astrocytes, chrondocytes, myoblasts and osteoblasts. Non-mitogenic actions of fibroblast growth factors include promotion of cell migration into a wound area (chemotaxis), initiation of new blood vessel formulation (angiogenesis), modulation of nerve regeneration and survival (neurotrophism), modulation of endocrine functions, and stimulation or suppression of specific cellular protein expression, extracellular matrix production and cell survival. Baird, A. & Bohlen, P. , Handbook of Exp. Phrmacol 95(1): 369-418 (1990). These properties provide a basis for using fibroblast growth factors in therapeutic approaches to accelerate wound healing, nerve repair, collateral blood vessel formation, and the like. For example, fibroblast growth factors, have been suggested to minimize myocardium damage in heart disease and surgery (U.S. P. 4,378,437). Since the PR0245 polypeptide and nucleic acid encoding it possess sequence homology to a transmembrane protein tyrosine kinase protein and its encoding nucleic acid, probes based upon the PR0245 nucleotide sequence may be employed to identify other novel transmembrane tyrosine kinase proteins. Soluble forms of the PR0245 polypeptide may be employed as antagonists of membrane bound PR0245 activity both in vitro and in vivo. PR0245 polypeptides may be employed in screening assays designed to identify agonists or antagonists of the native PR0245 polypeptide, wherein such assays may take the form of any conventional cell-type or biochemical binding assay. Moreover, the PR0245 polypeptide may serve as a molecular marker for the tissues in which the polypeptide is specifically expressed.
PRO220, PR0221 and PR0227 all have leucine rich repeats. Additionally, PRO220 and PR0221 have homology to SLIT and leucine rich repeat protein. Therefore, these proteins are useful in assays described in the literature, supra, wherein the SLIT and leucine rich repeat protein are used. Regarding the SLIT protein, PR0227 can be used in an assay to determine the affect of PR0227 on neurodegenerative disease. Additionally, PR0227 has homology to human glycoprotein V. In the case of PR0227, this polypeptide is used in an assay to determine its affect on bleeding, clotting, tissue repair and scarring.
The PR0266 polypeptide can be used in assays to determine if it has a role in neurodegenerative diseases or their reversal.
PR0269 polypeptides and portions thereof which effect the activity of thrombin may also be useful for in vivo therapeutic purposes, as well as for various in vitro applications. In addition, PR0269 polypeptides and portions thereof may have therapeutic use as an antithrombotic agent with reduced risk for hemorrhage as compared with heparin. Peptides having homology to thrombomodulin are particularly desirable. PR0287 polypeptides and portions thereof which effect the activity of bone morphogenic protein
" BMP 1 "/procollagen C-proteinase (PCP) may also be useful for in vivo therapeutic purposes, as well as for various in vitro applications. In addition, PR0287 polypeptides and portions thereof may have therapeutic applications in wound healing and tissue repair. Peptides having homology to procollagen C-proteinase enhancer protein and its precursor may also be used to induce bone and/or cartilage formation and are therefore of particular interest to the scientific and medical communities.
Therapeutic indications for PR0214 polypeptides include disorders associated with the preservation and maintenance of gastrointestinal mucosa and the repair of acute and chronic mucosal lesions (e.g., enterocolitis,
Zollinger-Ellison syndrome, gastrointestinal ulceration and congenital microvillus atrophy), skin diseases associated with abnormal keratinocyte differentiation (e.g., psoriasis, epithelial cancers such as lung squamous cell carcinoma, epidermoid carcinoma of the vulva and gliomas.
Studies on the generation and analysis of mice deficient in members of the TGF- superfamily are reported in Matzuk, Trends in Endocrinol. and MetaboL. 6: 120-127 (1995).
The PR0317 polypeptide, as well as PR0317-specific antibodies, inhibitors, agonists, receptors, or their analogs, herein are useful in treating PR0317-associated disorders. Hence, for example, they may be employed in modulating endometrial bleeding angiogenesis, and may also have an effect on kidney tissue. Endometrial bleeding can occur in gynecological diseases such as endometrial cancer as abnormal bleeding. Thus, the compositions herein may find use in diagnosing and treating abnormal bleeding conditions in the endometrium, as by reducing or eliminating the need for a hysterectomy. The molecules herein may also find use in angiogenesis applications such as anti-tumor indications for which the antibody against vascular endothelial growth factor is used, or, conversely, ischemic indications for which vascular endothelial growth factor is employed.
Bioactive compositions comprising PR0317 or agonists or antagonists thereof may be administered in a suitable therapeutic dose determined by any of several methodologies including clinical smdies on mammalian species to determine maximal tolerable dose and on normal human subjects to determine safe dose. Additionally, the bioactive agent may be complexed with a variety of well established compounds or compositions which enhance stability or pharmacological properties such as half-life. It is contemplated that the therapeutic, bioactive composition may be delivered by intravenous infusion into the bloodstream or any other effective means which could be used for treating problems of the kidney, uterus, endometrium, blood vessels, or related tissue, e.g., in the heart or genital tract.
Dosages and administration of PR0317, PR0317 agonist, or PR0317 antagonist in a pharmaceutical composition may be determined by one of ordinary skill in the art of clinical pharmacology or pharmacokinetics. See, for example, Mordenti and Rescigno, Pharmaceutical Research. 9: 17-25 (1992); Morenti et al , Pharmaceutical Research. 8: 1351-1359 (1991); and Mordenti and Chappell, "The use of interspecies scaling in toxicokinetics" in Toxicokinetics and New Drug Development. Yacobi etal. (eds) (Pergamon Press: NY, 1989), pp. 42-96. An effective amount of PR0317, PR0317 agonist, or PR0317 antagonist to be employed therapeutically will depend, for example, upon the therapeutic objectives, the route of administration, and the condition of the mammal. Accordingly, it will be necessary for the therapist to titer the dosage and modify the route of administration as required to obtain the optimal therapeutic effect. A typical daily dosage might range from about 10 ng/kg to up to 100 mg/kg of the mammal's body weight or more per day, preferably about 1 μg/kg/day to 10 mg/kg/day. Typically, the clinician will administer PR0317, PR0317 agonist, or PR0317 antagonist, until a dosage is reached that achieves the desired effect for treatment of the above mentioned disorders. PR0317 or an PR0317 agonist or PR0317 antagonist may be administered alone or in combination with another to achieve the desired pharmacological effect . PR0317 itself, or agonists or antagonists of PR0317 can provide different effects when administered therapeutically. Such compounds for treatment will be formulated in a nontoxic, inert, pharmaceutically acceptable aqueous carrier medium preferably at a pH of about 5 to 8, more preferably 6 to 8, although the pH may vary according to the characteristics of the PR0317, agonist, or antagonist being formulated and the condition to be treated. Characteristics of the treatment compounds include solubility of the molecule, half-life, and antigenicity/immunogenicity; these and other characteristics may aid in defining an effective carrier.
PR0317 or PR0317 agonists or PR0317 antagonists may be delivered by known routes of administration including but not limited to topical creams and gels; transmucosal spray and aerosol, transdermal patch and bandage; injectable, intravenous, and lavage formulations; and orally administered liquids and pills, particularly formulated to resist stomach acid and enzymes. The particular formulation, exact dosage, and route of administration will be determined by the attending physician and will vary according to each specific situation. Such determinations of administration are made by considering multiple variables such as the condition to be treated, the type of mammal to be treated, the compound to be administered, and the pharmacokinetic profile of the particular treatment compound. Additional factors which may be taken into account include disease state (e.g. severity) of the patient, age, weight, gender, diet, time of administration, drug combination, reaction sensitivities, and tolerance/response to therapy. Long-acting treatment compound formulations (such as liposomally encapsulated PR0317 or PEGylated PR0317 or PR0317 polymeric microspheres, such as polylactic acid-based microspheres) might be administered every 3 to 4 days, every week, or once every two weeks depending on half-life and clearance rate of the particular treatment compound.
Normal dosage amounts may vary from about 10 ng/kg to up to 100 mg/kg of mammal body weight or more per day, preferably about 1 μg/kg/day to 10 mg/kg/day, depending upon the route of administration. Guidance as to particular dosages and methods of delivery is provided in the literature; see, for example, U.S. Pat. Nos. 4,657,760; 5,206,344; or 5,225,212. It is anticipated that different formulations will be effective for different treatment compounds and different disorders, that administration targeting the uterus, for example, may necessitate delivery in a manner different from that to another organ or tissue, such as cardiac tissue.
Where sustained-release administration of PR0317 is desired in a formulation with release characteristics suitable for the treatment of any disease or disorder requiring administration of PR0317, microencapsulation of PR0317 is contemplated. Microencapsulation of recombinant proteins for sustained release has been successfully performed with human growth hormone (rhGH), interferon- (rhIFN- ), interleukin-2, and MN rgpl20. Johnson et al , Nat. Med.. 2: 795-799 (1996); Yasuda. Biomed. Ther.. 27: 1221-1223 (1993); Hora etal . Bio/Technology. 8: 755-758 (1990); Cleland, "Design and Production of Single Immunization Vaccines Using Polylactide Polyglycolide Microsphere Systems, " in Vaccine Design: The Subunit and Adjuvant Approach , Powell and Newman, eds, (Plenum Press: New York, 1995), pp. 439-462; WO 97/03692, WO 96/40072, WO 96/07399; and U.S Pat. No. 5,654,010.
It is contemplated that conditions or diseases of the uterus, endometrial tissue, or other genital tissues or cardiac tissues may precipitate damage that is treatable with PR0317 or PR0317 agonist where PR0317 expression is reduced in the diseased state; or with antibodies to PR0317 or other PR0317 antagonists where the expression of PR0317 is increased in the diseased state. These conditions or diseases may be specifically diagnosed by the probing tests discussed above for physiologic and pathologic problems which affect the function of the organ.
The PR0317, PR0317 agonist, or PR0317 antagonist may be administered to a mammal with another biologically active agent, either separately or in the same formulation to treat a common indication for which they are appropriate. For example, it is contemplated that PR0317 can be administered together with EBAF-1 for those indications on which they demonstrate the same qualitative biological effects . Alternatively , where they have opposite effects, EBAF-1 may be administered together with an antagonist to PR0317, such as an anti-
PR0317 antibody. Further, PR0317 may be administered together with VEGF for coronary ischemia where such indication is warranted, or with an anti-VEGF for cancer as warranted, or, conversely, an antagonist to
PR0317 may be administered with VEGF for coronary ischemia or with anti-VEGF to treat cancer as warranted.
These administrations would be in effective amounts for treating such disorders. Native PRO301 (SEQ ID NO: 119) has a Blast score of 246 and 30% homology at residues 24 to 282 of Figure 44 with A33 HUMAN, an A33 antigen precursor. A33 antigen precursor, as explained in the Background is a tumor-specific antigen, and as such, is a recognized marker and therapeutic target for the diagnosis and treatment of colon cancer. The expression of tumor-specific antigens is often associated with the progression of neoplastic tissue disorders. Native PRO301 (SEQ ID NO: 119) and A33 HUMAN also show a Blast score of 245 and 30% homology at residues 21 to 282 of Fig. 44 with A33_HUMAN, the variation dependent upon how spaces are inserted into the compared sequences. Native PRO301 (SEQ ID NO: 119) also has a Blast score of 165 and 29% homology at residues 60 to 255 of Fig. 44 with HS46KDA_1 , a human coxsackie and adenovirus receptor protein, also known as cell surface protein HCAR. This region of PRO301 also shows a similar Blast score and homology with HSU90716_1. Expression of such proteins is usually associated with viral infection and therapeutics for the prevention of such infection may be accordingly conceived. As mentioned in the Background, the expression of viral receptors is often associated with neoplastic tumors.
Therapeutic uses for the PR0234 polypeptides of the invention includes treatments associated with leukocyte homing or the interaction between leukocytes and the endothelium during an inflammatory response. Examples include asthma, rheumatoid arthritis, psoriasis and multiple sclerosis.
Since the PR0231 polypeptide and nucleic acid encoding it possess sequence homology to a putative acid phosphatase and its encoding nucleic acid, probes based upon the PR0231 nucleotide sequence may be employed to identify other novel phosphatase proteins. Soluble forms of the PR0231 polypeptide may be employed as antagonists of membrane bound PR0231 activity both in vitro and in vivo. PR0231 polypeptides may be employed in screening assays designed to identify agonists or antagonists of the native PR0231 polypeptide, wherein such assays may take the form of any conventional cell-type or biochemical binding assay. Moreover, the PR0231 polypeptide may serve as a molecular marker for the tissues in which the polypeptide is specifically expressed.
PR0229 polypeptides can be fused with peptides of interest to determine whether the fusion peptide has an increased half-life over the peptide of interest. The PR0229 polypeptides can be used accordingly to increase the half-life of polypeptides of interest. Portions of PR0229 which cause the increase in half-life are an embodiment of the invention herein.
PR0238 can be used in assays which measure its ability to reduce substrates, including oxygen and Aceyl-CoA, and particularly, measure PR0238's ability to produce oxygen free radicals. This is done by using assays which have been previously described. PR0238 can further be used to assay for candidates which block, reduce or reverse its reducing abilities. This is done by performing side by side assays where candidates are added in one assay having PR0238 and a substrate to reduce, and not added in another assay, being the same but for the lack of the presence of the candidate.
PR0233 polypeptides and portions thereof which have homology to reductase may also be useful for in vivo therapeutic purposes, as well as for various other applications. The identification of novel reductase proteins and related molecules may be relevant to a number of human disorders such as inflammatory disease, organ failure, atherosclerosis, cardiac injury, infertility, birth defects, premature aging, AIDS, cancer, diabetic complications and mutations in general. Given that oxygen free radicals and antioxidants appear to play important roles in a number of disease processes, the identification of new reductase proteins and reductase-like molecules is of special importance in that such proteins may serve as potential therapeutics for a variety of different human disorders. Such polypeptides may also play important roles in biotechnological and medical research, as well as various industrial applications. As a result, there is particular scientific and medical interest in new molecules, such as PR0233.
The PR0223 polypeptides of the present invention which exhibit serine carboxypeptidease activity may be employed in vivo for therapeutic purposes as well as for in vitro purposes. Those of ordinary skill in the art will well know how to employ PR0223 polypeptides for such uses.
PR0235 polypeptides and portions thereof which may be involved in cell adhesion are also useful for in vivo therapeutic purposes, as well as for various in vitro applications. In addition, PR0235 polypeptides and portions thereof may have therapeutic applications in disease states which involve cell adhesion. Given the physiological importance of cell adhesion mechanisms in vivo, efforts are currently being under taken to identify new, native proteins which are involved in cell adhesion. Therefore, peptides having homology to plexin are of particular interest to the scientific and medical communities. Because the PR0236 and PR0262 polypeptides disclosed herein are homologous to various known β- galactosidase proteins, the PR0236 and PR0262 polypeptides disclosed herein will find use in conjugates of monoclonal antibodies and the polypeptide for specific killing of mmor cells by generation of active drug from a galactosylated prodrug (e.g., the generation of 5-fluorouridine from the prodrug β-D-galactosyl-5- fluorouridine). The PR0236 and PR0262 polypeptides disclosed herein may also find various uses both in vivo and in vitro, wherein those uses will be similar or identical to uses for which β-galactosidase proteins are now employed. Those of ordinary skill in the art will well know how to employ PR0236 and PR0262 polypeptides for such uses.
PR0239 polypeptides and portions thereof which have homology to densin may also be useful for in vivo therapeutic purposes, as well as for various in vitro applications. In addition, PR0239 polypeptides and portions thereof may have therapeutic applications in disease states which involve synaptic mechanisms, regeneration or cell adhesion. Given the physiological importance of synaptic processes, regeneration and cell adhesion mechanisms in vivo, efforts are currently being under taken to identify new, native proteins which are involved in synaptic machinery and cell adhesion. Therefore, peptides having homology to densin are of particular interest to the scientific and medical communities. The PRO260 polypeptides described herein can be used in assays to determine their relation to fucosidase. In particular, the PRO260 polypeptides can be used in assays in determining their ability to remove fucose or other sugar residues from proteoglycans. The PRO260 polypeptides can be assayed to determine if they have any functional or locational similarities as fucosidase. The PRO260 polypeptides can then be used to regulate the systems in which they are integral. PR0263 can be used in assays wherein CD44 antigen is generally used to determine PR0263 activity relative to that of CD44. The results can be used accordingly. PRO270 polypeptides and portions thereof which effect reduction-oxidation (redox) state may also be useful for in vivo therapeutic purposes, as well as for various in vitro applications. More specifically, PRO270 polypeptides may affect the expression of a large variety of genes thought to be involved in the pathogenesis of AIDS, cancer, atherosclerosis, diabetic complications and in pathological conditions involving oxidative stress such as stroke and inflammation. In addition, PRO270 polypeptides and portions thereof may affect the expression of a genes which have a role in apoptosis. Therefore, peptides having homology to thioredoxin are particularly desirable to the scientific and medical communities.
PR0272 polypeptides and portions thereof which possess the ability to bind calcium may also have numerous in vivo therapeutic uses, as well as various in vitro applications. Therefore, peptides having homology to reticulocalbin are particularly desirable. Those with ordinary skill in the art will know how to employ PR0272 polypeptides and portions thereof for such purposes.
PR0294 polypeptides and portions thereof which have homology to collagen may also be useful for in vivo therapeutic purposes, as well as for various other applications. The identification of novel collagens and collage-like molecules may have relevance to a number of human disorders. Thus, the identification of new collagens and collage-like molecules is of special importance in that such proteins may serve as potential therapeutics for a variety of different human disorders. Such polypeptides may also play important roles in biotechnological and medical research as well as various industrial applications. Given the large number of uses for collagen, there is substantial interest in polypeptides with homology to the collagen molecule.
PR0295 polypeptides and portions thereof which have homology to integrin may also be useful for in vivo therapeutic purposes, as well as for various other applications. The identification of novel integrins and integrin-like molecules may have relevance to a number of human disorders such as modulating the binding or activity of cells of the immune system. Thus, the identification of new integrins and integrin-like molecules is of special importance in that such proteins may serve as potential therapeutics for a variety of different human disorders. Such polypeptides may also play important roles in biotechnological and medical research as well as various industrial applications. As a result, there is particular scientific and medical interest in new molecules, such as PR0295.
As the PR0293 polypeptide is clearly a leucine rich repeat polypeptide homologue, the peptide can be used in all applications that the known NLRR-1 and NLRR-2 polypeptides are used. The activity can be compared between these peptides and thus applied accordingly.
The PR0247 polypeptides described herein can be used in assays in which densin is used to determine the activity of PR0247 relative to densin or these other proteins. The results can be used accordingly in diagnostics and/or therapeutic applications with PR0247.
PRO302, PRO303, PRO304, PRO307 and PR0343 polypeptides ofthe present invention which possess protease activity may be employed both in vivo for therapeutic purposes and in vitro. Those of ordinary skill in the art will well know how to employ the PRO302, PRO303, PRO304, PRO307 and PR0343 polypeptides of the present invention for such purposes.
PR0328 polypeptides and portions thereof which have homology to GLIP and CRISP may also be useful for in vivo therapeutic purposes, as well as for various other applications. The identification of novel GLIP and CRISP-like molecules may have relevance to a number of human disorders which involve transcriptional regulation or are over expressed in human tumors. Thus, the identification of new GLIP and CRISP-like molecules is of special importance in that such proteins may serve as potential therapeutics for a variety of different human disorders. Such polypeptides may also play important roles in biotechnological and medical research as well as in various industrial applications. As a result, there is particular scientific and medical interest in new molecules, such as PR0328.
Uses for PR0335, PR0331 or PR0326 including uses in competitive assays with LIG-1, ALS and decorin to determine their relative activities. The results can be used accordingly. PR0335, PR0331 or PR0326 can also be used in assays where LIG-1 would be used to determine if the same effects are incurred. PR0332 contains GAG repeat (GKEK) at amino acid positions 625-628 in Fig. 108 (SEQ ID NO:310). Slippage in such repeats can be associated with human disease. Accordingly, PR0332 can use useful for the treatment of such disease conditions by gene therapy, i.e. by introduction of a gene containing the correct GKEK sequence motif.
Other uses of PR0334 include use in assays in which fibrillin or fibulin would be used to determine the relative activity of PR0334 to fibrillin or fibulin. In particular, PR0334 can be used in assays which require the mechanisms imparted by epidermal growth factor repeats.
Native PR0346 (SEQ ID NO:320) has a Blast score of 230, corresponding to 27% homology between amino acid residues 21 to 343 with residues 35 to 1040 CGM6_HUMAN, a carcinoembryonic antigen cgm6 precursor. This homology region includes nearly all but 2 N-terminal extracellular domain residues, including an immunoglobulin superfamily homology at residues 148 to 339 of PR0346 in addition to several transmembrane residues (340-343). Carcinoembryonic antigen precursor, as explained in the Background is a tumor-specific antigen, and as such, is a recognized marker and therapeutic target for the diagnosis and treatment of colon cancer. The expression of tumor-specific antigens is often associated with the progression of neoplastic tissue disorders. Native PR0346 (SEQ ID NO:320) and P W06874, a human carcinoembryonic antigen CEA-d have a Blast score of 224 and homology of 28% between residues 2 to 343 and 67 to 342, respectively. This homology includes the entire extracellular domain residues of native PR0346, minus the initiator methionine (residues 2 to 18) as well as several transmembrane residues (340-343).
PR0268 polypeptides which have protein disulfide isomerase activity will be useful for many applications where protein disulfide isomerase activity is desirable including, for example, for use in promoting proper disulfide bond formation in recombinantly produced proteins so as to increase the yield of correctly folded protein. Those of ordinary skill in the art will readily know how to employ such PR0268 polypeptides for such purposes.
PRO330 polypeptides of the present invention which possess biological activity related to that of the prolyl 4-hydroxylase alpha subunit protein may be employed both in vivo for therapeutic purposes and in vitro. Those of ordinary skill in the art will well know how to employ the PRO330 polypeptides of the present invention for such purposes.
Uses of the herein disclosed molecules may also be based upon the positive functional assay hits disclosed and described below. F. Anti-PRO Antibodies
The present invention further provides anti-PRO antibodies. Exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heteroconjugate antibodies.
1. Polyclonal Antibodies The anti-PRO antibodies may comprise polyclonal antibodies. Methods of preparing polyclonal antibodies are known to the skilled artisan. Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. The immunizing agent may include the PRO polypeptide or a fusion protein thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. Examples of adjuvants which may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). The immunization protocol may be selected by one skilled in the art without undue experimentation.
2. Monoclonal Antibodies
The anti-PRO antibodies may, alternatively, be monoclonal antibodies. Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature. 256:495 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes may be immunized in vitro.
The immunizing agent will typically include the PRO polypeptide or a fusion protein thereof. Generally, either peripheral blood lymphocytes ("PBLs") are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell [Goding, Monoclonal Antibodies: Principles and Practice. Academic Press, (1986) pp. 59-103]. Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine ("HAT medium"), which substances prevent the growth of HGPRT-deficient cells.
Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, California and the American Type Culture Collection, Manassas, Virginia. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies [Kozbor, J. Immunol.. 133:3001 (1984); BrodeuretaL. Monoclonal Antibody Production Techniques and Applications. Marcel Dekker, Inc., New York, (1987) pp. 51-63].
The culture medium in which the hybridoma cells are cultured can then be assayed for the presence o monoclonal antibodies directed against PRO. Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem.. 107:220 (1980).
After the desired hybridoma cells are identified, the clones may be subcloned by limiting dilution procedures and grown by standard methods [Goding, supra] . Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells may be grown in vivo as ascites in a mammal.
The monoclonal antibodies secreted by the subclones may be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
The monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Patent No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA may be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also may be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences [U.S. Patent No. 4,816,567; Morrison et al., supra] or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody. The antibodies may be monovalent antibodies. Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chain and modified heavy chain. The heavy chain is truncated generally at any point in the Fc region so as to prevent heavy chain crosslinking. Alternatively, the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent crosslinking. In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly, Fab fragments, can be accomplished using routine techniques known in the art. 3. Human and Humanized Antibodies
The anti-PRO antibodies of the invention may further comprise humanized antibodies or human antibodies. Humanized forms of non-human (e.g. , murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity. In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol.. 2:593-596 (1992)].
Methods for humanizing non-human antibodies are well known in the art. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non- human amino acid residues are often referred to as "import" residues, which are typically taken from an "import" variable domain. Humanization can be essentially performed following the method of Winter and co-workers [Jones et al. , Nature. 321 :522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science. 239: 1534-1536 (1988)], by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such "humanized" antibodies are chimeric antibodies (U.S. Patent No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
Human antibodies can also be produced using various techniques known in the art, including phage display libraries [Hoogenboom and Winter, J. Mol. Biol.. 227:381 (1991); Marks et al., J. Mol. Biol.. 222:581 (1991)]. The techniques of Cole et al. and Boemer et al. are also available for the preparation of human monoclonal antibodies (Cole et al.. Monoclonal Antibodies and Cancer Therapy. Alan R. Liss, p. 77 (1985) and Boerner et al., J. Immunol.. 147(l):86-95 (1991)]. Similarly, human antibodies can be made by introducing of human immunoglobulin loci into transgenic animals, e.g. , mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Patent Nos. 5,545,807; 5,545,806; 5,569,825; 5,625, 126; 5,633,425; 5,661,016, and in the following scientific publications: Marks et al, Bio/Technology 10. 779-783 (1992): Lonberg etal. Nature 368856-859 (1994): Morrison. Nature 368. 812-13 (1994); Fishwild et al., Nature Biotechnology 14, 845-51 (1996); Neuberger, Nature Biotechnology M, 826 (1996); Lonberg and Huszar. Intern. Rev. Immunol. 13 65-93 (1995).
4. Bispecific Antibodies Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for the PRO, the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit.
Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities [Milstein and Cuello, Nature. 305:537-539 (1983)]. Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixmre of ten different antibody molecules, of which only one has the correct bispecific strucmre. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published 13 May 1993, and in Traunecker et al., EMBO , 10:3655-3659 (1991).
Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CHI) containing the site necessary for light-chain binding present in at least one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of generating bispecific antibodies see, for example, Suresh et al. , Methods in Enzymology. 121:210 (1986). According to another approach described in WO 96/27011, the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture. The preferred interface comprises at least a part of the CH3 region of an antibody constant domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g. tyrosine or tryptophan). Compensatory "cavities" of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g. alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.
Bispecific antibodies can be prepared as full length antibodies or antibody fragments (e.g. F(ab')2 bispecific antibodies). Techniques for generating bispecific antibodies from antibody fragments have been described in the literature. For example, bispecific antibodies can be prepared can be prepared using chemical linkage . Brennan et al. , Science 229:81 (1985) describe a procedure wherein intact antibodies are proteoly tically cleaved to generate F(ab')2 fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The Fab' fragments generated are then converted to thionitrobenzoate (TNB) derivatives. One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB derivative to form the bispecific antibody. The bispecific antibodies produced can be used as agents for the selective immobilization of enzymes. Fab' fragments may be directly recovered from E. coli and chemically coupled to form bispecific antibodies. Shalaby et al , J. Exp. Med. 175:217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab')2 molecule. Each Fab' fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast mmor targets.
Various technique for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al , J. Immunol. 148(5): 1547-1553 (1992). The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab' portions of two different antibodies by gene fusion. The antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers. The "diabody" technology described by Hollinger et al , Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the VH and VL domains of one fragment are forced to pair with the complementary VL and VH domains of another fragment, thereby forming two antigen-binding sites. Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See, Gruber et al , J. Immunol. 152:5368 (1994). Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared. Tutt et al. , J. Immunol. 147:60 (1991).
Exemplary bispecific antibodies may bind to two different epitopes on a given PRO polypeptide herein. Alternatively, an anti-PRO polypeptide arm may be combined with an arm which binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3, CD28, or B7), or Fc receptors for IgG (FcγR), such as FcγRI (CD64), FcγRII (CD32) and FcγRIII (CD16) so as to focus cellular defense mechanisms to the cell expressing the particular PRO polypeptide. Bispecific antibodies may also be used to localize cytotoxic agents to cells which express a particular PRO polypeptide. These antibodies possess a PRO-binding arm and an arm which binds a cytotoxic agent or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or TETA. Another bispecific antibody of interest binds the PRO polypeptide and further binds tissue factor (TF).
5. Heteroconjugate Antibodies
Heteroconjugate antibodies are also within the scope of the present invention. Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells [U.S. Patent No. 4,676,980], and for treatment of HIV infection [WO 91/00360; WO 92/200373; EP 03089]. It is contemplated that the antibodies may be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins may be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Patent No. 4,676,980.
6. Effector Function Engineering
It may be desirable to modify the antibody of the invention with respect to effector function, so as to enhance, e.g. , the effectiveness of the antibody in treating cancer. For example, cysteine residue(s) may be introduced into the Fc region, thereby allowing interchain disulfide bond formation in this region. The homodimeric antibody thus generated may have improved intemalization capability and/or increased complement- mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al. , J. Exp Med. , 176: 1191-1195 (1992) and Shopes, J. Immunol.. 148: 2918-2922 (1992). Homodimeric antibodies with enhanced anti-tumor activity may also be prepared using heterobifunctional cross-linkers as described in Wolff et al. Cancer Research. 53: 2560-2565 (1993). Alternatively, an antibody can be engineered that has dual Fc regions and may thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design. 3: 219-230 (1989).
7. Immunoconjugates
The invention also pertains to immunoconjugates comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g. , an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).
Chemotherapeutic agents useful in the generation of such immunoconjugates have been described above . Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. A variety of radionuclides are available for the production of radioconjugated antibodies. Examples include 212Bi, 131I, 131In, ^Y, and 186Re.
Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutareldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis- diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as tolyene 2,6- diisocyanate), and bis-active fluorine compounds (such as 1 ,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al , Science. 238: 1098 (1987). Carbon- 14-labeled 1- isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See W094/11026.
In another embodiment, the antibody may be conjugated to a "receptor" (such streptavidin) for utilization in mmor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand" (e.g., avidin) that is conjugated to a cytotoxic agent (e.g., a radionucleotide).
8. Immunoliposomes
The antibodies disclosed herein may also be formulated as immunoliposomes. Liposomes containing the antibody are prepared by methods known in the art, such as described in Epstein et al, Proc. Natl. Acad. Sci. USA. 82: 3688 (1985); Hwang et al, Proc. Natl Acad. Sci. USA. 77: 4030 (1980); and U.S. Pat. Nos. 4,485,045 and 4,544,545. Liposomes with enhanced circulation time are disclosed in U.S. Patent No. 5,013,556.
Particularly useful liposomes can be generated by the reverse-phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol, and PEG-derivatizedphosphatidylethanolamine (PEG- PE). Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter. Fab' fragments of the antibody of the present invention can be conjugated to the liposomes as described in Martin et al .. J. Biol. Chem.. 257: 286-288 (1982) via a disulfide-interchange reaction. A chemotherapeutic agent (such as Doxorubicin) is optionally contained within the liposome. See Gabizon et al. , J. National Cancer Inst.. 81(19): 1484 (1989).
9. Pharmaceutical Compositions of Antibodies
Antibodies specifically binding a PRO polypeptide identified herein, as well as other molecules identified by the screening assays disclosed hereinbefore, can be administered for the treatment of various disorders in the form of pharmaceutical compositions. If the PRO polypeptide is intracellular and whole antibodies are used as inhibitors, internalizing antibodies are preferred. However, lipofections or liposomes can also be used to deliver the antibody, or an antibody fragment, into cells. Where antibody fragments are used, the smallest inhibitory fragment that specifically binds to the binding domain of the target protein is preferred. For example, based upon the variable- region sequences of an antibody, peptide molecules can be designed that retain the ability to bind the target protein sequence. Such peptides can be synthesized chemically and/or produced by recombinant DNA technology. See, e.g., Marasco et al, Proc. Natl. Acad. Sci. USA. 90: 7889-7893 (1993). The formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other. Alternatively, or in addition, the composition may comprise an agent that enhances its function, such as, for example, a cytotoxic agent, cytokine, chemotherapeutic agent, or growth-inhibitory agent. Such molecules are suitably present in combination in amounts that are effective for the purpose intended.
The active ingredients may also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles, and nanocapsules) or in macroemulsions. Such techniques are disclosed in Remington's Pharmaceutical Sciences, supra.
The formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes.
Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), orpoly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic acid and γ ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOT ™ (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(-)-3- hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods. When encapsulated antibodies remain in the body for a long time, they may denamre or aggregate as a result of exposure to moismre at 37°C, resulting in a loss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S-S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling moismre content, using appropriate additives, and developing specific polymer matrix compositions.
G. Uses for anti-PRO Antibodies
The anti-PRO antibodies of the invention have various utilities. For example, anti-PRO antibodies may be used in diagnostic assays for PRO, e.g. , detecting its expression in specific cells, tissues, or serum. Various diagnostic assay techniques known in the art may be used, such as competitive binding assays, direct or indirect sandwich assays and immunoprecipitation assays conducted in either heterogeneous or homogeneous phases [Zola, Monoclonal Antibodies: A Manual of Techniques, CRC Press, Inc. (1987) pp. 147-158]. The antibodies used in the diagnostic assays can be labeled with a detectable moiety. The detectable moiety should be capable of producing, either directly or indirectly, a detectable signal. For example, the detectable moiety may be a radioisotope, such as 3H, 14C, 32P, 35S, or l25I, a fluorescent or chemiluminescent compound, such as fluorescein isothiocyanate, rhodamine, or luciferin, or an enzyme, such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase. Any method known in the art for conjugating the antibody to the detectable moiety may be employed, including those methods described by Hunter et al., Nature, 144:945 (1962); David et al., Biochemistry. 13: 1014 (1974); Pain et al., J. Immunol. Meth.. 40:219 (1981); and Nygren, J. Histochem. and Cvtochem.. 30:407 (1982).
Anti-PRO antibodies also are useful for the affinity purification of PRO from recombinant cell culture or natural sources. In this process, the antibodies against PRO are immobilized on a suitable support, such a Sephadex resin or filter paper, using methods well known in the art. The immobilized antibody then is contacted with a sample containing the PRO to be purified, and thereafter the support is washed with a suitable solvent that will remove substantially all the material in the sample except the PRO, which is bound to the immobilized antibody. Finally, the support is washed with another suitable solvent that will release the PRO from the antibody. The following examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way.
All patent and literature references cited in the present specification are hereby incorporated by reference in their entirety.
EXAMPLES
Commercially available reagents referred to in the examples were used according to manufacturer's instructions unless otherwise indicated. The source of those cells identified in the following examples, and throughout the specification, by ATCC accession numbers is the American Type Culture Collection, Rockville, Maryland.
EXAMPLE 1: Extracellular Domain Homology Screening to Identify Novel Polypeptides and cDNA Encoding Therefor The extracellular domain (ECD) sequences (including the secretion signal sequence, if any) from about 950 known secreted proteins from the Swiss-Prot public database were used to search EST databases. The EST databases included public databases (e.g. , Dayhoff, GenBank), and proprietary databases (e.g. LIFESEQ™, Incyte Pharmaceuticals, Palo Alto, CA). The search was performed using the computer program BLAST or BLAST2 (Altschul, and Gish, Methods in Enzymology 266: 460-80 ( 1996) ; http://blast.wustl/edu/blast/README.html) as a comparison of the ECD protein sequences to a 6 frame translation of the EST sequences. Those comparisons with a Blast score of 70 (or in some cases 90) or greater that did not encode known proteins were clustered and assembled into consensus DNA sequences with the program "phrap" (Phil Green, University of Washington, Seattle, Washington).
Using this extracellular domain homology screen, consensus DNA sequences were assembled relative to the other identified EST sequences. In addition, the consensus DNA sequences obtained were often (but not always) extended using repeated cycles of BLAST and phrap to extend the consensus sequence as far as possible using the sources of EST sequences discussed above.
Based upon the consensus sequences obtained as described above, oligonucleotides were then synthesized and used to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for a PRO polypeptide. Forward (.f) and reverse (.r) PCR primers generally range from 20 to 30 nucleotides and are often designed to give a PCR product of about 100-1000 bp in length. The probe (.p) sequences are typically 40-55 bp in length. In some cases, additional oligonucleotides are synthesized when the consensus sequence is greater than about 1-1.5kbρ. In order to screen several libraries for a full-length clone, DNA from the libraries was screened by PCR amplification, as per Ausubel et al., Current Protocols in Molecular Biology, with the PCR primer pair. A positive library was then used to isolate clones encoding the gene of interest using the probe oligonucleotide and one of the primer pairs.
The cDNA libraries used to isolate the cDNA clones were constructed by standard methods using commercially available reagents such as those from Invitrogen, San Diego, CA. The cDNA was primed with oligo dT containing a Notl site, linked with blunt to Sail hemikinased adaptors, cleaved with Notl, sized appropriately by gel electrophoresis, and cloned in a defined orientation into a suitable cloning vector (such as pRKB or pRKD; pRK5B is a precursor of pRK5D that does not contain the Sfil site; see, Holmes et al. , Science. 253: 1278-1280 (1991)) in the unique Xhol and Notl sites.
EXAMPLE 2: Isolation of cDNA Clones Encoding PRQ211 and PRQ217
Consensus DNA sequences were assembled as described in Example 1 above and were designated as
DNA28730 and DNA28760, respectively. Based on these consensus sequences, oligonucleotides were synthesized and used to identify by PCR a cDNA library that contained the sequences of interest and for use as probes to isolate a clone of the full-length coding sequence for the PR0211 and PR0217 polypeptides. The libraries used to isolate DNA32292-1131 and DNA33094-1131 were fetal lung libraries. cDNA clones were sequenced in their entirety. The entire nucleotide sequences of PR0211
(DNA32292-1131) and PR0217 (UNQ191) are shown in Figure 1 (SEQ ID NO: 1) and Figure 3 (SEQ ID
NO:3), respectively. The predicted polypeptides are 353 and 379 amino acid in length, respectively, with respective molecular weights of approximately 38,190 and 41,520 daltons. The oligonucleotide sequences used in the above procedures were the following:
28730-p (OLI 516) (SEQ ID NO:5)
5 ' -AGGGAGC ACGG AC AGTGTGC AGATGTGGACGAGTGCTC ACTAGC A-3 '
28730T (OLI 517) (SEQ ID NO:6)
5 ' -AGAGTGTATCTCTGGCTACGC-3 ' 28730.r (OLI 518) (SEQ ID NO:7)
5 ' -TA AGTCCGGCAC ATTAC AGGTC-3 '
28760.p (OLI 617) (SEQ ID NO:8)
5'-CCCACGATGTATGAATGGTGGACTTTGTGTGACTCCTGGTTTCTGCATC-3'
28760.f (OLI 618) (SEQ ID NO:9) 5'-AAAGACGCATCTGCGAGTGTCC-3'
28760.r (OLI 619) (SEQ ID NO:10)
5'-TGCTGATTTCACACTGCTCTCCC-3'
EXAMPLE 3: Isolation of cDNA Clones Encoding Human PRO230 A consensus DNA sequence was assembled relative to the other identified EST sequences as described in Example 1 above, wherein the consensus sequence is designated herein as DNA30857. An EST proprietary to Genentech was employed in the consensus assembly. The EST is designated as DNA20088 and has the nucleotide sequence shown in Figure 7 (SEQ ID NO: 13).
Based on the DNA30857 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDN A library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for PRO230.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-TTCGAGGCCTCTGAGAAGTGGCCC-3' (SEQ ID NO: 14) reverse PCR primer 5'-GGCGGTATCTCTCTGGCCTCCC-3' (SEQ ID NO: 15)
Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA30857 sequence which had the following nucleotide sequence hybridization probe 5'-TTCTCCACAGCAGCTGTGGCATCCGATCGTGTCTCAATCCATTCTCTGGG-3' (SEQ ID NO: 16)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PRO230 gene using the probe oligonucleotide and one of the PCR primers.
RNA for construction of the cDNA libraries was isolated from human fetal lung tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO230 (herein designated as DNA33223-1136 and the derived protein sequence for PRO230.
The entire nucleotide sequence of DNA33223-1136 is shown in Figure 5 (SEQ ID NO: 11). Clone DNA33223-1136 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 100-103 and ending at the stop codon at nucleotide positions 1501-1503 (Figure 5; SEQ ID NO: 11). The predicted polypeptide precursor is 467 amino acids long (Figure 6).
EXAMPLE 4: Isolation of cDNA Clones Encoding Human PRQ232
A consensus DNA sequence was assembled relative to the other identified EST sequences as described in Example 1 above, wherein the consensus sequence is designated herein as DNA30935. Based on the DNA30935 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for
PR0232.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-TGCTGTGCTACTCCTGCAAAGCCC-3' (SEQ ID NO: 19) reverse PCR primer 5'-TGCACAAGTCGGTGTCACAGCACG-3' (SEQ ID NO:20)
Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA30935 sequence which had the following nucleotide sequence hybridization probe
5'-AGCAACGAGGACTGCCTGCAGGTGGAGAACTGCACCCAGCTGGG-3' (SEQ ID NO:21) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0232 gene using the probe oligonucleotide and one of the PCR primers. RNA for construction of the cDNA libraries was isolated from human fetal kidney tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0232 [herein designated as DNA34435-1140] and the derived protein sequence for PR0232.
The entire nucleotide sequence of DNA34435-1140 is shown in Figure 8 (SEQ ID NO: 17). Clone DNA34435-1140 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 17-19 and ending at the stop codon at nucleotide positions 359-361 (Fig. 8; SEQ ID NO: 17). The predicted polypeptide precursor is 1 14 amino acids long (Fig. 9). Clone DNA34435-1140 has been deposited with ATCC on September 16, 1997 and is assigned ATCC deposit no. ATCC 209250.
Analysis of the amino acid sequence of the full-length PR0232 suggests that it possesses 35 % sequence identity with a stem cell surface antigen from Gallus gallus.
EXAMPLE 5: Isolation of cDNA Clones Encoding PRO 187
A proprietary expressed sequence tag (EST) DNA database (LIFESEQ™, Incyte Pharmaceuticals, Palo
Alto, CA) was searched and an EST (#843193) was identified which showed homology to fibroblast growth factor (FGF-8) also known as androgen-induced growth factor. mRNA was isolated from human fetal lung tissue using reagents and protocols from Invitrogen, San Diego, CA (Fast Track 2). The cDNA libraries used to isolate the cDNA clones were constructed by standard methods using commercially available reagents (e.g.,
Invitrogen, San Diego, CA, Life Technologies, Gaithersburg, MD). The cDNA was primed with oligo dT containing a Notl site, linked with blunt to Sail hemikinased adaptors, cleaved with Notl, sized appropriately by gel electrophoresis, and cloned in a defined orientation into the cloning vector ρRK5D using reagents and protocols from Life Technologies, Gaithersburg, MD (Super Script Plasmid System). The double-stranded cDNA was sized to greater than 1000 bp and the Sall/Notl linkered cDNA was cloned into Xhol/Notl cleaved vector. pRK5D is a cloning vector that has an sp6 transcription initiation site followed by an Sfil restriction enzyme site preceding the Xhol/Notl cDNA cloning sites.
Several libraries from various tissue sources were screened by PCR amplification with the following oligonucleotide probes:
IN843193.f (OLI315) (SEQ ID NO: 24)
5 ' -CAGTACGTGAGGGACCAGGGCGCCATGA-3 '
IN843193.r (OLI 317) (SEQ ID NO:25)
5 ' -CCGGTG ACCTGC ACGTGCTTGCC A-3 ' A positive library was then used to isolate clones encoding the PRO 187 gene using one of the above oligonucleotides and the following oligonucleotide probe:
IN843193.p (OLI 316) (SEQ ID NO:26)
5'-GCGGATCTGCCGCCTGCTCANCTGGTCGGTCATGGCGCCCT-3'
A cDNA clone was sequenced in entirety. The entire nucleotide sequence of PR0187 (DNA27864- 1155) is shown in Figure 10 (SEQ ID NO:22). Clone DNA27864-1155 contains a single open reading frame with an apparent translational initiation site at nucleotide position 1 (Figure 10; SEQ ID NO:22). The predicted polypeptide precursor is 205 amino acids long. Clone DNA27864-1155 has been deposited with the ATCC (designation: DNA27864-1155) and is assigned ATCC deposit no. ATCC 209375.
Based on a BLAST and FastA sequence alignment analysis (using the ALIGN computer program) of the full-length sequence, the PR0187 polypeptide shows 74% amino acid sequence identity (Blast score 310) to human fibroblast growth factor-8 (androgen-induced growth factor).
EXAMPLE 6: Isolation of cDNA Clones Encoding PRQ265
A consensus DNA sequence was assembled relative to other EST sequences as described in Example
1 above using phrap. This consensus sequence is herein designated DNA33679. Based on the DNA33679 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0265.
PCR primers (two forward and one reverse) were synthesized: forward PCR primer A: 5'-CGGTCTACCTGTATGGCAACC-3' (SEQ ID NO:29); forward PCR primer B: 5 ' -GCAGGACAACCAGATAAACCAC-3 ' (SEQ ID NO:30); reverse PCR primer 5'-ACGCAGATTTGAGAAGGCTGTC-3' (SEQ ID NO:31) Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA33679 sequence which had the following nucleotide sequence hybridization probe 5'-TTCACGGGCTGCTCTTGCCCAGCTCTTGAAGCTTGAAGAGCTGCAC-3' (SEQ ID NO:32)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PR0265 gene using the probe oligonucleotide and one of the PCR primers. RNA for construction of the cDNA libraries was isolated from human a fetal brain library. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0265 [herein designated as DNA36350-1158] (SEQ ID NO:27) and the derived protein sequence for PR0265.
The entire nucleotide sequence of DNA36350-1 158 is shown in Figure 12 (SEQ ID NO:27). Clone
DNA36350-1158 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 352-354 and ending at the stop codon at positions 2332-2334 (Figure 12). The predicted polypeptide precursor is 660 amino acids long (Figure 13). Clone DNA36350-1158 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209378.
Analysis of the amino acid sequence of the full-length PR0265 polypeptide suggests that portions of it possess significant homology to the fibromodulin and the fibromodulin precursor, thereby indicating that PR0265 may be a novel member of the leucine rich repeat family, particularly related to fibromodulin.
EXAMPLE 7: Isolation of cDNA Clones Encoding Human PRQ219
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA28729. Based on the DNA28729 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0219.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-GTGACCCTGGTTGTGAATACTCC-3' (SEQ ID NO:35) reverse PCR primer 5'-ACAGCCATGGTCTATAGCTTGG-3' (SEQ ID NO:36)
Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA28729 sequence which had the following nucleotide sequence hybridization probe
5'-GCCTGTCAGTGTCCTGAGGGACACGTGCTCCGCAGCGATGGGAAG-3' (SEQ ID NO:37) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0219 gene using the probe oligonucleotide and one of the PCR primers.
RNA for construction of the cDNA libraries was isolated from human fetal kidney tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0219 [herein designated as DNA32290-1164] (SEQ ID NO:33) and the derived protein sequence for PR0219.
The entire nucleotide sequence of DNA32290-1164 is shown in Figure 14 (SEQ ID NO:33). Clone
DNA32290-1164 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 204-206 and ending at the stop codon at nucleotide positions 2949-2951 (Figure 14). The predicted polypeptide precursor is 915 amino acids long (Figure 15). Clone DNA32290-1164 has been deposited with
ATCC and is assigned ATCC deposit no. ATCC 209384.
Analysis of the amino acid sequence of the full-length PR0219 polypeptide suggests that portions of it possess significant homology to the mouse and human matrilin-2 precursor polypeptides.
EXAMPLE 8: Isolation of cDNA Clones Encoding Human PRQ246
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA30955. Based on the DNA30955 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0246.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-AGGGTCTCCAGGAGAAAGACTC-3' (SEQ ID NO:40) reverse PCR primer 5'-ATTGTGGGCCTTGCAGACATAGAC-3' (SEQ ID NO:41)
Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA30955 sequence which had the following nucleotide sequence hybridization probe 5'-GGCCACAGCATCAAAACCTTAGAACTCAATGTACTGGTTCCTCCAGCTCC-3' (SEQ ID NO:42) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0246 gene using the probe oligonucleotide and one of the PCR primers.
RNA for construction of the cDNA libraries was isolated from human fetal liver tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0246 [herein designated as DNA35639-1 172] (SEQ ID NO:38) and the derived protein sequence for PR0246.
The entire nucleotide sequence of DNA35639-1172 is shown in Figure 16 (SEQ ID NO:38). Clone
DNA35639-1172 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 126-128 and ending at the stop codon at nucleotide positions 1296-1298 (Figure 16). The predicted polypeptide precursor is 390 amino acids long (Figure 17). Clone DNA35639-1172 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209396.
Analysis of the amino acid sequence of the full-length PR0246 polypeptide suggests that it possess significant homology to the human cell surface protein HCAR, thereby indicating that PR0246 may be a novel cell surface vims receptor.
EXAMPLE 9: Isolation of cDNA Clones Encoding Human PRQ228
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA28758. An EST proprietary to Genentech was employed in the consensus assembly. This EST is shown in Figure 20 (SEQ ID NO:50) and is herein designated as DNA21951. Based on the DNA28758 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full- length coding sequence for PR0228.
PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-GGTAATGAGCTCCATTACAG-3' (SEQ ID NO:51) forward PCR primer 5'-GGAGTAGAAAGCGCATGG-3' (SEQ ID NO: 52) forward PCR primer 5'-CACCTGATACCATGAATGGCAG-3' (SEQ ID NO:53) reverse PCR primer 5'-CGAGCTCGAATTAATTCG-3' (SEQ ID NO:54) reverse PCR primer 5'-GGATCTCCTGAGCTCAGG-3' (SEQ ID NO:55) reverse PCR primer 5'-CCTAGTTGAGTGATCCTTGTAAG-3' (SEQ ID NO:56) Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA28758 sequence which had the following nucleotide sequence hybridization probe
5'-ATGAGACCCACACCTCATGCCGCTGTAATCACCTGACACATTTTGCAATT-3' (SEQ ID NO:57) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PR0228 gene using the probe oligonucleotide and one of the PCR primers. RNA for construction of the cDNA libraries was isolated from human fetal kidney tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0228 [herein designated as DNA33092-1202] (SEQ ID NO:48) and the derived protein sequence for PR0228.
The entire nucleotide sequence of DNA33092-1202 is shown in Figure 18 (SEQ ID NO:48). Clone
DNA33092-1202 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 24-26 of SEQ ID NO:48 and ending at the stop codon after nucleotide position 2093 of SEQ ID
NO:48. The predicted polypeptide precursor is 690 amino acids long (Figure 19). Clone DNA33092-1202 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209420.
Analysis of the amino acid sequence of the full-length PR0228 polypeptide suggests that portions of it possess significant homology to the secretin-related proteins CD97 and EMRl as well as the secretin member, latrophilin, thereby indicating that PR0228 may be a new member of the secretin related proteins.
EXAMPLE 10: Isolation of cDNA Clones Encoding Human PRQ533
The EST sequence accession number AF007268, a murine fibroblast growth factor (FGF-15) was used to search various public EST databases (e.g., GenBank, Dayhoff, etc.). The search was performed using the computer program BLAST or BLAST2 [Altschul et al., Methods in Enzymology, 266:460-480 (1996); http://blast.wustl/edu/blast/README.html] as a comparison of the ECD protein sequences to a 6 frame translation of the EST sequences. The search resulted in a hit with GenBank EST AA220994, which has been identified as stratagene NT2 neuronal precursor 937230.
Based on the Genbank EST AA220994 sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence. Forward and reverse PCR primers may range from 20 to 30 nucleotides (typically about 24), and are designed to give a PCR product of 100-1000 bp in length. The probe sequences are typically 40-55 bp (typically about 50) in length. In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification, as per Ausubel et al, Current Protocols in Molecular Biology, with the PCR primer pair. A positive library was then used to isolate clones encoding the gene of interest using the probe oligonucleotide and one of the PCR primers.
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified below. A positive library was then used to isolate clones encoding the PR0533 gene using the probe oligonucleotide and one of the PCR primers. RNA for construction of the cDNA libraries was isolated from human fetal retina. The cDNA libraries used to isolated the cDNA clones were constructed by standard methods using commercially available reagents (e.g., Invitrogen, San Diego, CA; Clontech, etc.) The cDNA was primed with oligo dT containing a Notl site, linked with blunt to Sail hemikinased adaptors, cleaved with Notl, sized appropriately by gel electrophoresis, and cloned in a defined orientation into a suitable cloning vector (such as pRKB or pRKD; pRK5B is a precursor of pRK5D that does not contain the Sfil site; see, Holmes et al., Science, 253: 1278-1280 (1991)) in the unique Xhol and Notl sites. A cDNA clone was sequenced in its entirety. The full length nucleotide sequence of PR0533 is shown in Figure 21 (SEQ ID NO:58). Clone DNA49435-1219 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 459-461 (Figure 21; SEQ ID NO:58). The predicted polypeptide precursor is 216 amino acids long. Clone DNA47412-1219 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209480. Based on a BLAST-2 and FastA sequence alignment analysis of the full-length sequence, PR0533 shows amino acid sequence identity to fibroblast growth factor (53%). The oligonucleotide sequences used in the above procedure were the following: FGF15. forward: 5'-ATCCGCCCAGATGGCTACAATGTGTA-3' (SEQ ID NO:60); FGF15.probe: 5'-GCCTCCCGGTCTCCCTGAGCAGTGCCAAACAGCGGCAGTGTA-3' (SEQ ID NO:61); FGF15.reverse: 5'-CCAGTCCGGTGACAAGCCCAAA-3' (SEQ ID NO:62).
EXAMPLE 11: Isolation of cDNA Clones Encoding Human PRQ245
A consensus DNA sequence was assembled relative to the other identified EST sequences as described in Example 1 above, wherein the consensus sequence is designated herein as DNA30954. Based on the DNA30954 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for PR0245.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-ATCGTTGTGAAGTTAGTGCCCC-3' (SEQ ID NO:65) reverse PCR primer 5'-ACCTGCGATATCCAACAGAATTG-3' (SEQ ID NO: 66)
Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA30954 sequence which had the following nucleotide sequence hybridization probe
5'-GGAAGAGGATACAGTCACTCTGGAAGTATTAGTGGCTCCAGCAGTTCC-3' (SEQ ID NO:67) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0245 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal liver tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0245 [herein designated as DNA35638-1141] and the derived protein sequence for PR0245.
The entire nucleotide sequence of DNA35638-1141 is shown in Figure 23 (SEQ ID NO:63). Clone
DNA35638-1 141 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 89-91 and ending at the stop codon at nucleotide positions 1025-1027 (Fig. 23; SEQ ID NO:63). The predicted polypeptide precursor is 312 amino acids long (Fig. 24). Clone DNA35638-1141 has been deposited with ATCC on September 16, 1997 and is assigned ATCC deposit no. ATCC 209265.
Analysis of the amino acid sequence of the full-length PR0245 suggests that a portion of it possesses
60% amino acid identity with the human c-myb protein and, therefore, may be a new member of the transmembrane protein receptor tyrosine kinase family.
EXAMPLE 12: Isolation of cDNA Clones Encoding Human PRO220. PRQ221 and PRQ227
(a) PRO220
A consensus DNA sequence was assembled relative to the other identified EST sequences as described in Example 1 above, wherein the consensus sequence is designated herein as DNA28749. Based on the
DNA28749 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for
PRO220.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-TCACCTGGAGCCTTTATTGGCC-3' (SEQ ID NO:74) reverse PCR primer 5'-ATACCAGCTATAACCAGGCTGCG-3' (SEQ ID NO: 75)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA28749 sequence which had the following nucleotide sequence: hybridization probe 5'-CAACAGTAAGTGGTTTGATGCTCTTCCAAATCTAGAGATTCTGATGATTGGG-3' (SEQ ID NO:76). In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PRO220 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO220 [herein designated as DNA32298-1132 and the derived protein sequence for PRO220.
The entire nucleotide sequence of DNA32298-1132 is shown in Figure 25 (SEQ ID NO:68). Clone
DNA32298-1132 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 480-482 and ending at the stop codon at nucleotide positions 2604-2606 (Figure 25). The predicted polypeptide precursor is 708 amino acids long (Figure 26). Clone DNA32298-1132 has been deposited with
ATCC and is assigned ATCC deposit no. ATCC 209257.
Analysis of the amino acid sequence of the full-length PRO220 shows it has homology to member of the leucine rich repeat protein superfamily, including the leucine rich repeat protein and the neuronal leucine-rich repeat protein 1.
(b) PRQ221
A consensus DNA sequence was assembled relative to the other identified EST sequences as described in Example 1 above, wherein the consensus sequence is designated herein as DNA28756. Based on the
DNA28756 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for
PR0221. A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-CCATGTGTCTCCTCCTACAAAG-3' (SEQ ID NO:77) reverse PCR primer 5'-GGGAATAGATGTGATCTGATTGG-3' (SEQ ID NO:78)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA28756 sequence which had the following nucleotide sequence: hybridization probe
5'-CACCTGTAGCAATGCAAATCTCAAGGAAATACCTAGAGATCTTCCTCCTG-3' (SEQ ID NO:79)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0221 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0221 [herein designated as DNA33089-1132 and the derived protein sequence for PR0221.
The entire nucleotide sequence of DNA33089-1132 is shown in Figure 27 (SEQ ID NO:70). Clone DNA33089-1 132 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 179-181 and ending at the stop codon at nucleotide positions 956-958 (Figure 27). The predicted polypeptide precursor is 259 amino acids long (Figure 28). PR0221 is believed to have a transmembrane region at amino acids 206-225. Clone DNA33089-1132 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209262.
Analysis of the amino acid sequence of the full-length PR0221 shows it has homology to member of the leucine rich repeat protein superfamily, including the SLIT protein.
(c) PRQ227
A consensus DNA sequence was assembled relative to the other identified EST sequences as described in Example 1 above, wherein the consensus sequence is designated herein as DNA28740. Based on the DNA28740 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for
PR0227.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-AGCAACCGCCTGAAGCTCATCC-3' (SEQ ID NO: 80) reverse PCR primer 5'-AAGGCGCGGTGAAAGATGTAGACG-3' (SEQ ID NO:81)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA28740 sequence which had the following nucleotide sequence: hybridization probe
5'GACTACATGTTTCAGGACCTGTACAACCTCAAGTCACTGGAGGTTGGCGA-3' (SEQ ID NO:82). In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0227 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0227 [herein designated as DNA33786-1132 and the derived protein sequence for PR0227.
The entire nucleotide sequence of DNA33786-1132 is shown in Figure 29 (SEQ ID NO:72). Clone DNA33786-1132 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 33-35 and ending at the stop codon at nucleotide positions 1893-1895 (Figure 29). The predicted polypeptide precursor is 620 amino acids long (Figure 30). PR0227 is believed to have a transmembrane region. Clone DNA33786-1132 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209253.
Analysis of the amino acid sequence of the full-length PR0221 shows it has homology to member of the leucine rich repeat protein superfamily, including the platelet glycoprotein V precursor and the human glycoprotein V.
EXAMPLE 13: Isolation of cDNA Clones Encoding Human PRQ258
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA28746.
Based on the DNA28746 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full- length coding sequence for PR0258.
PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-GCTAGGAATTCCACAGAAGCCC-3' (SEQ ID NO:85) reverse PCR primer 5'-AACCTGGAATGTCACCGAGCTG-3' (SEQ ID NO: 86) reverse PCR primer 5'-CCTAGCACAGTGACGAGGGACTTGGC-3' (SEQ ID NO:87)
Additionally, synthetic oligonucleotide hybridization probes were constmcted from the consensus DNA28740 sequence which had the following nucleotide sequence: hybridization probe
5'-AAGACACAGCCACCCTAAACTGTCAGTCTTCTGGGAGCAAGCCTGCAGCC-3' (SEQ ID NO:88) 5'-GCCCTGGCAGACGAGGGCGAGTACACCTGCTCAATCTTCACTATGCCTGT-3' (SEQ ID NO:89)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0258 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0258 [herein designated as DNA35918-1174] (SEQ ID NO:83) and the derived protein sequence for PR0258.
The entire nucleotide sequence of DNA35918-1174 is shown in Figure 31 (SEQ ID NO:83). Clone DNA35918-1174 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 147-149 of SEQ ID NO: 83 and ending at the stop codon after nucleotide position 1340 of SEQ ID
NO:83 (Figure 31). The predicted polypeptide precursor is 398 amino acids long (Figure 32). Clone DNA35918-1174 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209402.
Analysis of the amino acid sequence of the full-length PR0258 polypeptide suggests that portions of it possess significant homology to the CRTAM and the poliovims receptor and have an Ig domain, thereby indicating that PR0258 is a new member of the Ig superfamily.
EXAMPLE 14: Isolation of cDNA Clones Encoding Human PRQ266
An expressed sequence tag database was searched for ESTs having homology to SLIT, resulting in the identification of a single EST sequence designated herein as T73996. Based on the T73996 EST sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0266. A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-GTTGGATCTGGGCAACAATAAC-3' (SEQ ID NO: 92) reverse PCR primer 5'-ATTGTTGTGCAGGCTGAGTTTAAG-3' (SEQ ID NO:93)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted which had the following nucleotide sequence hybridization probe
5'-GGTGGCTATACATGGATAGCAATTACCTGGACACGCTGTCCCGGG-3' (SEQ ID NO:94)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0266 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal brain tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0266 [herein designated as DNA37150-1178] (SEQ ID NO:90) and the derived protein sequence for PR0266.
The entire nucleotide sequence of DNA37150-1178 is shown in Figure 33 (SEQ ID NO:90). Clone DNA37150-1178 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 167-169 and ending at the stop codon after nucleotide position 2254 of SEQ ID NO:90. The predicted polypeptide precursor is 696 amino acids long (Figure 34). Clone DNA37150-1 178 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209401.
Analysis of the amino acid sequence of the full-length PR0266 polypeptide suggests that portions of it possess significant homology to the SLIT protein, thereby indicating that PR0266 may be a novel leucine rich repeat protein.
EXAMPLE 15: Isolation of cDNA Clones Encoding Human PRQ269
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA35705. Based on the DNA35705 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PR0269. Forward and reverse PCR primers were synthesized: forward PCR primer .fl 5'-TGGAAGGAGATGCGATGCCACCTG -3'
(SEQ ID NO: 97) forward PCR primer (.f2) 5'-TGACCAGTGGGGAAGGACAG-3' (SEQ ID NO:98) forward PCR primer (.f3) 5'-ACAGAGCAGAGGGTGCCTTG-3' (SEQ ID NO: 99) reverse PCR primer (.rl) 5'-TCAGGGACAAGTGGTGTCTCTCCC-3'
(SEQ ID NO: 100) reverse PCR primer (.r2) 5'-TCAGGGAAGGAGTGTGCAGTTCTG-3'
(SEQ ID NO: 101)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA35705 sequence which had the following nucleotide sequence: hybridization probe 5'-ACAGCTCCCGATCTCAGTTACTTGCATCGCGGACGAAATCGGCGCTCGCT-3' (SEQ ID NO: 102)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PR0269 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal kidney tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0269 [herein designated as DNA38260- 1180] (SEQ ID NO:95) and the derived protein sequence for PR0269. The entire nucleotide sequence of DNA38260-1180 is shown in Figure 35 (SEQ ID NO:95). Clone
DNA38260-1180 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 314-316 and ending at the stop codon at nucleotide positions 1784-1786 (Fig. 35; SEQ ID NO:95). The predicted polypeptide precursor is 490 amino acids long (Fig. 36). Clone DNA38260-1180 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209397. Analysis of the amino acid sequence of the full-length PR0269 suggests that portions of it possess significant homology to the human thrombomodulin proteins, thereby indicating that PR0269 may possess one or more thrombomodulin-like domains.
EXAMPLE 16: Isolation of cDNA Clones Encoding Human PRQ287 A consensus DNA sequence encoding PR0287 was assembled relative to the other identified EST sequences as described in Example 1 above, wherein the consensus sequence is designated herein as DNA28728.
Based on the DNA28728 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for PR0287. A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5 ' -CCGATTCATAGACCTCGAGAGT-3 ' (SEQ ID NO : 105) reverse PCR primer 5'-GTCAAGGAGTCCTCCACAATAC-3' (SEQ ID NO: 106) Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA28728 sequence which had the following nucleotide sequence hybridization probe
5 ' -GTGTACA ATGGCC ATGCCAATGGCC AGCGC ATTGGCCGCTTCTGT-3 ' (SEQ ID NO: 107) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0287 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal kidney tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0287 [herein designated as DNA39969-1185, SEQ ID NO: 103] and the derived protein sequence for PR0287.
The entire nucleotide sequence of DNA39969-1185 is shown in Figure 37 (SEQ ID NO: 103). Clone
DNA39969-1185 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 307-309 and ending at the stop codon at nucleotide positions 1552-1554 (Fig. 37; SEQ ID NO: 103). The predicted polypeptide precursor is 415 amino acids long (Fig. 38). Clone DNA39969-1185 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209400.
Analysis of the amino acid sequence of the full-length PR0287 suggests that it may possess one or more procollagen C-proteinase enhancer protein precursor or procollagen C-proteinase enhancer protein-like domains.
Based on a BLAST and FastA sequence alignment analysis of the full-length sequence, PR0287 shows nucleic acid sequence identity to procollagen C-proteinase enhancer protein precursor and procollagen C-proteinase enhancer protein (47 and 54% , respectively).
EXAMPLE 17: Isolation of cDNA Clones Encoding Human PRQ214
A consensus DNA sequence was assembled using phrap as described in Example 1 above. This consensus DNA sequence is designated herein as DNA28744. Based on this consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence.
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified below. A positive library was then used to isolate clones encoding the PR0214 gene using the probe oligonucleotide and one of the PCR primers.
RNA for construction of the cDNA libraries was isolated from human fetal lung tissue.
A cDNA clone was sequenced in its entirety. The full length nucleotide sequence of DNA32286-1191 is shown in Figure 39 (SEQ ID NO: 108). DNA32286-1191 contains a single open reading frame with an apparent translational initiation site at nucleotide position 103 (Fig. 39; SEQ ID NO: 108). The predicted polypeptide precursor is 420 amino acids long (SEQ ID NO: 109).
Based on a BLAST and FastA sequence alignment analysis of the full-length sequence, PR0214 polypeptide shows amino acid sequence identity to HT protein and/or Fibulin (49% and 38%, respectively). The oligonucleotide sequences used in the above procedure were the following: 28744.p (OLI555)
5'-CCTGGCTATCAGCAGGTGGGCTCCAAGTGTCTCGATGTGGATGAGTGTGA-3' (SEQ ID NO: 110) 28744.f (OLI556)
5'-ATTCTGCGTGAACACTGAGGGC-3' (SEQ ID NO: 111) 28744. r (OLI557)
5'-ATCTGCTTGTAGCCCTCGGCAC-3' (SEQ ID NO: 112)
EXAMPLE 18: Isolation of cDNA Clones Encoding Human PRQ317
A consensus DNA sequence was assembled using phrap as described in Example 1 above, wherein the consensus sequence is herein designated as DNA28722. Based on this consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence. The forward and reverse PCR primers, respectively, synthesized for this purpose were:
5'-AGGACTGCCATAACTTGCCTG (OLI489) (SEQ ID NO: 115) and 5'-ATAGGAGTTGAAGCAGCGCTGC (OLI490) (SEQ ID NO: 116). The probe synthesized for this purpose was:
5'-TGTGTGGACATAGACGAGTGCCGCTACCGCTACTGCCAGCACCGC (OLI488) (SEQ ID NO: 117) mRNA for construction of the cDNA libraries was isolated from human fetal kidney tissue. In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification, as per Ausubel et al. , Current Protocols in Molecular Biology ( 1989) , with the
PCR primer pair identified above. A positive library was then used to isolate clones containing the PR0317 gene using the probe oligonucleotide identified above and one of the PCR primers.
A cDNA clone was sequenced in its entirety. The entire nucleotide sequence of DNA33461-1199
(encoding PR0317) is shown in Figure 41 (SEQ ID NO: 113). Clone DNA33461-1199 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 68-70 (Fig. 41; SEQ ID
NO: 113). The predicted polypeptide precursor is 366 amino acids long. The predicted signal sequence is amino acids 1-18 of Figure 42 (SEQ ID NO: 114). There is one predicted N-linked glycosylation site at amino acid residue 160. Clone DNA33461-1199 has been deposited with ATCC and is assigned ATCC deposit no. ATCC
209367. Based on BLAST™ and FastA™ sequence alignment analysis (using the ALIGN™ computer program) of the full-length PR0317sequence, PR0317 shows the most amino acid sequence identity to EBAF-1 (92%).
The results also demonstrate a significant homology between human PR0317 and mouse LEFTY protein. The
C-terminal end of the PR0317 protein contains many conserved sequences consistent with the pattern expected of a member of the TGF- superfamily. In situ expression analysis in human tissues performed as described below evidences that there is distinctly strong expression of the PR0317 polypeptide in pancreatic tissue. EXAMPLE 19: Isolation of cDNA clones Encoding Human PRO301
A consensus DNA sequence designated herein as DNA35936 was assembled using phrap as described in Example 1 above. Based on this consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence. In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified below. A positive library was then used to isolate clones encoding the PRO301 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal kidney.
A cDNA clone was sequenced in its entirety. The full length nucleotide sequence of native sequence PRO301 is shown in Figure 43 (SEQ ID NO: 118). Clone DNA40628- 1216 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 52-54 (Fig. 43; SEQ ID NO: 118). The predicted polypeptide precursor is 299 amino acids long with a predicted molecular weight of 32,583 daltons and pi of 8.29. Clone DNA40628-1216 has been deposited with ATCC and is assigned ATCC deposit No. ATCC 209432. Based on a BLAST and FastA sequence alignment analysis of the full-length sequence, PRO301 shows amino acid sequence identity to A33 antigen precursor (30%) and coxsackie and adenovirus receptor protein (29%).
The oligonucleotide sequences used in the above procedure were the following:
OLI2162 (35936.fl) 5'-TCGCGGAGCTGTGTTCTGTTTCCC-3' (SEQ ID NO: 120) OLI2163 (35936.pl)
5'-TGATCGCGATGGGGACAAAGGCGCAAGCTCGAGAGGAAACTGTTGTGCCT-3' (SEQ ID NO: 121)
OLI2164 (35936.f2)
5'-ACACCTGGTTCAAAGATGGG-3' (SEQ ID NO: 122)
OLI2165 (35936.rl) 5'-TAGGAAGAGTTGCTGAAGGCACGG-3' (SEQ ID NO: 123)
OLI2166 (35936.f3)
5'-TTGCCTTACTCAGGTGCTAC-3' (SEQ ID NO: 124)
OLI2167 (35936.r2)
5'-ACTCAGCAGTGGTAGGAAAG-3' (SEQ ID NO: 125)
EXAMPLE 20: Isolation of cDNA Clones Encoding Human PRQ224
A consensus DNA sequence assembled relative to the other identified EST sequences as described in
Example 1 , wherein the consensus sequence is designated herein as DNA30845. Based on the DNA30845 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for PR0224. A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-AAGTTCCAGTGCCGCACCAGTGGC-3' (SEQ ID NO: 128) reverse PCR primer 5'-TTGGTTCCACAGCCGAGCTCGTCG-3' (SEQ ID NO:129)
Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA30845 sequence which had the following nucleotide sequence hybridization probe 5'-GAGGAGGAGTGCAGGATTGAGCCATGTACCCAGAAAGGGCAATGCCCACC-3' (SEQ ID NO: 130)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0224 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal liver tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0224 [herein designated as DNA33221-1133] and the derived protein sequence for PR0224.
The entire nucleotide sequence of DNA33221-1133 is shown in Figure 45 (SEQ ID NO: 126). Clone DNA33221-1133 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 33-35 and ending at the stop codon at nucleotide positions 879-899 (Figure 45; SEQ ID NO: 126). The start of a transmembrane region begins at nucleotide position 777. The predicted polypeptide precursor is 282 amino acids long (Figure 46). Clone DNA33221-1133 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209263.
Analysis of the amino acid sequence of the full-length PR0224 suggests that it has homology to very low-density lipoprotein receptors, apolipoprotein E receptor and chicken oocyte receptors P95. Based on a
BLAST and FastA sequence alignment analysis of the full-length sequence, PR0224 has amino acid identity to portions of these proteins in the range from 28% to 45%, and overall identity with these proteins in the range from 33% to 39% .
EXAMPLE 21: Isolation of cDNA Clones Encoding Human PRQ222
A consensus DNA sequence was assembled relative to the other identified EST sequences as described in Example 1 above, wherein the consensus sequence is designated herein as DNA28771. Based on the
DNA28771 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for PR0222.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5 ' -ATCTCCTATCGCTGCTTTCCCGG-3 ' (SEQ ID NO : 133) reverse PCR primer 5'-AGCCAGGATCGCAGTAAAACTCC-3' (SEQ ID NO: 134)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA28771 sequence which had the following nucleotide sequence: hybridization probe 5'-ATTTAAACTTGATGGGTCTGCGTATCTTGAGTGCTTACAAAACCTTATCT-3' (SEQ ID NO: 135)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0222 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal kidney tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0222 [herein designated as DNA33107-1135] and the derived protein sequence for PR0222.
The entire nucleotide sequence of DNA33107-1135 is shown in Figure 47 (SEQ ID NO: 131). Clone
DNA33107-1135 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 159-161 and ending at the stop codon at nucleotide positions 1629-1631 (Fig. 47; SEQ ID NO: 131). The predicted polypeptide precursor is 490 amino acids long (Fig. 48). Clone DNA33107-1135 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209251.
Based on a BLAST and FastA sequence alignment analysis of the full-length sequence, PR0222 shows amino acid sequence identity to mouse complement factor h precursor (25-26%), complement receptor (27-29%), mouse complement C3b receptor type 2 long form precursor (25-47 % ) and human hypothetical protein kiaa0247 (40%).
EXAMPLE 22: Isolation of cDNA clones Encoding PRQ234
A consensus DNA sequence was assembled (DNA30926) using phrap as described in Example 1 above.
Based on this consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence.
RNA for the constmction of the cDNA libraries was isolated using standard isolation protocols, e.g. ,
Ausubel et al. , Current Protocols in Molecular Biology , from tissue or cell line sources or it was purchased from commercial sources (e.g., Clontech). The cDNA libraries used to isolate the cDNA clones were constmcted by standard methods (e.g. , Ausubel et al.) using commercially available reagents (e.g. , Invitrogen). This library was derived from 22 week old fetal brain tissue.
A cDNA clone was sequenced in its entirety. The entire nucleotide sequence of PR0234 is shown in Figure 49 (SEQ ID NO: 136). The predicted polypeptide precursor is 382 amino acids long and has a calculated molecular weight of approximately 43.1 kDa.
The oligonucleotide sequences used in the above procedure were the following: 30926-p (OLI826) (SEQ ID NO: 138): 5'-GTTCATTGAAAACCTCTTGCCATCT GATGGTGACTTCTGGATTGGGCTC A-3 '
30926.f (OLI827) (SEQ ID NO: 139): 5'-AAGCCAAAGAAGCCTGCAGGAGGG-3' 30926.r (OLI828) (SEQ ID NO: 140): 5'-CAGTCCAAGCATAAAGGTCCTGGC-3'
EXAMPLE 23: Isolation of cDNA Clones Encoding Human PRQ231
A consensus DNA sequence was assembled relative to the other identified EST sequences as described in Example 1 above, wherein the consensus sequence was designated herein as DNA30933. Based on the
DNA30933 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for PR0231.
Three PCR primers (two forward and one reverse) were synthesized: forward PCR primer 1 5'-CCAACTACCAAAGCTGCTGGAGCC-3' (SEQ ID NO: 143) forward PCR primer 2 5 ' -GCAGCTCTATTACCACGGGAAGGA-3 ' (SEQ ID NO: 144) reverse PCR primer 5'-TCCTTCCCGTGGTAATAGAGCTGC-3' (SEQ ID NO: 145)
Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA30933 sequence which had the following nucleotide sequence hybridization probe 5'-GGCAGAGAACCAGAGGCCGGAGGAGACTGCCTCTTTACAGCCAGG-3' (SEQ ID NO: 146)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PR0231 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal liver tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for
PR0231 [herein designated as DNA34434-1139] and the derived protein sequence for PR0231.
The entire nucleotide sequence of DNA34434-1139 is shown in Figure 51 (SEQ ID NO: 141). Clone
DNA34434-1139 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 173-175 and ending at the stop codon at nucleotide positions 1457-1459 (Fig. 51; SEQ ID NO: 141). The predicted polypeptide precursor is 428 amino acids long (Fig. 52). Clone DNA34434-1139 has been deposited with ATCC on September 16, 1997 and is assigned ATCC deposit no. ATCC 209252.
Analysis of the amino acid sequence of the full-length PR0231 suggests that it possesses 30% and 31 % amino acid identity with the human and rat prostatic acid phosphatase precursor proteins, respectively.
EXAMPLE 24: Isolation of cDNA Clones Encoding Human PRQ229
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA28762. Based on the DNA28762 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0229.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-TTCAGCTCATCACCTTCACCTGCC-3' (SEQ ID NO: 149) reverse PCR primer 5 ' -GGCTCATACAAAATACCACTAGGG-3 ' (SEQ ID NO: 150)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA28762 sequence which had the following nucleotide sequence hybridization probe
5'-GGGCCTCCACCGCTGTGAAGGGCGGGTGGAGGTGGAACAGAAAGGCCAGT-3' (SEQ ID NO: 151) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0229 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal liver tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0229 [herein designated as DNA33100-1159] (SEQ ID NO: 147) and the derived protein sequence for PR0229.
The entire nucleotide sequence of DNA33100-1159 is shown in Figure 53 (SEQ ID NO: 147). Clone DNA33100- 1159 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 98-100 and ending at the stop codon at nucleotide positions 1139-1141 (Figure 53). The predicted polypeptide precursor is 347 amino acids long (Figure 54). Clone DNA33100-1159 has been deposited with ATCC and is assigned ATCC deposit no.ATCC 209377
Analysis of the amino acid sequence of the full-length PR0229 polypeptide suggests that portions of it possess significant homology to antigen wcl. l, M130 antigen and CD6.
EXAMPLE 25: Isolation of cDNA Clones Encoding Human PRQ238
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described above in Example 1. This consensus sequence is herein designated DNA30908. Based on the DNA30908 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PR0238.
PCR primers (forward and reverse) were synthesized: forward PCR primer 1 5'-GGTGCTAAACTGGTGCTCTGTGGC-3' (SEQ ID NO: 154) forward PCR primer 2 5'-CAGGGCAAGATGAGCATTCC-3' (SEQ ID NO: 155) reverse PCR primer 5'-TCATACTGTTCCATCTCGGCACGC-3* (SEQ ID NO: 156)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA30908 sequence which had the following nucleotide sequence hybridization probe
5'-AATGGTGGGGCCCTAGAAGAGCTCATCAGAGAACTCACCGCTTCTCATGC-3' (SEQ ID NO: 157) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0238 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal liver tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0238 and the derived protein sequence for PR0238.
The entire nucleotide sequence of DNA35600-1162 is shown in Figure 55 (SEQ ID NO: 152). Clone
DNA35600-1162 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 134-136 and ending prior to the stop codon at nucleotide positions 1064-1066 (Figure 55). The predicted polypeptide precursor is 310 amino acids long (Figure 56). Clone DNA35600-1162 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209370.
Analysis of the amino acid sequence of the full-length PR0238 polypeptide suggests that portions of it possess significant homology to reductase, particularly oxidoreductase, thereby indicating that PR0238 may be a novel reductase.
EXAMPLE 26: Isolation of cDNA Clones Encoding Human PRQ233
The extracellular domain (ECD) sequences (including the secretion signal, if any) of from about 950 known secreted proteins from the Swiss-Prot public protein database were used to search expressed sequence tag (EST) databases. The EST databases included public EST databases (e.g. , GenBank) and a proprietary EST
DNA database (LIFESEQ™, Incyte Pharmaceuticals, Palo Alto, CA). The search was performed using the computer program BLAST or BLAST2 (Altshul et al., Methods in Enzymology 266:460-480 (1996)) as a comparison of the ECD protein sequences to a 6 frame translation of the EST sequence. Those comparisons resulting in a BLAST score of 70 (or in some cases 90) or greater that did not encode known proteins were clustered and assembled into consensus DNA sequences with the program "phrap" (Phil Green, University of
Washington, Seattle, Washington; http://bozeman.mbt.washington.edu/phrap.docs/phrap.html).
An expressed sequence tag (EST) was identified by the EST database search and a consensus DNA sequence was assembled relative to other EST sequences using phrap. This consensus sequence is herein designated DNA30945. Based on the DNA30945 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0233.
Forward and reverse PCR primers were synthesized: forward PCR primer 5'-GGTGAAGGCAGAAATTGGAGATG-3' (SEQ ID NO: 160) reverse PCR primer 5'-ATCCCATGCATCAGCCTGTTTACC-3' (SEQ ID NO: 161) Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA30945 sequence which had the following nucleotide sequence hybridization probe
5 ' -GCTGGTGTAGTCTATAC ATC AG ATTTGTTTGCTAC AC AAGATCCTC AG-3 '
(SEQ ID NO: 162) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0233 gene using the probe oligonucleotide.
RNA for constmction of the cDNA libraries was isolated from human fetal brain tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0233 [herein designated as DNA34436-1238] (SEQ ID NO: 158) and the derived protein sequence for
PR0233.
The entire nucleotide sequence of DNA34436-1238 is shown in Figure 57 (SEQ ID NO: 158). Clone
DNA34436-1238 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 101-103 and ending at the stop codon at nucleotide positions 1001-1003 (Figure 57). The predicted polypeptide precursor is 300 amino acids long (Figure 58). The full-length PR0233 protein shown in Figure
58 has an estimated molecular weight of about 32,964 daltons and a pi of about 9.52. Clone DNA34436-1238 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209523. Analysis of the amino acid sequence of the full-length PR0233 polypeptide suggests that portions of it possess significant homology to reductase proteins, thereby indicating that PR0233 may be a novel reductase.
EXAMPLE 27: Isolation of cDNA Clones Encoding Human PRQ223
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA30836. Based on the DNA30836 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PR0223.
PCR primer pairs (one forward'and two reverse) were synthesized: forward PCR primer 5'-TTCCATGCCACCTAAGGGAGACTC-3' (SEQ ID NO: 165) reverse PCR primer 1 5'-TGGATGAGGTGTGCAATGGCTGGC-3' (SEQ ID NO: 166) reverse PCR primer 2 5'-AGCTCTCAGAGGCTGGTCATAGGG-3' (SEQ ID NO: 167) Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA30836 sequence which had the following nucleotide sequence hybridization probe
5*-GTCGGCCCTTTCCCAGGACTGAACATGAAGAGTTATGCCGGCTTCCTCAC-3' (SEQ ID NO: 168) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0223 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal liver tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0223 [herein designated as DNA33206-1165] (SEQ ID NO: 163) and the derived protein sequence for PR0223.
The entire nucleotide sequence of DNA33206-1165 is shown in Figure 59 (SEQ ID NO: 163). Clone DNA33206-1165 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 97-99 and ending at the stop codon at nucleotide positions 1525-1527 (Figure 59). The predicted polypeptide precursor is 476 amino acids long (Figure 60). Clone DNA33206-1165 has been deposited with
ATCC and is assigned ATCC deposit no. ATCC 209372.
Analysis of the amino acid sequence of the full-length PR0223 polypeptide suggests that it possesses significant homology to various serine carboxypeptidase proteins , thereby indicating that PR0223 may be a novel serine carboxypeptidase.
EXAMPLE 28: Isolation of cDNA Clones Encoding Human PRQ235
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated "DNA30927" . Based on the DNA30927 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0235.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-TGGAATACCGCCTCCTGCAG-3' (SEQ ID NO: 171) reverse PCR primer 5 ' -CTTCTGCCCTTTGGAGA AGATGGC-3 ' (SEQ ID NO: 172)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA30927 sequence which had the following nucleotide sequence hybridization probe 5'-GGACTCACTGGCCCAGGCCTTCAATATCACCAGCCAGGACGAT-3' (SEQ ID NO: 173)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0235 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal liver tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0235 [herein designated as DNA35558-1167] (SEQ ID NO: 169) and the derived protein sequence for PR0235. The entire nucleotide sequence of DNA35558-1167 is shown in Figure 61 (SEQ ID NO: 169). Clone
DNA35558-1167 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 667-669 and ending at the stop codon at nucleotide positions 2323-2325 (Figure 61). The predicted polypeptide precursor is 552 amino acids long (Figure 62). Clone DNA35558-1167 has been deposited with ATCC and is assigned ATCC deposit no. 209374. Analysis of the amino acid sequence of the full-length PR0235 polypeptide suggests that portions of it possess significant homology to the human, mouse and Xenopus plexin protein, thereby indicating that PR0235 may be a novel plexin protein.
EXAMPLE 29: Isolation of cDNA Clones Encoding Human PRQ236 and Human PRQ262 Consensus DNA sequences were assembled relative to other EST sequences using phrap as described in Example 1 above. These consensus sequences are herein designated DNA30901 and DNA30847. Based on the DNA30901 and DNA30847 consensus sequences, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full- length coding sequence for PR0236 and PR0262, respectively. Based upon the DNA30901 consensus sequence, a pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-TGGCTACTCCAAGACCCTGGCATG-3' (SEQ ID NO: 178) reverse PCR primer 5'-TGGACAAATCCCCTTGCTCAGCCC-3' (SEQ ID NO: 179)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA30901 sequence which had the following nucleotide sequence hybridization probe 5'-GGGCTTCACCGAAGCAGTGGACCTTTATTTTGACCACCTGATGTCCAGGG-3' (SEQ ID NO: 180) Based upon the DNA30847 consensus sequence, a pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-CCAGCTATGACTATGATGCACC-3' (SEQ ID NO: 181) reverse PCR primer 5 '-TGGCACCCAGAATGGTGTTGGCTC-3 ' (SEQ ID NO: 182)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA30847 sequence which had the following nucleotide sequence hybridization probe 5'-CGAGATGTCATCAGCAAGTTCCAGGAAGTTCCTTTGGGACCTTTACCTCC-3' (SEQ ID NO: 183)
In order to screen several libraries for a source of full-length clones, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. Positive libraries were then used to isolate clones encoding the PR0236 and PR0262 genes using the probe oligonucleotides and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue for PR0236 and human fetal liver tissue for PR0262.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0236 [herein designated as DNA35599-1168] (SEQ ID NO: 174), the derived protein sequence for PR0236, the full-length DNA sequence for PR0262 [herein designated as DNA36992-1168] (SEQ ID NO: 176) and the derived protein sequence for PR0262.
The entire nucleotide sequence of DNA35599-1168 is shown in Figure 63 (SEQ ID NO: 174). Clone
DNA35599-1168 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 69-71 and ending at the stop codon at nucleotide positions 1977-1979 (Figure 63). The predicted polypeptide precursor is 636 amino acids long (Figure 64). Clone DNA35599-1168 has been deposited with
ATCC and is assigned ATCC deposit no. ATCC 209373.
The entire nucleotide sequence of DNA36992-1168 is shown in Figure 65 (SEQ ID NO: 176). Clone
DNA36992-1168 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 240-242 and ending at the stop codon at nucleotide positions 2202-2204 (Figure 65). The predicted polypeptide precursor is 654 amino acids long (Figure 66). Clone DNA36992-1168 has been deposited with
ATCC and is assigned ATCC deposit no. ATCC 209382.
Analysis of the amino acid sequence of the full-length PR0236 and PR0262 polypeptides suggests that portions of those polypeptides possess significant homology to β-galactosidase proteins derived from various sources, thereby indicating that PR0236 and PR0262 may be novel β-galactosidase homologs.
EXAMPLE 30: Isolation of cDNA Clones Encoding Human PRQ239
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA30909. Based on the DNA30909 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PR0239. A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-CCTCCCTCTATTACCCATGTC-3' (SEQ ID NO: 186) reverse PCR primer 5'-GACCAACTTTCTCTGGGAGTGAGG-3' (SEQ ID NO: 187)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA30909 sequence which had the following nucleotide sequence hybridization probe
5'-GTCACTTTATTTCTCTAACAACAAGCTCGAATCCTTACCAGTGGCAG-3' (SEQ ID NO:188)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0239 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0239 [herein designated as DNA34407-1169] (SEQ ID NO: 184) and the derived protein sequence for PR0239. The entire nucleotide sequence of DNA34407-1169 is shown in Figure 67 (SEQ ID NO: 184). Clone
DNA34407-1169 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 72-74 and ending at the stop codon at nucleotide positions 1575-1577 (Figure 67). The predicted polypeptide precursor is 501 amino acids long (Figure 68). Clone DNA34407-1169 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209383. Analysis of the amino acid sequence of the full-length PR0239 polypeptide suggests that portions of it possess significant homology to the densin protein, thereby indicating that PR0239 may be a novel molecule in the densin family.
EXAMPLE 31 : Isolation of cDNA Clones Encoding Human PRQ257 A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA28731. Based on the DNA28731 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0257. A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-TCTCTATTCCAAACTGTGGCG-3' (SEQ ID NO: 191) reverse PCR primer 5'-TTTGATGACGATTCGAAGGTGG-3' (SEQ ID NO: 192)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA28731 sequence which had the following nucleotide sequence hybridization probe
5'-GGAAGGATCCTTCACCAGCCCCAATTACCCAAAGCCGCATCCTGAGC-3' (SEQ ID NO: 193) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0257 gene using the probe oligonucleotide and one of the PCR primers.
RNA for construction of the cDNA libraries was isolated from human fetal kidney tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0257 [herein designated as DNA35841-1173 (SEQ ID NO: 189) and the derived protein sequence for PR0257.
The entire nucleotide sequence of DNA35841-1173 is shown in Figure 69 (SEQ ID NO: 189). Clone
DNA35841-1173 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 964-966 and ending at the stop codon at nucleotide positions 2785-2787 (Figure 69). The predicted polypeptide precursor is 607 amino acids long (Figure 70). Clone DN A35841-1173 has been deposited with
ATCC and is assigned ATCC deposit no. ATCC 209403.
Analysis of the amino acid sequence of the full-length PR0257 polypeptide suggests that portions of it possess significant homology to the ebnerin protein, thereby indicating that PR0257 may be a novel protein member related to the ebnerin protein.
EXAMPLE 32: Isolation of cDNA Clones Encoding Human PRO260
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA30834. Based on the DNA30834 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PRO260.
PCR primers (forward and two reverse) were synthesized: forward PCR primer: 5'-TGGTTTGACCAGGCCAAGTTCGG-3' (SEQ ID NO: 196); reverse PCR primer A: 5'-GGATTCATCCTCAAGGAAGAGCGG-3' (SEQ ID NO: 197); and reverse PCR primer B: 5ΑACTTGCAGCATCAGCCACTCTGC-3' (SEQ ID NO: 198)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA30834 sequence which had the following nucleotide sequence: hybridization probe:
5'-TTCCGTGCCCAGCTTCGGTAGCGAGTGGTTCTGGTGGTATTGGCA-3' (SEQ ID NO: 199) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PRO260 gene using the probe oligonucleotide and one of the PCR primers.
RNA for construction of the cDNA libraries was isolated from human fetal kidney tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO260 [herein designated as DNA33470-1175] (SEQ ID NO: 194) and the derived protein sequence for PRO260. The entire nucleotide sequence of DNA33470-1175 is shown in Figure 71 (SEQ ID NO: 194). Clone DNA33470-1175 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 67-69 and ending at the stop codon 1468-1470 (see Figure 71). The predicted polypeptide precursor is 467 amino acids long (Figure 72). Clone DNA33470-1175 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209398. Analysis of the amino acid sequence of the full-length PRO260 polypeptide suggests that portions of it possess significant homology to the alpha-1-fucosidase precursor, thereby indicating that PRO260 may be a novel fucosidase.
EXAMPLE 33: Isolation of cDNA Clones Encoding Human PRQ263 A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA30914. Based on the DNA30914 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PR0263. PCR primers (tow forward and one reverse) were synthesized: forward PCR primer 1 : 5'-GAGCTTTCCATCCAGGTGTCATGC-3' (SEQ ID NO:202); forward PCR primer 2: 5'-GTCAGTGACAGTACCTACTCGG-3' (SEQ ID NO:203): reverse PCR primer: 5'-TGGAGCAGGAGGAGTAGTAGTAGG-3' (SEQ ID NO:204)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA30914 sequence which had the following nucleotide sequence: hybridization probe:
5'-AGGAGGCCTGTAGGCTGCTGGGACTAAGTTTGGCCGGCAAGGACCAAGTT-3' (SEQ ID NO:205) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0263 gene using the probe oligonucleotide and one of the PCR primers. RNA for construction of the cDNA libraries was isolated from human fetal liver tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for
PR0263 [herein designated as DNA34431-1177] (SEQ ID NO:200) and the derived protein sequence for
PR0263. The entire nucleotide sequence of DNA34431-1177 is shown in Figure 73 (SEQ ID NO:200). Clone
DNA34431-1177 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 160-162 of SEQ ID NO:200 and ending at the stop codon after the nucleotide at position 1126-1128 of SEQ ID NO:200 (Figure 73). The predicted polypeptide precursor is 322 amino acids long (Figure 74).
Clone DNA34431-1177 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209399. Analysis of the amino acid sequence of the full-length PR0263 polypeptide suggests that portions of it possess significant homology to CD44 antigen, thereby indicating that PR0263 may be a novel cell surface adhesion molecule. EXAMPLE 34: Isolation of cDNA Clones Encoding Human PRO270
A consensus DNA sequence was assembled relative to the other identified EST sequences as described in Example 1 above, wherein the consensus sequence was designated herein as DNA35712. Based on the
DNA35712 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PRO270. Forward and reverse PCR primers were synthesized: forward PCR primer (.fl) 5'-GCTTGGATATTCGCATGGGCCTAC-3' (SEQ ID NO: 208) forward PCR primer (.f2) 5'-TGGAGACAATATCCCTGAGG-3' (SEQ ID NO.209) reverse PCR primer (.rl) 5'-AACAGTTGGCCACAGCATGGCAGG-3' (SEQ ID NO:210) Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA35712 sequence which had the following nucleotide sequence hybridization probe
5 ' -CCATTGATGAGGAACTAGAACGGGACAAGAGGGTCACTTGGATTGTGGAG-3 ' (SEQ ID NO:211)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PRO270 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO270 [herein designated as DNA39510-1181] (SEQ ID NO:206) and the derived protein sequence for PRO270.
The entire nucleotide sequence of DNA39510-1181 is shown in Figure 75 (SEQ ID NO:206). Clone
DNA39510-1181 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 3-5 and ending at the stop codon at nucleotide positions 891-893 (Fig. 75; SEQ ID NO:206). The predicted polypeptide precursor is 296 amino acids long (Fig. 76). Clone DNA39510-1181 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209392.
Analysis of the amino acid sequence of the full-length PRO270 suggests that portions of it possess significant homology to the thioredoxin-protein, thereby indicating that the PRO270 protein may be a novel member of the thioredoxin family.
EXAMPLE 35: Isolation of cDNA Clones Encoding Human PRQ271
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA35737. Based on the DNA35737 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0271.
Forward and reverse PCR primers were synthesized: forward PCR primer 1 5'-TGCTTCGCTACTGCCCTC-3' (SEQ ID NO:214) forward PCR primer 2 5'-TTCCCTTGTGGGTTGGAG-3' (SEQ ID NO:215) forward PCR primer 3 5'-AGGGCTGGAAGCCAGTTC-3' (SEQ ID NO:216) reverse PCR primer 1 5'-AGCCAGTGAGGAAATGCG-3' (SEQ ID NO:217) reverse PCR primer 2 5'-TGTCCAAAGTACACACACCTGAGG-3' (SEQ ID NO:218) Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA35737 sequence which had the following nucleotide sequence hybridization probe 5'-GATGCCACGATCGCCAAGGTGGGACAGCTCTTTGCCGCCTGGAAG-3' (SEQ ID NO:219)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0271 gene using the probe oligonucleotide and one of the PCR primers.
RNA for construction of the cDNA libraries was isolated from human fetal brain tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0271 [herein designated as DNA39423-1182] (SEQ ID NO:212) and the derived protein sequence for PR0271. The entire nucleotide sequence of DNA39423-1182 is shown in Figure 77 (SEQ ID NO:212). Clone
DNA39423-1182 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 101-103 and ending at the stop codon at nucleotide positions 1181-1183 (Figure 77). The predicted polypeptide precursor is 360 amino acids long (Figure 78). Clone DNA39423-1182 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209387. Analysis of the amino acid sequence of the full-length PR0271 polypeptide suggests that it possess significant homology to the proteoglycan link protein, thereby indicating that PR0271 may be a link protein homolog.
EXAMPLE 36: Isolation of cDNA Clones Encoding Human PRQ272 A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA36460. Based on the DNA36460 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0272. Forward and reverse PCR primers were synthesized: forward PCR primer (.fl) 5'-CGCAGGCCCTCATGGCCAGG-3' (SEQ ID NO:222) forward PCR primer (.f2) 5'-GAAATCCTGGGTAATTGG-3' (SEQ ID NO:223) reverse PCR primer 5'-GTGCGCGGTGCTCACAGCTCATC-3' (SEQ ID NO:224)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA36460 sequence which had the following nucleotide sequence hybridization probe 5'-CCCCCCTGAGCGACGCTCCCCCATGATGACGCCCACGGGAACTTC-3' (SEQ ID NO: 225) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PR0272 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0272 [herein designated as DNA40620-1183] (SEQ ID NO:220) and the derived protein sequence for PR0272.
The entire nucleotide sequence of DNA40620-1183 is shown in Figure 79 (SEQ ID NO:220). Clone
DNA40620-1183 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 35-37 and ending at the stop codon at nucleotide positions 1019-1021 (Figure 79). The predicted polypeptide precursor is 328 amino acids long (Figure 80). Clone DNA40620-1183 has been deposited with
ATCC and is assigned ATCC deposit no. ATCC 209388.
Analysis of the amino acid sequence of the full-length PR0272 polypeptide suggests that portions of it possess significant homology to the human and mouse reticulocalbin proteins, respectively, thereby indicating that PR0272 may be a novel reticulocalbin protein.
EXAMPLE 37: Isolation of cDNA Clones Encoding Human PRQ294
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA35731. Based on the DNA35731 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PR0294.
Forward and reverse PCR primers were synthesized: forward PCR primer (.fl) 5'-TGGTCTCGCACACCGATC-3' (SEQ ID NO: 228) forward PCR primer (.f2) 5'-CTGCTGTCCACAGGGGAG-3' (SEQ ID NO: 229) forward PCR primer (.13) 5'-CCTTGAAGCATACTGCTC-3' (SEQ ID NO: 230) forward PCR primer (.f4) 5'-GAGATAGCAATTTCCGCC-3' (SEQ ID NO:231) reverse PCR primer (.rl) 5'-TTCCTCAAGAGGGCAGCC-3' (SEQ ID NO:232) reverse PCR primer (.r2) 5'-CTTGGCACCAATGTCCGAGATTTC-3'
(SEQ ID NO:233) Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA35731 sequence which had the following nucleotide sequence hybridization probe
5 ' -GCTCTGAGGA AGGTGACGCGCGGGGCCTCCGAACCCTTGGCCTTG-3 ' (SEQ ID NO:234) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PR0294 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal brain tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0294 [herein designated as DNA40604-1187] (SEQ ID NO: 226) and the derived protein sequence for PR0294.
The entire nucleotide sequence of DNA40604-1187 is shown in Figure 81 (SEQ ID NO:226). Clone DNA40604-1187 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 396-398 and ending at the stop codon at nucleotide positions 2046-2048 (Figure 81). The predicted polypeptide precursor is 550 amino acids long (Figure 82). Clone DNA40604-1187 has been deposited with
ATCC and is assigned ATCC deposit no. 209394.
Analysis of the amino acid sequence of the full-length PR0294 polypeptide suggests that portions of it possess significant homology to portions of various collagen proteins, thereby indicating that PR0294 may be collagen-like molecule.
EXAMPLE 38: Isolation of cDNA Clones Encoding Human PRQ295
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA35814. Based on the DNA35814 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PR0295.
Forward and reverse PCR primers were synthesized: forward PCR primer (.fl) 5'-GCAGAGCGGAGATGCAGCGGCTTG-3'
(SEQ ID NO:238) forward PCR primer Lf2) 5'-CCCAGCATGTACTGCCAG-3' (SEQ ID NO:239) forward PCR primer CO) 5'-TTGGCAGCTTCATGGAGG-3' (SEQ ID NO:240) forward PCR primer (,f4) 5'-CCTGGGCAAAAATGCAAC-3' (SEQ ID NO:241) reverse PCR primer (.rl) 5'-CTCCAGCTCCTGGCGCACCTCCTC-3' (SEQ ID NO: 242)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA35814 sequence which had the following nucleotide sequence hybridization probe
5'-GGCTCTCAGCTACCGCGCAGGAGCGAGGCCACCCTCAATGAGATG-3' (SEQ ID NO:243)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PR0295 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for
PR0295 [herein designated as DNA38268-1188] (SEQ ID N0:235) and the derived protein sequence for
PR0295. The entire nucleotide sequence of DNA38268-1188 is shown in Figure 83 (SEQ ID NO:235). Clone DNA38268-1188 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 153-155 and ending at the stop codon at nucleotide positions 1202-1204 (Figure 83). The predicted polypeptide precursor is 350 amino acids long (Figure 84). Clone DNA38268-1188 has been deposited with ATCC and is assigned ATCC deposit no. 209421. Analysis of the amino acid sequence of the full-length PR0295 polypeptide suggests that portions of it possess significant homology to the integrin proteins, thereby indicating that PR0295 may be a novel integrin.
EXAMPLE 39: Isolation of cDNA Clones Encoding Human PRQ293
The extracellular domain (ECD) sequences (including the secretion signal, if any) of from about 950 known secreted proteins from the Swiss-Prot public protein database were used to search expressed sequence tag (EST) databases. The EST databases included public EST databases (e.g. , GenBank) and a proprietary EST DNA database (LIFESEQ™, Incyte Pharmaceuticals, Palo Alto, CA). The search was performed using the computer program BLAST or BLAST2 (Altshul et al., Methods in Enzymology 266:460-480 (1996)) as a comparison of the ECD protein sequences to a 6 frame translation of the EST sequence. Those comparisons resulting in a BLAST score of 70 (or in some cases 90) or greater that did not encode known proteins were clustered and assembled into consensus DNA sequences with the program "phrap" (Phil Green, University of Washington, Seattle, Washington; http://bozeman.mbt.washington.edu/phrap.docs/phrap.html).
Based on an expression tag sequence designated herein as T08294 identified in the above analysis, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0293.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-AACAAGGTAAGATGCCATCCTG-3' (SEQ ID NO: 246) reverse PCR primer 5'-AAACTTGTCGATGGAGACCAGCTC-3' (SEQ ID NO: 247)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the expression sequence tag which had the following nucleotide sequence hybridization probe 5'-AGGGGCTGCAAAGCCTGGAGAGCCTCTCCTTCTATGACAACCAGC-3' (SEQ ID NO:248)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0293 gene using the probe oligonucleotide and one of the PCR primers.
RNA for construction of the cDNA libraries was isolated from human fetal brain tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0293 [herein designated as DNA37151-1193] (SEQ ID NO: 244) and the derived protein sequence for PR0293. The entire nucleotide sequence of DNA37151-1 193 is shown in Figure 85 (SEQ ID NO:244). Clone
DNA37151 - 1193 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 881-883 and ending at the stop codon after nucleotide position 3019 of SEQ ID NO:244, Figure 85). The predicted polypeptide precursor is 713 amino acids long (Figure 86). Clone DNA37151-1193 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209393.
Analysis of the amino acid sequence of the full-length PR0293 polypeptide suggests that portions of it possess significant homology to the NLRR proteins, thereby indicating that PR0293 may be a novel NLRR protein.
EXAMPLE 40: Isolation of cDNA Clones Encoding Human PRQ247
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA33480. Based on the DNA33480 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PR0247.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-CAACAATGAGGGCACCAAGC-3' (SEQ ID NO:251) reverse PCR primer 5'-GATGGCTAGGTTCTGGAGGTTCTG-3' (SEQ ID NO:252) Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the DNA33480 expression sequence tag which had the following nucleotide sequence hybridization probe 5'-CAACCTGCAGGAGATTGACCTCAAGGACAACAACCTCAAGACCATCG-3' (SEQ ID NO:253)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0247 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal brain tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0247 [herein designated as DNA35673-1201] (SEQ ID NO:249) and the derived protein sequence for PR0247.
The entire nucleotide sequence of DNA35673-1201 is shown in Figure 89 (SEQ ID NO:249). Clone
DNA35673-1201 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 80-82 of SEQ ID NO: 249 and ending at the stop codon after nucleotide position 1717 of SEQ ID
NO: 249 (Figure 89). The predicted polypeptide precursor is 546 amino acids long (Figure 88). Clone DNA35673-1201 has been deposited with ATCC and is assigned ATCC deposit no. 209418.
Analysis of the amino acid sequence of the full-length PR0247 polypeptide suggests that portions of it possess significant homology to the densin molecule and KIAA0231 , thereby indicating that PR0247 may be a novel leucine rich repeat protein. EXAMPLE 41 : Isolation of cDNA Clones Encoding Human PRO302. PRO303. PRO304. PRO307 and
PRQ343
Consensus DNA sequences were assembled relative to other EST sequences using phrap as described in Example 1 above. These consensus sequences are herein designated DNA35953, DNA35955, DNA35958,
DNA37160 and DNA30895. Based on the DNA35953 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PRO302.
PCR primers (forward and reverse) were synthesized: forward PCR primer 1 5'-GTCCGCAAGGATGCCTACATGTTC-3' (SEQ ID NO:264) forward PCR primer 2 5'-GCAGAGGTGTCTAAGGTTG-3' (SEQ ID NO:265) reverse PCR primer 5'-AGCTCTAGACCAATGCCAGCTTCC-3' (SEQ ID NO: 266)
Also, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA35953 sequence which had the following nucleotide sequence hybridization probe
5'-GCCACCAACTCCTGCAAGAACTTCTCAGAACTGCCCCTGGTCATG-3' (SEQ ID NO:267) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PRO302 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal kidney tissue (LIB228). DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO302 [herein designated as DNA40370-1217] (SEQ ID NO:254) and the derived protein sequence for PRO302.
The entire nucleotide sequence of DNA40370-1217 is shown in Figure 89 (SEQ ID NO:254). Clone DNA40370-1217 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 34-36 and ending at the stop codon at nucleotide positions 1390-1392 (Figure 89). The predicted polypeptide precursor is 452 amino acids long (Figure 90). Various unique aspects of the PRO302 protein are shown in Figure 90. Clone DNA40370-1217 has been deposited with the ATCC on November 21, 1997 and is assigned ATCC deposit no. ATCC 209485.
Based on the DNA35955 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full- length coding sequence for PRO303.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-GGGGAATTCACCCTATGACATTGCC-3' (SEQ ID NO:268) reverse PCR primer 5'-GAATGCCCTGCAAGCATCAACTGG-3' (SEQ ID NO: 269)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA35955 sequence which had the following nucleotide sequence: hybridization probe 5'-GCACCTGTCACCTACACTAAACACATCCAGCCCATCTGTCTCCAGGCCTC-3' (SEQ ID NO:270) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PRO303 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue (LIB25).
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO303 [herein designated as DNA42551-1217] (SEQ ID NO:256) and the derived protein sequence for PRO303.
The entire nucleotide sequence of DNA42551-1217 is shown in Figure 91 (SEQ ID NO:256). Clone DNA42551-1217 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 20-22 and ending at the stop codon at nucleotide positions 962-964 (Figure 91). The predicted polypeptide precursor is 314 amino acids long (Figure 92). Various unique aspects of the PRO303 protein are shown in Figure 92. Clone DNA42551-1217 has been deposited on November 21, 1997 with the ATCC and is assigned ATCC deposit no. ATCC 209483.
Based on the DNA35958 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full- length coding sequence for PRO304.
Pairs of PCR primers (forward and reverse) were synthesized: forward PCR primer 1 5'-GCGGAAGGGCAGAATGGGACTCCAAG-3' (SEQ ID NO:271) forward PCR primer 2 5'-CAGCCCTGCCACATGTGC-3' (SEQ ID NO:272) forward PCR primer 3 5'-TACTGGGTGGTCAGCAAC-3' (SEQ ID NO:273) reverse PCR primer 5'-GGCGAAGAGCAGGGTGAGACCCCG-3' (SEQ ID NO: 274)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA35958 sequence which had the following nucleotide sequence hybridization probe
5'-GCCCTCATCCTCTCTGGCAAATGCAGTTACAGCCCGGAGCCCGAC-3' (SEQ ID NO:275) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PRO304 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from 22 week human fetal brain tissue (LIB153). DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for
PRO304 [herein designated as DNA39520-1217] (SEQ ID NO:258) and the derived protein sequence for PRO304.
The entire nucleotide sequence of DNA39520-1217 is shown in Figure 93 (SEQ ID NO:258). Clone
DNA39520-1217 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 34-36 and ending at the stop codon at nucleotide positions 1702-1704 (Figure 93). The predicted polypeptide precursor is 556 amino acids long (Figure 94). Various unique aspects of the PRO304 protein are shown in Figure 94. Clone DNA39520-1217 has been deposited with ATCC on November 21, 1997 and is assigned ATCC deposit no. ATCC 209482.
Based on the DNA37160 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full- length coding sequence for PRO307.
Pairs of PCR primers (forward and reverse) were synthesized: forward PCR primer 1 5'-GGGCAGGGATTCCAGGGCTCC-3' (SEQ ID NO:276) forward PCR primer 2 5'-GGCTATGACAGCAGGTTC-3' (SEQ ID NO:277) forward PCR primer 3 5'-TGACAATGACCGACCAGG-3' (SEQ ID NO:278) reverse PCR primer 5'-GCATCGCATTGCTGGTAGAGCAAG-3' (SEQ ID NO:279)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA37160 sequence which had the following nucleotide sequence hybridization probe 5'-TTACAGTGCCCCCTGGAAACCCACTTGGCCTGCATACCGCCTCCC-3' (SEQ ID NO:280)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PRO307 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal liver tissue (LIB229).
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO307 [herein designated as DNA41225-1217] (SEQ ID NO: 260) and the derived protein sequence for PRO307. The entire nucleotide sequence of DNA41225-1217 is shown in Figure 95 (SEQ ID NO:260). Clone
DNA41225-1217 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 92-94 and ending at the stop codon at nucleotide positions 1241-1243 (Figure 95). The predicted polypeptide precursor is 383 amino acids long (Figure 96). Various unique aspects of the PRO307 protein are shown in Figure 96. Clone DNA41225-1217 has been deposited with ATCC on November 21, 1997 and is assigned ATCC deposit no. ATCC 209491.
Based on the DNA30895 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full- length coding sequence for PR0343.
A pair of PCR primers (forward and reverse) were synthesized: forward PCR primer 5'-CGTCTCGAGCGCTCCATACAGTTCCCTTGCCCCA-3' (SEQ ID NO:281) reverse PCR primer
5 ' -TGGAGGGGGAGCGGGATGCTTGTCTGGGCGACTCCGGGGGCC CCCTCATGTGCCAGGTGGA-3' (SEQ ID NO:282)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA30895 sequence which had the following nucleotide sequence hybridization probe
5'-CCCTCAGACCCTGCAGAAGCTGAAGGTTCCTATCATCGACTCGGAAGTCTGCAGCCATCTG TACTGGCGGGGAGCAGGACAGGGACCCATCACTGAGGACATGCTGTGTGCCGGCTACT-3' (SEQID NO:283)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PR0343 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue (LIB26).
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0343 [herein designated as DNA43318-1217] (SEQ ID NO:262) and the derived protein sequence for PR0343.
The entire nucleotide sequence of DNA43318-1217 is shown in Figure 97 (SEQ ID NO:262). Clone DNA43318-1217 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 53-55 and ending at the stop codon at nucleotide positions 1004-1006 (Figure 97). The predicted polypeptide precursor is 317 amino acids long (Figure 98). Various unique aspects of the PR0343 protein are shown in Figure 98. Clone DNA43318-1217 has been deposited with ATCC on November 21, 1997 and is assigned ATCC deposit no. ATCC 209481.
EXAMPLE 42: Isolation of cDNA Clones Encoding Human PRQ328
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA35615. Based on the DNA35615 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PR0328.
Forward and reverse PCR primers were synthesized: forward PCR primer 5'-TCCTGCAGTTTCCTGATGC-3' (SEQ ID NO:286) reverse PCR primer 5'-CTCATATTGCACACCAGTAATTCG-3' (SEQ ID NO:287)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA35615 sequence which had the following nucleotide sequence hybridization probe 5 ' -ATGAGGAGAAACGTTTGATGGTGGAGCTGCAC AACCTCTACCGGG-3 '
(SEQ ID NO:288)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0328 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal kidney tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for
PR0328 [herein designated as DNA40587-1231] (SEQ ID NO:284) and the derived protein sequence for PR0328.
The entire nucleotide sequence of DNA40587-1231 is shown in Figure 99 (SEQ ID NO:284). Clone
DNA40587-1231 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 15-17 and ending at the stop codon at nucleotide positions 1404-1406 (Figure 99). The predicted polypeptide precursor is 463 amino acids long (Figure 100). Clone DNA40587-1231 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209438.
Analysis of the amino acid sequence of the full-length PR0328 polypeptide suggests that portions of it possess significant homology to the human glioblastoma protein and to the cysteine rich secretory protein thereby indicating that PR0328 may be a novel glioblastoma protein or cysteine rich secretory protein.
EXAMPLE 43: Isolation of cDNA Clones Encoding Human PRQ335. PRQ331 or PRQ326
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA36685. Based on the DNA36685 consensus sequence, and Incyte EST sequence no. 2228990, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0335, PR0331 or PR0326.
Forward and reverse PCR primers were synthesized for the determination of PR0335: forward PCR primer 5'-GGAACCGAATCTCAGCTA-3' (SEQ ID NO:295) forward PCR primer 5'-CCTAAACTGAACTGGACCA-3' (SEQ ID NO:296) forward PCR primer 5'-GGCTGGAGACACTGAACCT-3' (SEQ ID NO:297) forward PCR primer 5'-ACAGCTGCACAGCTCAGAACAGTG-3' (SEQ ID NO:298) reverse PCR primer 5'-CATTCCCAGTATAAAAATTTTC-3' (SEQ ID NO: 299) reverse PCR primer 5'-GGGTCTTGGTGAATGAGG-3' (SEQ ID NO:300) reverse PCR primer 5'-GTGCCTCTCGGTTACCACCAATGG-3' (SEQ ID NO:301)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted for the determination of PR0335 which had the following nucleotide sequence hybridization probe
5 '-GCGGCCACTGTTGGACCGAACTGTAACCAAGGGAGAAACAGCCGTCCTAC-3 ' (SEQ ID NO: 302)
Forward and reverse PCR primers were synthesized for the determination of PR0331 : forward PCR primer 5'-GCCTTTGACAACCTTCAGTCACTAGTGG-3' (SEQ ID NO:303) reverse PCR primer 5'-CCCCATGTGTCCATGACTGTTCCC-3' (SEQ ID NO:304)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted for the determination of PR0331 which had the following nucleotide sequence hybridization probe 5'-TACTGCCTCATGACCTCTTCACTCCCTTGCATCATCTTAGAGCGG-3' (SEQ ID NO:305) Forward and reverse PCR primers were synthesized for the determination of PR0326: forward PCR primer 5'-ACTCCAAGGAAATCGGATCCGTTC-3' (SEQ ID NO:306) reverse PCR primer 5'-TTAGCAGCTGAGGATGGGCACAAC-3' (SEQ ID NO:307)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted for the determination of PR0331 which had the following nucleotide sequence hybridization probe
5 ' -GCCTTC ACTGGTTTGGATGC ATTGGAGC ATCTAGACCTG AGTGAC AACGC-3 ' (SEQ ID NO:308)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PR0335, PR0331 or PR0326 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal kidney tissue (PR0335 and PR0326) and human fetal brain (PR0331).
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0335, PR0331 or PR0326 [herein designated as SEQ ID NOS:289, 291 and 293, respectively; see Figures 101, 103 and 105, respectively], and the derived protein sequence for PR0335, PR0331 or PR0326 (see Figures 102, 104 and 106, respectively; SEQ ID NOS:290, 292 and 294, respectively).
The entire nucleotide sequences are shown in Figures 101, 103 and 105, deposited with the ATCC on June 2, 1998, November 7, 1997 and November 21, 1997, respectively. Analysis of the amino acid sequence of the full-length PR0335, PR0331 or PR0326 polypeptide suggests that portions of it possess significant homology to the LIG-1 protein, thereby indicating that PR0335, PR0331 and PR0326 may be a novel LIG-1 -related protein.
EXAMPLE 44: Isolation of cDNA clones Encoding Human PRQ332 Based upon an ECD homology search performed as described in Example 1 above, a consensus DNA sequence designated herein as DNA36688 was assembled. Based on the DNA36688 consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for PR0332. A pair of PCR primers (forward and reverse) were synthesized: 5'-GCATTGGCCGCGAGACTTTGCC-3' (SEQ ID NO:311)
5 '-GCGGCCACGGTCCTTGGAAATG-3 ' (SEQ ID NO:312)
A probe was also synthesized: 5 ' -TGGAGGAGCTC AACCTC AGCTAC AACCGC ATC ACCAGCCC AC AGG-3 ' (SEQ ID NO:313) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0332 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from a human fetal liver library (LIB229).
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for DNA40982-1235 and the derived protein sequence for PR0332.
The entire nucleotide sequence of DNA40982-1235 is shown in Figure 107 (SEQ ID NO:309). Clone
DNA40982- 1235 contains a single open reading frame (with an apparent translational initiation site at nucleotide positions 342-344, as indicated in Figure 107). The predicted polypeptide precursor is 642 amino acids long, and has a calculated molecular weight of 72,067 (pi: 6.60). Clone DNA40982-1235 has been deposited with
ATCC and is assigned ATCC deposit no. ATCC 209433.
Based on a BLAST and FastA sequence alignment analysis of the full-length sequence, PR0332 shows about 30-40% amino acid sequence identity with a series of known proteoglycan sequences, including, for example, fibromodulin and fibromodulin precursor sequences of various species (FMOD_BOVIN, FMOD CHICK, FMOD_RAT, FMOD.MOUSE, FMOD.HUMAN, P_R36773), osteomodulin sequences (AB000114 1, AB007848.1), decorin sequences (CFU83141.1, OCU03394.1, P R42266, P R42267, P R42260, P R89439), keratan sulfate proteoglycans (BTU48360_1, AF022890_1), corneal proteoglycan (AF022256_1), and bone/cartilage proteoglycans and proteoglycane precursors (PGS1.BOVIN, PGS2. MOUSE, PGS2.HUMAN).
EXAMPLE 45: Isolation of cDNA clones Encoding Human PRQ334
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. Based on the consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full- length coding sequence for PR0334.
Forward and reverse PCR primers were synthesized for the determination of PR0334: forward PCR primer 5 ' -G ATGGTTCCTGCTC A AGTGCCCTG-3 ' (SEQ ID NO : 316) reverse PCR primer 5'-TTGCACTTGTAGGACCCACGTACG-3' (SEQ ID NO:317)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted for the determination of PR0334 which had the following nucleotide sequence hybridization probe
5 ' -CTGATGGGAGGACCTGTGTAGATGTTGATGAATGTGCTACAGGAAGAGCC-3 ' (SEQ ID NO:318)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0334 gene using the probe oligonucleotide and one of the PCR primers.
Human fetal kidney cDNA libraries used to isolate the cDNA clones were constmcted by standard methods using commercially available reagents such as those from Invitrogen, San Diego, CA.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0334 [herein designated as DNA41379-1236] (SEQ ID NO:314) and the derived protein sequence for PR0334. The entire nucleotide sequence of DNA41379-1236 (also referred to as UNQ295) is shown in Figure 109 (SEQ ID NO:314). Clone DNA41379-1236 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 203-205 and ending at the stop codon at nucleotide positions 1730-1732 (Figure 109). The predicted polypeptide precursor is 509 amino acids long (Figure 110). Clone DNA41379-1236 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209488. Analysis of the amino acid sequence of the full-length PR0334 polypeptide suggests that portions of it possess significant homology to the fibulin and fibrillin proteins, thereby indicating that PR0334 may be a novel member of the EGF protein family.
EXAMPLE 46: Isolation of cDNA Clones Encoding Human PRQ346 A consensus DNA sequence was identified using phrap as described in Example 1 above. Specifically, this consensus sequence is herein designated DNA38240. Based on the DNA38240 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length PR0346 coding sequence.
RNA for constmction of the cDNA libraries was isolated from human fetal liver. The cDNA libraries used to isolated the cDNA clones were constmcted by standard methods using commercially available reagents (e.g., Invitrogen, San Diego, CA; Clontech, etc.) The cDNA was primed with oligo dT containing a Notl site, linked with blunt to Sail hemikinased adaptors, cleaved with Notl, sized appropriately by gel electrophoresis, and cloned in a defined orientation into a suitable cloning vector (such as pRKB or pRKD; pRK5B is a precursor of pRK5D that does not contain the Sfil site; see, Holmes et al., Science, 253: 1278-1280 (1991)) in the unique Xhol and Notl sites.
A cDNA clone was sequenced in entirety. The entire nucleotide sequence of DNA44167- 1243 is shown in Figure 111 (SEQ ID NO: 319). Clone DNA44167- 1243 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 64-66 (Fig. I l l; SEQ ID NO:319). The predicted polypeptide precursor is 450 amino acids long. Clone DNA44167-1243 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209434 (designation DNA44167-1243).
Based on a BLAST, BLAST-2 and FastA sequence alignment analysis (using the ALIGN computer program) of the full-length sequence, PR0346 shows amino acid sequence identity to carcinoembryonic antigen (28%).
The oligonucleotide sequences used in the above procedure were the following: OLI2691 (38240.fl)
5'-GATCCTGTCACAAAGCCAGTGGTGC-3' (SEQ ID NO:321) OLI2693 (38240.rl)
5'-CACTGACAGGGTTCCTCACCCAGG-3' (SEQ ID NO:322)
OLI2692 (38240.pl) 5'-CTCCCTCTGGGCTGTGGAGTATGTGGGGAACATGACCCTGACATG-3' (SEQ ID NO:323) EXAMPLE 47: Isolation of cDNA Clones Encoding Human PRQ268
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA35698. Based on the DNA35698 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0268.
Forward and reverse PCR primers were synthesized: forward PCR primer 1 5'-TGAGGTGGGCAAGCGGCGAAATG-3' (SEQ ID NO:326) forward PCR primer 2 5'-TATGTGGATCAGGACGTGCC-3' (SEQ ID NO: 327) forward PCR primer 3 5'-TGCAGGGTTCAGTCTAGATTG-3' (SEQ ID NO:328) reverse PCR primer 5'-TTGAAGGACAAAGGCAATCTGCCAC-3' (SEQ ID NO:329)
Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus DNA35698 sequence which had the following nucleotide sequence hybridization probe
5'-GGAGTCTTGCAGTTCCCCTGGCAGTCCTGGTGCTGTTGCTTTGGG-3' (SEQ ID NO:330) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0268 gene using the probe oligonucleotide and one of the PCR primers.
RNA for constmction of the cDNA libraries was isolated from human fetal lung tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0268 [herein designated as DNA39427-1179] (SEQ ID NO:324) and the derived protein sequence for PR0268.
The entire nucleotide sequence of DNA39427-1179 is shown in Figure 113 (SEQ ID NO:324). Clone
DNA39427-1179 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 13-15 and ending at the stop codon at nucleotide positions 853-855 (Figure 113). The predicted polypeptide precursor is 280 amino acids long (Figure 114). Clone DNA39427-1179 has been deposited with
ATCC and is assigned ATCC deposit no. ATCC 209395.
Analysis of the amino acid sequence of the full-length PR0268 polypeptide suggests that it possess significant homology to protein disulfide isomerase, thereby indicating that PR0268 may be a novel protein disulfide isomerase.
EXAMPLE 48: Isolation of cDNA Clones Encoding Human PRO330
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA35730. Based on the DNA35730 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for
PRO330. Forward and reverse PCR primers were synthesized: forward PCR primer 1 5'-CCAGGCACAATTTCCAGA-3' (SEQ ID NO: 333) forward PCR primer 2 5'-GGACCCTTCTGTGTGCCAG-3' (SEQ ID NO:334) reverse PCR primer 1 5'-GGTCTCAAGAACTCCTGTC-3' (SEQ ID NO: 335) reverse PCR primer 2 5'-ACACTCAGCATTGCCTGGTACTTG-3' (SEQ ID NO:336) Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus sequence which had the following nucleotide sequence hybridization probe 5'-GGGCACATGACTGACCTGATTTATGCAGAGAAAGAGCTGGTGCAG-3' (SEQ ID NO:337)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PRO330 gene using the probe oligonucleotide and one of the PCR primers.
RNA for construction of the cDNA libraries was isolated from human fetal liver tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO330 [herein designated as DNA40603-1232] (SEQ ID NO:331) and the derived protein sequence for PRO330.
The entire nucleotide sequence of DNA40603-1232 is shown in Figure 115 (SEQ ID NO:331). Clone
DNA40603-1232 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 167-169 and ending at the stop codon at nucleotide positions 1766-1768 (Figure 115). The predicted polypeptide precursor is 533 amino acids long (Figure 116). Clone DNA40603-1232 has been deposited with ATCC and is assigned ATCC deposit no.ATCC 209486 on November 21, 1997.
Analysis of the amino acid sequence of the full-length PRO330 polypeptide suggests that portions of it possess significant homology to the mouse prolyl 4-hydroxylase alpha subunit protein, thereby indicating that PRO330 may be a novel prolyl 4-hydroxylase alpha subunit polypeptide.
EXAMPLE 49: Isolation of cDNA Clones Encoding Human PRO310
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA40553. Based on the DNA40553 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PRO310.
Forward and reverse PCR primers were synthesized: forward PCR primer 1 5'-TCCCCAAGCCGTTCTAGACGCGG-3' (SEQ ID NO:342) forward PCR primer 2 5'-CTGGTTCTTCCTTGCACG-3' (SEQ ID NO:343) reverse PCR primer 5'-GCCCAAATGCCCTAAGGCGGTATACCCC-3' (SEQ ID NO:344) Additionally, a synthetic oligonucleotide hybridization probe was constmcted from the consensus sequence which had the following nucleotide sequence hybridization probe 5'-GGGTGTGATGCTTGGAAGCATTTTCTGTGCTTTGATCACTATGCTAGGAC-3' (SEQ ID NO:345)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PRO310 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal liver tissue.
DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PR0310 [herein designated as DNA43046-1225 (SEQ ID NO: 340) and the derived protein sequence for PR0310 (SEQ ID NO:341).
The entire nucleotide sequence of DNA43046-1225 is shown in Figure 119 (SEQ ID NO:340). Clone DNA43046-1225 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 81-83 and ending at the stop codon at nucleotide positions 1035-1037 (Figure 119). The predicted polypeptide precursor is 318 amino acids long (Figure 120) and has a calculated molecular weight of approximately 36,382 daltons. Clone DNA43046-1225 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209484. Analysis of the amino acid sequence of the full-length PRO310 polypeptide suggests that portions of it possess homology to C. elegans proteins and to fringe, thereby indicating that PRO310 may be involved in development.
EXAMPLE 50: Isolation of cDNA clones Encoding Human PRQ339 An expressed sequence tag (EST) DNA database (LIFESEQ™, Incyte Pharmaceuticals, Palo Alto, CA) was searched and ESTs were identified. An assembly of Incyte clones and a consensus sequence was formed using phrap as described in Example 1 above.
Forward and reverse PCR primers were synthesized based upon the assembly-created consensus sequence: forward PCR primer 1 5'-GGGATGCAGGTGGTGTCTCATGGGG-3' (SEQ ID NO:346) forward PCR primer 2 5'-CCCTCATGTACCGGCTCC-3' (SEQ ID NO:347) forward PCR primer 3 5'-GTGTGACACAGCGTGGGC-3' (SEQ ID NO:43) forward PCR primer 4 5'-GACCGGCAGGCTTCTGCG-3' (SEQ ID NO:44) reverse PCR primer 1 5'-CAGCAGCTTCAGCCACCAGGAGTGG-3' (SEQ ID NO:45) reverse PCR primer 2 5'-CTGAGCCGTGGGCTGCAGTCTCGC-3' (SEQ ID NO:46)
Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus sequence which had the following nucleotide sequence hybridization probe
5'-CCGACTACGACTGGTTCTTCATCATGCAGGATGACACATATGTGC-3' (SEQ ID NO:47) In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PR0339 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from human fetal liver tissue.
A cDNA clone was sequenced in entirety. The entire nucleotide sequence of DNA43466-1225 is shown in Figure 117 (SEQ ID NO:338). Clone DNA43466-1225 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 333-335 and ending at the stop codon found at nucleotide positions 2649-2651 (Figure 117; SEQ ID NO:338). The predicted polypeptide precursor is 772 amino acids long and has a calculated molecular weight of approximately 86,226 daltons. Clone DNA43466-1225 has been deposited with ATCC and is assigned ATCC deposit no. ATCC 209490.
Based on a BLAST and FastA sequence alignment analysis (using the ALIGN computer program) of the full-length sequence, PR0339 has homology to C. elegans proteins and collagen-like polymer sequences as well as to fringe, thereby indicating that PR0339 may be involved in development or tissue growth.
EXAMPLE 51 : Isolation of cDNA Clones Encoding Human PRQ244
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. Based on this consensus sequence, oligonucleotides were synthesized to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for PR0244.
A pair of PCR primers (forward and reverse) were synthesized:
5'-TTCAGCTTCTGGGATGTAGGG-3' (30923. fl) (SEQ ID NO:378)
5'-TATTCCTACCATTTCACAAATCCG-3' (30923.rl) (SEQ ID NO:379)
A probe was also synthesized: 5'-GGAGGACTGTGCCACCATGAGAGACTCTTCAAACCCAAGGCAAAATTGG-3' (30923.pl) (SEQ ID
NO:380)
In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pair identified above. A positive library was then used to isolate clones encoding the PR0244 gene using the probe oligonucleotide and one of the PCR primers. RNA for constmction of the cDNA libraries was isolated from a human fetal kidney library. DNA sequencing of the clones isolated as described above gave the full-length DNA sequence and the derived protein sequence for PR0244.
The entire nucleotide sequence of PR0244 is shown in Figure 121 (SEQ ID NO:376). Clone
DNA35668-1171 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 106-108 (Fig. 121). The predicted polypeptide precursor is 219 amino acids long. Clone DNA35668-
1171 has been deposited with ATCC (designated as DNA35663-1 171) and is assigned ATCC deposit no.
ATCC209371. The protein has a cytoplasmic domain (aa 1-20), a transmembrane domain (aa 21-46), and an extracellular domain (aa 47-219), with a C-lectin domain at aa 55-206.
Based on a BLAST and FastA sequence alignment analysis of the full-length sequence, PR0244 shows notable amino acid sequence identity to hepatic lectin gallus gallus (43%), HIC hpl20-binding C-type lectin
(42%), macrophage lectin 2 (HUMHML2-1 , 41 %), and sequence PR32188 (44%). EXAMPLE 52: Use of PRO Polvpeptide-Encoding Nucleic Acid as Hybridization Probes
The following method describes use of a nucleotide sequence encoding a PRO polypeptide as a hybridization probe.
DNA comprising the coding sequence of of a PRO polypeptide of interest as disclosed herein may be employed as a probe or used as a basis from which to prepare probes to screen for homologous DNAs (such as those encoding naturally-occurring variants of the PRO polypeptide) in human tissue cDN A libraries or human tissue genomic libraries.
Hybridization and washing of filters containing either library DNAs is performed under the following high stringency conditions. Hybridization of radiolabeled PRO polypeptide-encoding nucleic acid-derived probe to the filters is performed in a solution of 50% formamide, 5x SSC, 0.1 % SDS, 0.1 % sodium pyrophosphate, 50 mM sodium phosphate, pH 6.8, 2x Denhardt's solution, and 10% dextran sulfate at 42°C for 20 hours.
Washing of the filters is performed in an aqueous solution of 0. lx SSC and 0.1 % SDS at 42°C.
DNAs having a desired sequence identity with the DNA encoding full-length native sequence PRO polypeptide can then be identified using standard techniques known in the art.
EXAMPLE 53: Expression of PRO Polypeptides in E. coli
This example illustrates preparation of an unglycosylated form of a desired PRO polypeptide by recombinant expression in E. coli.
The DNA sequence encoding the desired PRO polypeptide is initially amplified using selected PCR primers. The primers should contain restriction enzyme sites which correspond to the restriction enzyme sites on the selected expression vector. A variety of expression vectors may be employed. An example of a suitable vector is pBR322 (derived from E. coli; see Bolivar et al., Gene. 2:95 (1977)) which contains genes for ampicillin and tetracycline resistance. The vector is digested with restriction enzyme and dephosphorylated. The PCR amplified sequences are then ligated into the vector. The vector will preferably include sequences which encode for an antibiotic resistance gene, a trp promoter, a polyhis leader (including the first six STII codons, polyhis sequence, and enterokinase cleavage site), the specific PRO polypeptide coding region, lambda transcriptional terminator, and an argU gene.
The ligation mixmre is then used to transform a selected E. coli strain using the methods described in Sambrook et al. , supra. Transformants are identified by their ability to grow on LB plates and antibiotic resistant colonies are then selected. Plasmid DNA can be isolated and confirmed by restriction analysis and DNA sequencing.
Selected clones can be grown overnight in liquid culture medium such as LB broth supplemented with antibiotics. The overnight culture may subsequently be used to inoculate a larger scale culture. The cells are then grown to a desired optical density, during which the expression promoter is turned on.
After culturing the cells for several more hours, the cells can be harvested by centrifugation. The cell pellet obtained by the centrifugation can be solubilized using various agents known in the art, and the solubilized PRO polypeptide can then be purified using a metal chelating column under conditions that allow tight binding of the protein.
PR0187, PR0317, PRO301 , PR0224 and PR0238 were successfully expressed inE. coli in a poly-His tagged form, using the following procedure. The DNA encoding PR0187, PR0317, PRO301, PR0224 or PR0238 was initially amplified using selected PCR primers. The primers contained restriction enzyme sites which correspond to the restriction enzyme sites on the selected expression vector, and other useful sequences providing for efficient and reliable translation initiation, rapid purification on a metal chelation column, and proteolytic removal with enterokinase. The PCR-amplified, poly-His tagged sequences were then ligated into an expression vector, which was used to transform an E. coli host based on strain 52 (W3110 fuhA(tonA) Ion galE rpoHts(htpRts) clpP(lacIq). Transformants were first grown in LB containing 50 mg/ml carbenicillin at 30°C with shaking until an O.D.600 of 3-5 was reached. Cultures were then diluted 50-100 fold into CRAP media (prepared by mixing 3.57 g (NH4)2S04, 0.71 g sodium citrate-2H20, 1.07 g KCl, 5.36 g Difco yeast extract, 5.36 g Sheffield hycase SF in 500 mL water, as well as 110 mM MPOS, pH 7.3, 0.55% (w/v) glucose and 7 mM MgS04) and grown for approximately 20-30 hours at 30 °C with shaking. Samples were removed to verify expression by SDS-PAGE analysis, and the bulk culture is centrifuged to pellet the cells. Cell pellets were frozen until purification and refolding. E. coli paste from 0.5 to 1 L fermentations (6-10 g pellets) was resuspended in 10 volumes (w/v) in 7
M guanidine, 20 mM Tris, pH 8 buffer. Solid sodium sulfite and sodium tetrathionate is added to make final concentrations of 0.1M and 0.02 M, respectively, and the solution was stirred overnight at 4°C. This step results in a denatured protein with all cysteine residues blocked by sulfitolization. The solution was centrifuged at 40,000 rpm in a Beckman Ultracentifuge for 30 min. The supernatant was diluted with 3-5 volumes of metal chelate column buffer (6 M guanidine, 20 mM Tris, pH 7.4) and filtered through 0.22 micron filters to clarify. Depending the clarified extract was loaded onto a 5 ml Qiagen Ni-NTA metal chelate column equilibrated in the metal chelate column buffer. The column was washed with additional buffer containing 50 mM imidazole (Calbiochem, Utrol grade), pH 7.4. The protein was eluted with buffer containing 250 mM imidazole. Fractions containing the desired protein were pooled and stored at 4°C. Protein concentration was estimated by its absorbance at 280 nm using the calculated extinction coefficient based on its amino acid sequence.
The proteins were refolded by diluting sample slowly into freshly prepared refolding buffer consisting of: 20 mM Tris, pH 8.6, 0.3 M NaCl, 2.5 M urea, 5 mM cysteine, 20 mM glycine and 1 mM EDTA. Refolding volumes were chosen so that the final protein concentration was between 50 to 100 micrograms/ml. The refolding solution was stirred gently at 4°C for 12-36 hours. The refolding reaction was quenched by the addition of TFA to a final concentration of 0.4% (pH of approximately 3). Before further purification of the protein, the solution was filtered through a 0.22 micron filter and acetonitrile was added to 2-10% final concentration. The refolded protein was chromatographed on a Poros Rl/H reversed phase column using a mobile buffer of 0.1 % TFA with elution with a gradient of acetonitrile from 10 to 80% . Aliquots of fractions with A280 absorbance were analyzed on SDS polyacrylamide gels and fractions containing homogeneous refolded protein were pooled. Generally, the properly refolded species of most proteins are eluted at the lowest concentrations of acetonitrile since those species are the most compact with their hydrophobic interiors shielded from interaction with the reversed phase resin. Aggregated species are usually eluted at higher acetonitrile concentrations. In addition to resolving misfolded forms of proteins from the desired form, the reversed phase step also removes endotoxin from the samples.
Fractions containing the desired folded PR0187, PR0317, PRO301, PR0224 and PR0238 proteins, respectively, were pooled and the acetonitrile removed using a gentle stream of nitrogen directed at the solution.
Proteins were formulated into 20 mM Hepes, pH 6.8 with 0.14 M sodium chloride and 4% mannitol by dialysis or by gel filtration using G25 Superfine (Pharmacia) resins equilibrated in the formulation buffer and sterile filtered.
EXAMPLE 54: Expression of PRO Polypeptides in Mammalian Cells
This example illustrates preparation of a glycosylated form of a desired PRO polypeptide by recombinant expression in mammalian cells.
The vector, pRK5 (see EP 307,247, published March 15, 1989), is employed as the expression vector. Optionally, the PRO polypeptide-encoding DNA is ligated into pRK5 with selected restriction enzymes to allow insertion of the PRO polypeptide DNA using ligation methods such as described in Sambrook et al. , supra. The resulting vector is called pRK5-PRO polypeptide. In one embodiment, the selected host cells may be 293 cells. Human 293 cells (ATCC CCL 1573) are grown to confluence in tissue culmre plates in medium such as DMEM supplemented with fetal calf serum and optionally, nutrient components and/or antibiotics. About 10 μg pRK5-PRO polypeptide DNA is mixed with about 1 μg DNA encoding the VA RNA gene [Thimmappaya et al., Cell. 3 543 (1982)] and dissolved in 500 μl of 1 mM Tris-HCl, 0.1 mM EDTA, 0.227 M CaCl2. To this mixmre is added, dropwise, 500 μl of 50 mM HEPES (pH 7.35), 280 mM NaCl, 1.5 mM NaP04, and a precipitate is allowed to form for 10 minutes at 25°C. The precipitate is suspended and added to the 293 cells and allowed to settle for about four hours at 37°C. The culture medium is aspirated off and 2 ml of 20% glycerol in PBS is added for 30 seconds. The 293 cells are then washed with serum free medium, fresh medium is added and the cells are incubated for about 5 days.
Approximately 24 hours after the transfections, the culture medium is removed and replaced with culmre medium (alone) or culmre medium containing 200 μCi/ml 35S-cysteine and 200 μCi/ml 35S-methionine. After a 12 hour incubation, the conditioned medium is collected, concentrated on a spin filter, and loaded onto a 15 % SDS gel. The processed gel may be dried and exposed to film for a selected period of time to reveal the presence of PRO polypeptide. The cultures containing transfected cells may undergo further incubation (in semm free medium) and the medium is tested in selected bioassays. In an alternative technique, PRO polypeptide may be introduced into 293 cells transiently using the dextran sulfate method described by Somparyrac et al., Proc. Natl. Acad. Sci.. 12:7575 (1981). 293 cells are grown to maximal density in a spinner flask and 700 μg ρRK5-PRO polypeptide DNA is added. The cells are first concentrated from the spinner flask by centrifugation and washed with PBS. The DNA-dextran precipitate is incubated on the cell pellet for four hours. The cells are treated with 20% glycerol for 90 seconds, washed with tissue culture medium, and re-introduced into the spinner flask containing tissue culmre medium, 5 μg/ml bovine insulin and 0.1 μg/ml bovine transferrin. After about four days, the conditioned media is centrifuged and filtered to remove cells and debris. The sample containing expressed PRO polypeptide can then be concentrated and purified by any selected method, such as dialysis and/or column chromatography.
In another embodiment, PRO polypeptides can be expressed in CHO cells. The pRK5-PRO polypeptide can be transfected into CHO cells using known reagents such as CaP04 or DEAE-dextran. As described above, the cell cultures can be incubated, and the medium replaced with culmre medium (alone) or medium containing a radiolabel such as 35S-methionine. After determining the presence of PRO polypeptide, the culture medium may be replaced with semm free medium. Preferably, the cultures are incubated for about 6 days, and then the conditioned medium is harvested. The medium containing the expressed PRO polypeptide can then be concentrated and purified by any selected method.
Epitope-tagged PRO polypeptide may also be expressed in host CHO cells. The PRO polypeptide may be subcloned out of the pRK5 vector. The subclone insert can undergo PCR to fuse in frame with a selected epitope tag such as a poly-his tag into a Baculovims expression vector. The poly-his tagged PRO polypeptide insert can then be subcloned into a SV40 driven vector containing a selection marker such as DHFR for selection of stable clones. Finally, the CHO cells can be transfected (as described above) with the SV40 driven vector. Labeling may be performed, as described above, to verify expression. The culmre medium containing the expressed poly-His tagged PRO polypeptide can then be concentrated and purified by any selected method, such as by Ni2+-chelate affinity chromatography.
PR0211 , PR0217, PRO230, PR0219, PR0245, PR0221, PR0258, PRO301, PR0224, PR0222, PR0234, PR0229, PR0223, PR0328 and PR0332 were successfully expressed in CHO cells by both a transient and a stable expression procedure. In addition, PR0232, PR0265, PR0246, PR0228, PR0227, PRO220, PR0266, PR0269, PR0287, PR0214, PR0231, PR0233, PR0238, PR0244, PR0235, PR0236, PR0262, PR0239, PR0257, PRO260, PR0263, PRO270, PR0271, PR0272, PR0294, PR0295, PR0293, PR0247, PRO303 and PR0268 were successfully transiently expressed in CHO cells.
Stable expression in CHO cells was performed using the following procedure. The proteins were expressed as an IgG constmct (immunoadhesin), in which the coding sequences for the soluble forms (e.g. extracellular domains) of the respective proteins were fused to an IgGl constant region sequence containing the hinge, CH2 and CH2 domains and/or is a poly-His tagged form.
Following PCR amplification, the respective DNAs were subcloned in a CHO expression vector using standard techniques as described in Ausubel et al., Current Protocols of Molecular Biology, Unit 3.16, John Wiley and Sons (1997). CHO expression vectors are constmcted to have compatible restriction sites 5' and 3' of the DNA of interest to allow the convenient shuttling of cDNA's. The vector used expression in CHO cells is as described in Lucas et al, Nucl. Acids Res. 24: 9 (1774-1779 (1996), and uses the SV40 early promoter/enhancer to drive expression of the cDNA of interest and dihydrofolate reductase (DHFR). DHFR expression permits selection for stable maintenance of the plasmid following transfection.
Twelve micrograms of the desired plasmid DNA were introduced into approximately 10 million CHO cells using commercially available transfection reagents Superfect* (Quiagen), Dosper* or Fugene* (Boehringer Mannheim). The cells were grown and described in Lucas et al , supra. Approximately 3 x IO 7 cells are frozen in an ampule for further growth and production as described below. The ampules containing the plasmid DNA were thawed by placement into water bath and mixed by vortexing. The contents were pipetted into a centrifuge tube containing 10 mLs of media and centrifuged at 1000 rpm for 5 minutes. The supernatant was aspirated and the cells were resuspended in 10 mL of selective media (0.2 μm filtered PS20 with 5 % 0.2 μm diafiltered fetal bovine semm). The cells were then aliquoted into a 100 mL spinner containing 90 mL of selective media. After 1-2 days, the cells were transferred into a 250 mL spinner filled with 150 mL selective growth medium and incubated at 37°C. After another 2-3 days, a 250 mL, 500 mL and 2000 mL spinners were seeded with 3 x 105 cells/mL. The cell media was exchanged with fresh media by centrifugation and resuspension in production medium. Although any suitable CHO media may be employed, a production medium described in US Patent No. 5, 122,469, issued June 16, 1992 was actually used. 3L production spinner is seeded at 1.2 x IO6 cells/mL. On day 0, the cell number pH were determined. On day 1, the spinner was sampled and sparging with filtered air was commenced. On day 2, the spinner was sampled, the temperature shifted to 33 °C, and 30 mL of 500 g/L glucose and 0.6 mL of 10% antifoam (e.g., 35% polydimethylsiloxane emulsion, Dow Coming 365 Medical Grade Emulsion). Throughout the production, pH was adjusted as necessary to keep at around 7.2. After 10 days, or until viability dropped below 70% , the cell culmre was harvested by centrifugtion and filtering through a 0.22 μm filter. The filtrate was either stored at 4°C or immediately loaded onto columns for purification.
For the poly-His tagged constructs, the proteins were purified using a Ni-NTA column (Qiagen). Before purification, imidazole was added to the conditioned media to a concentration of 5 mM. The conditioned media was pumped onto a 6 ml Ni-NTA column equilibrated in 20 mM Hepes, pH 7.4, buffer containing 0.3 M NaCl and 5 mM imidazole at a flow rate of 4-5 ml/min. at 4°C. After loading, the column was washed with additional equilibration buffer and the protein eluted with equilibration buffer containing 0.25 M imidazole. The highly purified protein was subsequently desalted into a storage buffer containing 10 mM Hepes, 0.14 M NaCl and 4% mannitol, pH 6.8, with a 25 ml G25 Superfine (Pharmacia) column and stored at -80°C.
Immunoadhesin (Fc containing) constmcts of were purified from the conditioned media as follows. The conditioned medium was pumped onto a 5 ml Protein A column (Pharmacia) which had been equilibrated in 20 mM Na phosphate buffer, pH 6.8. After loading, the column was washed extensively with equilibration buffer before elution with 100 mM citric acid, pH 3.5. The eluted protein was immediately neutralized by collecting 1 ml fractions into tubes containing 275 μL of 1 M Tris buffer, pH 9. The highly purified protein was subsequently desalted into storage buffer as described above for the poly-His tagged proteins. The homogeneity was assessed by SDS polyacrylamide gels and by N-terminal amino acid sequencing by Edman degradation. PR0211, PR0217, PRO230, PR0232, PR0187, PR0265, PR0219, PR0246, PR0228, PR0533,
PR0245, PR0221, PR0227, PRO220, PR0258, PR0266, PR0269, PR0287, PR0214, PR0317, PRO301, PR0224, PR0222, PR0234, PR0231, PR0229, PR0233, PR0238, PR0223, PR0235, PR0236, PR0262, PR0239, PR0257, PRO260, PR0263, PRO270, PR0271, PR0272, PR0294, PR0295, PR0293, PR0247, PRO304, PRO302, PRO307, PRO303, PR0343, PR0328, PR0326, PR0331, PR0332, PR0334, PR0346, PR0268, PRO330, PRO310 and PR0339 were also successfully transiently expressed in COS cells. EXAMPLE 55: Expression of PRO Polypeptides in Yeast
The following method describes recombinant expression of a desired PRO polypeptide in yeast.
First, yeast expression vectors are constmcted for intracellular production or secretion of PRO polypeptides from the ADH2/GAPDH promoter. DNA encoding a desired PRO polypeptide, a selected signal peptide and the promoter is inserted into suitable restriction enzyme sites in the selected plasmid to direct intracellular expression of the PRO polypeptide. For secretion, DNA encoding the PRO polypeptide can be cloned into the selected plasmid, together with DNA encoding the ADH2/GAPDH promoter, the yeast alpha- factor secretory signal/leader sequence, and linker sequences (if needed) for expression of the PRO polypeptide.
Yeast cells, such as yeast strain AB110, can then be transformed with the expression plasmids described above and cultured in selected fermentation media. The transformed yeast supernatants can be analyzed by precipitation with 10% trichloroacetic acid and separation by SDS-PAGE, followed by staining of the gels with Coomassie Blue stain.
Recombinant PRO polypeptide can subsequently be isolated and purified by removing the yeast cells from the fermentation medium by centrifugation and then concentrating the medium using selected cartridge filters. The concentrate containing the PRO polypeptide may further be purified using selected column chromatography resins.
EXAMPLE 56: Expression of PRO Polypeptides in Baculovirus-Infected Insect Cells
The following method describes recombinant expression of PRO polypeptides in Baculovims-infected insect cells. The desired PRO polypeptide is fused upstream of an epitope tag contained with a baculovims expression vector. Such epitope tags include poly-his tags and immunoglobulin tags (like Fc regions of IgG).
A variety of plasmids may be employed, including plasmids derived from commercially available plasmids such as pVL1393 (Novagen). Briefly, the PRO polypeptide or the desired portion of the PRO polypeptide (such as the sequence encoding the extracellular domain of a transmembrane protein) is amplified by PCR with primers complementary to the 5' and 3' regions. The 5' primer may incorporate flanking (selected) restriction enzyme sites. The product is then digested with those selected restriction enzymes and subcloned into the expression vector.
Recombinant baculovims is generated by co-transfecting the above plasmid and BaculoGold™ vims
DNA (Pharmingen) into Spodopterafrugiperda ("Sf9") cells (ATCC CRL 1711) using lipofectin (commercially available from GIBCO-BRL). After 4-5 days of incubation at 28°C, the released vimses are harvested and used for further amplifications. Viral infection and protein expression is performed as described by O'Reilley et al. ,
Baculovims expression vectors: A laboratory Manual, Oxford: Oxford University Press (1994).
Expressed poly-his tagged PRO polypeptide can then be purified, for example, by Ni2+-chelate affinity chromatography as follows. Extracts are prepared from recombinant vims-infected Sf9 cells as described by Rupert et al., Nature, 362: 175-179 (1993). Briefly, Sf9 cells are washed, resuspended in sonication buffer (25 mL Hepes, pH 7.9; 12.5 mM MgCl2; 0.1 mM EDTA; 10% Glycerol; 0.1 % NP-40; 0.4 M KCl), and sonicated twice for 20 seconds on ice. The sonicates are cleared by centrifugation, and the supernatant is diluted 50-fold in loading buffer (50 mM phosphate, 300 mM NaCl, 10% Glycerol, pH 7.8) and filtered through a 0.45 μm filter. A Ni2+-NTA agarose column (commercially available from Qiagen) is prepared with a bed volume of 5 mL, washed with 25 mL of water and equilibrated with 25 mL of loading buffer. The filtered cell extract is loaded onto the column at 0.5 mL per minute. The column is washed to baseline A280 with loading buffer, at which point fraction collection is started. Next, the column is washed with a secondary wash buffer (50 mM phosphate; 300 M NaCl, 10% Glycerol, pH 6.0), which elutes nonspecifically bound protein. After reaching A280 baseline again, the column is developed with a 0 to 500 mM Imidazole gradient in the secondary wash buffer. One mL fractions are collected and analyzed by SDS-PAGE and silver staining or western blot with Ni2+-NTA-conjugated to alkaline phosphatase (Qiagen). Fractions containing the eluted His10-tagged PRO polypeptide are pooled and dialyzed against loading buffer. Alternatively, purification of the IgG tagged (or Fc tagged) PRO polypeptide can be performed using known chromatography techniques, including for instance, Protein A or protein G column chromatography.
PR0211 , PR0217, PRO230, PR0187, PR0265, PR0246, PR0228, PR0533, PR0245, PR0221, PRO220, PR0258, PR0266, PR0269, PR0287, PR0214, PRO301, PR0224, PR0222, PR0234, PR0231 , PR0229, PR0235, PR0239, PR0257, PR0272, PR0294, PR0295, PR0328, PR0326, PR0331, PR0334, PR0346 and PRO310 were successfully expressed in baculovims infected Sf9 or high5 insect cells. While the expression was actually performed in a 0.5-2 L scale, it can be readily scaled up for larger (e.g. 8 L) preparations. The proteins were expressed as an IgG constmct (immunoadhesin), in which the protein extracellular region was fused to an IgGl constant region sequence containing the hinge, CH2 and CH3 domains and/or in poly-His tagged forms. Following PCR amplification, the respective coding sequences were subcloned into a baculovims expression vector (pb.PH.IgG for IgG fusions and pb.PH.His.c for poly-His tagged proteins), and the vector and Baculogold® baculovims DNA (Pharmingen) were co-transfected into 105 Spodopterafrugiperda ("Sf9") cells (ATCC CRL 1711), using Lipofectin (Gibco BRL). pb.PH.IgG and pb.PH.His are modifications of the commercially available baculovims expression vector pVL1393 (Pharmingen), with modified polylinker regions to include the His or Fc tag sequences. The cells were grown in Hink's TNM-FH medium supplemented with 10% FBS (Hyclone). Cells were incubated for 5 days at 28°C. The supernatant was harvested and subsequently used for the first viral amplification by infecting Sf9 cells in Hink's TNM-FH medium supplemented with 10% FBS at an approximate multiplicity of infection (MOI) of 10. Cells were incubated for 3 days at 28°C. The supernatant was harvested and the expression of the constmcts in the baculovims expression vector was determined by batch binding of 1 ml of supernatant to 25 mL of Ni-NTA beads (QIAGEN) for histidine tagged proteins or Protein-A Sepharose CL-4B beads (Pharmacia) for IgG tagged proteins followed by SDS-PAGE analysis comparing to a known concentration of protein standard by Coomassie blue staining.
The first viral amplification supernatant was used to infect a spinner culmre (500 ml) of Sf9 cells grown in ESF-921 medium (Expression Systems LLC) at an approximate MOI of 0.1. Cells were incubated for 3 days at 28°C. The supernatant was harvested and filtered. Batch binding and SDS-PAGE analysis was repeated, as necessary, until expression of the spinner culmre was confirmed. The conditioned medium from the transfected cells (0.5 to 3 L) was harvested by centrifugation to remove the cells and filtered through 0.22 micron filters. For the poly-His tagged constmcts, the protein construct were purified using a Ni-NTA column (Qiagen). Before purification, imidazole was added to the conditioned media to a concentration of 5 mM. The conditioned media were pumped onto a 6 ml Ni-NTA column equilibrated in 20 mM Hepes, pH 7.4, buffer containing 0.3 M NaCl and 5 mM imidazole at a flow rate of 4-5 ml/min. at 4°C. After loading, the column was washed with additional equilibration buffer and the protein eluted with equilibration buffer containing 0.25 M imidazole. The highly purified protein was subsequently desalted into a storage buffer containing 10 mM Hepes, 0.14 M NaCl and 4% mannitol, pH 6.8, with a 25 ml G25 Superfine (Pharmacia) column and stored at -80 °C.
Immunoadhesin (Fc containing) constmcts of proteins were purified from the conditioned media as - follows. The conditioned media were pumped onto a 5 ml Protein A column (Pharmacia) which had been equilibrated in 20 mM Na phosphate buffer, pH 6.8. After loading, the column was washed extensively with equilibration buffer before elution with 100 mM citric acid, pH 3.5. The eluted protein was immediately neutralized by collecting 1 ml fractions into tubes containing 275 mL of 1 M Tris buffer, pH 9. The highly purified protein was subsequently desalted into storage buffer as described above for the poly-His tagged proteins. The homogeneity of the proteins was verified by SDS polyacrylamide gel (PEG) electrophoresis and N-terminal amino acid sequencing by Edman degradation.
EXAMPLE 57: Preparation of Antibodies that Bind to PRO Polypeptides
This example illustrates preparation of monoclonal antibodies which can specifically bind to a PRO polypeptide.
Techniques for producing the monoclonal antibodies are known in the art and are described, for instance, in Goding, supra. Immunogens that may be employed include purified PRO polypeptide, fusion proteins containing the PRO polypeptide, and cells expressing recombinant PRO polypeptide on the cell surface. Selection of the immunogen can be made by the skilled artisan without undue experimentation. Mice, such as Balb/c, are immunized with the PRO polypeptide immunogen emulsified in complete
Freund's adjuvant and injected subcutaneously or intraperitoneally in an amount from 1-100 micrograms. Alternatively, the immunogen is emulsified in MPL-TDM adjuvant (Ribi Immunochemical Research, Hamilton, MT) and injected into the animal's hind foot pads. The immunized mice are then boosted 10 to 12 days later with additional immunogen emulsified in the selected adjuvant. Thereafter, for several weeks, the mice may also be boosted with additional immunization injections. Semm samples may be periodically obtained from the mice by retro-orbital bleeding for testing in ELISA assays to detect anti-PRO polypeptide antibodies.
After a suitable antibody titer has been detected, the animals "positive" for antibodies can be injected with a final intravenous injection of PRO polypeptide. Three to four days later, the mice are sacrificed and the spleen cells are harvested. The spleen cells are then fused (using 35 % polyethylene glycol) to a selected murine myeloma cell line such as P3X63AgU. l, available from ATCC, No. CRL 1597. The fusions generate hybridoma cells which can then be plated in 96 well tissue culmre plates containing HAT (hypoxanthine, aminopterin, and thymidine) medium to inhibit proliferation of non-fused cells, myeloma hybrids, and spleen cell hybrids.
The hybridoma cells will be screened in an ELISA for reactivity against the PRO polypeptide. Determination of "positive" hybridoma cells secreting the desired monoclonal antibodies against the PRO polypeptide is within the skill in the art.
The positive hybridoma cells can be injected intraperitoneally into syngeneic Balb/c mice to produce ascites containing the anti-PRO polypeptide monoclonal antibodies. Alternatively, the hybridoma cells can be grown in tissue culmre flasks or roller bottles. Purification of the monoclonal antibodies produced in the ascites can be accomplished using ammonium sulfate precipitation, followed by gel exclusion chromatography. Alternatively, affinity chromatography based upon binding of antibody to protein A or protein G can be employed.
EXAMPLE 58: Chimeric PRO Polypeptides
PRO polypeptides may be expressed as chimeric proteins with one or more additional polypeptide domains added to facilitate protein purification. Such purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS™ extension/affinity purification system (Immunex Corp., Seattle Wash.). The inclusion of a cleavable linker sequence such as Factor XA or enterokinase (Invitrogen, San Diego Calif.) between the purification domain and the PRO polypeptide sequence may be useful to facilitate expression of DNA encoding the PRO polypeptide.
EXAMPLE 59: Purification of PRO Polypeptides Using Specific Antibodies
Native or recombinant PRO polypeptides may be purified by a variety of standard techniques in the art of protein purification. For example, pro-PRO polypeptide, mature PRO polypeptide, or pre-PRO polypeptide is purified by immunoaffinity chromatography using antibodies specific for the PRO polypeptide of interest. In general, an immunoaffinity column is constmcted by covalently coupling the anti-PRO polypeptide antibody to an activated chromatographic resin.
Polyclonal immunoglobulins are prepared from immune sera either by precipitation with ammonium sulfate or by purification on immobilized Protein A (Pharmacia LKB Biotechnology, Piscataway, N.J.). Likewise, monoclonal antibodies are prepared from mouse ascites fluid by ammonium sulfate precipitation or chromatography on immobilized Protein A. Partially purified immunoglobulin is covalently attached to a chromatographic resin such as CnBr-activated SEPHAROSE™ (Pharmacia LKB Biotechnology). The antibody is coupled to the resin, the resin is blocked, and the derivative resin is washed according to the manufacturer's instructions.
Such an immunoaffinity column is utilized in the purification of PRO polypeptide by preparing a fraction from cells containing PRO polypeptide in a soluble form. This preparation is derived by solubilization of the whole cell or of a subcellular fraction obtained via differential centrifugation by the addition of detergent or by other methods well known in the art. Alternatively, soluble PRO polypeptide containing a signal sequence may be secreted in useful quantity into the medium in which the cells are grown.
A soluble PRO polypeptide-containing preparation is passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of PRO polypeptide (e.g. , high ionic strength buffers in the presence of detergent). Then, the column is eluted under conditions that dismpt antibody/PRO polypeptide binding (e.g. , a low pH buffer such as approximately pH 2-3, or a high concentration of a chaotrope such as urea or thiocyanate ion), and PRO polypeptide is collected.
EXAMPLE 60: Dmg Screening
This invention is particularly useful for screening compounds by using PRO polypeptides or binding fragment thereof in any of a variety of dmg screening techniques. The PRO polypeptide or fragment employed in such a test may either be free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly. One method of dmg screening utilizes eukaryotic or prokaryotic host cells which are stably transformed with recombinant nucleic acids expressing the PRO polypeptide or fragment. Dmgs are screened against such transformed cells in competitive binding assays. Such cells, either in viable or fixed form, can be used for standard binding assays. One may measure, for example, the formation of complexes between PRO polypeptide or a fragment and the agent being tested. Alternatively, one can examine the diminution in complex formation between the PRO polypeptide and its target cell or target receptors caused by the agent being tested.
Thus, the present invention provides methods of screening for drugs or any other agents which can affect a PRO polypeptide-associated disease or disorder. These methods comprise contacting such an agent with an PRO polypeptide or fragment thereof and assaying (I) for the presence of a complex between the agent and the PRO polypeptide or fragment, or (ii) for the presence of a complex between the PRO polypeptide or fragment and the cell, by methods well known in the art. In such competitive binding assays, the PRO polypeptide or fragment is typically labeled. After suitable incubation, free PRO polypeptide or fragment is separated from that present in bound form, and the amount of free or uncomplexed label is a measure of the ability of the particular agent to bind to PRO polypeptide or to interfere with the PRO polypeptide/cell complex. Another technique for dmg screening provides high throughput screening for compounds having suitable binding affinity to a polypeptide and is described in detail in WO 84/03564, published on September 13, 1984. Briefly stated, large numbers of different small peptide test compounds are synthesized on a solid substrate, such as plastic pins or some other surface. As applied to a PRO polypeptide, the peptide test compounds are reacted with PRO polypeptide and washed. Bound PRO polypeptide is detected by methods well known in the art. Purified PRO polypeptide can also be coated directly onto plates for use in the aforementioned drag screening techniques. In addition, non-neutralizing antibodies can be used to capture the peptide and immobilize it on the solid support.
This invention also contemplates the use of competitive dmg screening assays in which neutralizing antibodies capable of binding PRO polypeptide specifically compete with a test compound for binding to PRO polypeptide or fragments thereof. In this manner, the antibodies can be used to detect the presence of any peptide which shares one or more antigenic determinants with PRO polypeptide. EXAMPLE 61: Rational Dmg Design
The goal of rational dmg design is to produce structural analogs of biologically active polypeptide of interest (i.e., a PRO polypeptide) or of small molecules with which they interact, e.g., agonists, antagonists, or inhibitors. Any of these examples can be used to fashion drags which are more active or stable forms of the
PRO polypeptide or which enhance or interfere with the function of the PRO polypeptide in vivo (c.f., Hodgson, Bio/Technology. 9: 19-21 (1991)).
In one approach, the three-dimensional strucmre of the PRO polypeptide, or of an PRO polypeptide-inhibitor complex, is determined by x-ray crystallography, by computer modeling or, most typically, by a combination of the two approaches. Both the shape and charges of the PRO polypeptide must be ascertained to elucidate the strucmre and to determine active site(s) of the molecule. Less often, useful information regarding the strucmre of the PRO polypeptide may be gained by modeling based on the stmcture of homologous proteins. In both cases, relevant structural information is used to design analogous PRO polypeptide-like molecules or to identify efficient inhibitors. Useful examples of rational drag design may include molecules which have improved activity or stability as shown by Braxton and Wells, Biochemistry. 31:7796-7801 (1992) or which act as inhibitors, agonists, or antagonists of native peptides as shown by Athauda et al. , J. Biochem.. 113:742-746 (1993).
It is also possible to isolate a target-specific antibody, selected by functional assay, as described above, and then to solve its crystal structure. This approach, in principle, yields a pharmacore upon which subsequent drag design can be based. It is possible to bypass protein crystallography altogether by generating anti-idiotypic antibodies (anti-ids) to a functional, pharmacologically active antibody. As a mirror image of a mirror image, the binding site of the anti-ids would be expected to be an analog of the original receptor. The anti-id could then be used to identify and isolate peptides from banks of chemically or biologically produced peptides. The isolated peptides would then act as the pharmacore.
By virtue of the present invention, sufficient amounts of the PRO polypeptide may be made available to perform such analytical smdies as X-ray crystallography. In addition, knowledge of the PRO polypeptide amino acid sequence provided herein will provide guidance to those employing computer modeling techniques in place of or in addition to x-ray crystallography.
EXAMPLE 62: Diagnostic Test Using PRQ317 Polvpeptide-Specific Antibodies
Particular anti-PR0317 polypeptide antibodies are useful for the diagnosis of prepathologic conditions, and chronic or acute diseases such as gynecological diseases or ischemic diseases which are characterized by differences in the amount or distribution of PR0317. PR0317 has been found to be expressed in human kidney and is thus likely to be associated with abnormalities or pathologies which affect this organ. Further, since it is so closely related to EBAF-1 , it is likely to affect the endometrium and other genital tissues. Further, due to library sources of certain ESTs, it appears that PR0317 may be involved as well in forming blood vessels and hence to be a modulator of angiogenesis.
Diagnostic tests for PR0317 include methods utilizing the antibody and a label to detect PR0317 in human body fluids, tissues, or extracts of such tissues. The polypeptide and antibodies of the present invention may be used with or without modification. Frequently, the polypeptide and antibodies will be labeled by joining them, either covalently or noncovalently, with a substance which provides for a detectable signal. A wide variety of labels and conjugation techniques are known and have been reported extensively in both the scientific and patent literature. Suitable labels include radionuclides, enzymes, substrates, cofactors, inhibitors, fluorescent agents, chemiluminescent agents, magnetic particles, and the like. Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275, 149; and 4,366,241. Also, recombinant immunoglobulins may be produced as shown in U.S. Pat. No. 4,816,567.
A variety of protocols for measuring soluble or membrane-bound PRo317, using either polyclonal or monoclonal antibodies specific for that PR0317, are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), radioreceptor assay (RRA), and fluorescent activated cell sorting (FACS). A two-site monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on PR0317 is preferred, but a competitive binding assay may be employed. These assays are described, among other places, in Maddox et al. J Exp. Med.. 158: 1211 (1983).
EXAMPLE 63: Identification of PRQ317 Receptors Purified PR0317 is useful for characterization and purification of specific cell surface receptors and other binding molecules. Cells which respond to PR0317 by metabolic changes or other specific responses are likely to express a receptor for PR0317. Such receptors include, but are not limited to, receptors associated with and activated by tyrosine and serine/threonine kinases. See Kolodziejczyk and Hall, supra, for a review on known receptors for the TGF- superfamily. Candidate receptors for this superfamily fall into two primary groups, termed type I and type II receptors. Both types are serine/threonine kinases. Upon activation by the appropriate ligand, type I and type II receptors physically interact to form hetero-oligomers and subsequently activate intracellular signaling cascades, ultimately regulating gene transcription and expression. In addition, TGF- binds to a third receptor class, type III, a membrane-anchored proteoglycan lacking the kinase activity typical of signal transducing molecules. PR0317 receptors or other PR0317-binding molecules may be identified by interaction with radiolabeled PR0317. Radioactive labels may be incorporated into PR0317 by various methods known in the art. A preferred embodiment is the labeling of primary amino groups in PR0317 with125I Bolton-Hunter reagent (Bolton and Hunter, Biochem. J.. 133:529 (1973)), which has been used to label other polypeptides without concomitant loss of biological activity (Hebert et al , J. Biol. Chem.. 266: 18989 (1991); McColl et al, J. Immunol.. 150:4550-4555 (1993)). Receptor-bearing cells are incubated with labeled PR0317. The cells are then washed to removed unbound PR0317, and receptor-bound PR0317 is quantified. The data obtained using different concentrations of PR0317 are used to calculate values for the number and affinity of receptors.
Labeled PR0317 is useful as a reagent for purification of its specific receptor. In one embodiment of affinity purification, PR0317 is covalently coupled to a chromatography column. Receptor-bearing cells are extracted, and the extract is passed over the column. The receptor binds to the column by virtue of its biological affinity for PR0317. The receptor is recovered from the column and subjected to N-terminal protein sequencing. This amino acid sequence is then used to design degenerate oligonucleotide probes for cloning the receptor gene. In an alternative method, mRNA is obtained from receptor-bearing cells and made into a cDNA library. The library is transfected into a population of cells, and those cells expressing the receptor are selected using fluorescently labeled PR0317. The receptor is identified by recovering and sequencing recombinant DNA from highly labeled cells.
In another alternative method, antibodies are raised against the surface of receptor bearing cells, specifically monoclonal antibodies. The monoclonal antibodies are screened to identify those which inhibit the binding of labeled PR0317. These monoclonal antibodies are then used in affinity purification or expression cloning of the receptor.
Soluble receptors or other soluble binding molecules are identified in a similar manner. Labeled PR0317 is incubated with extracts or other appropriate materials derived from the uterus. After incubation, PR0317 complexes larger than the size of purified PR0317 are identified by a sizing technique such as size- exclusion chromatography or density gradient centrifugation and are purified by methods known in the art. The soluble receptors or binding protein(s) are subjected to N-terminal sequencing to obtain information sufficient for database identification, if the soluble protein is known, or for cloning, if the soluble protein is unknown.
EXAMPLE 64: Determination of PRQ317-Induced Cellular Response
The biological activity of PR0317 is measured, for example, by binding of an PR0317 of the invention to an PR0317 receptor. A test compound is screened as an antagonist for its ability to block binding of PR0317 to the receptor. A test compound is screened as an agonist of the PR0317 for its ability to bind an PR0317 receptor and influence the same physiological events as PR0317 using, for example, the KIRA-ELISA assay described by Sadick et al, Analytical Biochemistry. 235:207-214 (1996) in which activation of a receptor tyrosine kinase is monitored by immuno-capture of the activated receptor and quantitation of the level of ligand- induced phosphorylation. The assay may be adapted to monitor PR0317-induced receptor activation through the use of an PR0317 receptor-specific antibody to capture the activated receptor. These techniques are also applicable to other PRO polypeptides described herein.
EXAMPLE 65: Use of PRQ224 for Screening Compounds
PR0224 is expressed in a cell stripped of membrane proteins and capable of expressing PR0224. Low density lipoproteins having a detectable label are added to the cells and incubated for a sufficient time for endocytosis. The cells are washed. The cells are then analysed for label bound to the membrane and within the cell after cell lysis. Detection of the low density lipoproteins within the cell determines that PR0224 is within the family of low density lipoprotein receptor proteins. Members found within this family are then used for screening compounds which affect these receptors, and particularly the uptake of cholesterol via these receptors.
EXAMPLE 66: Ability of PRO Polypeptides to Inhibit Vascular Endothelial Growth Factor (VEGF) Stimulated Proliferation of Endothelial Cell Growth (Assay 9)
The ability of various PRO polypeptides to inhibit VEGF stimulated proliferation of endothelial cells was tested. Polypeptides testing positive in this assay are useful for inhibiting endothelial cell growth in mammals where such an effect would be beneficial, e.g., for inhibiting mmor growth.
Specifically, bovine adrenal cortical capillary endothelial cells (ACE) (from primary culmre, maximum of 12-14 passages) were plated in 96-well plates at 500 cells/well per 100 microliter. Assay media included low glucose DMEM, 10% calf serum, 2 mM glutamine, and IX penicillin/streptomycin/fungizone. Control wells included the following: (1) no ACE cells added; (2) ACE cells alone; (3) ACE cells plus 5 ng/ml FGF; (4) ACE cells plus 3 ng/ml VEGF; (5) ACE cells plus 3 ng/ml VEGF plus 1 ng/ml TGF-beta; and (6) ACE cells plus 3 ng/ml VEGF plus 5 ng/ml LIF. The test samples, poly-his tagged PRO polypeptides (in 100 microliter volumes), were then added to the wells (at dilutions of 1 % , 0.1 % and 0.01 % , respectively). The cell cultures were incubated for 6-7 days at 37°C/5% C02. After the incubation, the media in the wells was aspirated, and the cells were washed IX with PBS. An acid phosphatase reaction mixmre (100 microliter; 0.1M sodium acetate, pH 5.5, 0.1 % Triton X-100, 10 mM p-nitrophenyl phosphate) was then added to each well. After a 2 hour incubation at 37 °C , the reaction was stopped by addition of 10 microliters 1 N NaOH . Optical density (OD) was measured on a microplate reader at 405 nm.
The activity of PRO polypeptides was calculated as the percent inhibition of VEGF (3 ng/ml) stimulated proliferation (as determined by measuring acid phosphatase activity at OD 405 nm) relative to the cells without stimulation. TGF-beta was employed as an activity reference at 1 ng/ml, since TGF-beta blocks 70-90% of VEGF-stimulated ACE cell proliferation. The results are indicative of the utility of the PRO polypeptides in cancer therapy and specifically in inhibiting mmor angiogenesis. Numerical values (relative inhibition) are determined by calculating the percent inhibition of VEGF stimulated proliferation by the PRO polypeptides relative to cells without stimulation and then dividing that percentage into the percent inhibition obtained by TGF- β at 1 ng/ml which is known to block 70-90 % of VEGF stimulated cell proliferation. The results are considered positive if the PRO polypeptide exhibits 30% or greater inhibition of VEGF stimulation of endothelial cell growth (relative inhibition 30% or greater).
The following polypeptides tested positive in this assay: PR0211 , PR0217, PRO 187, PR0219, PR0246, PR0228, PR0245, PR0221 , PR0258, PRO301 , PR0224, PR0272, PR0328, PR0331 , PR0224, PR0328, PR0272, PRO301, PR0331 and PR0214.
EXAMPLE 67: Retinal Neuron Survival (Assay 52)
This example demonstrates that certain PRO polypeptides have efficacy in enhancing the survival of retinal neuron cells and, therefore, are useful for the therapeutic treatment of retinal disorders or injuries including, for example, treating sight loss in mammals due to retinitis pigmentosum, AMD, etc.
Sprague Dawley rat pups at postnatal day 7 (mixed population: glia and retinal neuronal types) are killed by decapitation following C02 anesthesia and the eyes are removed under sterile conditions. The neural retina is dissected away from the pigment epithelium and other ocular tissue and then dissociated into a single cell suspension using 0.25 % trypsin in Ca2+, Mg2+-free PBS. The retinas are incubated at 37°C for 7-10 minutes after which the trypsin is inactivated by adding 1 ml soybean trypsin inhibitor. The cells are plated at 100,000 cells per well in 96 well plates in DMEM/F12 supplemented with N2 and with or without the specific test PRO polypeptide. Cells for all experiments are grown at 37°C in a water saturated atmosphere of 5% C02. After 2-3 days in culmre, cells are stained with calcein AM then fixed using 4% paraformaldehyde and stained with DAPI for determination of total cell count. The total cells (fluorescent) are quantified at 20X objective magnification using CCD camera and NIH image software for Macintosh. Fields in the well are chosen at random.
The effect of various concentration of PRO polypeptides are reported herein where percent survival is calculated by dividing the total number of calcein AM positive cells at 2-3 days in culmre by the total number of DAPI-labeled cells at 2-3 days in culture. Anything above 30% survival is considered positive.
The following PRO polypeptides tested positive in this assay using polypeptide concentrations within the range of 0.01 % to 1.0% in the assay: PRO220 and PR0346.
EXAMPLE 68: Rod Photoreceptor Cell Survival (Assay 56)
This assay shows that certain polypeptides of the invention act to enhance the survival/proliferation of rod photoreceptor cells and, therefore, are useful for the therapeutic treatment of retinal disorders or injuries including, for example, treating sight loss in mammals due to retinitis pigmentosum, AMD, etc. Sprague Dawley rat pups at 7 day postnatal (mixed population: glia and retinal neuronal cell types) are killed by decapitation following C02 anesthesis and the eyes are removed under sterile conditions. The neural retina is dissected away form the pigment epithelium and other ocular tissue and then dissociated into a single cell suspension using 0.25% trypsin in Ca2+, Mg2+-free PBS. The retinas are incubated at 37°C for 7-10 minutes after which the trypsin is inactivated by adding 1 ml soybean trypsin inhibitor. The cells are plated at 100,000 cells per well in 96 well plates in DMEM/F12 supplemented with N2. Cells for all experiments are grown at 37°C in a water samrated atmosphere of 5% C02. After 2-3 days in culmre, cells are fixed using 4% paraformaldehyde, and then stained using CellTracker Green CMFDA. Rho 4D2 (ascites or IgG 1 : 100), a monoclonal antibody directed towards the visual pigment rhodopsin is used to detect rod photoreceptor cells by indirect immuno fluorescence. The results are calculated as % survival: total number of calcein - rhodopsin positive cells at 2-3 days in culmre, divided by the total number of rhodopsin positive cells at time 2-3 days in culmre. The total cells (fluorescent) are quantified at 20x objective magnification using a CCD camera and NIH image software for Macintosh. Fields in the well are chosen at random.
The following polypeptides tested positive in this assay: PRO220 and PR0346.
EXAMPLE 69: Induction of Endothelial Cell Apoptosis (Assay 73) The ability of PRO polypeptides to induce apoptosis in endothelial cells was tested in human venous umbilical vein endothelial cells (HUVEC, Cell Systems). A positive test in the assay is indicative of the usefulness of the polypeptide in therapeutically treating tumors as well as vascular disorders where inducing apoptosis of endothelial cells would be beneficial.
The cells were plated on 96-well microtiter plates (Amersham Life Science, cytostar-T scintillating microplate, RPNQ160, sterile, tissue-culmre treated, individually wrapped), in 10% serum (CSG-medium, Cell Systems), at a density of 2 x IO4 cells per well in a total volume of 100 μl. On day 2, test samples containing the PRO polypeptide were added in triplicate at dilutions of 1 % , 0.33 % and 0.11 %. Wells without cells were used as a blank and wells with cells only were used as a negative control. As a positive control 1 :3 serial dilutions of 50 μl of a 3x stock of staurosporine were used. The ability of the PRO polypeptide to induce apoptosis was determined by processing of the 96 well plates for detection of Annexin V, a member of the calcium and phospholipid binding proteins, to detect apoptosis.
0.2 ml Annexin V - Biotin stock solution (100 μg/ml) was diluted in 4.6 ml 2 x Ca2+ binding buffer and 2.5 % BSA (1 :25 dilution). 50 μl of the diluted Annexin V - Biotin solution was added to each well (except controls) to a final concentration of 1.0 μg/ml. The samples were incubated for 10-15 minutes with Annexin- Biotin prior to direct addition of 35S-Streptavidin. 35S-Streptavidin was diluted in 2x Ca2+ Binding buffer, 2.5 % BSA and was added to all wells at a final concentration of 3 x IO4 cpm/well. The plates were then sealed, centrifuged at 1000 rpm for 15 minutes and placed on orbital shaker for 2 hours. The analysis was performed on a 1450 Microbeta Trilux (Wallac). Percent above background represents the percentage amount of counts per minute above the negative controls. Percents greater than or equal to 30 % above background are considered positive.
The following PRO polypeptides tested positive in this assay: PR0228, PR0217 and PRO301.
EXAMPLE 70: PDB12 Cell Inhibition (Assay 40)
This example demonstrates that various PRO polypeptides have efficacy in inhibiting protein production by PDB12 pancreatic ductal cells and are, therefore, useful in the therapeutic treatment of disorders which involve protein secretion by the pancreas, including diabetes, and the like.
PDB12 pancreatic ductal cells are plated on fibronectin coated 96 well plates at 1.5xl03 cells per well in 100 μL/180 μL of growth media. 100 μL of growth media with the PRO polypeptide test sample or negative control lacking the PRO polypeptide is then added to well, for a final volume of 200 μL. Controls contain growth medium containing a protein shown to be inactive in this assay. Cells are incubated for 4 days at 37°C. 20 μL of Alamar Blue Dye (AB) is then added to each well and the flourescent reading is measured at 4 hours post addition of AB, on a microtiter plate reader at 530 nm excitation and 590 nm emission. The standard employed is cells without Bovine Pimitary Extract (BPE) and with various concentrations of BPE. Buffer or CM controls from unknowns are run 2 times on each 96 well plate.
These assays allow one to calculate a percent decrease in protein production by comparing the Alamar Blue Dye calculated protein concentration produced by the PRO polypeptide-treated cells with the Alamar Blue Dye calculated protein concentration produced by the negative control cells. A percent decrease in protein production of greater than or equal to 25% as compared to the negative control cells is considered positive. The following polypeptides tested positive in this assay: PR0211, PR0287, PRO301 and PR0293.
EXAMPLE 71 : Stimulation of Adult Heart Hypertrophy (Assay 2)
This assay is designed to measure the ability of various PRO polypeptides to stimulate hypertrophy of adult heart. PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of various cardiac insufficiency disorders.
Ventricular myocytes freshly isolated from adult (250g) Sprague Dawley rats are plated at 2000 cell/well in 180 μl volume. Cells are isolated and plated on day 1, the PRO polypeptide-containing test samples or growth medium only (negative control) (20 μl volume) is added on day 2 and the cells are then fixed and stained on day 5. After staining, cell size is visualized wherein cells showing no growth enhancement as compared to control cells are given a value of 0.0, cells showing small to moderate growth enhancement as compared to control cells are given a value of 1.0 and cells showing large growth enhancement as compared to control cells are given a value of 2.0. Any degree of growth enhancement as compared to the negative control cells is considered positive for the assay.
The following PRO polypeptides tested positive in this assay: PR0287, PRO301, PRO293 and PRO303.
EXAMPLE 72: PDB12 Cell Proliferation (Assay 29) This example demonstrates that various PRO polypeptides have efficacy in inducing proliferation of
PDB12 pancreatic ductal cells and are, therefore, useful in the therapeutic treatment of disorders which involve protein secretion by the pancreas, including diabetes, and the like.
PDB12 pancreatic ductal cells are plated on fibronectin coated 96 well plates at 1.5xl03 cells per well in 100 μL/180 μL of growth media. 100 μL of growth media with the PRO polypeptide test sample or negative control lacking the PRO polypeptide is then added to well, for a final volume of 200 μL. Controls contain growth medium containing a protein shown to be inactive in this assay. Cells are incubated for 4 days at 37°C. 20 μL of Alamar Blue Dye (AB) is then added to each well and the flourescent reading is measured at 4 hours post addition of AB, on a microtiter plate reader at 530 nm excitation and 590 nm emission. The standard employed is cells without Bovine Pimitary Extract (BPE) and with various concentrations of BPE. Buffer or growth medium only controls from unknowns are run 2 times on each 96 well plate.
Percent increase in protein production is calculated by comparing the Alamar Blue Dye calculated protein concentration produced by the PRO polypeptide-treated cells with the Alamar Blue Dye calculated protein concentration produced by the negative control cells. A percent increase in protein production of greater than or equal to 25% as compared to the negative control cells is considered positive. The following PRO polypeptides tested positive in this assay: PRO301 and PRO303.
EXAMPLE 73: Enhancement of Heart Neonatal Hypertrophy (Assay 1)
This assay is designed to measure the ability of PRO polypeptides to stimulate hypertrophy of neonatal heart. PRO polypeptides testing positive in this assay are expected to be useful for the therapeutic treatment of various cardiac insufficiency disorders.
Cardiac myocytes from 1-day old Harlan Sprague Dawley rats were obtained. Cells (180 μl at 7.5 x 104/ml, serum < 0.1 % , freshly isolated) are added on day 1 to 96- well plates previously coated with DMEM/F12 + 4% FCS. Test samples containing the test PRO polypeptide or growth medium only (hegative control) (20 μl/well) are added directly to the wells on day 1. PGF (20 μl/well) is then added on day 2 at final concentration of IO"6 M. The cells are then stained on day 4 and visually scored on day 5, wherein cells showing no increase in size as compared to negative controls are scored 0.0, cells showing a small to moderate increase in size as compared to negative controls are scored 1.0 and cells showing a large increase in size as compared to negative controls are scored 2.0. A positive result in the assay is a score of 1.0 or greater.
The following polypeptides tested positive in this assay: PR0224 and PR0231.
EXAMPLE 74: Stimulatory Activity in Mixed Lymphocyte Reaction (MLR) Assay (Assay 24)
This example shows that certain polypeptides of the invention are active as a stimulator of the proliferation of stimulated T-lymphocytes. Compounds which stimulate proliferation of lymphocytes are useful therapeutically where enhancement of an immune response is beneficial. A therapeutic agent may take the form of antagonists of the polypeptide of the invention, for example, murine-human chimeric, humanized or human antibodies against the polypeptide.
The basic protocol for this assay is described in Current Protocols in Immunology, unit 3.12; edited by J E Coligan, A M Kmisbeek, D H Marglies, E M Shevach, W Strober, National Insitutes of Health, Published by John Wiley & Sons, Inc.
More specifically, in one assay variant, peripheral blood mononuclear cells (PBMC) are isolated from mammalian individuals, for example a human volunteer, by leukopheresis (one donor will supply stimulator PBMCs, the other donor will supply responder PBMCs). If desired, the cells are frozen in fetal bovine semm and DMSO after isolation. Frozen cells may be thawed overnight in assay media (37°C, 5% C02) and then washed and resuspended to 3xl06 cells/ml of assay media (RPMI; 10% fetal bovine semm, 1% penicillin/streptomycin, 1 % glutamine, 1 % HEPES, 1 % non-essential amino acids, 1 % pyruvate). The stimulator PBMCs are prepared by irradiating the cells (about 3000 Rads). The assay is prepared by plating in triplicate wells a mixmre of: 100:1 of test sample diluted to 1 % or to 0.1 % ,
50 :1 of irradiated stimulator cells, and 50 :1 of responder PBMC cells. 100 microliters of cell culmre media or 100 microliter of CD4-IgG is used as the control. The wells are then incubated at 37°C, 5% C02 for 4 days. On day 5, each well is pulsed with tritiated thymidine (1.0 mC/well; Amersham). After 6 hours the cells are washed 3 times and then the uptake of the label is evaluated.
In another variant of this assay, PBMCs are isolated from the spleens of Balb/c mice and C57B6 mice. The cells are teased from freshly harvested spleens in assay media (RPMI; 10% fetal bovine semm, 1 % penicillin/streptomycin, 1 % glutamine, 1 % HEPES, 1 % non-essential amino acids, 1 % pyruvate) and the PBMCs are isolated by overlaying these cells over Lympholyte M (Organon Teknika), centrifuging at 2000 rpm for 20 minutes, collecting and washing the mononuclear cell layer in assay media and resuspending the cells to lxlO7 cells/ml of assay media. The assay is then conducted as described above.
Positive increases over control are considered positive with increases of greater than or equal to 180% being preferred. However, any value greater than control indicates a stimulatory effect for the test protein. The following PRO polypeptides tested positive in this assay: PR0245, PR0269, PR0217, PRO301, PR0266, PR0335, PR0331, PR0533 and PR0326. EXAMPLE 75: Pericvte c-Fos Induction (Assay 93)
This assay shows that certain polypeptides of the invention act to induce the expression of c-fos in pericyte cells and, therefore, are useful not only as diagnostic markers for particular types of pericyte-associated tumors but also for giving rise to antagonists which would be expected to be useful for the therapeutic treatment of pericyte-associated tumors. Specifically, on day 1, pericytes are received from VEC Technologies and all but 5 ml of media is removed from flask. On day 2, the pericytes are trypsinized, washed, spun and then plated onto 96 well plates. On day 7, the media is removed and the pericytes are treated with 100 μl of PRO polypeptide test samples and controls (positive control = DME+5% serum +/- PDGF at 500 ng/ml; negative control = protein 32). Replicates are averaged and SD/CV are determined. Fold increase over Protein 32 (buffer control) value indicated by chemiluminescence units (RLU) luminometer reading verses frequency is plotted on a histogram. Two-fold above Protein 32 value is considered positive for the assay. ASY Matrix: Growth media = low glucose DMEM = 20% FBS + IX pen strep + IX fungizone. Assay Media = low glucose DMEM +5% FBS.
The following polypeptides tested positive in this assay: PR0214, PR0219, PR0221 and PR0224.
EXAMPLE 76: Ability of PRO Polypeptides to Stimulate the Release of Proteoglycans from Cartilage (Assay 97}
The ability of various PRO polypeptides to stimulate the release of proteoglycans from cartilage tissue was tested as follows.
The metacarphophalangeal joint of 4-6 month old pigs was aseptically dissected, and articular cartilage was removed by free hand slicing being careful to avoid the underlying bone. The cartilage was minced and cultured in bulk for 24 hours in a humidified atmosphere of 95 % air, 5 % C02 in semm free (SF) media (DME/F12 1: 1) woth 0.1 % BSA and lOOU/ml penicillin and lOOμg/ml streptomycin. After washing three times, approximately 100 mg of articular cartilage was aliquoted into micronics tubes and incubated for an additional 24 hours in the above SF media. PRO polypeptides were then added at 1 % either alone or in combination with 18 ng/ml interleukin-lα, a known stimulator of proteoglycan release from cartilage tissue. The supernatant was then harvested and assayed for the amount of proteoglycans using the 1,9-dimethyl- methylene blue (DMB) colorimetric assay (Farndale and Buttle, Biochem. Biophys. Acta 883: 173-177 (1985)). A positive result in this assay indicates that the test polypeptide will find use, for example, in the treatment of sports-related joint problems, articular cartilage defects, osteoarthritis or rheumatoid arthritis. When various PRO polypeptides were tested in the above assay, the polypeptides demonstrated a marked ability to stimulate release of proteoglycans from cartilage tissue both basally and after stimulation with interleukin-lα and at 24 and 72 hours after treatment, thereby indicating that these PRO polypeptides are useful for stimulating proteoglycan release from cartilage tissue. As such, these PRO polypeptides are useful for the treatment of sports-related joint problems, articular cartilage defects, osteoarthritis or rheumatoid arthritis. The polypeptides testing positive in this assay are : PR0211. EXAMPLE 77: Skin Vascular Permeability Assay (Assay 64)
This assay shows that certain polypeptides of the invention stimulate an immune response and induce inflammation by inducing mononuclear cell, eosinophil and PMN infiltration at the site of injection of the animal. Compounds which stimulate an immune response are useful therapeutically where stimulation of an immune response is beneficial. This skin vascular permeability assay is conducted as follows. Hairless guinea pigs weighing 350 grams or more are anesthetized with ketamine (75-80 mg/Kg) and 5 mg/Kg xylazine intramuscularly (IM). A sample of purified polypeptide of the invention or a conditioned media test sample is injected intradermally onto the backs of the test animals with 100 μl per injection site. It is possible to have about 10-30, preferably about 16-24, injection sites per animal. One μl of Evans blue dye (1 % in physiologic buffered saline) is injected intracardially. Blemishes at the injection sites are then measured (mm diameter) at 1 hr and 6 hr post injection. Animals were sacrificed at 6 hrs after injection. Each skin injection site is biopsied and fixed in formalin. The skins are then prepared for histopathologic evaluation. Each site is evaluated for inflammatory cell infiltration into the skin. Sites with visible inflammatory cell inflammation are scored as positive. Inflammatory cells may be neutrophilic, eosinophilic, monocytic or lymphocytic. At least a minimal perivascular infiltrate at the injection site is scored as positve, no infiltrate at the site of injection is scored as negative.
The following polypeptides tested positive in this assay: PR0245, PR0217, PR0326, PR0266, PR0272, PRO301, PR0331 and PR0335.
EXAMPLE 78: Enhancement of Heart Neonatal Hypertrophy Induced by F2a (Assay 37) This assay is designed to measure the ability of PRO polypeptides to stimulate hypertrophy of neonatal heart. PRO polypeptides testing positive in this assay are expected to be useful for the therapeutic treatment of various cardiac insufficiency disorders.
Cardiac myocytes from 1-day old Harlan Sprague Dawley rats were obtained. Cells (180 μl at 7.5 x 104/ml, serum < 0.1 % , freshly isolated) are added on day 1 to 96- well plates previously coated with DMEM/F12 + 4% FCS. Test samples containing the test PRO polypeptide (20 μl/well) are added directly to the wells on day 1. PGF (20 μl/well) is then added on day 2 at a final concentration of IO"6 M. The cells are then stained on day 4 and visually scored on day 5. Visual scores are based on cell size, wherein cells showing no increase in size as compared to negative controls are scored 0.0, cells showing a small to moderate increase in size as compared to negative controls are scored 1.0 and cells showing a large increase in size as compared to negative controls are scored 2.0. A score of 1.0 or greater is considered positive.
No PBS is included, since calcium concentration is critical for assay response. Plates are coated with DMEM/F12 plus 4% FCS (200 μl/well). Assay media included: DMEM/F12 (with 2.44 gm bicarbonate), 10 μg/ml transferrin, 1 μg/ml insulin, 1 μg/ml aprotinin, 2 mmol/L glutamine, 100 U/ml penicillin G, 100 μg/ml streptomycin. Protein buffer containing mannitol (4%) gave a positive signal (score 3.5) at 1/10 (0.4%) and 1/100 (0.04%), but not at 1/1000 (0.004%). Therefore the test sample buffer containing mannitol is not mn. The following PRO polypeptides tested positive in this assay: PR0224. EXAMPLE 79: Inhibitory Activity in Mixed Lymphocyte Reaction (MLR) Assay (Assay 67)
This example shows that one or more of the polypeptides of the invention are active as inhibitors of the proliferation of stimulated T-lymphocytes. Compounds which inhibit proliferation of lymphocytes are useful therapeutically where suppression of an immune response is beneficial.
The basic protocol for this assay is described in Current Protocols in Immunology, unit 3.12; edited by J E Coligan, A M Kmisbeek, D H Marglies, E M Shevach, W Strober, National Insitutes of Health, Published by John Wiley & Sons, Inc.
More specifically, in one assay variant, peripheral blood mononuclear cells (PBMC) are isolated from mammalian individuals, for example a human volunteer, by leukopheresis (one donor will supply stimulator PBMCs, the other donor will supply responder PBMCs). If desired, the cells are frozen in fetal bovine semm and DMSO after isolation. Frozen cells may be thawed overnight in assay media (37°C, 5% C02) and then washed and resuspended to 3xl06 cells/ml of assay media (RPMI; 10% fetal bovine semm, 1 % penicillin/streptomycin, 1 % glutamine, 1 % HEPES, 1 % non-essential amino acids, 1 % pymvate). The stimulator PBMCs are prepared by irradiating the cells (about 3000 Rads).
The assay is prepared by plating in triplicate wells a mixture of: 100 : 1- of test sample diluted to 1 % or to 0.1 % ,
50 :1 of irradiated stimulator cells, and
50 :1 of responder PBMC cells. 100 microliters of cell culture media or 100 microliter of CD4-IgG is used as the control. The wells are then incubated at 37°C, 5% C02 for 4 days. On day 5, each well is pulsed with tritiated thymidine (1.0 mC/well; Amersham). After 6 hours the cells are washed 3 times and then the uptake of the label is evaluated.
In another variant of this assay, PBMCs are isolated from the spleens of Balb/c mice and C57B6 mice. The cells are teased from freshly harvested spleens in assay media (RPMI; 10% fetal bovine serum, 1 % penicillin/streptomycin, 1 % glutamine, 1 % HEPES, 1 % non-essential amino acids, 1 % pyruvate) and the PBMCs are isolated by overlaying these cells over Lympholyte M (Organon Teknika), centrifuging at 2000 rpm for 20 minutes, collecting and washing the mononuclear cell layer in assay media and resuspending the cells to lxlO7 cells/ml of assay media. The assay is then conducted as described above.
Any decreases below control is considered to be a positive result for an inhibitory compound, with decreases of less than or equal to 80% being preferred. However, any value less than control indicates an inhibitory effect for the test protein. The following polypeptide tested positive in this assay: PR0235, PR0245 and PR0332.
EXAMPLE 80: Induction of Endothelial Cell Apoptosis (ELISA) (Assay 109)
The ability of PRO polypeptides to induce apoptosis in endothelial cells was tested in human venous umbilical vein endothelial cells (HUVEC, Cell Systems) using a 96-well format, in 0% serum media supplemented with 100 ng/ml VEGF, 0.1 % BSA, IX penn/strep. A positive result in this assay indicates the usefulness of the polypeptide for therapeutically treating any of a variety of conditions associated with undesired endothelial cell growth including, for example, the inhibition of mmor growth. The 96-well plates used were manufactured by Falcon (No. 3072). Coating of 96 well plates were prepared by allowing gelatinization to occur for > 30 minutes with 100 μl of 0.2% gelatin in PBS solution. The gelatin mix was aspirated thoroughly before plating HUVEC cells at a final concentration of 2 x IO4 cells/ml in 10% semm containing medium - 100 μl volume per well. The cells were grown for 24 hours before adding test samples containing the PRO polypeptide of interest. To all wells, 100 μl of 0% semm media (Cell Systems) complemented with 100 ng/ml VEGF, 0.1 %
BSA, IX penn/strep was added. Test samples containing PRO polypeptides were added in triplicate at dilutions of 1 % , 0.33 % and 0.11 % . Wells without cells were used as a blank and wells with cells only were used as a negative control. As a positive control, 1 :3 serial dilutions of 50 μl of a 3x stock of staurosporine were used. The cells were incubated for 24 to 35 hours prior to ELISA. ELISA was used to determine levels of apoptosis preparing solutions according to the Boehringer
Manual [Boehringer, Cell Death Detection ELISA plus, Cat No. 1 920 685]. Sample preparations: 96 well plates were spun down at 1 krpm for 10 minutes (200g); the supernatant was removed by fast inversion, placing the plate upside down on a paper towel to remove residual liquid. To each well, 200 μl of IX Lysis buffer was added and incubation allowed at room temperature for 30 minutes without shaking. The plates were spun down for 10 minutes at 1 krpm, and 20 μl of the lysate (cytoplasmic fraction) was transferred into streptavidin coated MTP. 80 μl of immunoreagent mix was added to the 20 μl lystate in each well. The MTP was covered with adhesive foil and incubated at room tempearature for 2 hours by placing it on an orbital shaker (200 rpm). After two hours, the supernatant was removed by suction and the wells rinsed three times with 250 μl of IX incubation buffer per well (removed by suction). Substrate solution was added (100 μl) into each well and incubated on an orbital shaker at room temperature at 250 rpm until color development was sufficient for a photometric analysis (approx. after 10-20 minutes). A 96 well reader was used to read the plates at 405 nm, reference wavelength, 492 nm. The levels obtained for PIN 32 (control buffer) was set to 100%. Samples with levels > 130% were considered positive for induction of apoptosis.
The following PRO polypeptides tested positive in this assay: PR0235.
EXAMPLE 81 : Human Venous Endothelial Cell Calcium Flux Assay (Assay 68)
This assay is designed to determine whether PRO polypeptides of the present invention show the ability to stimulate calcium flux in human umbilical vein endothelial cells (HUVEC, Cell Systems). Calcium influx is a well documented response upon binding of certain ligands to their receptors. A test compound that results in a positive response in the present calcium influx assay can be said to bind to a specific receptor and activate a biological signaling pathway in human endothelial cells. This could ultimately lead, for example, to endothelial cell division, inhibition of endothelial cell proliferation, endothelial tube formation, cell migration, apoptosis, etc.
Human venous umbilical vein endothelial cells (HUVEC, Cell Systems) in growth media (50:50 without glycine, 1 % glutamine, lOmM Hepes, 10% FBS, 10 ng/ml bFGF), were plated on 96-well microtiter ViewPlates-96 (Packard Instrument Company Part #6005182) microtiter plates at a cell density of 2 x IO4 cells/well. The day after plating, the cells were washed three times with buffer (HBSS plus 10 mM Hepes), leaving 100 μl/well. Then 100 μl/well of 8 μM Fluo-3 (2x) was added. The cells were incubated for 1.5 hours at 37°C/5% C02. After incubation, the cells were then washed 3x with buffer (described above) leaving 100 μl/well. Test samples of the PRO polypeptides were prepared on different 96-well plates at 5x concentration in buffer. The positive control corresponded to 50 μM ionomycin (5x); the negative control corresponded to Protein 32. Cell plate and sample plates were run on a FLIPR (Molecular Devices) machine. The FLIPR machine added 25 μl of test sample to the cells, and readings were taken every second for one minute, then every 3 seconds for the next three minutes.
The fluorescence change from baseline to the maximum rise of the curve (Δ change) was calculated, and replicates averaged. The rate of fluorescence increase was monitored, and only those samples which had a Δ change greater than 1000 and a rise within 60 seconds, were considered positive. The following PRO polypeptides tested positive in the present assay: PR0245.
EXAMPLE 82: Fibroblast (BHK-21) Proliferation (Assay 98)
This assay shows that certain PRO polypeptides of the invention act to induce proliferation of mammalian fibroblast cells in culmre and, therefore, function as useful growth factors in mammalian systems. The assay is performed as follows. BHK-21 fibroblast cells plated in standard growth medium at 2500 cells/well in a total volume of 100 μl. The PRO polypeptide, β-FGF (positive control) or nothing (negative control) are then added to the wells in the presence of lμg/ml of heparin for a total final volume of 200 μl. The cells are then incubated at 37°C for 6 to 7 days. After incubation, the media is removed, the cells are washed with PBS and then an acid phosphatase substrate reaction mixmre (100 μl/well) is added. The cells are then incubated at 37°C for 2 hours. 10 μl per well of IN NaOH is then added to stop the acid phosphatase reaction. The plates are then read at OD 405nm. A positive in the assay is acid phosphatase activity which is at least 50% above the negative control.
The following PRO polypeptide tested positive in this assay: PR0258.
EXAMPLE 83: Inhibition of Heart Adult Hypertrophy (Assay 42)
This assay is designed to measure the inhibition of heart adult hypertrophy. PRO polypeptides testing positive in this assay may find use in the therapeutic treatment of cardiac disorders associated with cardiac hypertrophy.
Ventricular myocytes are freshly isolated from adult (250g) Harlan Sprague Dawley rats and the cells are plated at 2000/well in 180 μl volume. On day two, test samples (20 μl) containing the test PRO polypeptide are added. On day five, the cells are fixed and then stained. An increase in ANP message can also be measured by PCR from cells after a few hours. Results are based on a visual score of cell size: 0 = no inhibition, -1 = small inhibition, -2 = large inhibition. A score of less than 0 is considered positive. Activity reference corresponds to phenylephrin (PE) at 0.1 mM, as a positive control. Assay media included: M199 (modified)- glutamine free, NaHC03, phenol red, supplemented with 100 nM insulin, 0.2% BSA, 5 mM cretine, 2 mM L- camitine, 5 mM taurine, 100 U/ml penicillin G, 100 μg/ml streptomycin (CCT medium). Only inner 60 wells are used in 96 well plates. Of these, 6 wells are reserved for negative and positive (PE) controls. The following PRO polypeptides provided a score of less than 0 in the above assay: PR0269.
EXAMPLE 84: Induction of c-fos in Endothelial Cells (Assay 34)
This assay is designed to determine whether PRO polypeptides show the ability to induce c-fos in endothelial cells. PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of conditions or disorders where angiogenesis would be beneficial including, for example, wound healing, and the like (as would agonists of these PRO polypeptides). Antagonists of the PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of cancerous tumors.
Human venous umbilical vein endothelial cells (HUVEC, Cell Systems) in growth media (50% Ham's F12 w/o GHT: low glucose, and 50% DMEM without glycine: with NaHC03, 1 % glutamine, 10 mM HEPES, 10% FBS, 10 ng/ml bFGF) were plated on 96-well microtiter plates at a cell density of 1x10" cells/well. The day after plating, the cells were starved by removing the growth media and treating the cells with 100 μl/well test samples and controls (positive control = growth media; negative control = Protein 32 buffer = 10 mM HEPES, 140 mM NaCl, 4% (w/v) mannitol, pH 6.8). The cells were incubated for 30 minutes at 37°C, in 5% C02. The samples were removed, and the first part of the bDNA kit protocol (Chiron Diagnostics, cat. #6005- 037) was followed, where each capitalized reagent/buffer listed below was available from the kit.
Briefly, the amounts of the TM Lysis Buffer and Probes needed for the tests were calculated based on information provided by the manufacmrer. The appropriate amounts of thawed Probes were added to the TM Lysis Buffer. The Capture Hybridization Buffer was warmed to room temperature. The bDNA strips were set up in the metal strip holders, and 100 μl of Capture Hybridization Buffer was added to each b-DNA well needed, followed by incubation for at least 30 minutes. The test plates with the cells were removed from the incubator, and the media was gently removed using the vacuum manifold. 100 μl of Lysis Hybridization Buffer with Probes were quickly pipetted into each well of the microtiter plates. The plates were then incubated at 55 °C for 15 minutes. Upon removal from the incubator, the plates were placed on the vortex mixer with the microtiter adapter head and vortexed on the #2 setting for one minute. 80 μl of the lysate was removed and added to the bDNA wells containing the Capture Hybridization Buffer, and pipetted up and down to mix. The plates were incubated at 53 °C for at least 16 hours.
On the next day, the second part of the bDNA kit protocol was followed. Specifically, the plates were removed from the incubator and placed on the bench to cool for 10 minutes. The volumes of additions needed were calculated based upon information provided by the manufacmrer. An Amplifier Working Solution was prepared by making a 1 : 100 dilution of the Amplifier Concentrate (20 fm/μl) in AL Hybridization Buffer. The hybridization mixmre was removed from the plates and washed twice with Wash A. 50 μl of Amplifier Working Solution was added to each well and the wells were incubated at 53 °C for 30 minutes. The plates were then removed from the incubator and allowed to cool for 10 minutes. The Label Probe Working Solution was prepared by making a 1 : 100 dilution of Label Concentrate (40 pmoles/μl) in AL Hybridization Buffer. After the 10-minute cool-down period, the amplifier hybridization mixmre was removed and the plates were washed twice with Wash A. 50 μl of Label Probe Working Solution was added to each well and the wells were incubated at 53 °C for 15 minutes. After cooling for 10 minutes, the Substrate was warmed to room temperature. Upon addition of 3 μl of Substrate Enhancer to each ml of Substrate needed for the assay, the plates were allowed to cool for 10 minutes, the label hybridization mixmre was removed, and the plates were washed twice with Wash A and three times with Wash D. 50 μl of the Substrate Solution with Enhancer was added to each well. The plates were incubated for 30 minutes at 37 °C and RLU was read in an appropriate luminometer. The replicates were averaged and the coefficient of variation was determined. The measure of activity of the fold increase over the negative control (Protein 32/HEPES buffer described above) value was indicated by chemiluminescence units (RLU). The results are considered positive if the PRO polypeptide exhibits at least a two-fold value over the negative buffer control. Negative control = 1.00 RLU at 1.00% dilution. Positive control = 8.39 RLU at 1.00% dilution. The following PRO polypeptides tested positive in this assay: PR0287.
EXAMPLE 85: Guinea Pig Vascular Leak (Assays 32 and 51)
This assay is designed to determine whether PRO polypeptides of the present invention show the ability to induce vascular permeability. Polypeptides testing positive in this assay are expected to be useful for the therapeutic treatment of conditions which would benefit from enhanced vascular permeability including, for example, conditions which may benefit from enhanced local immune system cell infiltration.
Hairless guinea pigs weighing 350 grams or more were anesthetized with Ketamine (75-80 mg/kg) and 5 mg/kg Xylazine intramuscularly. Test samples containing the PRO polypeptide or a physiological buffer without the test polypeptide are injected into skin on the back of the test animals with 100 μl per injection site intradermally. There were approximately 16-24 injection sites per animal. One ml of Evans blue dye (1 % in PBS) is then injected intracardially. Skin vascular permeability responses to the compounds (i.e. , blemishes at the injection sites of injection) are visually scored by measuring the diameter (in mm) of blue-colored leaks from the site of injection at 1 and 6 hours post administration of the test materials. The mm diameter of blueness at the site of injection is observed and recorded as well as the severity of the vascular leakage. Blemishes of at least 5 mm in diameter are considered positive for the assay when testing purified proteins, being indicative of the ability to induce vascular leakage or permeability. A response greater than 7 mm diameter is considered positive for conditioned media samples. Human VEGF at 0.1 μg/100 μl is used as a positive control, inducing a response of 15-23 mm diameter.
The following PRO polypeptides tested positive in this assay: PRO302 and PR0533.
EXAMPLE 86: Detection of Endothelial Cell Apoptosis (FACS) (Assay 96)
The ability of PRO polypeptides of the present invention to induce apoptosis in endothelial cells was tested in human venous umbilical vein endothelial cells (HUVEC, Cell Systems) in gelatinized T175 flasks using HUVEC cells below passage 10. PRO polypeptides testing positive in this assay are expected to be useful for therapeutically treating conditions where apoptosis of endothelial cells would be beneficial including, for example, the therapeutic treatment of tumors.
On day one, the cells were split [420,000 cells per gelatinized 6 cm dishes - (11 x 103 cells/cm2 Falcon, Primaria)] and grown in media containing serum (CS-C, Cell System) overnight or for 16 hours to 24 hours.
On day 2, the cells were washed lx with 5 ml PBS ; 3 ml of 0% semm medium was added with VEGF (100 ng/ml); and 30 μl of the PRO test compound (final dilution 1 %) or 0% semm medium (negative control) was added. The mixtures were incubated for 48 hours before harvesting.
The cells were then harvested for FACS analysis. The medium was aspirated and the cells washed once with PBS. 5 ml of 1 x trypsin was added to the cells in a T-175 flask, and the cells were allowed to stand until they were released from the plate (about 5-10 minutes). Trypsinization was stopped by adding 5 ml of growth media. The cells were spun at 1000 rpm for 5 minutes at 4°C. The media was aspirated and the cells were resuspended in 10 ml of 10% semm complemented medium (Cell Systems), 5 μl of Annexin-FITC (BioVison) added and chilled tubes were submitted for FACS. A positive result was determined to be enhanced apoptosis in the PRO polypeptide treated samples as compared to the negative control.
The following PRO polypeptides tested positive in this assay: PR0331.
EXAMPLE 87: Induction of c-fos in Cortical Neurons (Assay 83)
This assay is designed to determine whether PRO polypeptides show the ability to induce c-fos in cortical neurons. PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of nervous system disorders and injuries where neuronal proliferation would be beneficial.
Cortical neurons are dissociated and plated in growth medium at 10,000 cells per well in 96 well plates. After aproximately 2 cellular divisions, the cells are treated for 30 minutes with the PRO polypeptide or nothing (negative control). The cells are then fixed for 5 minutes with cold methanol and stained with an antibody directed against phosphorylated CREB. mRNA levels are then calculated using chemiluminescence. A positive in the assay is any factor that results in at least a 2-fold increase in c-fos message as compared to the negative controls.
The following PRO polypeptides tested positive in this assay: PR0229 and PR0269.
EXAMPLE 88: Stimulation of Endothelial Tube Formation (Assay 85)
This assay is designed to determine whether PRO polypeptides show the ability to promote endothelial vacuole and lumen formation in the absence of exogenous growth factors. PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of disorders where endothelial vacuole and/or lumen formation would be beneficial including, for example, where the stimulation of pinocytosis, ion pumping, vascular permeability and/or junctional formation would be beneficial.
HUVEC cells (passage < 8 from primary) are mixed with type I rat tail collagen (final concentration 2.6 mg/ml) at a density of 6xl05 cells per ml and plated at 50 μl per well of M199 culmre media supplemented with 1 % FBS and 1 μM 6-FAM-FITC dye to stain the vacuoles while they are forming and in the presence of the PRO polypeptide. The cells are then incubated at 37°C/5% C02 for 48 hours, fixed with 3.7% formalin at room temperamre for 10 minutes, washed 5 times with M199 medium and then stained with Rh-Phalloidin at 4°C overnight followed by nuclear staining with 4 μM DAPI. A positive result in the assay is when vacuoles are present in greater than 50% of the cells. The following PRO polypeptides tested positive in this assay: PRO230.
EXAMPLE 89: Detection of Polypeptides That Affect Glucose and/or FFA Uptake in Skeletal Muscle (Assay
106)
This assay is designed to determine whether PRO polypeptides show the ability to affect glucose or FFA uptake by skeletal muscle cells. PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of disorders where either the stimulation or inhibition of glucose uptake by skeletal muscle would be beneficial including, for example, diabetes or hyper- or hypo-insulinemia.
In a 96 well format, PRO polypeptides to be assayed are added to primary rat differentiated skeletal muscle, and allowed to incubate overnight. Then fresh media with the PRO polypeptide and +/- insulin are added to the wells. The sample media is then monitored to determine glucose and FFA uptake by the skeletal muscle cells. The insulin will stimulate glucose and FFA uptake by the skeletal muscle, and insulin in media without the PRO polypeptide is used as a positive control, and a limit for scoring. As the PRO polypeptide being tested may either stimulate or inhibit glucose and FFA uptake, results are scored as positive in the assay if greater than 1.5 times or less than 0.5 times the insulin control. The following PRO polypeptides tested positive as either stimulators or inhibitors of glucose and/or FFA uptake in this assay: PR0187, PR0211, PR0221 , PR0222, PR0224, PRO230, PR0239, PR0231 , PR0245,
PR0247, PR0258, PR0269, PR0328 and PR0533.
EXAMPLE 90: Rod Photoreceptor Cell Survival Assay (Assay 46) This assay shows that certain polypeptides of the invention act to enhance the survival/proliferation of rod photoreceptor cells and, therefore, are useful for the therapeutic treatment of retinal disorders or injuries including, for example, treating sight loss in mammals due to retinitis pigmentosum, AMD, etc.
Sprague Dawley rat pups (postnatal day 7, mixed population: glia and netinal neural cell types) are killed by decapitation following C02 anesthesia and the eyes removed under sterile conditions. The neural retina is dissected away from the pigment epithelium and other ocular tissue and then dissociated into a single cell suspension using 0.25% trypsin in Ca2+, Mg +-free PBS. The retinas are incubated at 37 °C in this solution for 7-10 minutes after which the trypsin is inactivated by adding 1 ml soybean trypsin inhibitor. The cells are plated at a density of approximately 10, 000 cells/ml into 96 well plates in DMEM/F12 supplemented with N2. Cells for all experiments are grown at 37°C in a water samrated atmosphere of 5 % C02. After 7-10 days in culmre, the cells are stained using calcein AM or CellTracker Green CMFDA and then fixed using 4% paraformaldehyde. Rho 4D2 (ascities or IgG 1: 100) monoclonal antibody directed towards the visual pigment rhodopsin is used to detect rod photoreceptor cells by indirect immunofluorescence. The results are calculated as % survival: total number of calcein - rhodopsin positive cells at 7-10 days in culmre, divided by the total number of rhodopsin positive cells at time 7-10 days in culmre. The total cells (fluorescent) are quantified at 20x objective magnification using a CCD camera and NIH image software for Macintosh. Fields in the well are chosen at random.
The following polypeptides tested positive in this assay: PR0245. Example 91 : In Vitro Antitumor Assay (Assay 161)
The antiproliferative activity of various PRO polypeptides was determined in the investigational, disease- oriented in vitro anti -cancer drag discovery assay of the National Cancer Institute (NCI), using a sulforhodamine B (SRB) dye binding assay essentially as described by Skehan et al., J. Natl. Cancer Inst. 82: 1107-1112 (1990). The 60 tumor cell lines employed in this study ("the NCI panel"), as well as conditions for their maintenance and culmre in vitro have been described by Monks et al. , J. Natl. Cancer Inst. 83 -.151-166 (1991). The purpose of this screen is to initially evaluate the cytotoxic and/or cytostatic activity of the test compounds against different types of tumors (Monks et al., supra; Boyd, Cancer: Princ. Pract. Oncol. Update 3(10): 1-12 [1989]).
Cells from approximately 60 human mmor cell lines were harvested with trypsin/EDTA (Gibco), washed once, resuspended in IMEM and their viability was determined. The cell suspensions were added by pipet (100 μL volume) into separate 96-well microtiter plates. The cell density for the 6-day incubation was less than for the 2-day incubation to prevent overgrowth. Inoculates were allowed a preincubation period of 24 hours at 37 °C for stabilization. Dilutions at twice the intended test concentration were added at time zero in 100 μL aliquots to the microtiter plate wells (1:2 dilution). Test compounds were evaluated at five half-log dilutions (1000 to 100,000-fold). Incubations took place for two days and six days in a 5% C02 atmosphere and 100% humidity.
After incubation, the medium was removed and the cells were fixed in 0.1 ml of 10% trichloroacetic acid at 40°C. The plates were rinsed five times with deionized water, dried, stained for 30 minutes with 0.1 ml of 0.4% sulforhodamine B dye (Sigma) dissolved in 1 % acetic acid, rinsed four times with 1 % acetic acid to remove unbound dye, dried, and the stain was extracted for five minutes with 0.1 ml of 10 mM Tris base [tris(hydroxymethyl)aminomethane], pH 10.5. The absorbance (OD) of sulforhodamine B at 492 nm was measured using a computer-interfaced, 96-well microtiter plate reader.
A test sample is considered positive if it shows at least 50% growth inhibitory effect at one or more concentrations. PRO polypeptides testing positive in this assay are shown in Table 7, where the abbreviations are as follows: NSCL = non-small cell lung carcinoma CNS = central nervous system
Iable_7 Test compound Tumor Cell Line Tvpe Cell Line Designation
PR0211 NSCL HOP62 PR0211 Leukemia RPMI-8226
PR0211 Leukemia HL-60 (TB)
PR0211 NSCL NCI-H522
PR0211 CNS SF-539
PR0211 Melanoma LOX IMVI PR0211 Breast MDA-MB-435
PR0211 Leukemia MOLT-4
PR0211 CNS U251
PR0211 Breast MCF7
PR0211 Leukemia HT-60 (TB) PR0211 Leukemia MOLT-4
PR0211 NSCL EKVX
PR0211 NSCL NCI-H23 Table 7 (cont')
PR0211 NSCL NCI-H322M PR0211 NSCL NCI-H460 PR0211 Colon HCT-116 PR0211 Colon HT29 PR0211 CNS SF-268 PR0211 CNS SF-295 PR0211 CNS SNB-19 PR0211 CNS U251 PR0211 Melanoma LOX IMVI PR0211 Melanoma SK-MEL-5 PR0211 Melanoma UACC-257 PR0211 Melanoma UACC-62 PR0211 Ovarian OVCAR-8 PR0211 Renal RXF 393 PR0211 Breast MCF7 PR0211 Breast NCI/ADR-REHS 578T PR0211 Breast T-47D PR0211 Leukemia HL-60 (TB) PR0211 Leukemia SR PR0211 NSCL NCI-H23 PR0211 Colon HCT-116 PR0211 Melanoma LOX-IMVI PR0211 Melanoma SK-MEL-5 PR0211 Breast T-47D PR0228 Leukemia MOLT-4 PR0228 NSCL EKVX PR0228 Colon KM12 PR0228 Melanoma UACC-62 PR0228 Ovarian OVCAR-3 PR0228 Renal TK10 PR0228 Renal SN12C PR0228 Breast MCF7 PR0228 Leukemia CCRF-CEM PR0228 Leukemia HL-60 (TB) PR0228 Colon COLO 205 PR0228 Colon HCT-15 PR0228 Colon KM 12 PR0228 CNS SF-268 PR0228 CNS SNB-75 PR0228 Melanoma LOX-IMVI PR0228 Melanoma SK-MEL2 PR0228 Melanoma UACC-257 PR0228 Ovarian IGROV1 PR0228 Ovarian OVCAR-4 PR0228 Ovarian OVCAR-5 PR0228 Ovarian OVCAR-8 PR0228 Renal 786-0 PR0228 Renal CAKI-1 PR0228 Renal RXF 393 PR0228 Renal TK-10 PR0228 Renal UO-31 PR0228 Prostate PC-3 PR0228 Prostate DU-145 PR0228 Breast MCF7 PR0228 Breast NCI/ADR-REHS 578T Table 7 (cont')
PR0228 Breast MDA-MB-435MDA-N PR0228 Breast T-47D PR0219 Leukemia SR PR0219 NSCL NCI-H5222 PR0219 Breast MCF7 PR0219 Leukemia K-562; RPMI-8226 PR0219 NSCL HOP-62; NCI-H322M PR0219 NSCL NCI -H460 PR0219 Colon HT29; KM12; HCT-116 PR0219 CNS SF-539; U251 PR0219 Prostate DU-145 PR0219 Breast MDA-N PR0219 Ovarian IGROV1 PR0219 NSCL NCI-H226 PR0219 Leukemia MOLT-4 PR0219 NSCL A549/ATCC; EKVX; NCI-H23 PR0219 Colon HCC-2998 PR0219 CNS SF-295; SNB-19 PR0219 Melanoma SK-MEL-2; SK-MEL-5 PR0219 Melanoma UACC-257; UACC-62 PR0219 Ovarian OCAR-4; SK-OV-3 PR0219 Renal 786-0; ACHN; CAKI-1; SN12C PR0219 Renal TK-10; UO-31 PR0219 Breast NCI/ADR-RES; BT-549; T-47D PR0219 Breast MDA-MB-435 PR0221 Leukemia CCRF-CEM PR0221 Leukemia MOLT-4 PR0221 NSCL HOP-62 PR0221 Breast MDA-N PR0221 Leukemia RPMI-8226; SR PR0221 NSCL NCI-H460 PR0221 Colon HCC-2998 PR0221 Ovarian IGROV1 PR0221 Renal TK-10 PR0221 Breast MCF7 PR0221 Leukemia K-562 PR0221 Breast MDA-MB-435 PR0224 Ovarian OVCAR-4 PR0224 Renal RXF 393 PR0224 Prostate DU-145 PR0224 NSCL HOP-62; NCI-H322M PR0224 Melanoma LOX IMVI PR0224 Ovarian OVCAR-8 PR0224 Leukemia SR PR0224 NSCL NCI-H460 PR0224 CNS SF-295 PR0224 Leukemia RPMI-8226 PR0224 Breast BT-549 PR0224 Leukemia CCRF-CEM; LH-60 (TB) PR0224 Colon HCT-116 PR0224 Breast MDA-MB-435 PR0224 Leukemia HL-60 (TB) PR0224 Colon HCC-2998 PR0224 Prostate PC-3 PR0224 CNS U251 Table 7 (cont')
PR0224 Colon HCT-15 PR0224 CNS SF-539 PR0224 Renal ACHN PR0328 Leukemia RPMI-8226 PR0328 NSCL A549/ATCC; EKVX; HOP-62 PR0328 NSCL NCI-H23; NCI-H322M PR0328 Colon HCT-15; KM12 PR0328 CNS SF-295; SF-539; SNB-19; U251 PR0328 Melanoma M14; UACC-257; UCAA-62 PR0328 Renal 786-0; ACHN PR0328 Breast MCF7 PR0328 Leukemia SR PR0328 Colon NCI-H23 PR0328 Melanoma SK-MEL-5 PR0328 Prostate DU-145 PR0328 Melanoma LOX IMVI PR0328 Breast MDA-MB-435 PR0328 Ovarian OVCAR-3 PR0328 Breast T-47D PRO301 NSCL NCI-H322M PRO301 Leukemia MOLT-4; SR PRO301 NSCL A549/ATCC; EKVX; PRO301 NSCL NCI-H23; NCI-460; NCI-H226 PRO301 Colon COLO 205; HCC-2998; PRO301 Colon HCT-15; KM 12; HT29; PRO301 Colon HCT-116 PRO301 CNS SF-268; SF-295; SNB-19 PRO301 Melanoma MALME-3M; SK-MEL-2; PRO301 Melanoma SK-MEL-5;UACC-257 PRO301 Melanoma UACC-62 PRO301 Ovarian IGROV1; OVCAR-4 PRO301 Ovarian OVCAR-5 PRO301 Ovarian OVCAR-8; SK0OV-3 PRO301 Renal ACHN;CAKI-1 ; TK-10; UO-31 PRO301 Prostate PC-3; DU-145 PRO301 Breast NCI/ADR-RES; HS 578T PRO301 Breast MDA-MB-435;MDA-N; T-47D PRO301 Melanoma M14 PRO301 Leukemia CCRF-CEM;HL-60(TB); K-562 PRO301 Leukemia RPMI-8226 PRO301 Melanoma LOX IMVI PRO301 Renal 786-0; SN12C PRO301 Breast MCF7; MDA-MB-231/ATCC PRO301 Breast BT-549 PRO301 NSCL HOP-62 PRO301 CNS SF-539 PRO301 Ovarian OVCAR-3 PR0326 NSCL NCI-H322M PR0326 CNS SF295 PR0326 CNS ST539 PR0326 CNS U251 The results of these assays demonstrate that the positive testing PRO polypeptides are useful for inhibiting neoplastic growth in a number of different tumor cell types and may be used therapeutically therefor.. Antibodies against these PRO polypeptides are useful for affinity purification of these useful polypeptides. Nucleic acids encoding these PRO polypeptides are useful for the recombinant preparation of these polypeptides.
EXAMPLE 92: Gene Amplification
This example shows that certain PRO polypeptide-encoding genes are amplified in the genome of certain human lung, colon and/or breast cancers and/or cell lines. Amplification is associated with overexpression of the gene product, indicating that the polypeptides are useful targets for therapeutic intervention in certain cancers such as colon, lung, breast and other cancers and diagnostic determination of the presence of those cancers. Therapeutic agents may take the form of antagonists of the PRO polypeptide, for example, murine-human chimeric, humanized or human antibodies against a PRO polypeptide.
The starting material for the screen was genomic DNA isolated from a variety cancers. The DNA is quantitated precisely, e.g., fluorometrically. As a negative control, DNA was isolated from the cells of ten normal healthy individuals which was pooled and used as assay controls for the gene copy in healthy individuals (not shown) . The 5 ' nuclease assay (for example, TaqMan™) and real-time quantitative PCR (for example, ABI Prizm 7700 Sequence Detection System™ (Perkin Elmer, Applied Biosystems Division, Foster City, CA)), were used to find genes potentially amplified in certain cancers. The results were used to determine whether the DNA encoding the PRO polypeptide is over-represented in any of the primary lung or colon cancers or cancer cell lines or breast cancer cell lines that were screened. The primary lung cancers were obtained from individuals with tumors of the type and stage as indicated in Table 8. An explanation of the abbreviations used for the designation of the primary tumors listed in Table 8 and the primary tumors and cell lines referred to throughout this example are given below.
The results of the TaqMan™ are reported in delta (Δ) Ct units. One unit corresponds to 1 PCR cycle or approximately a 2-fold amplification relative to normal, two units corresponds to 4-fold, 3 units to 8-fold amplification and so on. Quantitation was obtained using primers and a TaqMan™ fluorescent probe derived from the PRO polypeptide-encoding gene. Regions of the PRO polypeptide-encoding gene which are most likely to contain unique nucleic acid sequences and which are least likely to have spliced out introns are preferred for the primer and probe derivation, e.g., 3 '-untranslated regions. The sequences for the primers and probes (forward, reverse and probe) used for the PRO polypeptide gene amplification analysis were as follows: PRO 187 (DNA27864-1155) 27864.tm.p:
5'-GCAGATTTTGAGGACAGCCACCTCCA-3' (SEQ ID NO:381)
27864. tm.f: 5'-GGCCTTGCAGACAACCGT-3' (SEQ ID NO:382) 27864.tm.r:
5'-CAGACTGAGGGAGATCCGAGA-3' (SEQ ID NO:383) 27864.tm.p2:
5 ' -C AGCTGCCCTTCCCCA ACCA-3 ' (SEQ ID NO:384) 27864.tm.f2:
5 ' -C ATC AAGCGCCTCTACCA-3 ' (SEQ ID NO:385) 27864.tm.r2: 5'-CACAAACTCGAACTGCTTCTG-3' (SEQ ID NO:386)
PRQ214 (DNA32286-1191): 32286.3utr-5:
5 ' -GGGCC ATC AC AGCTCCCT-3 ' (SEQ ID NO:387) 32286.3utr-3b:
5 ' -GGGATGTGGTGAAC AC AG AAC A-3 ' (SEQ ID NO:388)
32286.3utr-ρrobe:
5 ' -TGCC AGCTGC ATGCTGCC AGTT-3 ' (SEQ ID NO:389)
PRQ211 (DNA32292-1131):
32292.3utr-5:
5 ' -C AG A AGGATGTCCCGTGGAA-3 ' (SEQ ID NO:390)
32292.3utr-3:
5 ' -GCCGCTGTCC ACTGC AG-3 ' (SEQ ID NO:391) 32292.3utr-ρrobe.rc:
5 ' -G ACGGC ATCCTC AGGGCC AC A-3 ' (SEQ ID NO:392)
PRO230 (DNA33223-1136):
33223.tm.p3: 5'-ATGTCCTCCATGCCCACGCG-3' (SEQ ID NO:393)
33223.tm.f3:
5 ' -GAGTGCGAC ATCGAGAGCTT-3 ' (SEQ ID NO:394)
33223. tm.r3:
5 ' -CCGC AGCCTC AGTGATGA-3 ' (SEQ ID NO:395) 33223.3utr-5:
5 ' -GAAGAGC AC AGCTGC AGATCC-3 ' (SEQ ID NO:396)
33223.3utr-3:
5 ' -G AGGTGTCCTGGCTTTGGTAGT-3 ' (SEQ ID NO:397)
33223.3utr-probe: 5'-CCTCTGGCGCCCCCACTCAA-3' (SEQ ID NO:398) PRQ317 (DNA33461 -1 199): 33461. tm.f:
5'-CCAGGAGAGCTGGCGATG-3' (SEQ ID NO:399)
33461. tm.r:
5'-GCAAATTCAGGGCTCACTAGAGA-3' (SEQ ID NO:400) 33461.tm.p:
5 '-C AC AG AGC ATTTGTCC ATC AGC AGTTC AG-3' (SEQ ID NO:401)
PRQ246 (DNA35639-1172):
35639.3utr-5: 5'-GGCAGAGACTTCCAGTCACTGA-3' (SEQ ID NO: 402)
35639.3utr-3:
5'-GCCAAGGGTGGTGTTAGATAGG-3' (SEQ ID NO:403)
35639.3utr-probe:
5'-CAGGCCCCCTTGATCTGTACCCCA-3' (SEQ ID NO:404)
PRQ533 (DNA49435-1219):
49435.tm.f:
5 '-GGGACGTGCTTCTACAAGAACAG-3 ' (SEQ ID NO:405)
49435. tm.r: 5 '-C AGGCTTAC A ATGTTATG ATC AGAC A-3' (SEQ ID NO: 406)
49435.tm.p:
5 '-TATTCAGAGTTTTCCATTGGCAGTGCC AGTT-3' (SEQ ID NO:407)
PRQ343 (DNA43318-1217): 43318.tm.fl
5'-TCTACATCAGCCTCTCTGCGC-3' (SEQ ID NO:408)
43318.tm.pl
5'-CGATCTTCTCCACCCAGGAGCGG-3' (SEQ ID NO:409)
43318.tm.rl 5'-GGAGCTGCACCCCTTGC-3" (SEQ ID NO:237)
PRQ232 (DNA34435-1140): 34435.3utr-5:
5'-GCCAGGCCTCACATTCGT-3' (SEQ ID NO:410) DNA34435.3utr-probe:
5'-CTCCCTGAATGGCAGCCTGAGCA-3' (SEQ ID NO:411) DNA34435.3utr-3: 5'-AGGTGTTTATTAAGGGCCTACGCT -3' (SEQ ID NO:412)
PR0269 (DNA38260-1180):
38260.tm.f:
5 ' -C AGAGCAGAGGGTGCCTTG-3 ' (SEQ ID NO:413
38260.tm.p:
5 ' -TGGCGGAGTCCCCTCTTGGCT-3 ' (SEQ ID NO:414)
38260.tm.r:
5 ' -CCCTGTTTCCCTATGCATC ACT-3 ' (SEQ ID NO:415)
PRO304 (DNA39520-1217):
39520.tm.f:
5'-TCAACCCCTGACCCTTTCCTA-3' (SEQ ID NO:416)
39520.tm.p:
5'-GGCAGGGGACAAGCCATCTCTCCT-3' (SEQ ID NO:417)
39520.tm.r:
5'-GGGACTGAACTGCCAGCTTC -3' (SEQ ID NO:418)
PR0339 (DNA43466-1225): 43466.tm.fl:
5'-GGGCCCTAACCTCATTACCTTT-3' (SEQ ID NO:419)
43466.tm.pl:
5'-TGTCTGCCTCAGCCCCAGGAAGG-3' (SEQ ID NO:420)
43466.tm.rl: 5'-TCTGTCCACCATCTTGCCTTG -3' (SEQ ID NO:421)
The 5' nuclease assay reaction is a fluorescent PCR-based technique which makes use of the 5' exonuclease activity of Taq DNA polymerase enzyme to monitor amplification in real time. Two oligonucleotide primers (forward [.f] and reverse [.r]) are used to generate an amplicon typical of a PCR reaction. A third oligonucleotide, or probe (.p), is designed to detect nucleotide sequence located between the two PCR primers. The probe is non-extendible by Taq DNA polymerase enzyme, and is labeled with a reporter fluorescent dye and a quencher fluorescent dye. Any laser-induced emission from the reporter dye is quenched by the quenching dye when the two dyes are located close together as they are on the probe. During the amplification reaction, the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner. The resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore. One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data. The 5 ' nuclease procedure is mn on a real-time quantitative PCR device such as the ABI Prism 7700TM Sequence Detection. The system consists of a thermocycler, laser, charge-coupled device (CCD) camera and computer. The system amplifies samples in a 96-well format on a thermocycler. During amplification, laser-induced fluorescent signal is collected in real-time through fiber optics cables for all 96 wells, and detected at the CCD. The system includes software for running the instrument and for analyzing the data. 5' Nuclease assay data are initially expressed as Ct, or the threshold cycle. This is defined as the cycle at which the reporter signal accumulates above the background level of fluorescence. The ΔCt values are used as quantitative measurement of the relative number of starting copies of a particular target sequence in a nucleic acid sample when comparing cancer DNA results to normal human DNA results.
Table 8 describes the stage, T stage and N stage of various primary tumors which were used to screen the PRO polypeptide compounds of the invention.
Table 8 Primary Lung and Colon Tumor Profiles
Primary Tumor Stage Stage Other Stage Dukes Stage T Stage N Stage
Human lung mmor AdenoCa (SRCC724) [LT1] IIA Tl Nl Human lung mmor SqCCa (SRCC725) [LTla] IIB T3 NO
Human lung mmor AdenoCa (SRCC726) [LT2] IB T2 NO
Human lung mmor AdenoCa (SRCC727) [LT3] IIIA Tl N2
Human lung tumor AdenoCa (SRCC728) [LT4] IB T2 NO
Human lung mmor SqCCa (SRCC729) [LT6] IB T2 NO Human lung mmor Aden/SqCCa (SRCC730) [LT7] I IAA Tl NO
Human lung mmor AdenoCa (SRCC731) [LT9] IB T2 NO
Human lung tumor SqCCa (SRCC732) [LT10] IIB T2 Nl
Human lung mmor SqCCa (SRCC733) [LT11] IIA Tl Nl
Human lung mmor AdenoCa (SRCC734) [LT12] IV T2 NO Human lung mmor AdenoSqCCa (SRCC735)[LT13] IIIBB T2 NO
Human lung tumor SqCCa (SRCC736) [LT15] IB T2 NO
Human lung mmor SqCCa (SRCC737) [LT16] IB T2 NO
Human lung tumor SqCCa (SRCC738) [LT17] IIB T2 Nl
Human lung tumor SqCCa (SRCC739) [LT18] IB T2 NO Human lung tumor SqCCa (SRCC740) [LT19] IB T2 NO
Human lung mmor LCCa (SRCC741) [LT21] IIB T3 Nl
Human lung AdenoCa (SRCC811) [LT22] IA Tl NO
Human colon AdenoCa (SRCC742) [CT2] Ml D pT4 NO
Human colon AdenoCa (SRCC743) [CT3] B pT3 NO Human colon AdenoCa (SRCC744) [CT8] B T3 NO
Human colon AdenoCa (SRCC745) [CT10] A pT2 NO
Human colon AdenoCa (SRCC746) [CT12] MO, Rl B T3 NO
Human colon AdenoCa (SRCC747) [CT14] pMO , RO B pT3 pNO
Human colon AdenoCa (SRCC748) [CT15] Ml , ] 2 D T4 N2 Human colon AdenoCa (SRCC749) [CT16] pMO B pT3 pNO
Human colon AdenoCa (SRCC750) [CT17] Cl pT3 pNl
Human colon AdenoCa (SRCC751) [CT1] MO, Rl B pT3 NO
Human colon AdenoCa (SRCC752) [CT4] B pT3 M0
Human colon AdenoCa (SRCC753) [CT5] G2 Cl pT3 pNO Human colon AdenoCa (SRCC754) [CT6] pMO , RO B pT3 pNO
Human colon AdenoCa (SRCC755) [CT7] Gl A pT2 pNO
Human colon AdenoCa (SRCC756) [CT9] G3 D pT4 pN2
Human colon AdenoCa (SRCC757) [CT11] B T3 NO
Human colon AdenoCa (SRCC758) [CT18] MO, RO B pT3 pNO
DNA Preparation:
DNA was prepared from cultured cell lines, primary tumors, normal human blood. The isolation was performed using purification kit, buffer set and protease and all from Quiagen, according to the manufacmrer's instmctions and the description below. Cell culture lysis:
Cells were washed and trypsinized at a concentration of 7.5 x 108 per tip and pelleted by centrifuging at 1000 rpm for 5 minutes at 4°C, followed by washing again with 1/2 volume of PBS recentrifugation. The pellets were washed a third time, the suspended cells collected and washed 2x with PBS. The cells were then suspended into 10 ml PBS. Buffer Cl was equilibrated at 4°C. Qiagen protease #19155 was diluted into 6.25 ml cold ddH20 to a final concentration of 20 mg/ml and equilibrated at 4°C. 10 ml of G2 Buffer was prepared by diluting Qiagen RNAse A stock (100 mg/ml) to a final concentration of 200 μg/ml. Buffer Cl (10 ml, 4°C) and ddH20 (40 ml, 4°C) were then added to the 10 ml of cell suspension, mixed by inverting and incubated on ice for 10 minutes. The cell nuclei were pelleted by centrifuging in a Beckman swinging bucket rotor at 2500 rpm at 4°C for 15 minutes. The supernatant was discarded and the nuclei were suspended with a vortex into 2 ml Buffer C 1 (at 4°C) and 6 ml ddH20, followed by a second 4°C centrifugation at 2500 rpm for 15 minutes. The nuclei were then resuspended into the residual buffer using 200 μl per tip. G2 buffer (10 ml) was added to the suspended nuclei while gentle vortexing was applied. Upon completion of buffer addition, vigorous vortexing was applied for 30 seconds. Quiagen protease (200 μl, prepared as indicated above) was added and incubated at 50°C for 60 minutes. The incubation and centrifugation was repeated until the lysates were clear (e.g., incubating additional 30-60 minutes, pelleting at 3000 x g for 10 min., 4°C).
Solid human tumor sample preparation and lysis: Tumor samples were weighed and placed into 50 ml conical tubes and held on ice. Processing was limited to no more than 250 mg tissue per preparation (1 tip /preparation). The protease solution was freshly prepared by diluting into 6.25 ml cold ddH20 to a final concentration of 20 mg/ml and stored at 4°C. G2 buffer
(20 ml) was prepared by diluting DNAse A to a final concentration of 200 mg/ml (from 100 mg/ml stock). The mmor tissue was homogenated in 19 ml G2 buffer for 60 seconds using the large tip of the polytron in a laminar- flow TC hood in order to avoid inhalation of aerosols, and held at room temperamre. Between samples, the polytron was cleaned by spinning at 2 x 30 seconds each in 2L ddH20, followed by G2 buffer (50 ml). If tissue was still present on the generator tip, the apparatus was disassembled and cleaned.
Quiagen protease (prepared as indicated above, 1.0 ml) was added, followed by vortexing and incubation at 50°C for 3 hours. The incubation and centrifugation was repeated until the lysates were clear (e.g. , incubating additional 30-60 minutes, pelleting at 3000 x g for 10 min., 4°C). Human blood preparation and lysis:
Blood was drawn from healthy volunteers using standard infectious agent protocols and citrated into 10 ml samples per tip. Quiagen protease was freshly prepared by dilution into 6.25 ml cold ddH20 to a final concentration of 20 mg/ml and stored at 4°C. G2 buffer was prepared by diluting RNAse A to a final concentration of 200 μg/ml from 100 mg/ml stock. The blood (10 ml) was placed into a 50 ml conical tube and 10 ml Cl buffer and 30 ml ddH20 (both previously equilibrated to 4°C) were added, and the components mixed by inverting and held on ice for 10 minutes. The nuclei were pelleted with a Beckman swinging bucket rotor at 2500 rpm, 4°C for 15 minutes and the supernatant discarded. With a vortex, the nuclei were suspended into 2 ml Cl buffer (4°C) and 6 ml ddH20 (4°C). Vortexing was repeated until the pellet was white. The nuclei were then suspended into the residual buffer using a 200 μl tip. G2 buffer (10 ml) were added to the suspended nuclei while gently vortexing, followed by vigorous vortexing for 30 seconds. Quiagen protease was added (200 μl) and incubated at 50°C for 60 minutes. The incubation and centrifugation was repeated until the lysates were clear (e.g., incubating additional 30-60 minutes, pelleting at 3000 x g for 10 min., 4°C). Purification of cleared lysates: (1) Isolation of genomic DNA:
Genomic DNA was equilibrated (1 sample per maxi tip preparation) with 10 ml QBT buffer. QF elution buffer was equilibrated at 50°C. The samples were vortexed for 30 seconds, then loaded onto equilibrated tips and drained by gravity. The tips were washed with 2 x 15 ml QC buffer. The DNA was eluted into 30 ml silanized, autoclaved 30 ml Corex tubes with 15 ml QF buffer (50°C). Isopropanol (10.5 ml) was added to each sample, the tubes covered with parafin and mixed by repeated inversion until the DNA precipitated. Samples were pelleted by centrifugation in the SS-34 rotor at 15,000 rpm for 10 minutes at 4°C. The pellet location was marked, the supernatant discarded, and 10 ml 70% ethanol (4°C) was added. Samples were pelleted again by centrifugation on the SS-34 rotor at 10,000 rpm for 10 minutes at 4°C. The pellet location was marked and the supernatant discarded. The tubes were then placed on their side in a drying rack and dried 10 minutes at 37°C, taking care not to overdry the samples.
After drying, the pellets were dissolved into 1.0 ml TE (pH 8.5) and placed at 50°C for 1-2 hours. Samples were held overnight at 4°C as dissolution continued. The DNA solution was then transferred to 1.5 ml tubes with a 26 gauge needle on a tuberculin syringe. The transfer was repeated 5x in order to shear the DNA. Samples were then placed at 50°C for 1-2 hours.
(2) Quantitation of genomic DNA and preparation for gene amplification assay:
The DNA levels in each tube were quantified by standard A260, A280 spectrophotometry on a 1:20 dilution (5 μl DNA + 95 μl ddH20) using the 0.1 ml quartz cuvetts in the Beckman DU640 spectrophotometer. A260/A280 ratios were in the range of 1.8-1.9. Each DNA samples was then diluted further to approximately 200 ng/ml in TE (pH 8.5). If the original material was highly concentrated (about 700 ng/μl), the material was placed at 50°C for several hours until resuspended.
Fluorometric DNA quantitation was then performed on the diluted material (20-600 ng/ml) using the manufacturer's guidelines as modified below. This was accomplished by allowing a Hoeffer DyNA Quant 200 fluorometer to warm-up for about 15 minutes. The Hoechst dye working solution (#H33258, 10 μl, prepared within 12 hours of use) was diluted into 100 ml 1 x TNE buffer. A 2 ml cuvette was filled with the fluorometer solution, placed into the machine, and the machine was zeroed. pGEM 3Zf(+) (2 μl, lot #360851026) was added to 2 ml of fluorometer solution and calibrated at 200 units. An additional 2 μl of pGEM 3Zf(+) DNA was then tested and the reading confirmed at 400 +/- 10 units. Each sample was then read at least in triplicate. When 3 samples were found to be within 10% of each other, their average was taken and this value was used as the quantification value.
The fluorometricly determined concentration was then used to dilute each sample to 10 ng/μl in ddH20. This was done simultaneously on all template samples for a single TaqMan plate assay, and with enough material to mn 500-1000 assays. The samples were tested in triplicate with Taqman™ primers and probe both B-actin and GAPDH on a single plate with normal human DNA and no-template controls. The diluted samples were used provided that the CT value of normal human DNA subtracted from test DNA was +/- 1 Ct. The diluted, lot-qualified genomic DNA was stored in 1.0 ml aliquots at -80°C. Aliquots which were subsequently to be used in the gene amplification assay were stored at 4°C. Each 1 ml aliquot is enough for 8-9 plates or 64 tests.
Gene amplification assay: The PRO polypeptide compounds of the invention were screened in the following primary tumors and the resulting ΔCt values greater than or equal to 1.0 are reported in Table 9 below. Table 9
ΔCt values in lung and colon primary tumors and cell line models
Primary Tumors PR0187 PR0533 PR0214 PR0343 PR0211 PRO230 PR0246 PR0317 PR0232 PR0269 PRO304 PR0339 or Cell lines
LT7 L52 L04 08
LT13 2 2..7744 1 1..8855 2 2..7711 1 1..8888 3 3..4422 1 1..6633 1 1..9900 1.27 1.29 1.04
10 2.98 1.83 2.23 2.26 3.22 1.68 2.24
2.44 2.84 2.93 2.15 2.75 2.53
15 1.82
LT3 1.57 1.97 1.06 1.86 1.17
LT4 1.17 1.18
20
LT9 1.42 1.04 1.80 1.03
LT12 2.70 1.38 2.23 1.51 . 2.86 1.54 2.54 2.40 1.14 1.15 1.26
2.90 1.49 1.50 1.27 2.96 2.47 1.74
25 2.27 2.92 1.25 2.68 2.28 1.34
30
LT30 1.67 2.13 1.36
Table 9 (Continued)
ΔCt values in lung and colon primary tumors and cell line models Primary Tumors PR0187 PR0533 PR0214 PR0343 PR0211 PRO230 PR0246 PR0317 PR0232 PR0269 PRO304 PR0339 or Cell lines
LT21 L26 L09 L50
LTl-a 1.02 1.18 1.29
10
LT6 1.93 LT10 1.96 1.07 2.57 15 LT11 1.09 1 1..6677 1 1..0000 2 2..0055 1 1..3322 3 3..4433 2 2..2200 1.14 1.51 1.39
1.80 1.89 1.14 1.41 2.33 1.54 1.02
-4
LT15 3.75 1 1..7777 33..6622 22..4444 44..3322 22..1111 2 2..0066 1.86 1.36 1.34
20 3.92 1.58 1.30 2.16 4.47 1.56 2.76 3.49 3.64 1.63 2.94 3.56 3.32
25 2.68
LT16 2.10 1.66 11..7700 11..2255 11..1155 11..5555 1.00 2.04 1.08 1.83 1.33
30
Figure imgf000239_0001
Table 9 (Continued)
ΔCt values in lung and colon primary mmors and cell line models
Primary Tumors PR0187 PR0533 PR0214 PR0343 PR0211 PRO230 PR0246 PR0317 PR0232 PR0269 PRO304 PR0339 or Cell lines
LT17 1.32 1.93 1.15 1.85 1.26 2.68 2.29 1.35 L42 L68 L63 1.87 2.30 1.39 1.69 2.03 1.30 1.10
10 1.33 1.30
LT18 1.17 1.04
15 L LTT1199 4 4..0055 1 1..6677 2 2..0099 3 3..8822 2 2..4422 4 4..0055 1 1..9911 2 2..5511 1 1..2211 1.60 1.15 3.99 1.98 2.55 4.92 1.68 2.03
90 4.93 1.16 3.78 4.76
20
HF-000840 1.58
Calu-1 1.08
25 SW900 1.86
CT2 3.56 2.49 1.95 1.42 2.75 3.49 2.36
Figure imgf000240_0001
Table 9 (Continued) ΔCt values in lung and colon primary mmors and cell line models
Primary Tumors PR0187 PR0533 PR0214 PR0343 PR0211 PRO230 PR0246 PR0317 PR0232 PR0269 PRO304 PR0339 or Cell lines
CT8 1.01 1.48 1.29 1.58
10 CT10 1.81 1.84 1.88 1.00 1.88 1.49 1.55
CT12 1.81 1.74 1.13
15 CT14 1.82 2.48 2.33 1.36 1.72 1.24 i 0
CT15 1.63 2.06 1.33 1.41 1.04
20
CT16 1.95 1.78 1.40 CT17 2.04 2.40 1.74
25 CT1 1.24 1.22 1.27 1.25 2.41 1.34 1.46 1.14
CT4 1.36 1.77 1.33 1.32 1.10 1.17 2.05
1.42 1.02
Figure imgf000241_0002
Figure imgf000241_0001
Table 9 (Continued) ΔCt values in lung and colon primary mmors and cell line models
Primary Tumors PR0187 PR0533 PR0214 PR0343 PR0211 PRO230 PR0246 PR0317 PR0232 PR02δ9 PRO304 PR0339 or Cell lines
CT5 2.96 1.56 2.68 1.76 2.27 1.33 1.59
2.99 2.76 1.64 2.39
10 CT6 1.10 1.33 1.01 1.14
CT7 1.40 1.66 1.39 1.00
15 CT9 1.39 1.16 1.09 1.24 1.13
CT11 2.22 2.05 1.55 2.01 1.75 1.48 1.92 2.26 1.85 1.83 1.12
20 HF000539 1.57
4-
©
SW620 1.14
HF000611 4.64
25
HF000733 1.93 2.33
HF000716 1.68
30 2.82
CT18 1.29
Summary
Because amplification of the various DNA's as described above occurs in various tumors, it is likely associated with mmor formation and/or growth. As a result, antagonists (e.g. , antibodies) directed against these polypeptides would be expected to be useful in cancer therapy.
EXAMPLE 94: Detection of PRO Polypeptides That Affect Glucose or FFA Uptake by Primary Rat Adipocytes (Assay 94)
This assay is designed to determine whether PRO polypeptides show the ability to affect glucose or FFA uptake by adipocyte cells. PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of disorders where either the stimulation or inhibition of glucose uptake by adipocytes would be beneficial including, for example, obesity, diabetes or hyper- or hypo-insulinemia.
In a 96 well format, PRO polypeptides to be assayed are added to primary rat adipocytes, and allowed to incubate overnight. Samples are taken at 4 and 16 hours and assayed for glycerol, glucose and FFA uptake. After the 16 hour incubation, insulin is added to the media and allowed to incubate for 4 hours. At this time, a sample is taken and glycerol, glucose and FFA uptake is measured. Media containing insulin without the PRO polypeptide is used as a positive reference control. As the PRO polypeptide being tested may either stimulate or inhibit glucose and FFA uptake, results are scored as positive in the assay if greater than 1.5 times or less than 0.5 times the insulin control.
The following PRO polypeptides tested positive as stimulators of glucose and/or FFA uptake in this assay: PR0221 , PR0235, PR0245, PR0295, PRO301 and PR0332. The following PRO polypeptides tested positive as inhibitors of glucose and/or FFA uptake in this assay: PR0214, PR0219, PR0228, PR0222, PR0231 and PR0265.
EXAMPLE 95: Chondrocvte Re-differentiation Assay (Assay 110)
This assay shows that certain polypeptides of the invention act to induce redifferentiation of chondrocytes, therefore, are expected to be useful for the treatment of various bone and/or cartilage disorders such as, for example, sports injuries and arthritis. The assay is performed as follows. Porcine chondrocytes are isolated by overnight collagenase digestion of articulary cartilage of metacarpophalangeal joints of 4-6 month old female pigs. The isolated cells are then seeded at 25,000 cells/cm2 in Ham F-12 containing 10% FBS and 4 μg/ml gentamycin. The culture media is changed every third day and the cells are then seeded in 96 well plates at 5,000 cells/well in lOOμl of the same media without serum and 100 μl of the test PRO polypeptide, 5 nM staurosporin (positive control) or medium alone (negative control) is added to give a final volume of 200 μl/well. After 5 days of incubation at 37°C, a picture of each well is taken and the differentiation state of the chondrocytes is determined. A positive result in the assay occurs when the redifferentiation of the chondrocytes is determined to be more similar to the positive control than the negative control. The following polypeptide tested positive in this assay: PR0214, PR0219, PR0229, PR0222, PR0224,
PRO230, PR0257, PR0272 and PRO301. EXAMPLE 96: Fetal Hemoglobin Induction in an Erythroblastic Cell Line (Assay 107)
This assay is useful for screening PRO polypeptides for the ability to induce the switch from adult hemoglobin to fetal hemoglobin in an erythroblastic cell line. Molecules testing positive in this assay are expected to be useful for therapeutically treating various mammalian hemoglobin-associated disorders such as the various thalassemias. The assay is performed as follows. Erythroblastic cells are plated in standard growth medium at 1000 cells/well in a 96 well format. PRO polypeptides are added to the growth medium at a concentration of 0.2% or 2% and the cells are incubated for 5 days at 37°C. As a positive control, cells are treated with 100μM hemin and as a negative control, the cells are untreated. After 5 days, cell lysates are prepared and analyzed for the expression of gamma globin (a fetal marker). A positive in the assay is a gamma globin level at least 2-fold above the negative control. The following polypeptides tested positive in this assay: PR0221 and PR0245.
EXAMPLE 97: Mouse Kidney Mesangial Cell Proliferation Assay (Assay 92)
This assay shows that certain polypeptides of the invention act to induce proliferation of mammalian kidney mesangial cells and, therefore, are useful for treating kidney disorders associated with decreased mesangial cell function such as Berger disease or other nephropathies associated with Schonlein-Henoch purpura, celiac disease, dermatitis herpetiformis or Crohn disease. The assay is performed as follows. On day one, mouse kidney mesangial cells are plated on a 96 well plate in growth media (3: 1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium, 95 % fetal bovine serum, 5 % supplemented with 14 mM HEPES) and grown overnight. On day 2, PRO polypeptides are diluted at 2 concentrations(l % and 0.1 %) in semm-free medium and added to the cells. Control samples are semm-free medium alone. On day 4, 20μl of the Cell Titer 96 Aqueous one solution reagent (Progema) was added to each well and the colormetric reaction was allowed to proceed for 2 hours. The absorbance (OD) is then measured at 490 nm. A positive in the assay is anything that gives an absorbance reading which is at least 15% above the control reading. The following polypeptide tested positive in this assay: PR0227.
EXAMPLE 98: Proliferation of Rat Utricular Supporting Cells (Assay 54)
This assay shows that certain polypeptides of the invention act as potent mitogens for inner ear supporting cells which are auditory hair cell progenitors and, therefore, are useful for inducing the regeneration of auditory hair cells and treating hearing loss in mammals. The assay is performed as follows. Rat UEC-4 utricular epithelial cells are aliquoted into 96 well plates with a density of 3000 cells/well in 200 μl of serum- containing medium at 33°C. The cells are cultured overnight and are then switched to serum-free medium at 37°C. Various dilutions of PRO polypeptides (or nothing for a control) are then added to the cultures and the cells are incubated for 24 hours. After the 24 hour incubation, 3H-thymidine (1 μCi/well) is added and the cells are then cultured for an additional 24 hours. The cultures are then washed to remove unincorporated radiolabel, the cells harvested and Cpm per well determined. Cpmofat least 30% or greater in the PRO polypeptide treated cultures as compared to the control cultures is considered a positive in the assay.
The following polypeptides tested positive in this assay: PRO310 and PR0346. EXAMPLE 99: Chondrocyte Proliferation Assay (Assay 111)
This assay is designed to determine whether PRO polypeptides of the present invention show the ability to induce the proliferation and/or redifferentiation of chondrocytes in culmre. PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of various bone and/or cartilage disorders such as, for example, sports injuries and arthritis. Porcine chondrocytes are isolated by overnight collagenase digestion of articular cartilage of the metacarpophalangeal joint of 4-6 month old female pigs. The isolated cells are then seeded at 25,000 cells/cm2 in Ham F-12 containing 10% FBS and 4 μg/ml gentamycin. The culmre media is changed every third day and the cells are reseeded to 25,000 cells/cm2 every five days. On day 12, the cells are seeded in 96 well plates at 5,000 cells/well in lOOμl of the same media without serum and 100 μl of either semm-free medium (negative control), staurosporin (final concentration of 5 nM; positive control) or the test PRO polypeptide are added to give a final volume of 200 μl/well. After 5 days at 37°C, 20 μl of Alamar blue is added to each well and the plates are incubated for an additional 3 hours at 37°C. The fluorescence is then measured in each well (Ex:530 nm; Em: 590 nm). The fluorescence of a plate containing 200 μl of the semm-free medium is measured to obtain the background. A positive result in the assay is obtained when the fluorescence of the PRO polypeptide treated sample is more like that of the positive control than the negative control.
The following PRO polypeptides tested positive in this assay: PR0219, PR0222, PR0317, PR0257, PR0265, PR0287, PR0272 and PR0533.
EXAMPLE 100: Inhibition of Heart Neonatal Hypertrophy Induced by LIF+ET-1 (Assay 74) This assay is designed to determine whether PRO polypeptides of the present invention show the ability to inhibit neonatal heart hypertrophy induced by LIF and endothelin-1 (ET-1). A test compound that provides a positive response in the present assay would be useful for the therapeutic treatment of cardiac insufficiency diseases or disorders characterized or associated with an undesired hypertrophy of the cardiac muscle.
Cardiac myocytes from 1-day old Harlan Sprague Dawley rats (180 μl at 7.5 x 104/ml, serum <0.1, freshly isolated) are introduced on day 1 to 96-well plates previously coated with DMEM/F12 + 4%FCS. Test PRO polypeptide samples or growth medium alone (negative control) are then added directly to the wells on day 2 in 20 μl volume. LIF + ET-1 are then added to the wells on day 3. The cells are stained after an additional 2 days in culmre and are then scored visually the next day. A positive in the assay occurs when the PRO polypeptide treated myocytes are visually smaller on the average or less numerous than the untreated myocytes. The following PRO polypeptides tested positive in this assay: PR0238.
EXAMPLE 101: Tissue Expression Distribution
Oligonucleotide probes were constmcted from some of the PRO polypeptide-encoding nucleotide sequences shown in the accompanying figures for use in quantitative PCR amplification reactions. The oligonucleotide probes were chosen so as to give an approximately 200-600 base pair amplified fragment from the 3' end of its associated template in a standard PCR reaction. The oligonucleotide probes were employed in standard quantitative PCR amplification reactions with cDNA libraries isolated from different human adult and/or fetal tissue sources and analyzed by agarose gel electrophoresis so as to obtain a quantitative determination of the level of expression of the PRO polypeptide-encoding nucleic acid in the various tissues tested. Knowledge of the expression pattern or the differential expression of the PRO polypeptide-encoding nucleic acid in various different human tissue types provides a diagnostic marker useful for tissue typing, with or without other tissue- specific markers, for determining the primary tissue source of a metastatic mmor, and the like. These assays provided the following results.
DNA Molecule Tissues With Significant Expression Tissues Lacking Significant Expression
DNA34436-1238 lung, placenta, brain testis
DNA35557-1137 lung, kidney, brain placenta
DNA35599-1168 kidney, brain liver, placenta
DNA35668-1171 liver, lung, kidney placenta, brain
DNA36992-1168 liver, lung, kidney, brain placenta
DNA39423-1182 kidney, brain liver
DNA40603-1232 liver brain, kidney, lung
DNA40604-1187 liver brain, kidney, lung
DNA41379-1236 lung, brain liver
DNA33206-1165 heart, spleen, dendrocytes substantia nigra, hippocampus, cartilage, prostate, HUVEC
DNA34431-1177 spleen, HUVEC, cartilage, heart, uterus brain, colon tumor, prostate, THP-1 macrophages DNA41225-1217 HUVEC, uterus, colon mmor, cartilage, spleen, brain, heart, IM-9 lymphoblasts prostate
EXAMPLE 102: In situ Hybridization
In situ hybridization is a powerful and versatile technique for the detection and localization of nucleic acid sequences within cell or tissue preparations. It may be useful, for example, to identify sites of gene expression, analyze the tissue distribution of transcription, identify and localize viral infection, follow changes in specific mRNA synthesis and aid in chromosome mapping. In situ hybridization was performed following an optimized version of the protocol by Lu and Gillett,
Cell Vision 1: 169-176 (1994), using PCR-generated 33P-labeled riboprobes. Briefly, formalin-fixed, paraffin- embedded human tissues were sectioned, deparaffinized, deproteinated in proteinase K (20 g/ml) for 15 minutes at 37°C, and further processed for in situ hybridization as described by Lu and Gillett, supra. A [33-P] UTP- labeled antisense riboprobe was generated from a PCR product and hybridized at 55 °C overnight. The slides were dipped in Kodak NTB2 nuclear track emulsion and exposed for 4 weeks. 33P-Riboprobe synthesis
6.0 μl (125 mCi) of "P-UTP (Amersham BF 1002, SA < 2000 Ci/mmol) were speed vac dried. To each tube containing dried 33P-UTP, the following ingredients were added:
2.0 μl 5x transcription buffer LO μl DTT (lOO mM)
2.0 μl NTP mix (2.5 mM : 10 μ; each of 10 mM GTP, CTP & ATP + 10 μl H20)
1.0 μl UTP (50 μM)
1.0 μl Rnasin
1.0 μl DNA template (lμg) 1.0 l H2O
1.0 μl RNA polymerase (for PCR products T3 = AS, T7 = S, usually)
The tubes were incubated at 37 °C for one hour. 1.0 μl RQ1 DNase were added, followed by incubation at 37°C for 15 minutes. 90 μl TE (10 mM Tris pH 7.6/lmM EDTA pH 8.0) were added, and the mixture was pipetted onto DE81 paper. The remaining solution was loaded in a Microcon-50 ultrafiltration unit, and spun using program 10 (6 minutes). The filtration unit was inverted over a second tube and spun using program 2 (3 minutes). After the final recovery spin, 100 μl TE were added. 1 μl of the final product was pipetted on DE81 paper and counted in 6 ml of Biofluor II.
The probe was mn on a TBE/urea gel. 1-3 μl of the probe or 5 μl of RNA Mrk III were added to 3 μl of loading buffer. After heating on a 95 °C heat block for three minutes, the gel was immediately placed on ice. The wells of gel were flushed, the sample loaded, and mn at 180-250 volts for 45 minutes. The gel was wrapped in saran wrap and exposed to XAR film with an intensifying screen in -70°C freezer one hour to overnight.
33P-Hvbridization A. Pretreatment of frozen sections
The slides were removed from the freezer, placed on aluminium trays and thawed at room temperature for 5 minutes. The trays were placed in 55 °C incubator for five minutes to reduce condensation. The slides were fixed for 10 minutes in 4% paraformaldehyde on ice in the fume hood, and washed in 0.5 x SSC for 5 minutes, at room temperamre (25 ml 20 x SSC + 975 ml SQ H20). After deproteination in 0.5 μg/ml proteinase K for 10 minutes at 37°C (12.5 μl of 10 mg/ml stock in 250 ml prewarmed RNase-free RNAse buffer), the sections were washed in 0.5 x SSC for 10 minutes at room temperamre. The sections were dehydrated in 70% , 95%, 100% ethanol, 2 minutes each. B. Pretreatment of paraffin-embedded sections
The slides were deparaffinized, placed in SQ H20, and rinsed twice in 2 x SSC at room temperamre, for 5 minutes each time. The sections were deproteinated in 20 μg/ml proteinase K (500 μl of 10 mg/ml in 250 ml RNase-free RNase buffer; 37°C, 15 minutes) - human embryo, or 8 x proteinase K (100 μl in 250 ml Rnase buffer, 37°C, 30 minutes) - formalin tissues. Subsequent rinsing in 0.5 x SSC and dehydration were performed as described above.
C. Prehvbridization
The slides were laid out in a plastic box lined with Box buffer (4 x SSC, 50% formamide) - samrated filter paper. The tissue was covered with 50 μl of hybridization buffer (3.75g Dextran Sulfate + 6 ml SQ H20), vortexed and heated in the microwave for 2 minutes with the cap loosened. After cooling on ice, 18.75 ml formamide, 3.75 ml 20 x SSC and 9 ml SQ H20 were added, the tissue was vortexed well, and incubated at
42 °C for 1-4 hours.
D. Hybridization
1.0 x 106 cpm probe and 1.0 μl tRNA (50 mg/ml stock) per slide were heated at 95 °C for 3 minutes.
The slides were cooled on ice, and 48 μl hybridization buffer were added per slide. After vortexing, 50 μl 33P t mix were added to 50 μl prehybridization on slide. The slides were incubated overnight at 55 °C.
E. Washes
Washing was done 2 x 10 minutes with 2xSSC, EDTA at room temperamre (400 ml 20 x SSC + 16 ml 0.25M EDTA, Vf=4L), followed by RNaseA treatment at 37°C for 30 minutes (500 μl of 10 mg/ml in 250 ml Rnase buffer = 20 μg/ml), The slides were washed 2 x 10 minutes with 2 x SSC, EDTA at room temperamre. The stringency wash conditions were as follows: 2 hours at 55 °C, 0.1 x SSC, EDTA (20 ml 20 x SSC + 16 ml EDTA, Vf=4L).
F. Oligonucleotides
In situ analysis was performed on a variety of DNA sequences disclosed herein. The oligonucleotides employed for these analyses are as follows. (1) DNA33094-1131 (PRQ217) pi 5'-GGATTCTAATACGACTCACTATAGGGCTCAGAAAAGCGCAACAGAGAA-3' (SEQ ID
NO:348) p2 5 '-CTATGAAATTAACCCTCACTAAAGGGATGTCTTCCATGCCAACCTTC-3 ' (SEQ ID NO:349) (2) DNA33223-1136 (PRO230) pi 5'-GGATTCTAATACGACTCACTATAGGGCGGCGATGTCCACTGGGGCTAC-3' (SEQ ID
NO:350) p2 5'-CTATGAAATTAACCCTCACTAAAGGGACGAGGAAGATGGGCGGATGGT-3' (SEQ ID
NO:351)
(3) DNA34435-1140 (PR0232) pi S'-GGATTCTAATACGACTCACTATAGGGCACCCACGCGTCCGGCTGCTT-S' (SEQ ID NO:352) p2 5'-CTATGAAATTAACCCTCACTAAAGGGACGGGGGACACCACGGACCAGA-3' (SEQ ID
NO:353)
(4) DNA35639-1172 (PR0246) pi 5 ' -GGATTCTAATACGACTCACTATAGGGCTTGCTGCGGTTTTTGTTCCTG-3 ' (SEQ ID NO:354) p2 5'-CTATGAAATTAACCCTCACTAAAGGGAGCTGCCGATCCCACTGGTATT-3' (SEQ ID
NO:355)
(5) DNA49435-1219 (PR0533) pi 5'-GGATTCTAATACGACTCACTATAGGGCGGATCCTGGCCGGCCTCTG-3' (SEQ ID NO:356) p2 5'-CTATGAAATTAACCCTCACTAAAGGGAGCCCGGGCATGGTCTCAGTTA-3' (SEQ ID
NO:357)
(6) DNA35638-1141 (PRQ245) pi 5'-GGATTCTAATACGACTCACTATAGGGCGGGAAGATGGCGAGGAGGAG-3' (SEQ ID NO:358) p2 5'-CTATGAAATTAACCCTCACTAAAGGGACCAAGGCCACAAACGGAAATC-3' (SEQ ID NO:359)
(7) DNA33089-1132 (PR0221) pi 5'-GGATTCTAATACGACTCACTATAGGGCTGTGCTTTCATTCTGCCAGTA-3' (SEQ ID
NO:360) p2 5'-CTATGAAATTAACCCTCACTAAAGGGAGGGTACAATTAAGGGGTGGAT-3' (SEQ ID
NO:361)
(8) DNA35918-1174 (PRQ258) pi 5'-GGATTCTAATACGACTCACTATAGGGCCCGCCTCGCTCCTGCTCCTG-3' (SEQ ID NO:362) p2 5'-CTATGAAATTAACCCTCACTAAAGGGAGGATTGCCGCGACCCTCACAG-3' (SEQ ID
NO:363) (9) DNA32286-1191 (PRQ214) pi 5'-GGATTCTAATACGACTCACTATAGGGCCCCTCCTGCCTTCCCTGTCC-3' (SEQ ID NO:364) p2 5'-CTATGAAATTAACCCTCACTAAAGGGAGTGGTGGCCGCGATTATCTGC-3' (SEQ ID
NO:365)
(10) DNA33221-1133 (PR0224) pi 5'-GGATTCTAATACGACTCACTATAGGGCGCAGCGATGGCAGCGATGAGG-3' (SEQ ID
NO:366) p2 5'-CTATGAAATTAACCCTCACTAAAGGGACAGACGGGGCAGAGGGAGTG-3' (SEQ ID
NO:367)
(11) DNA35557-1137 (PR0234) pi 5'-GGATTCTAATACGACTCACTATAGGGCCAGGAGGCGTGAGGAGAAAC-3' (SEQ ID
NO:368) p2 5'-CTATGAAATTAACCCTCACTAAAGGGAAAGACATGTCATCGGGAGTGG-3' (SEQ ID NO:369)
(12) DNA33100-1159 (PR0229) pi 5'-GGATTCTAATACGACTCACTATAGGGCCGGGTGGAGGTGGAACAGAAA-3' (SEQ ID
NO:370) p2 5'-CTATGAAATTAACCCTCACTAAAGGGACACAGACAGAGCCCCATACGC-3' (SEQ ID
NO:371)
(13) DNA34431-1 177 (PR0263) pi 5'-GGATTCTAATACGACTCACTATAGGGCCAGGGAAATCCGGATGTCTC-3' (SEQ ID NO:372) p2 5'-CTATGAAATTAACCCTCACTAAAGGGAGTAAGGGGATGCCACCGAGTA-3' (SEQ ID
NO:373)
(14) DNA38268-1188 (PRQ295) pi 5'-GGATTCTAATACGACTCACTATAGGGCCAGCTACCCGCAGGAGGAGG-3' (SEQ ID NO:374) p2 5'-CTATGAAATTAACCCTCACTAAAGGGATCCCAGGTGATGAGGTCCAGA-3' (SEQ ID
NO:375)
G. Results In situ analysis was performed on a variety of DNA sequences disclosed herein. The results from these analyses are as follows. (1) DNA33094-1131 (PRQ217)
Highly distinctive expression pattern, that does not indicate an obvious biological function. In the human embryo it was expressed in outer smooth muscle layer of the GI tract, respiratiry cartilage, branching respiratory epithelium, osteoblasts, tendons, gonad, in the optic nerve head and developing dermis. In the adult expression was observed in the epidermal pegs of the chimp tongue, the basal epithelial/myoepithelial cells of the prostate and urinary bladder. Also expressed in the alveolar lining cells of the adult lung, mesenchymal cells juxtaposed to erectile tissue in the penis and the cerebral cortex (probably glial cells). In the kidney, expression was only seen in disease, in cells surrounding thyroidized renal tubules.
Human fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and lower limb.
Adult human tissues examined: Kidney (normal and end-stage), adrenal, myocardium, aorta, spleen, lymph node, gall bladder, pancreas, lung, skin, eye (inc. retina), prostate, bladder, liver (normal, cirrhotic, acute failure).
Non-human primate tissues examined: (a) Chimp Tissues: Salivary gland, stomach, thyroid, parathyroid, skin, thymus, ovary, lymph node.
(b) Rhesus Monkey Tissues: Cerebral cortex, hippocampus, cerebellum, penis.
(2) DNA33223-1136 (PRO230) Sections show an intense signal associated with arterial and venous vessels in the fetus. In arteries the signal appeared to be confined to smooth-muscle/pericytic cells. The signal is also seen in capillary vessels and in glomeruli. It is not clear whether or not endothelial cells are expressing this mRNA. Expression is also observed in epithelial cells in the fetal lens. Strong expression was also seen in cells within placental trophoblastic villi, these cells lie between the trophoblast and the fibroblast-like cells that express HGF - uncertain histogenesis. In the adult, there was no evidence of expression and the wall of the aorta and most vessels appear to be negative. However, expression was seen over vascular channels in the normal prostate and in the epithelium lining the gallbladder. Insurers expression was seen in the vessels of the soft-tissue sarcoma and a renal cell carcinoma. In summary, this is a molecule that shows relatively specific vascular expression in the fetus as well as in some adult organs. Expression was also observed in the fetal lens and the adult gallbladder.
In a secondary screen, vascular expression was observed, similar to that observed above, seen in fetal blocks. Expression is on vascular smooth muscle, rather than endothelium. Expression also seen in smooth muscle of the developing oesophagus, so as reported previously, this molecule is not vascular specific. Expression was examined in 4 lung and 4 breast carcinomas. Substantial expression was seen in vascular smooth muscle of at least 3/4 lung cancers and 2/4 breast cancers. In addition, in one breast carcinoma, expression was observed in peritumoral stromal cells of uncertain histogenesis (possibly myofibroblasts). No endothelial cell expression was observed in this study. (3) DNA34435-1140 (PRQ232)
Strong expression in prostatic epithelium and bladder epithelium, lower level of expression in bronchial epithelium. High background / low level expression seen in a number of sites, including among others, bone, blood, chondrosarcoma, adult heart and fetal liver. It is felt that this level of signal represents background, partly because signal at this level was seen over the blood. All other tissues negative. Human fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis, testis and lower limb. Adult human tissues examined: Kidney (normal and end-stage), adrenal, spleen, lymph node, pancreas, lung, eye (inc. retina), bladder, liver (normal, cirrhotic, acute failure). Non-human primate tissues examined:
Chimp Tissues: adrenal
Rhesus Monkey Tissues: Cerebral cortex, hippocampus
In a secondary screen, expression was observed in the epithelium of the prostate, the superficial layers of the urethelium of the urinary bladder, the urethelium lining the renal pelvis and the urethelium of the ureter (1 out of 2 experiments). The urethra of a rhesus monkey was negative; it is unclear whether this represents a true lack of expression by the urethra, or if it is the result of a failure of the probe to cross react with rhesus tissue. The findings in the prostate and bladder are similar to those previously described using an isotopic detection technique. Expression of the mRNA for this antigen is NOT prostate epithelial specific. The antigen may serve as a useful marker for urethelial derived tissues. Expression in the superficial, post-mitotic cells, of the urinary tract epithelium also suggest that it is unlikely to represent a specific stem cell marker, as this would be expected to be expressed specifically in basal epithelium.
(4) DNA35639-1172 (PRQ246)
Strongly expressed in fetal vascular endothelium, including tissues of the CNS. Lower level of expression in adult vasculamre, including the CNS. Not obviously expressed at higher levels in tumor vascular endothelium. Signal also seen over bone matrix and adult spleen, not obviously cell associated, probably related to non-specific background at these sites.
Human fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis, testis and lower limb.
Adult human tissues examined: Kidney (normal and end-stage), adrenal, spleen, lymph node, pancreas, lung, eye (inc. retina), bladder, liver (normal, cirrhotic, acute failure).
Non-human primate tissues examined: Chimp Tissues: adrenal Rhesus Monkey Tissues: Cerebral cortex, hippocampus (5) DNA49435-1219 (PRQ533)
Moderate expression over cortical neurones in the fetal brain. Expression over the inner aspect of the fetal retina, possible expression in the developing lens. Expression over fetal skin, cartilage, small intestine, placental villi and umbilical cord. In adult tissues there is an extremely high level of expression over the gallbladder epithelium. Moderate expression over the adult kidney, gastric and colonic epithelia. Low-level expression was observed over many cell types in many tissues, this may be related to stickiness of the probe, these data should therefore be interpreted with a degree of caution.
Human fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis, testis and lower limb. Adult human tissues examined: Kidney (normal and end-stage), adrenal, spleen, lymph node, pancreas, lung, eye (inc. retina), bladder, liver (normal, cirrhotic, acute failure). Non-human primate tissues examined:
Chimp Tissues: adrenal
Rhesus Monkey Tissues: Cerebral cortex, hippocampus, cerebellum.
(6) DNA35638-1141 (PRQ245)
Expression observed in the endothelium lining a subset of fetal and placental vessels. Endothelial expression was confined to these tissue blocks. Expression also observed over intermediate trophoblast cells of placenta. Expression also observed tumor vasculamre but not in the vasculamre of normal tissues of the same type. All other tissues negative.
Fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and lower limb. Adult tissues examined: Liver, kidney, adrenal, myocardium, aorta, spleen, lymph node, pancreas, lung, skin, cerebral cortex (rm), hipρocampus(rm), cerebellum(rm), penis, eye, bladder, stomach, gastric carcinoma, colon, colonic carcinoma, thyroid (chimp), parathyroid (chimp) ovary (chimp) and chondrosarcoma. Acetominophen induced liver injury and hepatic cirrhosis
(7) DNA33089-1132 (PRQ221)
Specific expression over fetal cerebral white and grey matter, as well as over neurones in the spinal cord. Probe appears to cross react with rat. Low level of expression over cerebellar neurones in adult rhesus brain. All other tissues negative.
Fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and lower limb. Adult tissues examined: Liver, kidney, adrenal, myocardium, aorta, spleen, lymph node, pancreas, lung, skin, cerebral cortex (rm), hippocamρus(rm), cerebellum(rm), penis, eye, bladder, stomach, gastric carcinoma, colon, colonic carcinoma and chondrosarcoma. Acetominophen induced liver injury and hepatic cirrhosis
(8) DNA35918-1174 (PRQ258)
Strong expression in the nervous system. In the rhesus monkey brain expression is observed in cortical, hippocampal and cerebellar neurones. Expression over spinal neurones in the fetal spinal cord, the developing brain and the inner aspects of the fetal retina. Expression over developing dorsal root and autonomic ganglia as well as enteric nerves. Expression observed over ganglion cells in the adult prostate. In the rat, there is strong expression over the developing hind brain and spinal cord. Strong expression over interstitial cells in the placental villi. All other tissues were negative.
Fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and lower limb. Adult tissues examined: Liver, kidney, renal cell carcinoma, adrenal, aorta, spleen, lymph node, pancreas, lung, myocardium, skin, cerebral cortex (rm), hippocampus(rm), cerebellum(rm), bladder, prostate, stomach, gastric carcinoma, colon, colonic carcinoma, thyroid (chimp), parathyroid (chimp) ovary (chimp) and chondrosarcoma. Acetominophen induced liver injury and hepatic cirrhosis.
(9) DNA32286-1191 (PRQ214)
Fetal tissue: Low level throughout mesenchyme. Moderate expression in placental stromal cells in membranous tissues and in thyroid. Low level expression in cortical neurones. Adult tissue: all negative.
Fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and lower limb.
Adult tissues examined include: Liver, kidney, adrenal, myocardium, aorta, spleen, lymph node, pancreas, lung and skin.
(10) DNA33221-1133 (PRQ224) Expression limited to vascular endothelium in fetal spleen, adult spleen, fetal liver, adult thyroid and adult lymph node (chimp). Additional site of expression is the developing spinal ganglia. All other tissues negative.
Human fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and lower limb.
Adult human tissues examined: Kidney (normal and end-stage), adrenal, myocardium, aorta, spleen, lymph node, pancreas, lung, skin, eye (inc. retina), bladder, liver (normal, cirrhotic, acute failure). Non-human primate tissues examined:
Chimp Tissues: Salivary gland, stomach, thyroid, parathyroid, skin, thymus, ovary, lymph node. Rhesus Monkey Tissues: Cerebral cortex, hippocampus, cerebellum, penis.
(11) DNA35557-1137 (PRQ234) Specific expression over developing motor neurones in ventral aspect of the fetal spinal cord (will develop into ventral homs of spinal cord). All other tissues negative. Possible role in growth, differentiation and/or development of spinal motor neurons.
Fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and lower limb.
Adult tissues examined: Liver, kidney, adrenal, myocardium, aorta, spleen, lymph node, pancreas, lung, skin, cerebral cortex (rm), hippocampus(rm), cerebellum(rm), penis, eye, bladder, stomach, gastric carcinoma, colon, colonic carcinoma and chondrosarcoma. Acetominophen induced liver injury and hepatic cirrhosis
(12) DNA33100-1159 (PRQ229)
Striking expression in mononuclear phagocytes (macrophages) of fetal and adult spleen, liver, lymph node and adult thymus (in tingible body macrophages). The highest expression is in the spleen. All other tissues negative. Localisation and homology are entirely consistent with a role as a scavenger receptor for cells of the reticuloendothelial system. Expression also observed in placental mononuclear cells.
Human fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and lower limb.
Adult human tissues examined: Kidney (normal and end-stage), adrenal, myocardium, aorta, spleen, lymph node, gall bladder, pancreas, lung, skin, eye (inc. retina), prostate, bladder, liver (normal, cirrhotic, acute failure). Non-human primate tissues examined:
Chimp Tissues: Salivary gland, stomach, thyroid, parathyroid, skin, thymus, ovary, lymph node. Rhesus Monkey Tissues: Cerebral cortex, hippocampus, cerebellum, penis.
(13) DNA34431-1177 (PRQ263)
Widepread expression in human fetal tissues and placenta over mononuclear cells, probably macrophages +/- lymphocytes. The cellular distribution follows a perivascular pattern in many tissues. Strong expression also seen in epithelial cells of the fetal adrenal cortex. All adult tissues were negative. Fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and lower limb. Adult tissues examined: Liver, kidney, adrenal, spleen, lymph node, pancreas, lung, skin, cerebral cortex (rm), hippocampus(rm), cerebellum(rm), bladder, stomach, colon and colonic carcinoma. Acetominophen induced liver injury and hepatic cirrhosis.
A secondary screen evidenced expression over stromal mononuclear cells probably histiocytes.
(14) DNA38268-1188 (PRQ295)
High expression over ganglion cells in human fetal spinal ganglia and over large neurones in the anterior horns of the developing spinal cord. In the adult there is expression in the chimp adrenal medulla (neural), neurones of the rhesus monkey brain (hippocampus [ + + +] and cerebral cortex) and neurones in ganglia in the normal adult human prostate (the only section that contains ganglion cells, ie expression in this cell type is presumed NOT to be confined to the prostate). All other tissues negative.
Human fetal tissues examined (E12-E16 weeks) include: Placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, great vessels, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis, testis and lower limb.
Adult human tissues examined: Kidney (normal and end-stage), adrenal, spleen, lymph node, pancreas, lung, eye (inc. retina), bladder, liver (normal, cirrhotic, acute failure). Non-human primate tissues examined: Chimp Tissues: adrenal Rhesus Monkey Tissues: Cerebral cortex, hippocampus, cerebellum.
EXAMPLE 103: Isolation of cDNA clones Encoding Human PRQ1868
A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in Example 1 above. This consensus sequence is herein designated DNA49803. Based up an observed homology between the DNA49803 consensus sequence and an EST sequence contained within the Incyte EST clone no. 2994689, Incyte EST clone no. 2994689 was purchased and its insert obtained and sequenced. The sequence of that insert is shown in Figure 123 and is herein designated DNA77624-2515.
The entire nucleotide sequence of DNA77624-2515 is shown in Figure 123 (SEQ ID NO:422). Clone DNA77624-2515 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 51-53 and ending at the stop codon at nucleotide positions 981-983 (Figure 123). The predicted polypeptide precursor is 310 amino acids long (Figure 124). The full-length PR01868 protein shown in Figure 124 has an estimated molecular weight of about 35,020 daltons and a pi of about 7.90. Analysis of the full- length PR01868 sequence shown in Figure 124 (SEQ ID NO:423) evidences the presence of the following: a signal peptide from about amino acid 1 to about amino acid 30, a transmembrane domain from about amino acid 243 to about amino acid 263, potential N-glycosylation sites from about amino acid 104 to about amino acid 107 and from about amino acid 192 to about amino acid 195, a cAMP- and cGMP-dependent protein kinase phosphorylation site from about amino acid 107 to about amino acid 110, casein kinase II phosphorylation sites from about amino acid 106 to about amino acid 109 and from about amino acid 296 to about amino acid 299, a tyrosine kinase phosphorylation site from about amino acid 69 to about amino acid 77 and potential N- myristolation sites from about amino acid 26 to about amino acid 31 , from about amino acid 215 to about amino acid 220, from about amino acid 226 to about amino acid 231, from about amino acid 243 to about amino acid 248, from about amino acid 244 to about amino acid 249 and from about amino acid 262 to about amino acid 267. Clone DNA77624-2515 has been deposited with ATCC on December 22, 1998 and is assigned ATCC deposit no. 203553.
An analysis of the Dayhoff database (version 35.45 SwissProt 35), using a WU-BLAST2 sequence alignment analysis of the full-length sequence shown in Figure 124 (SEQ ID NO: 423), evidenced significant homology between the PRO 1868 amino acid sequence and the following Dayhoff sequences: HGS RC75, P W61379, A33 HUMAN, P W14146, P W14158, AMAL DROME, P R77437, 138346, NCM2 HUMAN and PTPD HUMAN.
EXAMPLE 104: Identification of Receptor/Li gand Interactions
In this assay, various PRO polypeptides are tested for ability to bind to a panel of potential receptor molecules for the purpose of identifying receptor/ligand interactions. The identification of a ligand for a known receptor, a receptor for a known ligand or a novel receptor/ligand pair is useful for a variety of indications including, for example, targeting bioactive molecules (linked to the ligand or receptor) to a cell known to express the receptor or ligand, use of the receptor or ligand as a reagent to detect the presence of the ligand or receptor in a composition suspected of containing the same, wherein the composition may comprise cells suspected of expressing the ligand or receptor, modulating the growth of or another biological or immunological activity of a cell known to express or respond to the receptor or ligand, modulating the immune response of cells or toward cells that express the receptor or ligand, allowing the preparaion of agonists, antagonists and/or antibodies directed against the receptor or ligand which will modulate the growth of or a biological or immunological activity of a cell expressing the receptor or ligand, and various other indications which will be readily apparent to the ordinarily skilled artisan.
The assay is performed as follows. A PRO polypeptide of the present invention suspected of being a ligand for a receptor is expressed as a fusion protein containing the Fc domain of human IgG (an immunoadhesin) . Receptor-ligand binding is detected by allowing interaction of the immunoadhesin polypeptide with cells (e.g. Cos cells) expressing candidate PRO polypeptide receptors and visualization of bound immunoadhesin with fluorescent reagents directed toward the Fc fusion domain and examination by microscope. Cells expressing candidate receptors are produced by transient transfection, in parallel, of defined subsets of a library of cDNA expression vectors encoding PRO polypeptides that may function as receptor molecules. Cells are then incubated for 1 hour in the presence of the PRO polypeptide immunoadhesin being tested for possible receptor binding. The cells are then washed and fixed with paraformaldehyde. The cells are then incubated with fluorescent conjugated antibody directed against the Fc portion of the PRO polypeptide immunoadhesin (e.g. FITC conjugated goat anti-human-Fc antibody). The cells are then washed again and examined by microscope. A positive interaction is judged by the presence of fluorescent labeling of cells transfected with cDN A encoding a particular PRO polypeptide receptor or pool of receptors and an absence of similar fluorescent labeling of similarly prepared cells that have been transfected with other cDNA or pools of cDNA. If a defined pool of cDNA expression vectors is judged to be positive for interaction with a PRO polypeptide immunoadhesin, the individual cDNA species that comprise the pool are tested individually (the pool is "broken down") to determine the specific cDNA that encodes a receptor able to interact with the PRO polypeptide immunoadhesin.
In another embodiment of this assay, an epitope-tagged potential ligand PRO polypeptide (e.g. 8 histidine "His" tag) is allowed to interact with a panel of potential receptor PRO polypeptide molecules that have been expressed as fusions with the Fc domain of human IgG (immunoadhesins). Following a 1 hour co-incubation with the epitope tagged PRO polypeptide, the candidate receptors are each immunoprecipitated with protein A beads and the beads are washed. Potential ligand interaction is determined by western blot analysis of the immunoprecipitated complexes with antibody directed towards the epitope tag. An interaction is judged to occur if a band of the anticipated molecular weight of the epitope tagged protein is observed in the western blot analysis with a candidate receptor, but is not observed to occur with the other members of the panel of potential receptors.
Using these assays, the following receptor/ligand interactions have been herein identified: PR0245 binds to PR01868.
Deposit of Material
The following materials have been deposited with the American Type Culmre Collection, 12301 Parklawn Drive, Rockville, MD, USA (ATCC):
Material ATCC Dep. No. Deposit Date
DNA32292-1131 ATCC 209258 September 16, 1997
DNA33094-1131 ATCC 209256 September 16, 1997
DNA33223-1136 ATCC 209264 September 16, 1997
DNA34435-1140 ATCC 209250 September 16, 1997
DNA27864-1155 ATCC 209375 October 16, 1997
DNA36350-1158 ATCC 209378 October 16, 1997
DNA32290-1164 ATCC 209384 October 16, 1997
DNA35639-1172 ATCC 209396 October 17, 1997
DNA33092-1202 ATCC 209420 October 28, 1997
DNA49435-1219 ATCC 209480 November 21 , 1997
DNA35638-1141 ATCC 209265 September 16, 1997
DNA32298-1132 ATCC 209257 September 16, 1997
DNA33089-1132 ATCC 209262 September 16, 1997
DNA33786-1132 ATCC 209253 September 16, 1997
DNA35918-1174 ATCC 209402 October 17, 1997
DNA37150-1178 ATCC 209401 October 17, 1997
DNA38260-1180 ATCC 209397 October 17, 1997
DNA39969-1185 ATCC 209400 October 17, 1997
DNA32286-1191 ATCC 209385 October 16, 1997
DNA33461-1199 ATCC 209367 October 15, 1997
DNA40628-1216 ATCC 209432 November 7, 1997
DNA33221-1133 ATCC 209263 September 16, 1997
DNA33107-1135 ATCC 209251 September 16, 1997
DNA35557-1137 ATCC 209255 September 16, 1997
DNA34434-1139 ATCC 209252 September 16, 1997
DNA33100- 1159 ATCC 209373 October 16, 1997
DNA35600-1162 ATCC 209370 October 16, 1997
DNA34436-1238 ATCC 209523 December 10, 1997
DNA33206-1165 ATCC 209372 October 16, 1997 DNA35558-1167 ATCC 209374 October 16, 1997 DNA35599-1168 ATCC 209373 October 16, 1997 DNA36992-1168 ATCC 209382 October 16, 1997 DNA34407-1169 ATCC 209383 October 16, 1997 DNA35841-1173 ATCC 209403 October 17, 1997 DNA33470-1175 ATCC 209398 October 17, 1997 DNA34431-1177 ATCC 209399 October 17, 1997 DNA39510-1181 ATCC 209392 October 17, 1997 DNA39423-1182 ATCC 209387 October 17, 1997 DNA40620-1183 ATCC 209388 October 17, 1997 DNA40604-1187 ATCC 209394 October 17, 1997 DNA38268-1188 ATCC 209421 October 28, 1997 DNA37151-1193 ATCC 209393 October 17, 1997 DNA35673-1201 ATCC 209418 October 28, 1997 DNA40370-1217 ATCC 209485 November 21, 1997 DNA42551-1217 ATCC 209483 November 21, 1997 DNA39520-1217 ATCC 209482 November 21, 1997 DNA41225-1217 ATCC 209491 November 21, 1997 DNA43318-1217 ATCC 209481 November 21, 1997 DNA40587-1231 ATCC 209438 November 7, 1997 DNA41338-1234 ATCC 209927 June 2, 1998 DNA40981-1234 ATCC 209439 November 7, 1997 DNA37140-1234 ATCC 209489 November 21, 1997 DNA40982-1235 ATCC 209433 November 7, 1997 DNA41379-1236 ATCC 209488 November 21, 1997 DNA44167-1243 ATCC 209434 November 7, 1997 DNA39427-1179 ATCC 209395 October 17, 1997 DNA40603-1232 ATCC 209486 November 21, 1997 DNA43466-1225 ATCC 209490 November 21, 1997 DNA43046-1225 ATCC 209484 November 21, 1997 DNA35668-1171 ATCC 209371 October 16, 1997 DNA77624-2515 ATCC 203553 December 22, 1998
These deposit were made under the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purpose of Patent Procedure and the Regulations thereunder (Budapest Treaty). This assures maintenance of a viable culmre of the deposit for 30 years from the date of deposit. The deposits will be made available by ATCC under the terms of the Budapest Treaty, and subject to an agreement between Genentech, Inc. and ATCC, which assures permanent and unrestricted availability of the progeny of the culmre of the deposit to the public upon issuance of the pertinent U.S. patent or upon laying open to the public of any U.S. or foreign patent application, whichever comes first, and assures availability of the progeny to one determined by the U.S. Commissioner of Patents and Trademarks to be entitled thereto according to 35 USC § 122 and the Commissioner's mles pursuant thereto (including 37 CFR § 1.14 with particular reference to 886 OG 638).
The assignee of the present application has agreed that if a culture of the materials on deposit should die or be lost or destroyed when cultivated under suitable conditions, the materials will be promptly replaced on notification with another of the same. Availability of the deposited material is not to be constraed as a license to practice the invention in contravention of the rights granted under the authority of any government in accordance with its patent laws. The foregoing written specification is considered to be sufficient to enable one skilled in the art to practice the invention. The present invention is not to be limited in scope by the constract deposited, since the deposited embodiment is intended as a single illustration of certain aspects of the invention and any constructs that are functionally equivalent are within the scope of this invention. The deposit of material herein does not constimte an admission that the written description herein contained is inadequate to enable the practice of any aspect of the invention, including the best mode thereof, nor is it to be constraed as limiting the scope of the claims to the specific illustrations that it represents. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and fall within the scope of the appended claims.

Claims

WHAT IS CLAIMED IS:
1. Isolated nucleic acid having at least 80% sequence identity to a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence selected from the group consisting of the amino acid sequence shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO: 12), Figure 9 (SEQ ID NO: 18), Figure 11 (SEQ ID NO:23), Figure 13 (SEQ ID NO:28), Figure 15 (SEQ ID NO:34), Figure 17 (SEQ ID NO:39), Figure 19 (SEQ ID NO:49), Figure 22 (SEQ ID NO:59), Figure 24 (SEQ ID NO:64), Figure 26 (SEQ ID NO:69), Figure 28 (SEQ ID NO:71), Figure 30 (SEQ ID NO:73), Figure 32 (SEQ ID NO:84), Figure 34 (SEQ ID NO:91), Figure 36 (SEQ ID NO:96), Figure 38 (SEQ ID NO: 104), Figure 40 (SEQ ID NO: 109), Figure 42 (SEQ ID NO: 114), Figure 44 (SEQ ID NO: 119), Figure 46 (SEQ ID NO: 127), Figure 48 (SEQ ID NO: 132), Figure 50 (SEQ ID NO: 137), Figure 52 (SEQ ID NO: 142), Figure 54 (SEQ ID NO: 148), Figure 56 (SEQ ID NO: 153), Figure 58 (SEQ ID NO: 159), Figure 60 (SEQ ID NO: 164), Figure 62 (SEQ ID NO:170), Figure 64 (SEQ ID NO: 175), Figure 66 (SEQ ID NO: 177), Figure 68 (SEQ ID NO: 185), Figure 70 (SEQ ID NO: 190), Figure 72 (SEQ ID NO: 195), Figure 74 (SEQ ID NO:201), Figure 76 (SEQ ID NO:207), Figure 78 (SEQ ID NO:213), Figure 80 (SEQ ID NO:221), Figure 82 (SEQ ID NO:227), Figure 84 (SEQ ID NO:236), Figure 86 (SEQ ID NO:245), Figure 88 (SEQ ID NO:250), Figure 90 (SEQ ID NO:255), Figure 92 (SEQ ID NO:257), Figure 94 (SEQ ID NO:259), Figure 96 (SEQ ID NO:261), Figure 98 (SEQ ID NO:263), Figure 100 (SEQ ID NO:285), Figure 102 (SEQ ID NO:290), Figure 104 (SEQ ID NO:292), Figure 106 (SEQ ID NO:294), Figure 108 (SEQ ID NO:310), Figure 110 (SEQ ID NO:315), Figure 112 (SEQ ID NO:320), Figure 114 (SEQ ID NO:325), Figure 116 (SEQ ID NO:332), Figure 118 (SEQ ID NO:339), Figure 120 (SEQ ID NO:341), Figure 122 (SEQ ID NO:377) and Figure 124 (SEQ ID NO:423).
2. The nucleic acid of Claim 1 , wherein said nucleotide sequence comprises a nucleotide sequence selected from the group consisting of the sequence shown in Figure 1 (SEQ ID NO: 1), Figure 3 (SEQ ID NO:3), Figure 5 (SEQ ID NO: 11), Figure 8 (SEQ ID NO: 17), Figure 10 (SEQ ID NO:22), Figure 12 (SEQ ID NO:27), Figure 14 (SEQ ID NO:33), Figure 16 (SEQ ID NO:38), Figure 18 (SEQ ID NO:48), Figure 21 (SEQ ID NO:58), Figure 23 (SEQ ID NO:63), Figure 25 (SEQ ID NO:68), Figure 27 (SEQ ID NO:70), Figure 29 (SEQ ID NO:72), Figure 31 (SEQ ID NO:83), Figure 33 (SEQ ID NO:90), Figure 35 (SEQ ID NO:95), Figure 37 (SEQ ID NO: 103), Figure 39 (SEQ ID NO: 108), Figure 41 (SEQ ID NO: 113), Figure 43 (SEQ ID NO: 118), Figure 45 (SEQ ID NO: 126), Figure 47 (SEQ ID NO: 131), Figure 49 (SEQ ID NO: 136), Figure 51 (SEQ ID NO: 141), Figure 53 (SEQ ID NO: 147), Figure 55 (SEQ ID NO: 152), Figure 57 (SEQ ID NO: 158), Figure 59 (SEQ ID NO: 163), Figure 61 (SEQ ID NO: 169), Figure 63 (SEQ ID NO: 174), Figure 65 (SEQ ID NO: 176), Figure 67 (SEQ ID NO: 184), Figure 69 (SEQ ID NO: 189), Figure 71 (SEQ ID NO: 194), Figure 73 (SEQ ID NO:200), Figure 75 (SEQ ID NO:206), Figure 77 (SEQ ID NO:212), Figure 79 (SEQ ID NO:220), Figure 81 (SEQ ID NO:226), Figure 83 (SEQ ID NO:235), Figure 85 (SEQ ID NO:244), Figure 87 (SEQ ID NO:249), Figure 89 (SEQ ID NO:254), Figure 91 (SEQ ID NO:256), Figure 93 (SEQ ID NO:258), Figure 95 (SEQ ID NO:260), Figure 97 (SEQ ID NO:262), Figure 99 (SEQ ID NO:284), Figure 101 (SEQ ID NO:289), Figure 103 (SEQ ID NO:291), Figure 105 (SEQ ID NO:293), Figure 107 (SEQ ID NO:309), Figure 109 (SEQ ID NO:314), Figure 111 (SEQ ID NO:319), Figure 113 (SEQ ID NO:324), Figure 115 (SEQ ID NO:331), Figure 117 (SEQ ID NO:338), Figure 119 (SEQ ID NO:340), Figure 121 (SEQ ID NO:376) and Figure 123 (SEQ ID NO: 422), or the complement thereof.
3. The nucleic acid of Claim 1 , wherein said nucleotide sequence comprises a nucleotide sequence selected from the group consisting of the full-length coding sequence of the sequence shown in Figure 1 (SEQ ID NO: 1), Figure 3 (SEQ ID NO:3), Figure 5 (SEQ ID NO: 11), Figure 8 (SEQ ID NO: 17), Figure 10 (SEQ ID NO:22), Figure 12 (SEQ ID NO:27), Figure 14 (SEQ ID NO:33), Figure 16 (SEQ ID NO:38), Figure 18 (SEQ ID NO:48), Figure 21 (SEQ ID NO:58), Figure 23 (SEQ ID NO:63), Figure 25 (SEQ ID NO:68), Figure 27 (SEQ ID NO:70), Figure 29 (SEQ ID NO:72), Figure 31 (SEQ ID NO:83), Figure 33 (SEQ ID NO:90), Figure 35 (SEQ ID NO:95), Figure 37 (SEQ ID NO: 103), Figure 39 (SEQ ID NO: 108), Figure 41 (SEQ ID NO: 113), Figure 43 (SEQ ID NO: 118), Figure 45 (SEQ ID NO: 126), Figure 47 (SEQ ID NO: 131), Figure 49 (SEQ ID NO: 136), Figure 51 (SEQ ID NO: 141), Figure 53 (SEQ ID NO: 147), Figure 55 (SEQ ID NO: 152), Figure 57 (SEQ ID NO: 158), Figure 59 (SEQ ID NO: 163), Figure 61 (SEQ ID NO: 169), Figure 63 (SEQ ID NO: 174), Figure 65 (SEQ ID NO: 176), Figure 67 (SEQ ID NO: 184), Figure 69 (SEQ ID NO: 189), Figure 71 (SEQ ID NO: 194), Figure 73 (SEQ ID NO:200), Figure 75 (SEQ ID NO:206), Figure 77 (SEQ ID NO:212), Figure 79 (SEQ ID NO:220), Figure 81 (SEQ ID NO:226), Figure 83 (SEQ ID NO:235), Figure 85 (SEQ ID NO:244), Figure 87 (SEQ ID NO:249), Figure 89 (SEQ ID NO:254), Figure 91 (SEQ ID NO:256), Figure 93 (SEQ ID NO:258), Figure 95 (SEQ ID NO:260), Figure 97 (SEQ ID NO:262), Figure 99 (SEQ ID NO:284), Figure 101 (SEQ ID NO:289), Figure 103 (SEQ ID NO:291), Figure 105 (SEQ ID NO:293), Figure 107 (SEQ ID NO:309), Figure 109 (SEQ ID NO:314), Figure 111 (SEQ ID NO:319), Figure 113 (SEQ ID NO:324), Figure 115 (SEQ ID NO:331), Figure 117 (SEQ ID NO:338), Figure 119 (SEQ ID NO:340), Figure 121 (SEQ ID NO:376) and Figure 123 (SEQ ID NO:422), or the complement thereof.
4. Isolated nucleic acid which comprises the full-length coding sequence of the DNA deposited under accession number ATCC 209258, ATCC 209256, ATCC 209264, ATCC 209250, ATCC 209375, ATCC 209378, ATCC 209384, ATCC 209396, ATCC 209420, ATCC 209480, ATCC 209265, ATCC 209257, ATCC 209262, ATCC 209253, ATCC 209402, ATCC 209401, ATCC 209397, ATCC 209400, ATCC 209385, ATCC 209367, ATCC 209432, ATCC 209263, ATCC 209251, ATCC 209255, ATCC 209252, ATCC 209373, ATCC 209370, ATCC 209523, ATCC 209372, ATCC 209374, ATCC 209373, ATCC 209382, ATCC 209383, ATCC 209403, ATCC 209398, ATCC 209399, ATCC 209392, ATCC 209387, ATCC 209388, ATCC 209394, ATCC 209421, ATCC 209393, ATCC 209418, ATCC 209485, ATCC 209483, ATCC 209482, ATCC 209491, ATCC 209481, ATCC 209438, ATCC 209927, ATCC 209439, ATCC 209489, ATCC 209433, ATCC 209488, ATCC 209434, ATCC 209395, ATCC 209486, ATCC 209490, ATCC 209484, ATCC 209371 or ATCC 203553.
5. A vector comprising the nucleic acid of Claim 1.
6. The vector of Claim 5 operably linked to control sequences recognized by a host cell transformed with the vector.
7. A host cell comprising the vector of Claim 5.
8. The host cell of Claim 7 wherein said cell is a CHO cell.
9. The host cell of Claim 7 wherein said cell is an E. coli.
10. The host cell of Claim 7 wherein said cell is a yeast cell.
11. A process for producing a PRO polypeptides comprising culmring the host cell of Claim 7 under conditions suitable for expression of said PRO polypeptide and recovering said PRO polypeptide from the cell culmre.
12. Isolated native sequence PRO polypeptide having at least 80% sequence identity to an amino acid sequence selected from the group consisting of the amino acid sequence shown in Figure 2 (SEQ ID NO: 2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO: 12), Figure 9 (SEQ ID NO: 18), Figure 11 (SEQ ID NO:23), Figure 13 (SEQ ID NO:28), Figure 15 (SEQ ID NO:34), Figure 17 (SEQ ID NO:39), Figure 19 (SEQ ID NO:49), Figure 22 (SEQ ID NO:59), Figure 24 (SEQ ID NO:64), Figure 26 (SEQ ID NO:69), Figure 28 (SEQ ID NO:71), Figure 30 (SEQ ID NO:73), Figure 32 (SEQ ID NO:84), Figure 34 (SEQ ID NO:91), Figure 36 (SEQ ID NO:96), Figure 38 (SEQ ID NO: 104), Figure 40 (SEQ ID NO: 109), Figure 42 (SEQ ID NO: 114), Figure 44 (SEQ ID NO: 119), Figure 46 (SEQ ID NO: 127), Figure 48 (SEQ ID NO: 132), Figure 50 (SEQ ID NO: 137), Figure 52 (SEQ ID NO: 142), Figure 54 (SEQ ID NO: 148), Figure 56 (SEQ ID NO: 153), Figure 58 (SEQ ID NO: 159), Figure 60 (SEQ ID NO: 164), Figure 62 (SEQ ID NO: 170), Figure 64 (SEQ ID NO: 175), Figure 66 (SEQ ID NO: 177), Figure 68 (SEQ ID NO: 185), Figure 70 (SEQ ID NO: 190), Figure 72 (SEQ ID NO: 195), Figure 74 (SEQ ID NO:201), Figure 76 (SEQ ID NO:207), Figure 78 (SEQ ID NO:213), Figure 80 (SEQ ID NO:221), Figure 82 (SEQ ID NO:227), Figure 84 (SEQ ID NO:236), Figure 86 (SEQ ID NO:245), Figure 88 (SEQ ID NO:250), Figure 90 (SEQ ID NO:255), Figure 92 (SEQ ID NO:257), Figure 94 (SEQ ID NO:259), Figure 96 (SEQ ID NO:261), Figure 98 (SEQ ID NO:263), Figure 100 (SEQ ID NO:285), Figure 102 (SEQ ID NO:290), Figure 104 (SEQ ID NO:292), Figure 106 (SEQ ID NO:294), Figure 108 (SEQ ID NO:310), Figure 110 (SEQ ID NO:315), Figure 112 (SEQ ID NO:320), Figure 114 (SEQ ID NO:325), Figure 116 (SEQ ID NO:332), Figure 118 (SEQ ID NO:339), Figure 120 (SEQ ID NO:341), Figure 122 (SEQ ID NO:377) and Figure 124 (SEQ ID NO:423).
13. Isolated PRO polypeptide having at least 80% sequence identity to the amino acid sequence encoded by the nucleotide deposited under accession number ATCC 209258, ATCC 209256, ATCC 209264, ATCC 209250, ATCC 209375, ATCC 209378, ATCC 209384, ATCC 209396, ATCC 209420, ATCC 209480, ATCC 209265, ATCC 209257, ATCC 209262, ATCC 209253, ATCC 209402, ATCC 209401, ATCC 209397, ATCC 209400, ATCC 209385, ATCC 209367, ATCC 209432, ATCC 209263, ATCC 209251 , ATCC 209255, ATCC 209252, ATCC 209373, ATCC 209370, ATCC 209523, ATCC 209372, ATCC 209374, ATCC 209373, ATCC 209382, ATCC 209383, ATCC 209403, ATCC 209398, ATCC 209399, ATCC 209392, ATCC 209387, ATCC 209388, ATCC 209394, ATCC 209421 , ATCC 209393, ATCC 209418, ATCC 209485, ATCC 209483, ATCC 209482, ATCC 209491 , ATCC 209481 , ATCC 209438, ATCC 209927, ATCC 209439, ATCC 209489, ATCC 209433, ATCC 209488, ATCC 209434, ATCC 209395, ATCC 209486, ATCC 209490, ATCC 209484, ATCC 209371 or ATCC 203553.
14. A chimeric molecule comprising a polypeptide according to Claim 12 fused to a heterologous amino acid sequence.
15. The chimeric molecule of Claim 14 wherein said heterologous amino acid sequence is an epitope tag sequence.
16. The chimeric molecule of Claim 14 wherein said heterologous amino acid sequence is a Fc region of an immunoglobulin.
17. An antibody which specifically binds to a PRO polypeptide according to Claim 12.
18. The antibody of Claim 17 wherein said antibody is a monoclonal antibody.
19. Isolated nucleic acid having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 2 (SEQ ID NO: 2), Figure 4
(SEQ ID NO:4), Figure 6 (SEQ ID NO: 12), Figure 9 (SEQ ID NO: 18), Figure 11 (SEQ ID NO:23), Figure 13 (SEQ ID NO:28), Figure 15 (SEQ ID NO:34), Figure 17 (SEQ ID NO:39), Figure 19 (SEQ ID NO:49), Figure 22 (SEQ ID NO:59), Figure 24 (SEQ ID NO:64), Figure 26 (SEQ ID NO:69), Figure 28 (SEQ ID NO:71), Figure 30 (SEQ ID NO:73), Figure 32 (SEQ ID NO:84), Figure 34 (SEQ ID NO:91), Figure 36 (SEQ ID NO:96), Figure 38 (SEQ ID NO: 104), Figure 40 (SEQ ID NO: 109), Figure 42 (SEQ ID NO: 114), Figure 44 (SEQ ID NO: 119), Figure 46 (SEQ ID NO: 127), Figure 48 (SEQ ID NO: 132), Figure 50 (SEQ ID NO: 137), Figure 52 (SEQ ID NO: 142), Figure 54 (SEQ ID NO: 148), Figure 56 (SEQ ID NO: 153), Figure 58 (SEQ ID NO: 159), Figure 60 (SEQ ID NO: 164), Figure 62 (SEQ ID NO: 170), Figure 64 (SEQ ID NO: 175), Figure 66 (SEQ ID NO: 177), Figure 68 (SEQ ID NO: 185), Figure 70 (SEQ ID NO: 190), Figure 72 (SEQ ID NO: 195), Figure 74 (SEQ ID NO:201), Figure 76 (SEQ ID NO:207), Figure 78 (SEQ ID NO:213), Figure 80 (SEQ ID NO:221), Figure 82 (SEQ ID NO:227), Figure 84 (SEQ ID NO:236), Figure 86 (SEQ ID NO:245), Figure 88 (SEQ ID NO:250), Figure 90 (SEQ ID NO:255), Figure 92 (SEQ ID NO:257), Figure 94 (SEQ ID NO:259), Figure 96 (SEQ ID NO:261), Figure 98 (SEQ ID NO:263), Figure 100 (SEQ ID NO:285), Figure 102 (SEQ ID NO:290), Figure 104 (SEQ ID NO:292), Figure 106 (SEQ ID NO:294), Figure 108 (SEQ ID NO:310), Figure 110 (SEQ ID NO:315), Figure 112 (SEQ ID NO:320), Figure 114 (SEQ ID NO:325), Figure 116 (SEQ ID NO:332), Figure 118 (SEQ ID NO:339), Figure 120 (SEQ ID NO:341), Figure 122 (SEQ ID NO:377) or Figure 124 (SEQ ID NO:423), lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO: 12), Figure 9 (SEQ ID NO: 18), Figure 11 (SEQ ID NO:23), Figure 13 (SEQ ID NO:28), Figure 15 (SEQ ID NO:34), Figure 17 (SEQ ID NO:39), Figure 19 (SEQ ID NO:49), Figure 22 (SEQ ID NO:59), Figure 24 (SEQ ID NO:64), Figure 26 (SEQ ID NO:69), Figure 28 (SEQ ID NO:71), Figure 30 (SEQ ID NO:73), Figure 32 (SEQ ID NO:84), Figure 34 (SEQ ID NO:91), Figure 36 (SEQ ID NO:96), Figure 38 (SEQ ID NO: 104), Figure 40 (SEQ ID NO: 109), Figure 42 (SEQ ID NO: l 14), Figure 44 (SEQ ID NO: 119), Figure 46 (SEQ ID NO: 127), Figure 48 (SEQ ID NO: 132), Figure 50 (SEQ ID NO: 137), Figure 52 (SEQ ID NO: 142), Figure 54 (SEQ ID NO: 148), Figure 56 (SEQ ID NO: 153), Figure 58 (SEQ ID NO: 159), Figure 60 (SEQ ID NO: 164), Figure 62 (SEQ ID NO: 170), Figure 64 (SEQ ID NO: 175), Figure 66 (SEQ ID NO: 177), Figure 68 (SEQ ID NO: 185), Figure 70 (SEQ ID NO: 190), Figure 72 (SEQ ID NO: 195), Figure 74 (SEQ ID NO:201), Figure 76 (SEQ ID NO:207), Figure 78 (SEQ ID NO:213), Figure 80 (SEQ ID NO:221), Figure 82 (SEQ ID NO:227), Figure 84 (SEQ ID NO:236), Figure 86 (SEQ ID NO:245), Figure 88 (SEQ ID NO:250), Figure 90 (SEQ ID NO:255), Figure 92 (SEQ ID NO:257), Figure 94 (SEQ ID NO:259), Figure 96 (SEQ ID NO:261), Figure 98 (SEQ ID NO:263), Figure 100 (SEQ ID NO:285), Figure 102 (SEQ ID NO:290), Figure 104 (SEQ ID NO:292), Figure 106 (SEQ ID NO:294), Figure 108 (SEQ ID NO:310), Figure 110 (SEQ ID NO:315), Figure 112 (SEQ ID NO:320), Figure 114 (SEQ ID NO:325), Figure 116 (SEQ ID NO:332), Figure 118 (SEQ ID NO:339), Figure 120 (SEQ ID NO:341), Figure 122 (SEQ ID NO:377) or Figure 124 (SEQ ID NO:423), with its associated signal peptide; or
(c) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO: 12), Figure 9 (SEQ ID NO: 18), Figure 11 (SEQ ID NO:23), Figure 13 (SEQ ID NO:28), Figure 15 (SEQ ID NO:34), Figure 17 (SEQ ID NO:39), Figure 19 (SEQ ID NO:49), Figure 22 (SEQ ID NO:59), Figure 24 (SEQ ID NO:64), Figure 26 (SEQ ID NO:69), Figure 28 (SEQ ID NO:71), Figure 30 (SEQ ID NO:73), Figure 32 (SEQ ID NO:84), Figure 34 (SEQ ID NO:91), Figure 36 (SEQ ID NO:96), Figure 38 (SEQ ID NO: 104), Figure 40 (SEQ ID NO: 109), Figure 42 (SEQ ID NO: 114), Figure 44 (SEQ ID NO: 119), Figure 46 (SEQ ID NO: 127), Figure 48 (SEQ ID NO: 132), Figure 50 (SEQ ID NO: 137), Figure 52 (SEQ ID NO: 142), Figure 54 (SEQ ID NO: 148), Figure 56 (SEQ ID NO: 153), Figure 58 (SEQ ID NO: 159), Figure 60 (SEQ ID NO: 164), Figure 62 (SEQ ID NO: 170), Figure 64 (SEQ ID NO: 175), Figure 66 (SEQ ID NO: 177), Figure 68 (SEQ ID NO: 185), Figure 70 (SEQ ID NO: 190), Figure 72 (SEQ ID NO: 195), Figure 74 (SEQ ID NO:201), Figure 76 (SEQ ID NO:207), Figure 78 (SEQ ID NO:213), Figure 80 (SEQ ID NO:221), Figure 82 (SEQ ID NO:227), Figure 84 (SEQ ID NO:236), Figure 86 (SEQ ID NO:245), Figure 88 (SEQ ID NO:250), Figure 90 (SEQ ID NO:255), Figure 92 (SEQ ID NO:257), Figure 94 (SEQ ID NO:259), Figure 96 (SEQ ID NO:261), Figure 98 (SEQ ID NO:263), Figure 100 (SEQ ID NO:285), Figure 102 (SEQ ID NO:290), Figure 104 (SEQ ID NO:292), Figure 106 (SEQ ID NO:294), Figure 108 (SEQ ID NO:310), Figure 110 (SEQ ID NO:315), Figure 112 (SEQ ID NO:320), Figure 114 (SEQ ID NO:325), Figure 116 (SEQ ID NO:332), Figure 118 (SEQ ID NO:339), Figure 120 (SEQ ID NO:341), Figure 122 (SEQ ID NO:377) or Figure 124 (SEQ ID NO:423), lacking its associated signal peptide.
20. An isolated polypeptide having at least 80% amino acid sequence identity to:
(a) the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO: 12), Figure 9 (SEQ ID NO: 18), Figure 11 (SEQ ID NO:23), Figure 13 (SEQ ID NO:28), Figure 15 (SEQ ID NO:34), Figure 17 (SEQ ID NO:39), Figure 19 (SEQ ID NO:49), Figure 22 (SEQ ID NO:59), Figure 24 (SEQ ID NO:64), Figure 26 (SEQ ID NO:69), Figure 28 (SEQ ID NO:71), Figure 30 (SEQ ID NO:73), Figure 32 (SEQ ID NO:84), Figure 34 (SEQ ID NO:91), Figure 36 (SEQ ID NO:96), Figure 38 (SEQ ID NO: 104), Figure 40 (SEQ ID NO: 109), Figure 42 (SEQ ID NO: 114), Figure 44 (SEQ ID NO: 119), Figure 46 (SEQ ID NO: 127), Figure 48 (SEQ ID NO: 132), Figure 50 (SEQ ID NO: 137), Figure 52 (SEQ ID NO: 142), Figure 54 (SEQ ID NO: 148), Figure 56 (SEQ ID NO: 153), Figure 58 (SEQ ID NO: 159), Figure 60 (SEQ ID NO: 164), Figure 62 (SEQ ID NO: 170), Figure 64 (SEQ ID NO: 175), Figure 66 (SEQ ID NO: 177), Figure 68 (SEQ ID NO: 185), Figure 70 (SEQ ID NO: 190), Figure 72 (SEQ ID NO: 195), Figure 74 (SEQ ID NO:201), Figure 76 (SEQ ID NO:207), Figure 78 (SEQ ID NO:213), Figure 80 (SEQ ID NO:221), Figure 82 (SEQ ID NO:227), Figure 84 (SEQ ID NO:236), Figure 86 (SEQ ID NO:245), Figure 88 (SEQ ID NO:250), Figure 90 (SEQ ID NO:255), Figure 92 (SEQ ID NO:257), Figure 94 (SEQ ID NO:259), Figure 96 (SEQ ID NO:261), Figure 98 (SEQ ID NO:263), Figure 100 (SEQ ID NO:285), Figure 102 (SEQ ID NO:290), Figure 104 (SEQ ID NO:292), Figure 106 (SEQ ID NO:294), Figure 108 (SEQ ID NO:310), Figure 110 (SEQ ID NO:315), Figure 112 (SEQ ID NO:320), Figure 114 (SEQ ID NO:325), Figure 116 (SEQ ID NO:332), Figure 118 (SEQ ID NO:339), Figure 120 (SEQ ID NO:341), Figure 122 (SEQ ID NO:377) or Figure 124 (SEQ ID NO:423), lacking its associated signal peptide;
(b) an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO: 12), Figure 9 (SEQ ID NO: 18), Figure 11 (SEQ ID NO:23), Figure 13 (SEQ
ID NO:28), Figure 15 (SEQ ID NO:34), Figure 17 (SEQ ID NO:39), Figure 19 (SEQ ID NO:49), Figure 22 (SEQ ID NO:59), Figure 24 (SEQ ID NO:64), Figure 26 (SEQ ID NO:69), Figure 28 (SEQ ID NO:71), Figure 30 (SEQ ID NO:73), Figure 32 (SEQ ID NO:84), Figure 34 (SEQ ID NO:91), Figure 36 (SEQ ID NO:96), Figure 38 (SEQ ID NO: 104), Figure 40 (SEQ ID NO: 109), Figure 42 (SEQ ID NO: 114), Figure 44 (SEQ ID NO: 119), Figure 46 (SEQ ID NO: 127), Figure 48 (SEQ ID NO: 132), Figure 50 (SEQ ID NO: 137), Figure 52 (SEQ ID NO: 142), Figure 54 (SEQ ID NO: 148), Figure 56 (SEQ ID NO: 153), Figure 58 (SEQ ID NO: 159), Figure 60 (SEQ ID NO: 164), Figure 62 (SEQ ID NO: 170), Figure 64 (SEQ ID NO: 175), Figure 66 (SEQ ID NO: 177), Figure 68 (SEQ ID NO: 185), Figure 70 (SEQ ID NO: 190), Figure 72 (SEQ ID NO: 195), Figure 74 (SEQ ID NO:201), Figure 76 (SEQ ID NO:207), Figure 78 (SEQ ID NO:213), Figure 80 (SEQ ID NO:221), Figure 82 (SEQ ID NO:227), Figure 84 (SEQ ID NO:236), Figure 86 (SEQ ID NO:245), Figure 88 (SEQ ID NO:250), Figure 90 (SEQ ID NO:255), Figure 92 (SEQ ID NO:257), Figure 94 (SEQ ID NO:259), Figure 96 (SEQ ID NO:261), Figure 98 (SEQ ID NO:263), Figure 100 (SEQ ID NO:285), Figure 102 (SEQ ID NO:290), Figure 104 (SEQ ID NO:292), Figure 106 (SEQ ID NO:294), Figure 108 (SEQ ID NO:310), Figure 110 (SEQ ID NO:315), Figure 112 (SEQ ID NO:320), Figure 114 (SEQ ID NO:325), Figure 116 (SEQ ID NO:332), Figure 118 (SEQ ID NO:339), Figure 120 (SEQ ID NO:341), Figure 122 (SEQ ID NO:377) or Figure 124 (SEQ ID NO:423), with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ
ID NO:4), Figure 6 (SEQ ID NO: 12), Figure 9 (SEQ ID NO: 18), Figure 11 (SEQ ID NO:23), Figure 13 (SEQ ID NO:28), Figure 15 (SEQ ID NO:34), Figure 17 (SEQ ID NO:39), Figure 19 (SEQ ID NO:49), Figure 22 (SEQ ID NO:59), Figure 24 (SEQ ID NO:64), Figure 26 (SEQ ID NO:69), Figure 28 (SEQ ID NO:71), Figure 30 (SEQ ID NO:73), Figure 32 (SEQ ID NO:84), Figure 34 (SEQ ID NO:91), Figure 36 (SEQ ID NO:96), Figure 38 (SEQ ID NO: 104), Figure 40 (SEQ ID NO: 109), Figure 42 (SEQ ID NO: 114), Figure 44 (SEQ ID NO: 119), Figure 46 (SEQ ID NO: 127), Figure 48 (SEQ ID NO: 132), Figure 50 (SEQ ID NO: 137), Figure 52 (SEQ ID NO: 142), Figure 54 (SEQ ID NO: 148), Figure 56 (SEQ ID NO: 153), Figure 58 (SEQ ID NO: 159), Figure 60 (SEQ ID NO: 164), Figure 62 (SEQ ID NO: 170), Figure 64 (SEQ ID NO: 175), Figure 66 (SEQ ID NO: 177), Figure 68 (SEQ ID NO: 185), Figure 70 (SEQ ID NO: 190), Figure 72 (SEQ ID NO: 195), Figure 74 (SEQ ID NO:201), Figure 76 (SEQ ID NO:207), Figure 78 (SEQ ID NO:213), Figure 80 (SEQ ID NO:221), Figure 82 (SEQ ID NO:227), Figure 84 (SEQ ID NO:236), Figure 86 (SEQ ID NO:245), Figure 88 (SEQ ID NO:250), Figure 90 (SEQ ID NO:255), Figure 92 (SEQ ID NO:257), Figure 94 (SEQ ID NO:259), Figure 96 (SEQ ID NO:261), Figure 98 (SEQ ID NO:263), Figure 100 (SEQ ID NO:285), Figure 102 (SEQ ID NO:290), Figure 104 (SEQ ID NO:292), Figure 106 (SEQ ID NO:294), Figure 108 (SEQ ID NO:310), Figure 1 10 (SEQ ID NO:315), Figure 112 (SEQ ID NO:320), Figure 114 (SEQ ID NO:325), Figure 116 (SEQ ID NO:332), Figure 118 (SEQ ID NO:339), Figure 120 (SEQ ID NO:341), Figure 122 (SEQ ID NO:377) or Figure 124 (SEQ ID NO: 423), lacking its associated signal peptide.
21. A method of detecting a PR0245 polypeptide in a sample suspected of containing a PR0245 polypeptide, said method comprising contacting said sample with a PRO 1868 polypeptide and determining the formation of a PR0245 /PRO 1868 polypeptide conjugate in said sample, wherein the formation of said conjugate is indicative of the presence of a PR0245 polypeptide in said sample.
22. The method according to Claim 21 , wherein said sample comprises cells suspected of expressing said PR0245 polypeptide.
23. The method according to Claim 21 , wherein said PRO 1868 polypeptide is labeled with a detectable label.
24. The method according to Claim 21, wherein said PR01868 polypeptide is attached to a solid support.
25. A method of detecting a PRO 1868 polypeptide in a sample suspected of containing a PRO 1868 polypeptide, said method comprising contacting said sample with a PR0245 polypeptide and determining the formation of a PR0245/PR01868 polypeptide conjugate in said sample, wherein the formation of said conjugate is indicative of the presence of a PRO 1868 polypeptide in said sample.
26. The method according to Claim 25, wherein said sample comprises cells suspected of expressing said PRO 1868 polypeptide.
27. The method according to Claim 25, wherein said PR0245 polypeptide is labeled with a detectable label.
28. The method according to Claim 25, wherein said PR0245 polypeptide is attached to a solid support.
29. A method of linking a bioactive molecule to a cell expressing a PR0245 polypeptide, said method comprising contacting said cell with a PR01868 polypeptide that is bound to said bioactive molecule and allowing said PR0245 and PRO 1868 polypeptides to bind to one another, thereby linking said bioactive molecules to said cell.
30. The method according to Claim 29, wherein said bioactive molecule is a toxin, a radiolabel or an antibody.
31. The method according to Claim 29, wherein said bioactive molecule causes the death of said cell.
32. A method of linking a bioactive molecule to a cell expressing a PRO 1868 polypeptide, said method comprising contacting said cell with a PR0245 polypeptide that is bound to said bioactive molecule and allowing said PR0245 and PRO 1868 polypeptides to bind to one another, thereby linking said bioactive molecules to said cell.
33. The method according to Claim 32, wherein said bioactive molecule is a toxin, a radiolabel or an antibody.
34. The method according to Claim 32, wherein said bioactive molecule causes the death of said cell.
35. A method of modulating at least one biological activity of a cell expressing a PR0245 polypeptide, said method comprising contacting said cell with a PRO 1868 polypeptide or an anti-PR0245 antibody, whereby said PRO 1868 polypeptide or said anti-PR0245 antibody binds to said PR0245 polypeptide, thereby modulating at least one biological activity of said cell.
36. The method according to Claim 35, wherein said cell is killed.
37. A method of modulating at least one biological activity of a cell expressing a PRO 1868 polypeptide, said method comprising contacting said cell with a PR0245 polypeptide or an anti-PR01868 antibody , whereby said PR0245 polypeptide or said anti-PRO 1868 antibody binds to said PRO 1868 polypeptide , thereby modulating at least one biological activity of said cell.
38. The method according to Claim 37, wherein said cell is killed.
PCT/US2000/004414 1994-09-08 2000-02-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same WO2001004311A1 (en)

Priority Applications (781)

Application Number Priority Date Filing Date Title
AU28839/00A AU2883900A (en) 1999-07-07 2000-02-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2000603378A JP2003531811A (en) 1999-03-08 2000-02-24 Promotion or inhibition of angiogenesis and cardiovascularization
KR1020017011378D KR20010104373A (en) 1999-03-08 2000-02-24 Promotion or Inhibition of Angiogenesis and Cardiovascularization
CA002361849A CA2361849A1 (en) 1999-03-08 2000-02-24 Promotion or inhibition of angiogenesis and cardiovascularization
EP00912015A EP1159419A1 (en) 1999-03-08 2000-02-24 Promotion or inhibition of angiogenesis and cardiovascularization
PCT/US2000/005004 WO2000053757A2 (en) 1999-03-08 2000-02-24 Promotion or inhibition of angiogenesis and cardiovascularization
AU33816/00A AU768694B2 (en) 1999-03-08 2000-02-24 Promotion or inhibition of angiogenesis and cardiovascularization
KR1020017011378A KR100553300B1 (en) 1999-03-08 2000-02-24 Promotion or Inhibition of Angiogenesis and Cardiovascularization
EP00913764A EP1220905A2 (en) 1999-03-08 2000-03-02 Composition and methods for the treatment of immune related diseases
JP2000603379A JP2004516227A (en) 1999-03-08 2000-03-02 Compositions and methods for treating immune-related diseases
CA002362427A CA2362427A1 (en) 1999-03-08 2000-03-02 Compositions and methods for the treatment of immune related diseases
KR1020017011406A KR20010103046A (en) 1999-03-08 2000-03-02 Compositions and Methods for the Treatment of Immune Related Diseases
PCT/US2000/005841 WO2000053758A2 (en) 1999-03-08 2000-03-02 Compositions and methods for the treatment of immune related diseases
AU35144/00A AU3514400A (en) 1999-03-08 2000-03-02 Compositions and methods for the treatment of immune related diseases
CA002384089A CA2384089A1 (en) 1999-09-08 2000-03-09 Fibroblast growth factor-19 (fgf-19) nucleic acids and polypeptides and methods of use for the treatment of obesity
ES00917878T ES2264929T3 (en) 1999-09-08 2000-03-09 NUCLEIC AND POLYPEPTIDE ACIDS OF FIBROBLASTIC GROWTH FACTOR 19 (FGF-19) AND PROCEDURES OF USE FOR THE TREATMENT OF OBESITY.
KR1020027003131A KR20020059591A (en) 1997-10-27 2000-03-09 Fibroblast Growth Factor-19 (FGF-19) Nucleic acid and Polypeptides and Methods of Use for the Treatment of Obesity
PT00917878T PT1214409E (en) 1999-09-08 2000-03-09 NUCLEIC AND POLYETHYDID ACIDS OF THE FIBROBLAST-GROWTH FACTOR-19 (FGF-19) AND METHODS OF USE FOR THE TREATMENT OF OBESITY
SI200030879T SI1214409T1 (en) 1999-09-08 2000-03-09 Fibroblast growth factor-19 (fgf-19) nucleic acids and polypeptides and methods of use for the treatment of obesity
JP2001521746A JP2004500037A (en) 1999-09-08 2000-03-09 Fibroblast growth factor-19 (FGF-19) nucleic acids and polypeptides and methods of use for treating obesity
MXPA02002491A MXPA02002491A (en) 1999-09-08 2000-03-09 Fibroblast growth factor 19 (fgf 19) nucleic acids and polypeptides and methods of use for the treatment of obesity.
AT00917878T ATE326532T1 (en) 1999-09-08 2000-03-09 FIBROBLAST GROWTH FACTOR-19 (FGF-19) NUCLEIC ACID AND POLYPEPTIDES AND METHOD OF USE THEREOF FOR TREATING OBESITY
DE60028054T DE60028054T2 (en) 1999-09-08 2000-03-09 FIBROBLAST GROWTH FACTOR-19 (FGF-19) NUCLEIC ACID AND POLYPEPTIDES AND METHOD FOR THE USE THEREOF FOR THE TREATMENT OF FATIBILITY
CNA2004100465359A CN1560249A (en) 1999-09-08 2000-03-09 Fibroblast growth factor-19 (FGF-19) nucleic acids and polypeptides and methods of use for the treatment of obesity
CN00815274A CN1387570A (en) 1999-09-08 2000-03-09 Fibroblast growth factor-19 (FGF-19) nucleic acids and polypeptides and methods of use for treatment of obesity
EP00917878A EP1214409B1 (en) 1999-09-08 2000-03-09 Fibroblast growth factor-19 (fgf-19) nucleic acids and polypeptides and methods of use for the treatment of obesity
AU38784/00A AU783117B2 (en) 1999-09-08 2000-03-09 Fibroblast growth factor-19 (FGF-19) nucleic acids and polypeptides and methods of use for the treatment of obesity
IL14818800A IL148188A0 (en) 1999-09-08 2000-03-09 Fibroblast growth factor-19 (fgf-19) nucleic acids and polypeptides and methods of use for the treatment of obesity
PCT/US2000/006471 WO2001018210A1 (en) 1999-09-08 2000-03-09 Fibroblast growth factor-19 (fgf-19) nucleic acids and polypeptides and methods of use for the treatment of obesity
DK00917878T DK1214409T3 (en) 1999-09-08 2000-03-09 Fibroblast Growth Factor-19 (FGF-19) Nucleic Acids and Polypeptides and Methods of Use for the Treatment of Obesity
AT00916675T ATE478145T1 (en) 1999-06-02 2000-03-30 SECRETED AND TRANSMEMBRANE POLYPEPTIDES AND NUCLEIC ACIDS CODING THEREFOR
CA002383254A CA2383254A1 (en) 1999-06-02 2000-03-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2001500766A JP2004522402A (en) 1999-06-02 2000-03-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP00916675A EP1210418B1 (en) 1999-06-02 2000-03-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
AU37743/00A AU3774300A (en) 1999-06-02 2000-03-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
PCT/US2000/008439 WO2000073454A1 (en) 1999-06-02 2000-03-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP07025116A EP1953173B1 (en) 1999-06-15 2000-05-22 Secreted and transmembrane polypeptides and nucleic acids endoding the same
AT07025118T ATE448246T1 (en) 1999-06-15 2000-05-22 SECRETED AND TRANSMEMBRANE POLYPEPTIDES AND NUCLEIC ACIDS FOR THE ENCODING THEM
CA2372511A CA2372511C (en) 1999-06-15 2000-05-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP07025118A EP1956030B1 (en) 1999-06-15 2000-05-22 Secreted and transmembrane polypeptides and nucleic acids endoding the same
JP2001503894A JP2003529324A (en) 1999-06-15 2000-05-22 Secreted and transmembrane polypeptides and nucleic acids encoding them
EP00936172A EP1208195A2 (en) 1999-06-15 2000-05-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same
AU51527/00A AU5152700A (en) 1999-06-15 2000-05-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same
AT07025116T ATE449109T1 (en) 1999-06-15 2000-05-22 SECRETED AND TRANSMEMBRANE POLYPEPTIDES AND NUCLEIC ACIDS FOR THE ENCODING THEM
EP07025117A EP1978029A3 (en) 1999-06-15 2000-05-22 Secreted and transmembrane polypeptides and nucleic acids endoding the same
PCT/US2000/014042 WO2000077037A2 (en) 1999-06-15 2000-05-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same
PCT/US2000/015264 WO2000073452A2 (en) 1999-06-02 2000-06-02 Compositions and methods for the treatment of immune related diseases
PCT/US2000/020710 WO2001009327A2 (en) 1999-07-28 2000-07-28 Method of preventing the injury or death of retinal cells and treating ocular diseases
AU63910/00A AU6391000A (en) 1999-07-28 2000-07-28 Method of preventing the injury or death of retinal cells and treating ocular diseases
EP05019540A EP1621620A3 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP00964919A EP1208202A2 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP05019536A EP1623991A3 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP05019538A EP1623992A3 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
CA002645727A CA2645727A1 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
CA002380355A CA2380355A1 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
ES05019537T ES2341257T3 (en) 1999-09-01 2000-08-24 SECRETED AND TRANSMEMBRANE POLIPEPTIDES AND NUCLEIC ACIDS THAT CODE THEM.
EP07019808A EP1892249A1 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
AT05019537T ATE459645T1 (en) 1999-09-01 2000-08-24 SECRETED POLYPEPTIDES AND TRANSMEMBRANE POLYPEPTIDES AND NUCLEIC ACIDS CODING THEREFOR
EP05019537A EP1637541B1 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP05019539A EP1623993A3 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
AU75730/00A AU7573000A (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
DE60043951T DE60043951D1 (en) 1999-09-01 2000-08-24 Secreted polypeptides and transmembrane polypeptides and nucleic acids coding therefor
PCT/US2000/023328 WO2001016318A2 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2001520864A JP3951035B2 (en) 1999-09-01 2000-08-24 Secreted and transmembrane polypeptides and nucleic acids encoding them
CA002490853A CA2490853A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
CA002391455A CA2391455A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
CA002490909A CA2490909A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP06000588A EP1690873A3 (en) 1999-12-01 2000-12-01 Composition and methods for the diagnosis of tumours
EP06000587A EP1690872A3 (en) 1999-12-01 2000-12-01 Composition and methods for the diagnosis of tumours
EP06000589A EP1661997A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
CA002492049A CA2492049A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
CA002492070A CA2492070A1 (en) 1999-12-01 2000-12-01 Lung tumor marker pro4329 polypeptides and nucleic acids encoding the same
CA002494705A CA2494705A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP06000585A EP1661996A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP06000586A EP1688497A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP06000581A EP1666494A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
CA002491258A CA2491258A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
CA2709291A CA2709291A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2001542531A JP2004522404A (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding them
CA002491433A CA2491433A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP05025102A EP1672070A3 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP10005292A EP2228446A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptieds and nucleic acids encoding the same
EP06000584A EP1669371A3 (en) 1999-12-01 2000-12-01 Composition and methods for the diagnosis of tumours
CA002496312A CA2496312A1 (en) 1999-12-01 2000-12-01 Colon tumour marker pro4799 polypeptides and nucleic acids encoding the same
EP06000582A EP1666495A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
CA002491610A CA2491610A1 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP00983846A EP1250426A2 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding same
PCT/US2000/032678 WO2001040466A2 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
EP06000583A EP1686134A3 (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
AU20554/01A AU2055401A (en) 1999-12-01 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/767,609 US20020042367A1 (en) 1997-11-25 2001-01-22 Fibroblast growth factor-19 (FGF-19) nucleic acids and polypeptides and methods of use for the treatment of obesity and related disorders
US09/828,366 US20020010137A1 (en) 1997-09-18 2001-04-05 Methods and compositions for inhibiting neoplastic cell growth
US09/866,028 US6642360B2 (en) 1997-12-03 2001-05-25 Secreted polypeptides that stimulate release of proteoglycans from cartilage
US09/902,692 US20030054400A1 (en) 1997-09-17 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,979 US20030113718A1 (en) 1997-09-17 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,572 US20030108983A1 (en) 1997-09-17 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,759 US20030077654A1 (en) 1997-09-17 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,713 US20030082541A1 (en) 1997-09-17 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,615 US20030092002A1 (en) 1997-09-17 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,903 US20030044839A1 (en) 1997-09-17 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,853 US20020192659A1 (en) 1997-09-17 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,775 US6686451B1 (en) 1997-10-24 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,736 US20030049676A1 (en) 1997-09-17 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,634 US20030082540A1 (en) 1997-09-17 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/902,736 US6894148B2 (en) 1997-11-12 2001-07-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/903,603 US20030148419A1 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/903,806 US20030130489A1 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,119 US20030049621A1 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids enconding the same
US09/903,603 US6767995B2 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/903,786 US20030044793A1 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/903,640 US7208308B2 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/903,520 US20030054401A1 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/903,749 US7147853B2 (en) 1997-09-17 2001-07-11 Anti-pro211 polypeptide antibodies
US09/904,011 US20030003530A1 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/903,925 US20030096233A1 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/903,562 US6965015B2 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/903,823 US20030104381A1 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/903,943 US20030054349A1 (en) 1997-09-17 2001-07-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/905,291 US20020160374A1 (en) 1997-09-17 2001-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/905,056 US20030054441A1 (en) 1997-09-17 2001-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,766 US20030152999A1 (en) 1997-09-17 2001-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,992 US20030135025A1 (en) 1997-09-17 2001-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,786 US7557192B2 (en) 1997-09-17 2001-07-12 Anti-PRO335 antibodies
US09/904,859 US20030036060A1 (en) 1997-09-17 2001-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,805 US20030211568A1 (en) 1997-10-27 2001-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,938 US20030211569A1 (en) 1997-09-17 2001-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/905,125 US6664376B2 (en) 1997-09-17 2001-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,877 US20030186358A1 (en) 1997-09-17 2001-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/905,088 US20030073077A1 (en) 1997-09-17 2001-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,485 US20030064367A1 (en) 1997-09-17 2001-07-13 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,462 US6878807B2 (en) 1997-09-17 2001-07-13 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/905,075 US7169906B2 (en) 1997-09-17 2001-07-13 PRO211 polypeptides
US09/904,920 US6806352B2 (en) 1997-09-17 2001-07-13 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/905,449 US6965011B2 (en) 1997-09-17 2001-07-13 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/905,381 US6818746B2 (en) 1997-09-17 2001-07-13 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,553 US20030059828A1 (en) 1997-09-17 2001-07-13 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,820 US20030036094A1 (en) 1997-09-17 2001-07-13 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,532 US7151160B2 (en) 1997-09-17 2001-07-13 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/905,348 US20030064923A1 (en) 1997-09-17 2001-07-13 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,838 US20030148370A1 (en) 1997-09-17 2001-07-13 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/904,956 US20030049622A1 (en) 1995-12-01 2001-07-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/906,618 US6828146B2 (en) 1997-09-17 2001-07-16 Nucleic acid encoding PRO229 polypeptides
US09/906,777 US20030148371A1 (en) 1997-09-17 2001-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/906,838 US7070979B2 (en) 1997-09-17 2001-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/906,700 US6723535B2 (en) 1997-09-17 2001-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/906,815 US7094567B2 (en) 1997-09-17 2001-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/906,722 US6946262B2 (en) 1997-09-17 2001-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/906,742 US20030023054A1 (en) 1997-09-17 2001-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/906,760 US20030096340A1 (en) 1997-09-17 2001-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/906,646 US6852848B2 (en) 1997-09-17 2001-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/906,679 US6974689B1 (en) 1997-09-18 2001-07-16 Nucleic acid encoding PRO211 polypeptides
US09/907,979 US20030082542A1 (en) 1994-09-08 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/907,613 US20030027145A1 (en) 1997-09-17 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/908,093 US20030017498A1 (en) 1997-09-17 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/907,728 US20030190611A1 (en) 1997-09-17 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/907,925 US20030054352A1 (en) 1997-09-17 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/907,794 US6635468B2 (en) 1997-09-17 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/907,841 US7033825B2 (en) 1997-09-17 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/907,575 US20030073079A1 (en) 1997-09-17 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/907,652 US20030104469A1 (en) 1997-09-17 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/907,942 US7087738B2 (en) 1997-09-17 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/907,824 US20020197671A1 (en) 1997-09-17 2001-07-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/909,088 US20020146709A1 (en) 1997-09-17 2001-07-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/909,064 US6818449B2 (en) 1997-09-17 2001-07-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/908,576 US20040005553A1 (en) 1997-09-17 2001-07-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/909,204 US20030036061A1 (en) 1997-09-17 2001-07-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/909,320 US7074592B2 (en) 1997-09-17 2001-07-18 Secreted and transmembrane polypeptides nucleic acid encoding
US09/924,647 US20020155543A1 (en) 1997-11-25 2001-08-07 Fibroblast growth factor-19 (FGF-19) nucleic acids and polypeptides and methods of use for the treatment of obesity and related disorders
US09/941,992 US20030082546A1 (en) 1996-11-06 2001-08-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,396 US20020132981A1 (en) 1997-12-03 2001-08-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/943,851 US20020150976A1 (en) 1997-12-03 2001-08-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,449 US20020102647A1 (en) 1997-12-03 2001-08-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/943,664 US20040091972A1 (en) 1997-12-03 2001-08-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/943,780 US20030096742A1 (en) 1997-12-03 2001-08-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,413 US20020156004A1 (en) 1998-09-16 2001-08-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,457 US6734288B2 (en) 1997-12-03 2001-08-30 Antibodies against a secreted polypeptide that stimulates release of proteoglycans from cartilage
US09/943,762 US20020142958A1 (en) 1998-09-16 2001-08-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,432 US20020142419A1 (en) 1998-09-16 2001-08-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,403 US20020165143A1 (en) 1997-12-03 2001-08-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,852 US20030083479A1 (en) 1997-12-03 2001-08-31 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,862 US20020115145A1 (en) 1997-12-03 2001-08-31 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,884 US7018837B2 (en) 1997-12-03 2001-08-31 Nucleic acids encoding secreted polypeptides that stimulate release of proteoglycans from cartilage
US09/944,896 US7189566B2 (en) 1997-12-03 2001-08-31 PRO347 nucleic acids
US09/944,654 US20020142959A1 (en) 1998-09-16 2001-08-31 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,907 US20020198147A1 (en) 1997-12-03 2001-08-31 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/945,584 US6908993B2 (en) 1997-12-03 2001-08-31 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/945,587 US6936254B2 (en) 1997-12-03 2001-08-31 Method of inducing fetal hemoglobin synthesis
US09/944,929 US7550573B2 (en) 1997-12-03 2001-08-31 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/944,944 US6929947B2 (en) 1997-12-03 2001-08-31 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/945,015 US20020132768A1 (en) 1997-12-03 2001-08-31 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/993,469 US20030068623A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/991,854 US20030059780A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/991,163 US20020132253A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/993,583 US7074897B2 (en) 1997-06-16 2001-11-14 Pro943 polypeptides
US09/990,440 US20030060407A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/992,521 US20030083461A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/991,073 US20020127576A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/990,427 US20030073809A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/992,598 US6956108B2 (en) 1997-06-16 2001-11-14 PRO1184 antibodies
US09/990,442 US20020132252A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/990,444 US6930170B2 (en) 1997-06-16 2001-11-14 PRO1184 polypeptides
US09/990,456 US20020137890A1 (en) 1997-03-31 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/990,443 US20030054987A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/990,438 US20030027754A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/990,562 US20030027985A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/990,436 US20020198148A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/993,748 US20030069403A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/993,687 US20020198149A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/990,726 US20030054359A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/993,667 US20030022187A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/990,711 US20030032023A1 (en) 1997-06-16 2001-11-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,666 US20030027163A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,666 US7244816B2 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,440 US20030059833A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,559 US20030054403A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,641 US20030224358A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/998,041 US20030119001A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,601 US7189814B2 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,529 US7309761B2 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,514 US7019116B2 (en) 1997-06-16 2001-11-15 PRO 1387 polypeptides
US09/997,384 US20030087305A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,641 US7112656B2 (en) 1997-06-16 2001-11-15 PRO1312 polypeptides
US09/998,041 US7309775B2 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,857 US20030064375A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/998,156 US20030044806A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,653 US7034122B2 (en) 1997-06-16 2001-11-15 Antibodies to PRO1159 polypeptides
US09/997,585 US20030119055A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,585 US7166282B2 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,529 US20030134284A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,573 US20030049682A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,628 US20030059782A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,384 US7119177B2 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,683 US20030059783A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,542 US20030068647A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,428 US20030027162A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,614 US20030124531A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/002,796 US20030032057A1 (en) 1997-08-26 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,601 US20030054404A1 (en) 1997-06-16 2001-11-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/997,349 US7034106B2 (en) 1997-06-16 2001-11-15 Pro1159 polypeptides
US09/997,333 US6953836B2 (en) 1997-06-16 2001-11-15 PRO844 polypeptides
US09/990,437 US20030045463A1 (en) 1997-06-16 2001-11-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/991,181 US6913919B2 (en) 1997-06-16 2001-11-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/991,157 US7101687B2 (en) 1997-06-16 2001-11-16 Nucleic acids encoding PRO943
US09/991,172 US20030050457A1 (en) 1997-06-16 2001-11-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/990,441 US7041804B2 (en) 1997-06-16 2001-11-16 Antibodies to PRO1387 polypeptides
US09/991,150 US20030194760A1 (en) 1997-06-16 2001-11-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,726 US7018811B2 (en) 1997-06-16 2001-11-19 Nucleic acids encoding PRO189 polypeptides
US09/989,723 US20020072092A1 (en) 1997-06-16 2001-11-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,862 US20030130182A1 (en) 1997-11-05 2001-11-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,732 US7037679B2 (en) 1997-06-16 2001-11-19 Nucleic acids encoding PRO1184 polypeptides
US09/989,722 US20020072067A1 (en) 1997-06-16 2001-11-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,729 US20030059831A1 (en) 1997-06-16 2001-11-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,735 US6972185B2 (en) 1997-06-16 2001-11-19 Nucleic acids encoding PRO844 polypeptides
US09/989,328 US7056736B2 (en) 1997-06-16 2001-11-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,734 US7491529B2 (en) 1997-06-16 2001-11-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,727 US20020072497A1 (en) 1997-06-16 2001-11-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,279 US7083978B2 (en) 1997-06-16 2001-11-19 Nucleic acid encoding PRO1111 polypeptides
US09/989,721 US20020142961A1 (en) 1997-06-16 2001-11-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,725 US20030139329A1 (en) 1997-06-16 2001-11-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,730 US7157247B2 (en) 1997-06-16 2001-11-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,728 US7029873B2 (en) 1997-06-16 2001-11-20 Nucleic acids to PRO1387 polypeptides
US09/989,731 US20020103125A1 (en) 1997-06-16 2001-11-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/989,293 US7034136B2 (en) 1997-06-16 2001-11-20 Nucleic acids encoding PRO1159 polypeptides
US10/006,867 US7160985B2 (en) 1997-10-29 2001-12-06 Pro180 polypeptide
US10/028,072 US20030004311A1 (en) 1997-06-18 2001-12-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/032,996 US20030054447A1 (en) 1998-08-04 2001-12-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/033,301 US20020098506A1 (en) 1998-08-04 2001-12-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/033,326 US20020098507A1 (en) 1998-08-04 2001-12-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/033,223 US20020164646A1 (en) 1998-08-04 2001-12-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/033,245 US20020160392A1 (en) 1998-08-04 2001-12-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/032,990 US20030032060A1 (en) 1998-08-04 2001-12-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/033,435 US20030027256A1 (en) 1998-08-04 2001-12-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/033,396 US20030077657A1 (en) 1998-08-04 2001-12-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/033,167 US20020182618A1 (en) 1998-08-04 2001-12-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/033,244 US20020192668A1 (en) 1998-08-04 2001-12-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/033,246 US20020098505A1 (en) 1998-08-04 2001-12-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/052,586 US20020127584A1 (en) 1997-09-18 2002-01-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/066,273 US7317092B2 (en) 1997-08-26 2002-02-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/066,193 US20030044902A1 (en) 1997-08-26 2002-02-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/066,203 US20030180796A1 (en) 1997-08-26 2002-02-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/066,211 US20030044844A1 (en) 1997-08-26 2002-02-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/066,198 US20030170721A1 (en) 1997-08-26 2002-02-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/066,494 US20030032063A1 (en) 1997-08-26 2002-02-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/066,500 US20020177165A1 (en) 1997-08-26 2002-02-01 Secreted and transmembrane polypeptides and nucleic acids encoding
US10/066,269 US20030040014A1 (en) 1997-08-26 2002-02-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/081,056 US20040043927A1 (en) 1997-09-19 2002-02-20 Compositions and methods for the diagnosis and treatment of disorders involving angiogenesis
US10/119,480 US20040087769A1 (en) 1998-09-10 2002-04-09 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,047 US20030077778A1 (en) 1997-03-31 2002-04-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,051 US20030092147A1 (en) 1997-03-31 2002-04-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,040 US20030082759A1 (en) 1997-03-31 2002-04-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,046 US20030194791A1 (en) 1997-03-31 2002-04-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,045 US20030073210A1 (en) 1997-03-31 2002-04-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,041 US20030077776A1 (en) 1997-03-31 2002-04-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,044 US20030190717A1 (en) 1997-03-31 2002-04-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,042 US20030096386A1 (en) 1997-03-31 2002-04-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,059 US20030190721A1 (en) 1997-03-31 2002-04-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,058 US20030190720A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,054 US20030199054A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,063 US20030199055A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,062 US20030077779A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,055 US20030190718A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,052 US20030199052A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,050 US20030054516A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,053 US20030199053A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,056 US20030082760A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,057 US20030190719A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,043 US7220831B2 (en) 1997-03-31 2002-04-12 PRO235 polypeptides
US10/121,048 US20030199051A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,060 US20030190722A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,061 US20030082761A1 (en) 1997-03-31 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/121,049 US20030022239A1 (en) 1997-06-18 2002-04-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,212 US7276577B2 (en) 1997-03-31 2002-04-15 PRO1866 polypeptides
US10/123,292 US20030073211A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,213 US7193048B2 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,108 US7635478B2 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,213 US20030199057A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,771 US20030199060A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,262 US20030049816A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,261 US20030068796A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,154 US20030190724A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,236 US20030068795A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,292 US7045603B2 (en) 1997-11-24 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,109 US20030190723A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,214 US7343721B2 (en) 1997-03-31 2002-04-15 PRO4406 polypeptide
US10/123,215 US7291329B2 (en) 1997-03-31 2002-04-15 Antibodies against PRO4406
US10/123,322 US20030199059A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,155 US20030068794A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,235 US20030082762A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,291 US20030199058A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,157 US20030190725A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,156 US20030194792A1 (en) 1997-03-31 2002-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,906 US20030190726A1 (en) 1997-03-31 2002-04-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,910 US7329404B2 (en) 1997-03-31 2002-04-16 Antibodies against PRO1310
US10/123,912 US20030100087A1 (en) 1997-03-31 2002-04-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,905 US7285625B2 (en) 1997-06-18 2002-04-16 PRO536 polypeptides
US10/123,907 US7084258B2 (en) 1997-03-31 2002-04-16 Antibodies against the PRO862 polypeptides
US10/123,902 US20030077781A1 (en) 1997-03-31 2002-04-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,911 US7408032B2 (en) 1997-03-31 2002-04-16 PRO1188 polypeptides
US10/123,908 US7335728B2 (en) 1997-03-31 2002-04-16 PRO1310 polypeptides
US10/123,903 US20030073212A1 (en) 1997-03-31 2002-04-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,909 US7193049B2 (en) 1997-03-31 2002-04-16 PRO862 polypeptides
US10/123,904 US20030022328A1 (en) 1997-03-31 2002-04-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,913 US20030203462A1 (en) 1997-03-31 2002-04-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/123,905 US20030087344A1 (en) 1997-06-18 2002-04-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/124,813 US7312307B2 (en) 1997-03-31 2002-04-17 PRO1056 polypeptides
US10/124,824 US20030077659A1 (en) 1997-03-31 2002-04-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/124,816 US20030190728A1 (en) 1997-03-31 2002-04-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/125,166 US20030039648A1 (en) 1998-09-16 2002-04-17 Compositions and methods for the diagnosis and treatment of tumor
US10/124,818 US20030082763A1 (en) 1997-03-31 2002-04-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/124,814 US7105335B2 (en) 1997-03-31 2002-04-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/125,704 US7357926B2 (en) 1997-03-31 2002-04-17 Antibodies against PRO1879 and the use thereof
US10/124,819 US7285626B2 (en) 1997-03-31 2002-04-17 PRO1076 polypeptides
US10/125,805 US20030194794A1 (en) 1997-03-31 2002-04-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/124,821 US20030199023A1 (en) 1997-03-31 2002-04-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/125,795 US7304131B2 (en) 1997-03-31 2002-04-17 PRO1483 polypeptides
US10/124,817 US20030077786A1 (en) 1997-03-31 2002-04-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/124,822 US7109305B2 (en) 1997-03-31 2002-04-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/124,823 US20030199062A1 (en) 1997-03-31 2002-04-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/124,820 US20030190729A1 (en) 1997-03-31 2002-04-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/125,922 US7309762B2 (en) 1997-03-31 2002-04-19 PRO1360 polypeptides
US10/125,931 US20030199063A1 (en) 1997-03-31 2002-04-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/125,927 US20030190731A1 (en) 1997-03-31 2002-04-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/125,924 US7342097B2 (en) 1997-03-31 2002-04-19 PRO1309 polypeptides
US10/125,932 US7317079B2 (en) 1997-03-31 2002-04-19 PRO812 polypeptides
US10/127,831 US20030082689A1 (en) 1997-03-31 2002-04-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/128,689 US20030087365A1 (en) 1997-03-31 2002-04-23 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/131,817 US7291701B2 (en) 1997-03-31 2002-04-24 PRO1777 polypeptides
US10/131,825 US7282566B2 (en) 1997-03-31 2002-04-24 PRO1779 polypeptide
US10/131,823 US7304132B2 (en) 1997-03-31 2002-04-24 PRO1693 polypeptides
US10/131,815 US20030092103A1 (en) 1998-12-22 2002-04-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/137,865 US20030032155A1 (en) 1997-03-31 2002-05-03 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/137,867 US20030207349A1 (en) 1997-03-31 2002-05-03 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/137,868 US20030082764A1 (en) 1997-03-31 2002-05-03 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/139,963 US7288625B2 (en) 1997-03-31 2002-05-06 PRO4395 polypeptides
US10/140,024 US20040058424A1 (en) 1997-03-31 2002-05-06 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,023 US20030207416A1 (en) 1997-03-31 2002-05-06 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,470 US20030022331A1 (en) 1997-03-31 2002-05-06 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,020 US20030207415A1 (en) 1997-03-31 2002-05-06 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/139,980 US7247710B2 (en) 1997-03-31 2002-05-06 PRO4395 antibodies
US10/140,474 US20030032156A1 (en) 1997-03-31 2002-05-06 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,808 US7425621B2 (en) 1997-03-31 2002-05-07 Antibodies against the PRO4401 polypeptide
US10/140,805 US20030207417A1 (en) 1997-03-31 2002-05-07 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,928 US20030068798A1 (en) 1997-03-31 2002-05-07 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,864 US20030207419A1 (en) 1997-03-31 2002-05-07 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,865 US20030207420A1 (en) 1997-03-31 2002-05-07 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,925 US20030073215A1 (en) 1997-03-31 2002-05-07 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,809 US20030207418A1 (en) 1997-03-31 2002-05-07 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,860 US7307151B2 (en) 1997-03-31 2002-05-07 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/140,921 US7317080B2 (en) 1997-03-31 2002-05-07 PRO4303 polypeptides
US10/063,651 US7193057B2 (en) 1997-10-29 2002-05-07 Antibodies to a polypeptide encoded by a nucleic acid underexpressed in rectal tumor
US10/141,756 US7488586B2 (en) 1997-03-31 2002-05-08 PRO4409 polypeptides
US10/141,701 US20030207421A1 (en) 1997-03-31 2002-05-08 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/141,760 US7342104B2 (en) 1997-03-31 2002-05-08 Antibodies against the PRO4320 polypeptide
US10/141,754 US7361732B2 (en) 1997-03-31 2002-05-08 PRO4400 polypeptides
US10/141,755 US7297764B2 (en) 1997-03-31 2002-05-08 PRO4318 polypeptides
US10/142,417 US7304133B2 (en) 1997-03-31 2002-05-09 PRO4389 polypeptides
US10/143,113 US7329730B2 (en) 1997-03-31 2002-05-09 PRO4348 polypeptides
US10/142,430 US7309766B2 (en) 1997-03-31 2002-05-09 PRO5774 polypeptides
US10/143,114 US20030036180A1 (en) 1997-03-31 2002-05-09 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/142,425 US20030207424A1 (en) 1997-03-31 2002-05-09 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/142,423 US20030049817A1 (en) 1997-03-31 2002-05-10 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/142,431 US7285629B2 (en) 1997-03-31 2002-05-10 Pro5005 polypeptides
US10/143,032 US7408033B2 (en) 1997-03-31 2002-05-10 PRO5995 polypeptides
US10/142,419 US7153941B2 (en) 1997-03-31 2002-05-10 Antibodies that bind PRO4994 polypeptides
US10/145,627 US20030180869A1 (en) 1997-09-17 2002-05-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/145,753 US20030207372A1 (en) 1997-11-03 2002-05-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/145,876 US20030134371A1 (en) 1997-10-29 2002-05-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/145,875 US20030166079A1 (en) 1997-09-17 2002-05-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/146,792 US20030207428A1 (en) 1997-03-31 2002-05-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/146,786 US20030203438A1 (en) 1997-11-24 2002-05-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/146,730 US20030207427A1 (en) 1997-03-31 2002-05-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/146,794 US20030207375A1 (en) 1997-10-24 2002-05-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/146,789 US20030180872A1 (en) 1997-11-24 2002-05-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/147,528 US20030219885A1 (en) 1997-03-31 2002-05-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/147,519 US20030077791A1 (en) 1997-03-31 2002-05-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/147,492 US20030082765A1 (en) 1997-03-31 2002-05-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/147,536 US20040077064A1 (en) 1997-03-31 2002-05-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/152,373 US20030186367A1 (en) 1998-12-22 2002-05-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/152,395 US7189534B2 (en) 1997-03-31 2002-05-21 PRO4320 polynucleotide
US10/153,934 US20030129695A1 (en) 1997-03-31 2002-05-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/156,843 US20030207805A1 (en) 1997-06-18 2002-05-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/157,782 US20030077792A1 (en) 1997-03-31 2002-05-29 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/157,786 US20030208055A1 (en) 1997-03-31 2002-05-29 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/158,791 US20030207429A1 (en) 1997-03-31 2002-05-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/158,782 US20030082766A1 (en) 1997-03-31 2002-05-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/160,498 US20030073216A1 (en) 1997-03-31 2002-05-30 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,689 US20030166104A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,694 US20030166107A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,695 US20030032101A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,699 US20030166109A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,693 US20030073169A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,706 US20030022293A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,707 US20030166110A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,708 US20030040053A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,690 US20030166105A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,702 US20030170793A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,698 US20030166108A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,692 US20030166188A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,691 US20030166106A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,700 US20030027262A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,697 US20030032102A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,696 US20030082767A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,703 US20030170794A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,701 US20030104538A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,705 US20030032103A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/173,704 US20030170795A1 (en) 1997-09-18 2002-06-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,570 US20030211572A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,578 US20030073170A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,590 US20030008352A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,579 US20030027264A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,569 US20030166111A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,589 US20030166114A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,588 US20030027266A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,576 US7125962B2 (en) 1997-09-18 2002-06-18 Anti-Pro268 antibodies
US10/174,582 US20030027265A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,587 US20030166113A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,572 US20030027263A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,591 US20030166115A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,574 US20030170796A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,740 US20030027268A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,586 US20030032106A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,585 US20030032105A1 (en) 1997-09-18 2002-06-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/174,581 US7153939B2 (en) 1997-09-18 2002-06-18 PRO354 antibodies
US10/174,583 US7211645B2 (en) 1997-09-18 2002-06-18 PRO268 polypeptides
US10/175,738 US20030022294A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,751 US20030166122A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,736 US20030166117A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,749 US20050196832A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,747 US20030032107A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,739 US20030027267A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,752 US20030022295A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,750 US20030073172A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,753 US20030077732A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,735 US20030082715A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,748 US20030166121A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,744 US20030166119A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,745 US20030166120A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,754 US20030166123A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,742 US20030166118A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,746 US20030027270A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,737 US20030013153A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,741 US20030073171A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/175,743 US20030027269A1 (en) 1997-09-18 2002-06-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,491 US20030087373A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,487 US20030032110A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,483 US20030017541A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,746 US20030068680A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,484 US20030059876A9 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,988 US20030170802A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,918 US7495083B2 (en) 1997-09-18 2002-06-20 PRO940 antibodies
US10/176,753 US20030044917A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,919 US20030032114A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,749 US20030017542A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,989 US20030170803A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,759 US20030166128A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,485 US20030032109A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,993 US20030027280A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,911 US20030032113A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,493 US20030032111A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,914 US20030017543A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,479 US20030040054A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,757 US7317082B2 (en) 1997-09-18 2002-06-20 PRO1018 polypeptides
US10/176,917 US20030044918A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,921 US20030027276A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,747 US20030027273A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,754 US7709602B2 (en) 1997-09-18 2002-06-20 PRO1078 polypeptides
US10/176,490 US20030170798A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,913 US20030022298A1 (en) 1997-09-15 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,981 US20030170800A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,920 US20030166129A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,990 US20030036119A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,482 US20030022296A1 (en) 1997-09-18 2002-06-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,991 US20030027324A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,922 US20030166130A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,480 US20030166124A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,986 US20030073173A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,481 US20030032108A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,751 US20030036117A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,752 US20030170799A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,756 US20030032112A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,925 US20030032115A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,992 US20030027279A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,923 US20030068681A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,924 US20030166131A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,916 US20030040056A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,760 US7339033B2 (en) 1998-06-26 2002-06-21 Pro1481
US10/176,915 US20030017544A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,978 US20030032116A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,985 US20030027277A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,750 US20030027274A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,987 US20030027278A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,982 US20030044919A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,486 US7354999B2 (en) 1997-09-18 2002-06-21 PRO1481 polypeptides
US10/176,748 US20030040055A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,979 US20030087374A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,755 US20030166127A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,758 US20030008353A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,983 US20030170801A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,488 US20030027271A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,489 US20030166125A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/176,492 US20030027272A1 (en) 1997-09-18 2002-06-21 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,506 US20030044920A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,525 US20030040060A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,521 US20030170806A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,519 US7339024B2 (en) 1997-09-18 2002-06-24 PRO1772 polypeptides
US10/179,515 US20030166135A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,507 US20030040057A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,513 US20030044921A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,523 US20030215909A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,511 US20030104539A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,522 US20030044923A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,516 US20030040058A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,514 US20030044922A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,508 US20030166133A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,520 US20030096353A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,517 US20030170805A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,526 US20030100061A1 (en) 1998-06-26 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,510 US20030032117A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,509 US20030207392A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,512 US20030166134A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/179,518 US20030104540A1 (en) 1997-09-18 2002-06-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,551 US20030036123A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,549 US20030032122A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,557 US20030022301A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,540 US20030040061A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,555 US20030032123A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,541 US20030036120A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,544 US20030032119A1 (en) 1998-06-26 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,543 US20030032118A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,554 US20050202526A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,560 US20030044925A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,548 US7696319B2 (en) 1997-09-18 2002-06-25 PRO1772 antibodies
US10/180,546 US20030032120A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,545 US20030040062A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,552 US7348415B2 (en) 1997-09-18 2002-06-25 PRO1316 antibodies
US10/180,542 US20030036121A1 (en) 1998-06-26 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,553 US7365156B2 (en) 1997-09-18 2002-06-25 PRO1316 polypeptides
US10/180,550 US20030064440A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,547 US20030032121A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,556 US7355000B2 (en) 1997-09-18 2002-06-25 PRO1380 polypeptides
US10/180,559 US20030032124A1 (en) 1997-09-18 2002-06-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/183,012 US7718770B2 (en) 1997-09-18 2002-06-26 PRO1305-polypeptides
US10/183,009 US7339034B2 (en) 1997-09-18 2002-06-26 PRO1305 antibodies
US10/183,001 US7084255B2 (en) 1997-09-18 2002-06-26 PRO1278 polypeptides
US10/180,999 US7297767B2 (en) 1997-09-18 2002-06-26 PRO1374 polypeptides
US10/183,002 US20030054454A1 (en) 1997-09-18 2002-06-26 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/183,010 US20030032126A1 (en) 1997-09-18 2002-06-26 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/183,008 US20030040064A1 (en) 1997-09-18 2002-06-26 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/183,005 US7317093B2 (en) 1997-09-18 2002-06-26 PRO1339 antibodies
US10/183,018 US20030104541A1 (en) 1997-09-18 2002-06-26 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/183,003 US20030082716A1 (en) 1997-09-18 2002-06-26 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/183,011 US20030068682A1 (en) 1998-06-26 2002-06-26 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/183,016 US20030082717A1 (en) 1997-09-18 2002-06-26 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/183,017 US20030040065A1 (en) 1997-09-18 2002-06-26 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/183,013 US7309769B2 (en) 1997-09-18 2002-06-26 PRO1487 polypeptides
US10/183,006 US7297776B2 (en) 1997-09-18 2002-06-26 PRO1374 antibodies
US10/183,014 US20030064441A1 (en) 1997-09-18 2002-06-26 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/181,000 US7319137B2 (en) 1997-09-18 2002-06-26 PRO1339 polypeptides
US10/183,015 US20030044926A1 (en) 1997-09-18 2002-06-26 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/180,998 US7087421B2 (en) 1997-09-18 2002-06-26 Pro1278 polypeptides
US10/183,019 US7425605B2 (en) 1997-09-18 2002-06-26 PRO1486 polypeptides
US10/184,618 US7393917B2 (en) 1997-09-18 2002-06-27 PRO1482 polypeptides
US10/184,638 US20030054456A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,612 US20030036127A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,628 US7309770B2 (en) 1997-09-18 2002-06-27 PRO1757 polypeptides
US10/184,633 US20030068683A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,631 US20030036134A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,641 US20030073174A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,615 US20030044927A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,627 US7282569B2 (en) 1997-09-18 2002-06-27 PRO1508 antibodies
US10/184,640 US7271250B2 (en) 1998-06-26 2002-06-27 PRO1757 antibodies
US10/184,619 US20030049738A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,630 US7304143B2 (en) 1997-09-18 2002-06-27 PRO1571 antibodies
US10/184,654 US7378486B2 (en) 1997-09-18 2002-06-27 PRO1482 antibodies
US10/184,616 US20030036128A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,614 US20030032128A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,627 US20030040070A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,613 US20030119105A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,652 US20030032134A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,630 US20030036133A1 (en) 1997-09-18 2002-06-27 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,651 US7291704B2 (en) 1997-09-18 2002-06-27 PRO1758 polypeptides
US10/184,642 US7332573B2 (en) 1997-09-18 2002-06-27 PRO1571 polypeptides
US10/184,658 US20030027281A1 (en) 1998-06-26 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,629 US20030036132A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,625 US20030040068A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,623 US20030032129A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,632 US20030036135A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,655 US20030040073A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,645 US7291718B2 (en) 1998-06-26 2002-06-28 PRO1758 antibodies
US10/184,650 US20030036138A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,647 US20030032133A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,656 US20030044931A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,635 US20030032130A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,643 US20030044929A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,617 US20030036129A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,644 US20030044930A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,646 US20030032132A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,634 US20030068684A1 (en) 1998-06-26 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,624 US20030104542A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,621 US20030054455A1 (en) 1998-06-26 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,620 US20030044928A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,657 US20030104543A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,636 US20030036136A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,626 US20030040069A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,637 US20030032131A1 (en) 1997-09-18 2002-06-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/184,622 US20030036130A1 (en) 1997-09-18 2002-06-29 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,597 US20030036141A1 (en) 1997-09-18 2002-07-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,739 US7291706B2 (en) 1998-06-26 2002-07-01 PRO4352 polypeptides
US10/187,747 US7291707B2 (en) 1997-09-18 2002-07-01 PRO1337 polypeptides
US10/187,884 US20030036155A1 (en) 1997-09-18 2002-07-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,886 US7291708B2 (en) 1997-09-18 2002-07-01 PRO1785 polypeptides
US10/187,588 US7351795B2 (en) 1998-06-26 2002-07-01 PRO19563 polypeptides
US10/187,598 US20030036142A1 (en) 1997-09-18 2002-07-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,601 US7291705B2 (en) 1997-09-18 2002-07-01 PRO19645 polypeptides
US10/187,887 US7285645B2 (en) 1997-09-18 2002-07-01 PRO4356 antibodies
US10/187,594 US7294335B2 (en) 1998-06-26 2002-07-01 PRO19645 antibodies
US10/188,766 US7351804B2 (en) 1998-06-26 2002-07-02 Antibodies against PRO4421
US10/187,741 US20030036147A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,600 US20030036143A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/188,775 US20030040075A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/188,781 US20030036160A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,602 US20030036145A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,747 US20030036150A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/188,769 US20030036157A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/188,780 US7268217B2 (en) 1998-06-26 2002-07-02 PRO4421 polypeptides
US10/187,885 US20030032138A1 (en) 1998-06-24 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,757 US7276578B2 (en) 1997-09-18 2002-07-02 PRO4334 polypeptides
US10/188,767 US7312310B2 (en) 1997-09-18 2002-07-02 PRO6015 polypeptides
US10/187,751 US20030036151A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,754 US20030036153A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/188,773 US20030036159A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,753 US20030036152A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/188,770 US7358340B2 (en) 1997-09-18 2002-07-02 PRO19563 antibodies
US10/187,743 US20030036148A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,603 US20030036146A1 (en) 1998-06-26 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,746 US20030036149A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,745 US7250490B2 (en) 1997-09-18 2002-07-02 PRO1480 polypeptides
US10/188,774 US20030040074A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/187,596 US20030032136A1 (en) 1997-09-18 2002-07-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/192,010 US20030044932A1 (en) 1997-09-18 2002-07-09 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/194,462 US7388073B2 (en) 1998-06-26 2002-07-12 PRO9835 polypeptides
US10/194,361 US20030036161A1 (en) 1998-06-26 2002-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/194,423 US7339025B2 (en) 1998-06-26 2002-07-12 PRO6246 polypeptides
US10/194,365 US7381791B2 (en) 1998-06-26 2002-07-12 PRO9739 polypeptides
US10/194,461 US20030054459A1 (en) 1998-06-26 2002-07-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/195,897 US20030036164A1 (en) 1997-09-18 2002-07-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/195,888 US20060073545A1 (en) 1998-06-26 2002-07-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/195,889 US7534856B2 (en) 1998-06-26 2002-07-15 PRO19624 antibodies
US10/195,892 US7385033B2 (en) 1998-06-26 2002-07-15 PRO12970 polypeptides
US10/195,901 US20030036165A1 (en) 1998-06-26 2002-07-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/195,883 US20060073544A1 (en) 1998-06-26 2002-07-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/195,894 US20030043176A1 (en) 1998-06-26 2002-07-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/195,893 US20030206188A1 (en) 1998-06-26 2002-07-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/195,902 US20030038826A1 (en) 1998-06-26 2002-07-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/196,743 US20030038827A1 (en) 1998-06-26 2002-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/196,762 US20030040078A1 (en) 1998-06-26 2002-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/196,745 US7423120B2 (en) 1997-09-18 2002-07-16 PRO19814 polypeptides
US10/196,756 US7304145B2 (en) 1998-06-26 2002-07-16 PRO19646 antibodies
US10/196,760 US7408034B2 (en) 1998-06-26 2002-07-16 PRO20025 polypeptides
US10/196,759 US20030071835A1 (en) 1998-06-26 2002-07-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/199,462 US20030054468A1 (en) 1998-06-26 2002-07-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/198,768 US20030049756A1 (en) 1998-06-26 2002-07-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/199,464 US20030032140A1 (en) 1997-09-18 2002-07-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/199,316 US20030068726A1 (en) 1998-06-26 2002-07-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/202,938 US20030104551A1 (en) 1997-10-31 2002-07-24 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/205,904 US20030073813A1 (en) 1998-06-26 2002-07-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/215,371 US20040137561A1 (en) 1997-10-17 2002-08-08 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/226,739 US7390879B2 (en) 1999-06-15 2002-08-23 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2002341509A JP4017507B2 (en) 1999-06-02 2002-09-25 Medicament containing polypeptide
US10/265,542 US20030171568A1 (en) 1998-09-16 2002-10-03 Use of A33 antigens and JAM-IT
US10/299,937 US20030185846A1 (en) 1998-09-16 2002-11-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/298,993 US20030211576A1 (en) 2000-02-22 2002-11-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/299,976 US20030180312A1 (en) 2000-02-22 2002-11-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/336,979 US20050026243A1 (en) 1997-11-25 2003-01-02 Fibroblast growth factor-19 (FGF-19) nucleic acids and polypeptides and methods of use for the treatment of obesity and related disorders
US10/425,447 US20040023331A1 (en) 1997-10-24 2003-04-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/429,667 US20030207401A1 (en) 1997-12-03 2003-05-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/439,249 US20030228664A1 (en) 1998-12-16 2003-05-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/448,713 US20040006211A1 (en) 1997-10-24 2003-05-29 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/449,656 US20040005665A1 (en) 1997-10-24 2003-05-29 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/448,923 US7241865B2 (en) 1997-10-24 2003-05-29 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/448,580 US7208312B1 (en) 1997-09-17 2003-05-29 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/633,008 US7192589B2 (en) 1998-09-16 2003-07-31 Treatment of inflammatory disorders with STIgMA immunoadhesins
US10/712,560 US20040146908A1 (en) 1997-11-25 2003-11-12 Fibroblast growth factor-19 (FGF-19) nucleic acids and polypeptides and methods of use for the treatment of obesity and related disorders
US10/735,014 US7442772B2 (en) 1997-12-03 2003-12-12 Antibodies to PRO361 polypeptide
JP2003420475A JP2004154140A (en) 1999-03-08 2003-12-18 Promotion or inhibition of angioplasty and cardiovascular neogenesis
US10/771,187 US7355002B2 (en) 1997-11-12 2004-02-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/797,366 US7378507B2 (en) 1997-09-18 2004-03-09 PRO217 polypeptides
US10/855,211 US20050026832A1 (en) 1997-11-25 2004-05-26 Fibroblast growth factor-19 (FGF-19) nucleic acids and polypeptides and methods of use for the treatment of obesity and related disorders
US10/916,250 US7368250B2 (en) 1997-10-28 2004-08-11 Compositions and methods for the diagnosis and treatment of tumor
US10/943,353 US20050059115A1 (en) 1997-12-03 2004-09-17 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/955,952 US20050153396A1 (en) 1998-09-16 2004-09-29 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/963,467 US7223586B2 (en) 1997-09-18 2004-10-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/964,241 US20070026487A1 (en) 1997-11-24 2004-10-12 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/970,823 US7307152B2 (en) 1997-10-17 2004-10-20 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/972,317 US7208321B2 (en) 1998-06-02 2004-10-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/050,154 US7122631B2 (en) 2000-02-22 2005-02-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/050,559 US7157267B2 (en) 1997-10-17 2005-02-02 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/057,268 US20060084144A1 (en) 1997-09-17 2005-02-11 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/057,966 US20050187379A1 (en) 1997-09-17 2005-02-14 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2005054646A JP2005224245A (en) 1999-09-01 2005-02-28 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/080,062 US7619062B2 (en) 1997-10-17 2005-03-14 PRO214 polypeptides
US11/081,485 US20050170465A1 (en) 1997-10-17 2005-03-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/100,159 US7425613B2 (en) 1997-11-05 2005-04-05 PRO1375 polypeptides
JP2005119030A JP2005261437A (en) 1999-09-01 2005-04-15 Secreted and transmembrane polypeptide and nucleic acid encoding the same
JP2005118817A JP2005245460A (en) 1999-09-01 2005-04-15 Secretory and transmembrane peptide and nucleic acid encoding the same
JP2005118968A JP2005270107A (en) 1999-09-01 2005-04-15 Secreted and transmembrane polypeptide and nucleic acid encoding the same
JP2005118579A JP2005253468A (en) 1999-09-01 2005-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2005118701A JP2005253469A (en) 1999-09-01 2005-04-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/110,133 US20050181445A1 (en) 1997-09-17 2005-04-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/176,863 US20050266490A1 (en) 1997-10-24 2005-07-06 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/189,442 US20060246465A1 (en) 1998-06-04 2005-07-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2005235120A JP2006068006A (en) 1999-06-15 2005-08-15 Secreted and transmembrane polypeptide and nucleic acid encoding the same
JP2005264293A JP2006068016A (en) 1999-12-01 2005-08-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2005238274A JP2006051032A (en) 1999-06-15 2005-08-19 Secreted and transmembrane polypeptide and nucleic acid encoding the same
JP2005238266A JP2006025795A (en) 1999-06-15 2005-08-19 Secreted and transmembrane polypeptide and nucleic acid encoding the same
JP2005238244A JP2006061156A (en) 1999-06-15 2005-08-19 Secreted and transmembrane polypeptide and nucleic acid encoding the same
JP2005238217A JP2006051031A (en) 1999-06-15 2005-08-19 Secreted and transmembrane polypeptide and nucleic acid encoding the same
US11/240,891 US20060246540A1 (en) 1997-08-26 2005-09-29 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/283,473 US20090142800A1 (en) 1998-08-04 2005-11-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/296,155 US20060127983A1 (en) 1997-12-03 2005-12-06 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/323,117 US20070092941A1 (en) 1998-09-16 2005-12-29 PRO1298 polypeptides
US11/341,175 US7468427B2 (en) 1997-03-31 2006-01-27 Antibodies to PRO1275 polypeptide
US11/353,554 US7417126B2 (en) 1997-10-17 2006-02-13 PRO246 antibodies
US11/355,441 US7449551B2 (en) 1997-09-18 2006-02-15 PRO211 polypeptides
US11/471,396 US20060233803A1 (en) 1998-09-16 2006-06-19 Use of A33 antigens and JAM-it
US11/518,609 US20070077623A1 (en) 1997-09-17 2006-09-07 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/542,578 US20070031405A1 (en) 1998-09-16 2006-10-02 Use of A33 antigens and jam-it
US11/642,816 US20070088151A1 (en) 1997-09-18 2006-12-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US11/725,076 US20070190049A1 (en) 1998-09-16 2007-03-15 Use of A33 antigens and JAM-IT
US11/725,063 US7741056B2 (en) 1998-09-16 2007-03-15 Use of A33 antigens and JAM-IT
US11/725,027 US20080312421A1 (en) 1998-09-16 2007-03-15 Use of A33 antigens and JAM-it
JP2007172879A JP5512073B2 (en) 1999-06-02 2007-06-29 Medicament containing polypeptide
JP2007326613A JP2008161190A (en) 1999-12-01 2007-12-18 Secreted and transmembrane polypeptide and nucleic acid encoding the same
JP2007326609A JP2008148701A (en) 1999-12-01 2007-12-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2007325484A JP2008148699A (en) 1999-12-01 2007-12-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2007326424A JP2008167749A (en) 1999-12-01 2007-12-18 Secreted and transmembrane polypeptide and nucleic acid encoding the same
US12/031,612 US7514538B2 (en) 1997-10-28 2008-02-14 Compositions and methods for the diagnosis and treatment of tumor
US12/079,178 US20090170158A1 (en) 1997-12-03 2008-03-25 Secreted and transmembrane polypeptides and nucleic acids encoding the same
JP2008256822A JP2009095345A (en) 1999-09-01 2008-10-01 Secreted and transmembrane polypeptide and nucleic acid encoding the same
US12/393,224 US20090227776A1 (en) 1997-10-28 2009-02-26 Compositions and methods for the diagnosis and treatment of tumor
JP2011138276A JP2011236224A (en) 1999-06-02 2011-06-22 Medicine containing polypeptide

Applications Claiming Priority (32)

Application Number Priority Date Filing Date Title
US14304899P 1999-07-07 1999-07-07
US60/143,048 1999-07-07
US14569899P 1999-07-26 1999-07-26
US60/145,698 1999-07-26
US14622299P 1999-07-28 1999-07-28
US60/146,222 1999-07-28
USPCT/US99/20594 1999-09-08
PCT/US1999/020594 WO2000015666A2 (en) 1998-09-10 1999-09-08 Compositions and methods for the treatment of tumors
USPCT/US99/20944 1999-09-13
PCT/US1999/020944 WO2000015792A2 (en) 1998-09-14 1999-09-13 Promotion or inhibition of angiogenesis and cardiovascularization
USPCT/US99/21547 1999-09-15
PCT/US1999/021090 WO2000015796A2 (en) 1998-09-16 1999-09-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
PCT/US1999/021547 WO2000015797A2 (en) 1998-09-17 1999-09-15 Compositions and methods for the treatment of immune related diseases
USPCT/US99/21090 1999-09-15
PCT/US1999/023089 WO2000021996A2 (en) 1998-10-13 1999-10-05 Methods and compositions for inhibiting neoplastic cell growth
USPCT/US99/23089 1999-10-05
USPCT/US99/28214 1999-11-29
PCT/US1999/028214 WO2001019987A1 (en) 1999-09-13 1999-11-29 Promotion or inhibition of angiogenesis and cardiovascularization
USPCT/US99/28313 1999-11-30
PCT/US1999/028313 WO2000032221A2 (en) 1998-12-01 1999-11-30 Promotion or inhibition of angiogenesis and cardiovascularization
USPCT/US99/28565 1999-12-02
PCT/US1999/028565 WO2000037638A2 (en) 1998-12-22 1999-12-02 Methods and compositions for inhibiting neoplastic cell growth
PCT/US1999/028564 WO2000055319A1 (en) 1999-03-12 1999-12-02 Methods and compositions for inhibiting neoplastic cell growth
USPCT/US99/28564 1999-12-02
USPCT/US99/30095 1999-12-16
PCT/US1999/030095 WO2000037640A2 (en) 1998-12-22 1999-12-16 Compositions and methods for the treatment of tumor
USPCT/US99/30911 1999-12-20
PCT/US1999/030999 WO2001005836A1 (en) 1999-07-20 1999-12-20 Polypeptidic compositions and methods for the treatment of tumors
PCT/US1999/030911 WO2000075316A1 (en) 1999-06-02 1999-12-20 Methods and compositions for inhibiting neoplastic cell growth
USPCT/US99/30999 1999-12-20
USPCT/US99/00219 2000-01-05
PCT/US2000/000219 WO2000053753A2 (en) 1999-03-08 2000-01-05 Promotion or inhibition of angiogenesis and cardiovascularization

Related Parent Applications (16)

Application Number Title Priority Date Filing Date
PCT/US1998/018824 Continuation-In-Part WO1999014327A2 (en) 1994-09-08 1998-09-10 Genes amplified in tumours, antibodies against the proteins coded thereby, and their use in diagnosis and treatment of cancer
PCT/US1998/019330 Continuation-In-Part WO1999014328A2 (en) 1994-09-08 1998-09-16 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09380139 Continuation-In-Part 1998-09-16
PCT/US1998/019437 Continuation-In-Part WO1999014241A2 (en) 1994-09-08 1998-09-17 Compositions and methods for the treatment of immune related diseases
US38013999A Continuation-In-Part 1996-11-06 1999-08-25
US38013899A Continuation-In-Part 1996-11-06 1999-08-25
PCT/US1999/023089 Continuation-In-Part WO2000021996A2 (en) 1994-09-08 1999-10-05 Methods and compositions for inhibiting neoplastic cell growth
PCT/US1999/028313 Continuation-In-Part WO2000032221A2 (en) 1994-09-08 1999-11-30 Promotion or inhibition of angiogenesis and cardiovascularization
PCT/US1999/030095 Continuation-In-Part WO2000037640A2 (en) 1994-09-08 1999-12-16 Compositions and methods for the treatment of tumor
PCT/US2000/000219 Continuation-In-Part WO2000053753A2 (en) 1994-09-08 2000-01-05 Promotion or inhibition of angiogenesis and cardiovascularization
PCT/US2000/003565 Continuation WO2001053486A1 (en) 1994-09-08 2000-02-11 Compositions and methods for the treatment of tumor
PCT/US2000/003565 Continuation-In-Part WO2001053486A1 (en) 1994-09-08 2000-02-11 Compositions and methods for the treatment of tumor
PCT/US2000/004341 Continuation-In-Part WO2000053756A2 (en) 1996-11-06 2000-02-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
PCT/US2000/004342 Continuation WO2000078961A1 (en) 1997-03-31 2000-02-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
PCT/US2000/004342 Continuation-In-Part WO2000078961A1 (en) 1997-03-31 2000-02-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
PCT/US2000/014042 Continuation-In-Part WO2000077037A2 (en) 1994-09-08 2000-05-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same

Related Child Applications (23)

Application Number Title Priority Date Filing Date
US09/284,663 Continuation US20020012961A1 (en) 1997-08-26 1998-11-25 Fibroblast growth factor- 19
PCT/US2000/005004 Continuation-In-Part WO2000053757A2 (en) 1994-09-08 2000-02-24 Promotion or inhibition of angiogenesis and cardiovascularization
PCT/US2000/005601 Continuation-In-Part WO2000056889A2 (en) 1997-03-31 2000-03-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
PCT/US2000/005601 Continuation WO2000056889A2 (en) 1997-03-31 2000-03-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
PCT/US2000/005841 Continuation-In-Part WO2000053758A2 (en) 1994-09-08 2000-03-02 Compositions and methods for the treatment of immune related diseases
PCT/US2000/005841 Continuation WO2000053758A2 (en) 1994-09-08 2000-03-02 Compositions and methods for the treatment of immune related diseases
US52234200A Continuation-In-Part 1997-08-26 2000-03-09
PCT/US2000/014042 Continuation-In-Part WO2000077037A2 (en) 1994-09-08 2000-05-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US66535000A Continuation 1994-09-08 2000-09-18
US66535000A Continuation-In-Part 1994-09-08 2000-09-18
PCT/US2000/032678 Continuation-In-Part WO2001040466A2 (en) 1996-11-06 2000-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US09/866,028 Continuation-In-Part US6642360B2 (en) 1996-11-06 2001-05-25 Secreted polypeptides that stimulate release of proteoglycans from cartilage
US09/903,749 Continuation US7147853B2 (en) 1997-09-17 2001-07-11 Anti-pro211 polypeptide antibodies
US09/944,862 Continuation US20020115145A1 (en) 1997-12-03 2001-08-31 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/028,072 Continuation-In-Part US20030004311A1 (en) 1997-03-31 2001-12-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/028,072 Continuation US20030004311A1 (en) 1997-03-31 2001-12-19 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/052,586 Continuation US20020127584A1 (en) 1997-09-15 2002-01-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/081,056 Continuation US20040043927A1 (en) 1997-09-19 2002-02-20 Compositions and methods for the diagnosis and treatment of disorders involving angiogenesis
US10/119,480 Continuation US20040087769A1 (en) 1998-09-10 2002-04-09 Secreted and transmembrane polypeptides and nucleic acids encoding the same
US10/125,166 Continuation-In-Part US20030039648A1 (en) 1997-10-28 2002-04-17 Compositions and methods for the diagnosis and treatment of tumor
US10/125,166 Continuation US20030039648A1 (en) 1997-10-28 2002-04-17 Compositions and methods for the diagnosis and treatment of tumor
US10/265,542 Continuation-In-Part US20030171568A1 (en) 1997-11-21 2002-10-03 Use of A33 antigens and JAM-IT
US11/542,578 Continuation-In-Part US20070031405A1 (en) 1998-09-16 2006-10-02 Use of A33 antigens and jam-it

Publications (1)

Publication Number Publication Date
WO2001004311A1 true WO2001004311A1 (en) 2001-01-18

Family

ID=56289994

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/004414 WO2001004311A1 (en) 1994-09-08 2000-02-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same

Country Status (2)

Country Link
AU (1) AU2883900A (en)
WO (1) WO2001004311A1 (en)

Cited By (42)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003025162A2 (en) * 2001-09-20 2003-03-27 Bayer Healthcare Ag Regulation of human prolyl 4-hydroxylase alpha subunit precursor
WO2002064776A3 (en) * 2001-02-14 2003-08-21 Axaron Bioscience Ag Signal transduction proteins 15b3, 15b3-1 and 15b3-2, and related dna sequences
WO2003072773A1 (en) * 2002-02-08 2003-09-04 Seikagaku Corporation Fused protein having glucuronyl transferase activity
WO2003083110A1 (en) * 2002-03-29 2003-10-09 National Institute Of Advanced Industrial Science And Technology Novel galactose transferases, peptides thereof and nucleic acid encoding the same
WO2004002515A1 (en) * 2002-06-28 2004-01-08 Takeda Chemical Industries, Ltd. Diagnostics/preventives/remedies for respiratory diseases
WO2004063226A2 (en) * 2002-12-27 2004-07-29 Applied Research Systems Ars Holding N.V. Novel fibrillin-like polypeptides
US6902892B1 (en) 1998-10-19 2005-06-07 Diadexus, Inc. Method of diagnosing, monitoring, staging, imaging and treating prostate cancer
EP1629088A2 (en) * 2003-05-30 2006-03-01 Agensys, Inc. Prostate stem cell antigen (psca) variants and subsequences thereof
US7034132B2 (en) 2001-06-04 2006-04-25 Anderson David W Therapeutic polypeptides, nucleic acids encoding same, and methods of use
US7057017B2 (en) 1997-04-16 2006-06-06 Millennium Pharmaceuticals, Inc. Human dickkopf-related protein and nucleic acid molecules and uses therefor
US7169906B2 (en) 1997-09-17 2007-01-30 Genentech, Inc. PRO211 polypeptides
US7192589B2 (en) 1998-09-16 2007-03-20 Genentech, Inc. Treatment of inflammatory disorders with STIgMA immunoadhesins
US7419663B2 (en) 1998-03-20 2008-09-02 Genentech, Inc. Treatment of complement-associated disorders
US7446181B2 (en) 1998-01-15 2008-11-04 Millennium Pharmaceuticals, Inc. Antibodies that bind human Dickkopf-1 proteins
US7449551B2 (en) 1997-09-18 2008-11-11 Genentech, Inc. PRO211 polypeptides
EP2014675A1 (en) * 2003-08-11 2009-01-14 Genentech, Inc. Compositions and methods for the treatment of immune related diseases
US7544659B2 (en) 2004-08-13 2009-06-09 Genentech, Inc. Promotion of axonal regeneration
US7705195B2 (en) 2002-06-07 2010-04-27 Genentech, Inc. Screening method
US7709611B2 (en) 2004-08-04 2010-05-04 Amgen Inc. Antibodies to Dkk-1
US7723478B2 (en) 1998-09-25 2010-05-25 Amgen Inc. DKR polypeptides
US7785829B2 (en) 2003-03-19 2010-08-31 Biogen Idec Ma, Inc. Nogo receptor binding protein
US8007791B2 (en) 2007-05-23 2011-08-30 Genentech, Inc. Prevention and treatment of complement-associated eye conditions
US8007798B2 (en) 1997-11-21 2011-08-30 Genentech, Inc. Treatment of complement-associated disorders
US8058406B2 (en) 2008-07-09 2011-11-15 Biogen Idec Ma Inc. Composition comprising antibodies to LINGO or fragments thereof
US8067002B2 (en) 2006-11-02 2011-11-29 Genentech, Inc. Humanized anti-factor D antibodies
US8088386B2 (en) 1998-03-20 2012-01-03 Genentech, Inc. Treatment of complement-associated disorders
US8128926B2 (en) 2007-01-09 2012-03-06 Biogen Idec Ma Inc. Sp35 antibodies and uses thereof
US8273352B2 (en) 2008-04-28 2012-09-25 Genentech, Inc. Humanized anti-factor D antibodies and uses thereof
US8486893B2 (en) 2004-06-24 2013-07-16 Biogen Idec Ma Inc. Treatment of conditions involving demyelination
US8551476B2 (en) 2005-07-08 2013-10-08 Biogen Idec Ma Inc. SP35 antibodies and uses thereof
US8753625B2 (en) 2005-11-04 2014-06-17 Genentech, Inc. Use of complement inhibitors to treat ocular diseases
US9212228B2 (en) 2005-11-24 2015-12-15 Ganymed Pharmaceuticals Ag Monoclonal antibodies against claudin-18 for treatment of cancer
US9234024B2 (en) 2008-05-06 2016-01-12 Genentech, Inc. Affinity matured CRIg variants
US9512232B2 (en) 2012-05-09 2016-12-06 Ganymed Pharmaceuticals Ag Antibodies against Claudin 18.2 useful in cancer diagnosis
US9775785B2 (en) 2004-05-18 2017-10-03 Ganymed Pharmaceuticals Ag Antibody to genetic products differentially expressed in tumors and the use thereof
US9796780B2 (en) 2012-05-14 2017-10-24 Biogen Ma Inc. LINGO-2 antagonists for treatment of conditions involving motor neurons
US10093978B2 (en) 2013-08-12 2018-10-09 Genentech, Inc. Compositions for detecting complement factor H (CFH) and complement factor I (CFI) polymorphisms
US10179821B2 (en) 2014-05-01 2019-01-15 Genentech, Inc. Anti-factor D antibodies
US10407510B2 (en) 2015-10-30 2019-09-10 Genentech, Inc. Anti-factor D antibodies and conjugates
US10414824B2 (en) 2002-11-22 2019-09-17 Ganymed Pharmaceuticals Ag Genetic products differentially expressed in tumors and the use thereof
US10435467B2 (en) 2015-01-08 2019-10-08 Biogen Ma Inc. LINGO-1 antagonists and uses for treatment of demyelinating disorders
US10654932B2 (en) 2015-10-30 2020-05-19 Genentech, Inc. Anti-factor D antibody variant conjugates and uses thereof

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997007198A2 (en) * 1995-08-11 1997-02-27 Genetics Institute, Inc. Dna sequences and secreted proteins encoded thereby
EP0834563A2 (en) * 1996-09-26 1998-04-08 Smithkline Beecham Corporation Human 7-transmembrane receptor, member of the chemokine receptor family, named Strl-33
WO1999014328A2 (en) * 1997-09-17 1999-03-25 Genentech, Inc. Secreted and transmembrane polypeptides and nucleic acids encoding the same
WO1999014327A2 (en) * 1997-09-17 1999-03-25 Genentech, Inc. Genes amplified in tumours, antibodies against the proteins coded thereby, and their use in diagnosis and treatment of cancer

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997007198A2 (en) * 1995-08-11 1997-02-27 Genetics Institute, Inc. Dna sequences and secreted proteins encoded thereby
EP0834563A2 (en) * 1996-09-26 1998-04-08 Smithkline Beecham Corporation Human 7-transmembrane receptor, member of the chemokine receptor family, named Strl-33
WO1999014328A2 (en) * 1997-09-17 1999-03-25 Genentech, Inc. Secreted and transmembrane polypeptides and nucleic acids encoding the same
WO1999014327A2 (en) * 1997-09-17 1999-03-25 Genentech, Inc. Genes amplified in tumours, antibodies against the proteins coded thereby, and their use in diagnosis and treatment of cancer

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
CHEN H ET AL: "Cricetulus griseus HT protein mRNA, complete cds", EMBL - EMROD, XP002095039 *
KLEIN R D ET AL: "Selection for genes encoding secreted proteins and receptors", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA,US,NATIONAL ACADEMY OF SCIENCE. WASHINGTON, no. 93, 1 July 1996 (1996-07-01), pages 7108 - 7113, XP002077277, ISSN: 0027-8424 *
REVELLE B M ET AL: "SINGLE AMINO ACID RESIDUES IN THE E- AND P-SELECTIN EPIDERMAL GROWTH FACTOR DOMAINS CAN DETERMINE CARBOHYDRATE BINDING SPECIFICITY", JOURNAL OF BIOLOGICAL CHEMISTRY,US,AMERICAN SOCIETY OF BIOLOGICAL CHEMISTS, BALTIMORE, MD, vol. 271, no. 27, 5 July 1996 (1996-07-05), pages 16160 - 16170, XP000644685, ISSN: 0021-9258 *
STRAUSBERG ET AL: "oo14f12.x1 Soares_NSF_F8_9W_OT_PA_P_S1 Homo sapiens cDNA clone IMAGE:1566191 3' similar to TR:Q60438 Q60438 HT PROTEIN.;, mRNA sequence", EMBL NUCLEOTIDE SEQU, XP002131427 *
YOKOYAMA-KOBAYASHI M ET AL: "A signal sequence detection system using secreted protease activity as an indicator", GENE,NL,ELSEVIER BIOMEDICAL PRESS. AMSTERDAM, vol. 163, no. 2, 3 October 1995 (1995-10-03), pages 193 - 196, XP004041983, ISSN: 0378-1119 *

Cited By (80)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7579168B2 (en) 1997-04-16 2009-08-25 Millennium Pharmaceuticals, Inc. Human Dickkopf-related nucleic acid molecules
US7057017B2 (en) 1997-04-16 2006-06-06 Millennium Pharmaceuticals, Inc. Human dickkopf-related protein and nucleic acid molecules and uses therefor
US8202966B2 (en) 1997-04-16 2012-06-19 Millennium Pharmaceuticals, Inc. Human Dickkopf-related protein and nucleic acid molecules and uses therefor
US7645451B2 (en) 1997-04-16 2010-01-12 Millennium Pharmaceuticals, Inc. Human dickkopf-related protein and nucleic acid molecules and uses therefor
US7169906B2 (en) 1997-09-17 2007-01-30 Genentech, Inc. PRO211 polypeptides
US7449551B2 (en) 1997-09-18 2008-11-11 Genentech, Inc. PRO211 polypeptides
US8007798B2 (en) 1997-11-21 2011-08-30 Genentech, Inc. Treatment of complement-associated disorders
US7446181B2 (en) 1998-01-15 2008-11-04 Millennium Pharmaceuticals, Inc. Antibodies that bind human Dickkopf-1 proteins
US7419663B2 (en) 1998-03-20 2008-09-02 Genentech, Inc. Treatment of complement-associated disorders
US8088386B2 (en) 1998-03-20 2012-01-03 Genentech, Inc. Treatment of complement-associated disorders
US7741056B2 (en) 1998-09-16 2010-06-22 Genentech, Inc. Use of A33 antigens and JAM-IT
US7192589B2 (en) 1998-09-16 2007-03-20 Genentech, Inc. Treatment of inflammatory disorders with STIgMA immunoadhesins
US7723478B2 (en) 1998-09-25 2010-05-25 Amgen Inc. DKR polypeptides
US6902892B1 (en) 1998-10-19 2005-06-07 Diadexus, Inc. Method of diagnosing, monitoring, staging, imaging and treating prostate cancer
US7432064B2 (en) 1998-10-19 2008-10-07 Diadexus, Inc. Method of diagnosing, monitoring, staging, imaging and treating prostate cancer
WO2002064776A3 (en) * 2001-02-14 2003-08-21 Axaron Bioscience Ag Signal transduction proteins 15b3, 15b3-1 and 15b3-2, and related dna sequences
US7034132B2 (en) 2001-06-04 2006-04-25 Anderson David W Therapeutic polypeptides, nucleic acids encoding same, and methods of use
WO2003025162A3 (en) * 2001-09-20 2003-09-04 Bayer Ag Regulation of human prolyl 4-hydroxylase alpha subunit precursor
WO2003025162A2 (en) * 2001-09-20 2003-03-27 Bayer Healthcare Ag Regulation of human prolyl 4-hydroxylase alpha subunit precursor
WO2003072773A1 (en) * 2002-02-08 2003-09-04 Seikagaku Corporation Fused protein having glucuronyl transferase activity
JPWO2003083110A1 (en) * 2002-03-29 2005-08-04 独立行政法人産業技術総合研究所 Novel galactose transferase, peptide thereof and nucleic acid encoding the same
WO2003083110A1 (en) * 2002-03-29 2003-10-09 National Institute Of Advanced Industrial Science And Technology Novel galactose transferases, peptides thereof and nucleic acid encoding the same
US7705195B2 (en) 2002-06-07 2010-04-27 Genentech, Inc. Screening method
WO2004002515A1 (en) * 2002-06-28 2004-01-08 Takeda Chemical Industries, Ltd. Diagnostics/preventives/remedies for respiratory diseases
EP1558766A4 (en) * 2002-10-03 2007-12-26 Genentech Inc Use of a33 antigens and jam-it
US10414824B2 (en) 2002-11-22 2019-09-17 Ganymed Pharmaceuticals Ag Genetic products differentially expressed in tumors and the use thereof
WO2004063226A2 (en) * 2002-12-27 2004-07-29 Applied Research Systems Ars Holding N.V. Novel fibrillin-like polypeptides
WO2004063226A3 (en) * 2002-12-27 2004-09-30 Applied Research Systems Novel fibrillin-like polypeptides
US8932821B2 (en) 2003-03-19 2015-01-13 Biogen Idec Ma Inc. NOGO receptor binding protein
US7785829B2 (en) 2003-03-19 2010-08-31 Biogen Idec Ma, Inc. Nogo receptor binding protein
US8765662B2 (en) 2003-03-19 2014-07-01 Biogen Idec Ma Inc. NOGO receptor binding protein
EP1629088B1 (en) * 2003-05-30 2012-01-11 Agensys, Inc. Prostate stem cell antigen (psca) variants and subsequences thereof
EP2319524A1 (en) * 2003-05-30 2011-05-11 Agensys, Inc. Prostate stem cell antigen (PSCA) variants and subsequences thereof
EP1629088A2 (en) * 2003-05-30 2006-03-01 Agensys, Inc. Prostate stem cell antigen (psca) variants and subsequences thereof
EP2182006A2 (en) * 2003-08-11 2010-05-05 Genentech, Inc. Compositions and methods for the treatment of immune related diseases
EP2014675A1 (en) * 2003-08-11 2009-01-14 Genentech, Inc. Compositions and methods for the treatment of immune related diseases
EP2182006A3 (en) * 2003-08-11 2010-09-15 Genentech, Inc. Compositions and methods for the treatment of immune related diseases
US9775785B2 (en) 2004-05-18 2017-10-03 Ganymed Pharmaceuticals Ag Antibody to genetic products differentially expressed in tumors and the use thereof
US8486893B2 (en) 2004-06-24 2013-07-16 Biogen Idec Ma Inc. Treatment of conditions involving demyelination
US9068992B2 (en) 2004-06-24 2015-06-30 Biogen Ma Inc. Screening methods for identifying Sp35 antagonists
US7709611B2 (en) 2004-08-04 2010-05-04 Amgen Inc. Antibodies to Dkk-1
US8101184B2 (en) 2004-08-04 2012-01-24 Amgen Inc. Treatment methods using Dkk-1 antibodies
US7544659B2 (en) 2004-08-13 2009-06-09 Genentech, Inc. Promotion of axonal regeneration
US8551476B2 (en) 2005-07-08 2013-10-08 Biogen Idec Ma Inc. SP35 antibodies and uses thereof
US9066984B2 (en) 2005-07-08 2015-06-30 Biogen Ma Inc. Sp35 antibodies and uses thereof
US8753625B2 (en) 2005-11-04 2014-06-17 Genentech, Inc. Use of complement inhibitors to treat ocular diseases
US10174104B2 (en) 2005-11-24 2019-01-08 Ganymed Pharmaceuticals Gmbh Monoclonal antibodies against claudin-18 for treatment of cancer
US9751934B2 (en) 2005-11-24 2017-09-05 Ganymed Pharmaceuticals Ag Monoclonal antibodies against claudin-18 for treatment of cancer
US9499609B2 (en) 2005-11-24 2016-11-22 Ganymed Pharmaceuticals Ag Monoclonal antibodies against claudin-18 for treatment of cancer
US9212228B2 (en) 2005-11-24 2015-12-15 Ganymed Pharmaceuticals Ag Monoclonal antibodies against claudin-18 for treatment of cancer
US10738108B2 (en) 2005-11-24 2020-08-11 Astellas Pharma Inc. Monoclonal antibodies against claudin-18 for treatment of cancer
US10017564B2 (en) 2005-11-24 2018-07-10 Ganymed Pharmaceuticals Gmbh Monoclonal antibodies against claudin-18 for treatment of cancer
US11739139B2 (en) 2005-11-24 2023-08-29 Astellas Pharma Inc. Monoclonal antibodies against Claudin-18 for treatment of cancer
US8193329B2 (en) 2006-11-02 2012-06-05 Genentech, Inc. Nucleic acids encoding anti-factor D antibodies
US8187604B2 (en) 2006-11-02 2012-05-29 Genentech, Inc. Methods of treating with anti-factor D antibodies
US8372403B2 (en) 2006-11-02 2013-02-12 Genentech, Inc. Humanized anti-factor D antibodies and uses thereof
US8753826B2 (en) 2006-11-02 2014-06-17 Genentech, Inc. Methods of detecting factor D with anti-factor D antibodies
US8067002B2 (en) 2006-11-02 2011-11-29 Genentech, Inc. Humanized anti-factor D antibodies
US8128926B2 (en) 2007-01-09 2012-03-06 Biogen Idec Ma Inc. Sp35 antibodies and uses thereof
US8609407B2 (en) 2007-01-09 2013-12-17 Biogen Idec Ma Inc. Sp35 antibodies and uses thereof
US8268310B2 (en) 2007-05-23 2012-09-18 Genentech, Inc. Prevention and treatment of complement-associated eye conditions
US8497094B2 (en) 2007-05-23 2013-07-30 Genentech, Inc. Prevention and treatment of complement-associated eye conditions
US8007791B2 (en) 2007-05-23 2011-08-30 Genentech, Inc. Prevention and treatment of complement-associated eye conditions
US9676868B2 (en) 2008-04-28 2017-06-13 Genentech, Inc. Humanized anti-factor D antibodies and uses thereof
US8273352B2 (en) 2008-04-28 2012-09-25 Genentech, Inc. Humanized anti-factor D antibodies and uses thereof
US8614306B2 (en) 2008-04-28 2013-12-24 Genentech, Inc. Polynucleotides encoding humanized anti-factor D antibodies
US9234024B2 (en) 2008-05-06 2016-01-12 Genentech, Inc. Affinity matured CRIg variants
US9745375B2 (en) 2008-07-09 2017-08-29 Biogen Ma Inc. Compositions comprising antibodies to LINGO or fragments thereof
US8425910B2 (en) 2008-07-09 2013-04-23 Biogen Idec Ma Inc. Composition comprising antibodies to LINGO or fragments thereof
US8058406B2 (en) 2008-07-09 2011-11-15 Biogen Idec Ma Inc. Composition comprising antibodies to LINGO or fragments thereof
US9512232B2 (en) 2012-05-09 2016-12-06 Ganymed Pharmaceuticals Ag Antibodies against Claudin 18.2 useful in cancer diagnosis
US10053512B2 (en) 2012-05-09 2018-08-21 Ganymed Pharmaceuticals Ag Antibodies against claudin 18.2 useful in cancer diagnosis
US9796780B2 (en) 2012-05-14 2017-10-24 Biogen Ma Inc. LINGO-2 antagonists for treatment of conditions involving motor neurons
US10947591B2 (en) 2013-08-12 2021-03-16 Genentech, Inc. Compositions and method for treating complement-associated conditions
US10093978B2 (en) 2013-08-12 2018-10-09 Genentech, Inc. Compositions for detecting complement factor H (CFH) and complement factor I (CFI) polymorphisms
US10179821B2 (en) 2014-05-01 2019-01-15 Genentech, Inc. Anti-factor D antibodies
US10435467B2 (en) 2015-01-08 2019-10-08 Biogen Ma Inc. LINGO-1 antagonists and uses for treatment of demyelinating disorders
US10407510B2 (en) 2015-10-30 2019-09-10 Genentech, Inc. Anti-factor D antibodies and conjugates
US10654932B2 (en) 2015-10-30 2020-05-19 Genentech, Inc. Anti-factor D antibody variant conjugates and uses thereof
US10961313B2 (en) 2015-10-30 2021-03-30 Genentech, Inc. Anti-factor D antibody variant conjugates and uses thereof

Also Published As

Publication number Publication date
AU2883900A (en) 2001-01-30

Similar Documents

Publication Publication Date Title
US6965011B2 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
US7208312B1 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
WO2001004311A1 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
US6908993B2 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
US20070077623A1 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
WO2000077037A2 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
WO2000015796A2 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
US7033825B2 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
US7449551B2 (en) PRO211 polypeptides
US20090170158A1 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
WO2000032776A2 (en) Secreted amd transmembrane polypeptides and nucleic acids encoding the same
US7241865B2 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
US6894148B2 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
US7169906B2 (en) PRO211 polypeptides
US7307152B2 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
US7417126B2 (en) PRO246 antibodies
US20040137561A1 (en) Secreted and transmembrane polypeptides and nucleic acids encoding the same
ZA200103574B (en) Secreted and transmembrane polypeptides and nucleic acids and encoding the same.

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A1

Designated state(s): AE AL AM AT AU AZ BA BB BG BR BY CA CH CN CR CU CZ DE DK DM EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A1

Designated state(s): GH GM KE LS MW SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
WWE Wipo information: entry into national phase

Ref document number: 10265542

Country of ref document: US

122 Ep: pct application non-entry in european phase
WWE Wipo information: entry into national phase

Ref document number: 11542578

Country of ref document: US

WWP Wipo information: published in national office

Ref document number: 11542578

Country of ref document: US

DPE2 Request for preliminary examination filed before expiration of 19th month from priority date (pct application filed from 20040101)