ZA200104218B

ZA200104218B - Compositions and methods for the treatment of tumor.

Info

Publication number: ZA200104218B
Application number: ZA200104218A
Authority: ZA
Inventors: David Botstein; Audrey Goddard; Austin L Gurney; Kenneth Hillan; David A Lawrence; Margaret Ann Roy; William I Wood
Original assignee: Genentech Inc
Priority date: 1998-12-22
Filing date: 2001-05-23
Publication date: 2002-05-23
Also published as: WO2000037640A2; ZA200103885B; IL143212A0; CA2353775A1; JP2003524390A; WO2000037640A3; MXPA01006345A; WO2000037640A9; AU2192800A; KR20010102960A; EP1141289A2

Description

ro, A WO 00/37640 PCT/US99/30095

COMPOSITIONS AND METHODS FOR THE TREATMENT OF TUMOR

Field of the Invention

The present invention relates to compositions and methods for the diagnosis and treatment of tumor.

Background of the Invention

Malignant tumors (cancers) are the second leading cause of death in the United States, after heart disease (Boring et al., CA Cancel J. Clin., 43:7 {1993]).

Cancer is characterized by an increase in the number of abnormal, or neoplasticcells derived froma normal tissue which proliferate to form a turnor mass, the invasion of adjacent tissues by these neoplastic tumor cells, and the generation of malignant cells which eventually spread via the blood or lymphatic system toregional lymph nodes and to distant sites (metastasis). In a cancerous state, a cell proliferates under conditions in which normal cells , would not grow. Cancer manifests itself in a wide variety of forms, characterized by different degrees of invasiveness and aggressiveness. } 20 Alteration of gene expression is intimately related to the uncontrolled cell growth and de-differentiation which are a common feature of all cancers. The genomes of certain well studied tumors have been found to show decreased expression of recessive genes, usually referred to as tumor suppression genes, which would normally function to prevent malignant cell growth, and/or overexpression of certain dominant genes, such as oncogenes, that act to promote malignant growth. Each of these genetic changes appears to be responsible for importing some of the traits that, in aggregate, represent the full neoplastic phenotype (Hunter, Cell, 64:1129 [1991] and Bishop,

Cell, 64:235-248 [1991)).

A well known mechanism of gene (e.g., oncogene) overexpression in cancer cells is gene amplification.

This is a process where in the chromosome of the ancestral cell multiple copies of a particular gene are produced.

The process involves unscheduled replication of the region of chromosome comprising the gene, followed by recombination of the replicated segments back into the chromosome (Alitalo er al., Adv. Cancer Res., 47:235-281 [1986)). Itis believed that the overexpression of the gene parallels gene amplification, i. e., is proportionate to the number of copies made.

Proto-oncogenes that encode growth factors and growth factor receptors have been identified to play important roles in the pathogenesis of various human malignancies, including breast cancer. For example, it has been found that the human ErbB2 gene (erbB2, also known as her2, or c-erbB-2), which encodes a 185-kd transmembrane glycoprotein receptor (p185%5%%; HER?) related to the epidermal growth factor receptor EGFR), is overexpressed in about 25% to 30% of human breast cancer (Slamon et al., Science, 235:177-182 [1987]; Slamon etal., Scieqce, 244:707-712 [1989]).

Ithas been reported that gene amplification of a proto-oncogene is an event typically involved in the more malignant forms of cancer, and could act as a predictor of clinical outcome (Schwab et al., Genes Chromosomes

Cancer, 1:181-193 [1990]; Alitalo et al., supra). Thus, erbB2 overexpression is commonly regarded as a predictor of a poor prognosis, especially in patients with primary disease that involves axillary lymph nodes (Slamon ez al.,

[1987] and[1989], supra; Ravdin and Chamness, Gene, 159:19-27 [1995]; and Hynes and Stern, Biochim. Biophys.

Acta, 1198:165-184 [1994]), and has been linked to sensitivity and/or resistance to hormone therapy and chemotherapeutic regimens, including CMF (cyclophosphamide, methotrexate, and fluoruracil) and anthracyclines (Baselga etal., Oncology, 11 (3 Suppl 1):43-48 [1997]). However, despite the association of erbB2 overexpression with poor prognosis, the odds of HER2-positive patients responding clinically to treatment with taxanes were greater than three times those of HER 2-negative patients (Ibid). A recombinant humanized anti-ErbB2 (anti-HER?2) monoclonal antibody (a humanized version of the murine anti-ErbB2 antibody 4D5, referred to as rhuMAb HER2 or Herceptin™) has been clinically active in patients with ErbB2-overexpressing metastatic breast cancers that had received extensive prior anticancer therapy. (Baselga et al., J. Clin. Oncol., 14:737-744 [1996]).

In light of the above, there is obvious interest in identifying novel methods and compositions which are useful for diagnosing and treating tumors which are associated with gene amplification.

Summary of the Invention

A. Embodiments

The present invention concerns compositions and methods for the diagnosis and treatment of neoplastic cell growth and proliferation in mammals, including humans. The present invention is based on the identification ) of genes that are amplified in the genome of tumor cells. Such gene amplification is expected to be associated with the overexpression of the gene product and contribute to tumorigenesis. Accordingly, the proteins encoded by the amplified genes are believed to be useful targets for the diagnosis and/or treatment (including prevention) of certain cancers, and may act as predictors of the prognosis of tumor treatment.

In one embodiment, the present invention concerns an isolated antibody which binds to a polypeptide desighated hereit as 4 FROZ01, FRO292, TRO327; PRO126S, PRO244, PRNO34R PRNUT PRO3ST. PROTLS. :

PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide. In one aspect, the isolated antibody specifically binds toa PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017,

PROI1112, PRO509, PRO853 or PRO882 polypeptide. In another aspect, the antibody induces the death of a cell which expresses a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PROI1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide. Often, the cell that expresses the PRO201,

PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509,

PROS53 or PRO882 polypeptide is a tumor cell that overexpresses the polypeptide as compared to a normal cell of the same tissue type. In yet another aspect, the antibody is a monoclonal antibody, which preferably has non- human complementarity determining region (CDR) residues and human framework region (FR) residues. The antibody may be labeled and may be immobilized on a solid support. In yet another aspect, the antibody is an antibody fragment, a single-chain antibody, or a humanized antibody which binds, preferably specifically, to a rv, a WO00/37640 PCT/US99/30095

PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112,

PROS509, PRO853 or PRO882 polypeptide.

In another embodiment, the invention concerns a composition of matter which comprises an antibody which binds, preferably specifically, to a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide in admixture with a pharmaceutically acceptable carrier. In one aspect, the composition of matter comprises a therapeutically effective amount of the antibody. In another aspect, the composition comprises a further active ingredient, which may, for example, be a further antibody or a cytotoxic or chemotherapeutic agent. Preferably, the composition is sterile.

In a further embodiment, the invention concerns isolated nucleic acid molecules which encode anti-

PRO201, anti-PR0O292, anti-PRO327, anti-PRO1265, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibodies, and vectors and recombinant host cells comprising such nucleic acid molecules.

In a still further embodiment, the invention concerns a method for producing an anti-PRO201, anti-

PRO292, anti-PRO327, anti-PRO1265, anti-PR0O344, anti-PR0O343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody, wherein the method comprises culturing a host cell transformed with a nucleic acid molecule which encodes the antibody under conditions sufficient to allow expression of the antibody, and recovering the antibody from the cell culture.

The invention further concerns antagonists of a PRO201, PRO292, PR0O327, PRO1265, PRO344,

PRO343,PR0347,PRO357, PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide that inhibit one or more of the biological and/or immunological functions or activities of a PRO201, PR0292, PRO327, ’ PRO1265, PRO344, PRO343, PRO347,PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide.

In a further embodiment, the invention concerns an isolated nucleic acid molecule that hybridizes to a nucleic acid molecule encoding a PRO201, PR0O292, PRO327, PRO1265, PRO344, PRO343, PR0O347, PRO357,

PRO715,PRO1017,PRO1112,PRO509, PRO853 or PRO882 polypeptide or the complement thereof. The isolated nucleic acid molecule is preferably DNA, and hybridization preferably occurs under stringent hybridization and wash conditions. Such nucleic acid molecules can act as antisense molecules of the amplified genes identified herein, which, in turn, can find use in the modulation of the transcription and/or translation of the respective amplified genes, or as antisense primers in amplification reactions. Furthermore, such sequences can be used as part of a ribozyme and/or a triple helix sequence which, in turn, may be used in regulation of the amplified genes.

In another embodiment, the invention provides a method for determining the presence of a PRO201,

PROS853 or PRO8S?2 polypeptide in a sample suspected of containing a PRO201, PR0O292, PRO327, PRO1265,

PRO344,PR0O343,PR0O347, PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide, wherein the method comprises exposing the sample to an anti-PR0O201, anti-PR0292, anti-PRO327, anti-PRO 1265, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PROI1112, anti-

PROS509, anti-PRO853 or anti-PRO882 antibody and determining binding of the antibody to a PRO201, PRO292,

PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357,PRO715, PRO1017, PRO1112, PRO509, PRO853 or _3-

PROB882 polypeptide in the sample. In another embodiment, the invention provides a method for determining the presence of a PRO201, PR0O292, PR0O327,PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,PRO1017,

PRO1112, PRO509, PRO853 or PRO882 polypeptide in a cell, wherein the method comprises exposing the cell to an anti-PRO201, anti-PR0O292, anti-PRO327, anti-PRO1265, anti-PR0O344, anti-PR0O343, anti-PR0O347, anti-

PRO357, anti-PRO715, anti-PRO1017, anti-PRO11 12, anti-PRO509, anti-PRO853 or anti-PRO882 antibody and determining binding of the antibody to the cell.

In yet another embodiment, the present invention concerns a method of diagnosing tumor in a mammal, comprising detecting the level of expression of a gene encoding aPR0O201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample as compared to the control sample, is indicative of the presence of tumor in the mammal from which the test tissue cells were obtained.

In another embodiment, the present invention concerns a method of diagnosing tumor in a mammal, comprising (a) contacting an anti-PR0201, anti-PR0O292, anti-PR0O327, anti-PRO1263, anti-PR0O344, anti-PR0343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-

PRO882 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of acomplex between the anti-PRO201, anti-PR0292, anti-PR0O327, anti-PR0O1265, anti-PR0O344, anti-PR0O343, anti-

PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PROS509, anti-PRO853 or anti-PRO882 ) antibody anda PRO201, PRO292,PRO327,PRO1265,PR0O344, PRO343, PRO347,PR0O357, PRO715,PRO1017,

PROI1112, PROS09, PRO853 or PROS882 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of a tumor in said mammal. The detection may be qualitative or quantitative, and may ) be performed in comparison with monitoring the complex formation in a control sample of known normal tissue cells of the same cell type. A larger quantity of complexes formed in the test sample indicates the presence of tumor in the mammal from which the test tissue cells were obtained. The antibody preferably carries a detectable label.

Complex formation can be monitored, for example, by light microscopy, flow cytometry, fluorimetry, or other techniques known in the art.

The test sample is usually sbtained from an individual cucpected to have neoplactic cell growth or proliferation (e.g. cancerous cells).

In another embodiment, the present invention concerns a cancer diagnostic kit comprising an anti-PRO201, anti-PRO292, anti-PR0327, anti-PR0O1265, anti-PRO344, anti-PR0343, anti-PRO347, anti-PR0O357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PROS509, anti-PRO853 or anti-PRO882 antibody and a carrier (e.g., a buffer) in suitable packaging. The kit preferably contains instructions for using the antibody to detect the presence of a

PRO509, PRO853 or PRO882 polypeptide in a sample suspected of containing the same.

In yet another embodiment, the invention concerns a method for inhibiting the growth of tumor cells comprising exposing tumor cells which express a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343,

PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide to an effective amount of an agent which inhibits a biological and/or immunological activity and/or the expression of a PRO201,

PR0O292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PROS09,

PROS853 or PRO8BS82 polypeptide, wherein growth of the tumor cells is thereby inhibited. The agent preferably is an anti-PRO201, anti-PRO292, anti-PRO327, anti-PRO1265, anti-PRO344, anti-PR0O343, anti-PRO347, ant-

PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody, a

S small organic and inorganic molecule, peptide, phosphopeptide, antisense or ribozyme molecule, or a triple helix molecule. In a specific aspect, the agent, e.g., the anti-PRO201, anti-PR0292, anti-PR0O327, anti-PRO1265, anti-

PRO344, anti-PR0O343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody, induces cell death. In a further aspect, the tumor cells are further exposed to radiation treatment and/or a cytotoxic or chemotherapeutic agent.

In a further embodiment, the invention concerns an article of manufacture, comprising: a container; a label on the container; and a composition comprising an active agent contained within the container; wherein the composition is effective for inhibiting the growth of tumor cells and the label on the container indicates that the composition can be used for treating conditions characterized by overexpression of a PRO201, PR0O292, PRO327, PRO1265,

PRO344,PR0O343,PRO347, PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide as compared to a normal cell of the same tissue type. In particular aspects, the active agent in the composition is an agent which inhibits an activity and/or the expression of a PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide. In preferred aspects, the active agent is an anti-PR0O201, anti-PR0O292, anti-PRO327, anti-PRO1265, anti-PRO344, ; anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-

PRO853 or anti-PRO882 antibody or an antisense oligonucleotide.

The invention also provides a method for identifying a compound that inhibits an activity of a PRO201,

PR0O292, PRO327, PRO1265, PRO344, PR0O343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509,

PROB853 or PRO882 polypeptide, comprising contacting a candidate compound witha PRO201, PRO292, PRO327,

PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide under conditions and for a time sufficient to allow these two components to interact and determining whether a biological and/or immunological activity of the PRO201, PR0O292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide is inhibited. In a specific aspect, either the candidate compound or the PRO201, PRO292, PRO327, PRO1265,

PRO344,PR0O343,PR0O347, PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide is immobilized on a solid support. In another aspect, the non-immobilized component carries a detectable label.

In a preferred aspect, this method comprises the steps of (a) contacting cells and a candidate compound to be screened in the presence of the PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357,

PRO715, PRO1017, PRO1112, PROS09, PRO853 or PRO&82 polypeptide under conditions suitable for the induction of a cellular response normally induced by a PRO201,PR0O292, PRO327, PRO1265, PRO344, PRO343,

PRO347,PR0O357,PRO715,PRO1017,PRO1112,PRO509,PRO853 or PRO882 polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist.

In another embodiment, the invention provides a method for identifying a compound that inhibits the expression of a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017,PRO1112,PRO509, PRO85 3 or PRO882 polypeptide in cells that express the polypeptide, wherein the method comprises contacting the cells with a candidate compound and determining whether the expression of the

PRO509, PRO853 or PRO882 polypeptide is inhibited. In a preferred aspect, this method comprises the steps of (a) contacting cells and a candidate compound to be screened under conditions suitable for allowing expression of the PRO201, PRO292, PRO327,PRO1265, PRO344, PRO343,PRO347,PRO357,PRO715,PRO1017,PRO1112,

PROS509, PRO853 or PRO882 polypeptide and (b) determining the inhibition of expression of said polypeptide.

B. Additional Embodiments

In other embodiments of the present invention, the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence that encodes a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343,

PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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% i 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 aPRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112,

PRO308, FRO833 ul FRO882 pulypeptide having & full length amine acid cequence ac dicclnced herein. an amino acid sequence lacking the signal peptide as disclosed herein, an extracellular domain of a transmembrane protein, with or without the signal peptide, as disclosed herein or any other specifically defined fragment of the full-length amino acid sequence 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 PRO201,PRO292, PRO327,PR0O1265, PRO344,PR0O343, PRO347, PRO357,

S PRO715,PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide cDNA as disclosed herein, the coding sequence of aPRO201, PR0292, PRO327,PRO1265,PRO344, PR0O343,PRO347,PRO357,PRO715,PRO1017,

PRO1112, PRO509, PRO853 or PRO882 polypeptide lacking the signal peptide as disclosed herein, the coding sequence of an extracellular domain of a transmembrane PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide, with or without the signal peptide, as disclosed herein or the coding sequence of any other specifically defined fragment of the full-length amino acid sequence 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 of the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence encoding a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017, PRO1112, PRO509, PRO853 or PRO882 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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptides are contemplated.

Another embodiment is directed to fragments of a PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO832 polypeptide coding sequence, or the complement thereof, that may find use as, for example, hybridization probes, for encoding fragments of aPR0O201,PRO292,PRO327,PRO1265, PR0O344,PR0O343,PR0O347,PRO357,PRO715,PRO1017,

PRO1112, PRO509, PRO853 or PRO882 polypeptide that may optionally encode a polypeptide comprising a binding site for an anti-PRO201, anti-PRO292, anti-PR0O327, anti-PRO1265, anti-PRO344, anti-PRO343, anti-

PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody or as antisense oligonucleotide probes. 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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357,PRO715, PRO1017,

PRO1112,PRO509, PRO853 or PRO882 polypeptide-encoding nucleotide sequence may be determined in aroutine manner by aligning the PRO201, PRO292, PR0O327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, i

PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide-encoding nucleotide sequence with other known nucleotide sequences using any of a number of well known sequence alignment programs and determining which

PROS509, PRO853 or PRO882 polypeptide-encoding nucleotide sequence fragmeni(s) are novel. All of such

PRU309, PROBI3 ul FROB8Z pulypcpiide-enesding nuclectide sequences are contemplated herein. Also conternplated are the PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide fragments encoded by these nucleotide molecule fragments, preferably those PRO201, PRO292, PRO327, PRO1265, PR0O344, PRO343, PRO347, PRO357,

PRO715, PRO1017, PRO1112, PROS509, PRO853 or PRO882 polypeptide fragments that comprise a binding site for an anti-PRO201, anti-PR0O292, anti-PRO327, anti-PRO1265, anti-PRO344, anti-PRO343, anti-PR0O347, anti-

PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody.

In another embodiment, the invention provides isolated PRO201, PRO292, PRO327,PROI 265,PR0O344,

PRO343,PR0O347, PRO357, PRO715, PRO1017, PRO1112, PROS09, PRO853 or PRO882 polypeptide encoded by any of the isolated nucleic acid sequences hereinabove identified.

In a certain aspect, the invention concerns an isolated PRO201, PRO292, PRO327,PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide,

’ a» WO 00/37640 PCT/US99/30095 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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, -PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide having a full-length amino acid sequence as disclosed herein, an amino acid sequence lacking the signal peptide as disclosed herein, an extracellular domain of a transmembrane protein, with or without the signal peptide, as disclosed herein or any other specifically defined fragment of the full-length amino acid sequence as disclosed herein.

In a further aspect, the invention concerns an isolated PRO201, PR0O292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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 PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO88B2 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 PRO201, PRO292, PR0327,PRO1265, PRO344, PRO343, PRO347, PRO357,

PRO715, PRO1017, PRO1112, PROS509, PRO853 or PRO882 polypeptide having a full-length amino acid sequence as disclosed herein, an amino acid sequence lacking the signal peptide as disclosed herein, an extracellular domain of a transmembrane protein, with or without the signal peptide, as disclosed herein or any other specifically defined fragment of the full-length amino acid sequence as disclosed herein.

In a specific aspect, the invention provides an isolated PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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 culturing a host cell comprising a vector which comprises the appropriate encoding nucleic acid molecule under conditions suitable for expression of the PRO201, PR0292,

PRO327,PRO1265, PRO344, PRO343, PRO347,PR0O357,PRO715, PRO1017, PRO1112,PRO509, PRO853 or

PRO882 polypeptide and recovering the PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide from the cell culture.

Another aspect of the invention provides an isolated PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide which : is either transmembrane domain-deleted or transmembrane domain-inactivated. Processes for producing the same are also herein described, wherein those processes comprise culturing a host cell comprising a vector which comprises the appropriate encoding nucleic acid molecule under conditions suitable for expression of the PRO201, ’

PRO853 or PRO882 polypeptide and recovering the PRO201, PR0292, PRO327, PRO1265, PRO344, PRO343,

PRO347,PR0O357,PRO715,PRO1017,PRO1112,PRO509, PRO853 or PRO882 polypeptide from the cell culture.

In yet another embodiment, the invention concerns antagonists of a native PRO201, PRO292, PRO327,

PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 pulgpeptide as defined licrcin. In a partiealar embodiment; the antagonist ic an anti. PROVOT anti-PROJG)._anti-

PRO327, anti-PRO1265, anti-PRO344, anti-PRO343, anti-PRO347, anti-PR0O357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody or a small molecule.

In a further embodiment, the invention concerns a method of identifying antagonists to a PRO201,

PRO853 or PRO882 polypeptide which comprise contacting the PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide with a candidate molecule and monitoring a biological activity mediated by said PRO201, PRO292, PRO327, PRO1265,

PRO344,PR0343,PRO347,PR0O357,PRO715,PRO1017,PRO1112,PRO509, PRO853 or PRO882 polypeptide.

Preferably, the PRO201, PRO292, PRO327,PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,PRO1017,

PRO1112, PROS09, PRO853 or PRO882 polypeptide is a native PRO201, PRO292, PR0327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide.

: eo WO 00/37640 PCT/US99/30095

In a still further embodiment, the invention concerns a composition of matter comprising a PRO201,

PRO853 or PRO882 polypeptide, or an antagonist of a PRO201,PR0292,PR0327, PRO1265, PRO344, PRO343,

PRO347,PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide as herein described, or an anti-PR0O201, anti-PRO292, anti-PR0O327, anti-PRO1265, anti-PR0O344, anti-PR0343, anti-PR0O347, anti-

PRO357, anti-PRO7135, anti-PRO1017, anti-PRO1112, anti-PROS09, anti-PRO853 or anti-PRO882 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 PRO201, PRO292, PRO327,

PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,PRO1017, PRO1112, PROS09, PRO853 or PRO882 polypeptide, or an antagonist thereof as hereinbefore described, or an anti-PRO201, anti-PR0292, anti-PRO327, anti-PRO12635, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-

PRO1112, anti-PR0O509, anti-PRO853 or anti-PRO882 antibody, for the preparation of a medicament useful in the treatment of a condition which is responsive to the PRO201, PRO292, PR0O327, PRO12635, PRO344, PRO343,

PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PROBB2 polypeptide, an antagonist thereof or an anti-PRO20I, anti-PR0O292, anti-PRO327, anti-PR0O1265, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO101 7, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody.

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, yeast, or Baculovirus-infected insect cells. 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 fromthe 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 or as antisense probes, wherein those probes may be derived from any of the above or below described nucleotide sequences.

Brief Description of the Figures

Figure 1 shows the nucleotide sequence (SEQ ID NO:1) of a cDNA containing a nucleotide sequence encoding native sequence PRO201, wherein the nucleotide sequence (SEQ ID NO:1) is a clone designated herein as DNA30676-1223. Also presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 2 shows the amino acid sequence (SEQ ID NO:2) of a native sequence PRO201 polypeptide as _11-

derived from the coding sequence of SEQ ID NO:1 shown in Figure 1.

Figure 3 shows the nucleotide sequence (SEQ ID NO:5) of a cDNA containing a nucleotide sequence encoding native sequence PRO292, wherein the nucleotide sequence (SEQ ID NO:5) is a clone designated herein as DNA35617. Also presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 4 shows the amino acid sequence (SEQ ID NO:6) of a native sequence PRO292 polypeptide as derived from the coding sequence of SEQ ID NO:5 shown in Figure 3.

Figure 5 shows the nucleotide sequence (SEQ ID NO:7) of a cDNA containing a nucleotide sequence encoding native sequence PRO327, wherein the nucleotide sequence (SEQ ID NO:7) is a clone designated herein as DNA38113-1230. Also presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 6 shows the amino acid sequence (SEQ ID NO:8) of a native sequence PRO327 polypeptide as derived from the coding sequence of SEQ ID NO:7 shown in Figure 3.

Figure 7 shows the nucleotide sequence (SEQ ID NO:12) of a cDNA containing a nucleotide sequence encoding native sequence PRO1265, wherein the nucleotide sequence (SEQ ID NO: 12) is a clone designated herein as DNA60764-1533. Also presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 8 shows the amino acid sequence (SEQ ID NO:13) of a native sequence PRO1265 polypeptide as derived from the coding sequence of SEQ ID NO:12 shown in Figure 7.

Figure 9 shows the nucleotide sequence (SEQ ID NO:14) of a cDNA containing a nucleotide sequence encoding native sequence PRO344, wherein the nucleotide sequence (SEQ ID NO:14) is a clone designated herein as DNA40592-1242. Also presented in bold font and underlined are the positions of the respective start and stop : codons.

Figure 10 shows the amino acid sequence (SEQ ID NO:15) of a native sequence PRO344 polypeptide as derived from the coding sequence of SEQ ID NO:14 shown in Figure 9.

Figure 11 shows the nucleotide sequence (SEQ 1D NO:22) of a cDNA containing a nucleotide sequence encoding native sequence PRO343, wherein the nucleotide sequence (SEQ ID NO:22) is a clone designated herein as DMA43318 1217: Aldss presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 12 shows the amino acid sequence (SEQ ID NO:23) of a native sequence PRO343 polypeptide as derived from the coding sequence of SEQ ID NO:22 shown in Figure 11.

Figure 13 shows the nucleotide sequence (SEQ ID NO:27) of a cDNA containing a nucleotide sequence encoding native sequence PRO347, wherein the nucleotide sequence (SEQ ID NO:27) is aclone designated herein as DNA44176-1244. Also presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 14 shows the amino acid sequence (SEQ ID NO:28) of a native sequence PRO347 polypeptide as derived from the coding sequence of SEQ ID NO:27 shown in Figure 13.

Figure 15 shows the nucleotide sequence (SEQ ID NO:32) of a cDNA containing a nucleotide sequence encoding native sequence PRO357, wherein the nucleotide sequence (SEQ ID NO:32)is a clone designated herein as DNA44804-1248. Also presented in bold font and underlined are the positions of the respective start and stop

. a WO 00/37640 PCT/US99/30095 codons.

Figure 16 shows the amino acid sequence (SEQ ID NO:33) of a native sequence PRO357 polypeptide as derived from the coding sequence of SEQ ID NO:32 shown in Figure 15.

Figure 17 shows the nucleotide sequence (SEQ ID NO:39) of a cDNA containing a nucleotide sequence encoding native sequence PRO715, wherein the nucleotide sequence (SEQ ID NO:39) is a clone designated herein as DNA52722-1229. Also presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 18 shows the amino acid sequence (SEQ ID NO:40) of a native sequence PRO715 polypeptide as derived from the coding sequence of SEQ ID NO:39 shown in Figure 17.

Figure 19 shows the nucleotide sequence (SEQ ID NO:41) of a cDNA containing a nucleotide sequence encoding native sequence PRO1017, wherein the nucleotide sequence (SEQ ID NO:41) is a clone designated herein as DNAS56112-1379. Also presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 20 shows the amino acid sequence (SEQ ID NO:42) of a native sequence PRO1017 polypeptide as derived from the coding sequence of SEQ ID NO:41 shown in Figure 19.

Figure 21 shows the nucleotide sequence (SEQ ID NO:43) of a cDNA containing a nucleotide sequence encoding native sequence PRO1112, wherein the nucleotide sequence (SEQ ID NO:43) is a clone designated herein as DNAS7702-1476. Also presented in bold font and underlined are the positions of the respective start and stop codons. . 20 Figure 22 shows the amino acid sequence (SEQ ID NO:44) of a native sequence PRO1112 polypeptide ’ as derived from the coding sequence of SEQ ID NO:43 shown in Figure 21.

Figure 23 shows the nucleotide sequence (SEQ ID NO:45) of a cDNA containing a nucleotide sequence encoding native sequence PRO509, wherein the nucleotide sequence (SEQ ID NO:45) is a clone designated herein as DNASOQ148. Also presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 24 shows the amino acid sequence (SEQ ID NO:46) of a native sequence PROS509 polypeptide as derived from the coding sequence of SEQ ID NO:45 shown in Figure 23.

Figure 25 shows the nucleotide sequence (SEQ ID NO:47) of a cDNA containing a nucleotide sequence encoding native sequence PRO853, wherein the nucleotide sequence (SEQ ID NO:47) is a clone designated herein as DNA48227-1350. Also presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 26 shows the amino acid sequence (SEQ ID NQO:48) of a native sequence PRO853 polypeptide as derived from the coding sequence of SEQ ID NO:47 shown in Figure 25.

Figure 27 shows the nucleotide sequence (SEQ ID NO:52) of a cDNA containing a nucleotide sequence encoding native sequence PRO882, wherein the nucleotide sequence (SEQ ID NO:52) is a clone designated herein as DNASBI25. Also presented in bold font and underlined are the positions of the respective start and stop codons.

Figure 28 shows the amino acid sequence (SEQ ID NO:53) of a native sequence PRO882 polypeptide as derived from the coding sequence of SEQ ID NO:52 shown in Figure 27.

Figure 29 is a map of chromosome 19 showing the mappingregions of DNA30676-1223, DNA38113-1230 and DNAG60764-1533.

Figure 30 is a map of chromosome 11 showing the mapping region of DNA35617.

Figure 31 is a map of chromosome 16 showing the mapping region of DNA43318-1217and DNA58125.

Figure 32 is a map of chromosome 7 showing the mapping region of DNA56112-1379.

Figure 33A is map of chromosome 17 showing the mapping region of DNA52722-1229.

Figure 33B is a map of chromosome 17 showing the mapping region of DNA48227-1350.

Figure 34 is a map of chromosome 16 showing the mapping region of DNA44804-1248.

Detailed Description of the Invention

IL Definitions

The phrases "gene amplification” and "gene duplication" are used interchangeably and refer to a process by which multiple copies of a gene or gene fragment are formed in a particular cell or cell line. The duplicated region (a stretch of amplified DNA) is often referred to as "amplicon." Usually, the amount of the messenger RNA (mRNA) produced, i.e., the level of gene expression, also increases in the proportion of the number of copies made of the particular gene expressed. "Tumor", as used herein, refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues.

The terms “cancer” and "cancerous" refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. Examples of cancer include but are not limited to, carcinoma, lymphoma, blastoma, sarcoma, and leukemia. More particular examples of such cancers include breast cancer, prostate cancer, colon cancer, squamous cell cancer, small-cell lung cancer, non-small cell lung cancer, gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, ) hepatoma, colorectal cancer, endometrial carcinoma, salivary gland carcinoma, kidney cancer, liver cancer, vulval cancer, thyroid cancer, hepatic carcinoma and various types of head and neck cancer. "Treatment" is an intervention performed with the intention of preventing the development or altering the pathology of a disorder. Accordingly, "treatment" refers to both therapeutic treatment and prophylactic or preventative measures. Those in need of treatment include those already with the disorder as well as those in which tite disutlet is iv be prescaicd. In tumor {¢:85 eanssr) Geatment 2 therapeutic agent may directly decrease the pathology of tumor cells, or render the tumor cells more susceptible to treatment by other therapeutic agents, e.g, radiation and/or chemotherapy.

The "pathology" of cancer includes all phenomena that compromise the well-being of the patient. This includes, without limitation, abnormal or uncontrollable cell growth, metastasis, interference with the normal functioning of neighboring cells, release of cytokines or other secretory products at abnormal levels, suppression or aggravation of inflammatory or immunological response, etc. "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, horses, cats, cattle, pigs, sheep, 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. Examples of physiologically acceptable s y» WO 00/37640 PCT/US99/30095 carriers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (ess than about 10 residues) polypeptides; proteins, such as seram 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™,

Administration "in combination with" one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.

The term "cytotoxic agent” as used herein refers to a substance that inhibits or prevents the function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes (e.g., I'*', I'*%, Y*" and

Re'®%), chemotherapeutic agents, and toxins such as enzymatically active toxins of bacterial, fungal, plant or animal origin, or fragments thereof.

A "chemotherapeutic agent” is a chemical compound useful in the treatment of cancer. Examples of chemotherapeutic agents include adriamycin, doxorubicin, epirubicin, 5-fluorouracil, cytosine arabinoside ("Ara-

C"), cyclophosphamide, thiotepa, busulfan, cytoxin, taxoids, e.g., paclitaxel (Taxol, Bristol-Myers Squibb

Oncology, Princeton, NJ), and doxetaxel (Taxotere, Rhone-Poulenc Rorer, Antony, Rnace), toxotere, methotrexate, cisplatin, melphalan, vinblastine, bleomycin, etoposide, ifosfamide, mitomycin C, mitoxantrone, vincristine, . vinorelbine, carboplatin, teniposide, daunomycin, carminomycin, aminopterin, dactinomycin, mitomycins, esperamicins (see U.S. Pat. No. 4,675,187), 5-FU, 6-thioguanine, 6-mercaptopurine, actinomycin D, VP-16, - chlorambucil, melphalan, and other related nitrogen mustards. Also included in this definition are hormonal agents that act to regulate or inhibit hormone action on tumors such as tamoxifen and onapristone.

A "growth inhibitory agent” when used herein refers to a compound or composition which inhibits growth of a cell, especially cancer cell overexpressing any of the genes identified herein, either in vitro or in vivo. Thus, the growth inhibitory agent is one which significantly reduces the percentage of cells overexpressing such genes in S phase. Examples of growth inhibitory agents include agents that block cell cycle progression (at a place other than S phase), such as agents that induce G1 arrest and M-phase arrest. Classical M-phase blockers include the vincas (vincristine and vinblastine), taxol, and topo II inhibitors such as doxorubicin, epirubicin, daunorubicin, etoposide, and bleomycin. Those agents that arrest G1 also spill over into S-phase arrest, for example, DNA alkylating agents such as tamoxifen, prednisone, dacarbazine, mechlorethamine, cisplatin, methotrexate, 5- fluorouracil, and ara-C. Further information can be found in The Molecular Basis of Cancer, Mendelsohn and

Israel, eds., Chapter 1, entitled "Cell cycle regulation, oncogens, and antineoplastic drugs" by Murakami ez al., (WB

Saunders: Philadelphia, 1995), especially p. 13. “Doxorubicin” is an anthracycline antibiotic. The full chemical name of doxorubicin is (8S-cis)-10-[(3- amino-2,3,6-trideoxy-a-L-lyxo-hexapyranosyl)oxy]-7,8,9,10-tetrahydro-6,8,11-trihydroxy-8-(hydroxyacetyl)-1- methoxy-5,12-naphthacenedione.

The term "cytokine" is a generic term for proteins released by one cell population which act on another cell as intercellular mediators. Examples of such cytokines are lymphokines, monokines, and traditional polypeptide hormones. Included among the cytokines are growth hormone such as human growth hormone, N-methiony! human growth hormone, and bovine growth hormone; parathyroid hormone; thyroxine; insulin; proinsulin; relaxin; prorelaxin; glycoprotein hormones such as follicle stimulating hormone (FSH), thyroid stimulating hormone (TSH), and luteinizing hormone (LH); hepatic growth factor; fibroblast growth factor; prolactin; placental lactogen; tumor necrosis factor-«¢ and -f; mullerian-inhibiting substance; mouse gonadotropin-associated peptide; inhibin; activin; vascular endothelial growth factor; integrin; thrombopoietin (TPO); nerve growth factors such as NGF-f; platelet- growth factor; transforming growth factors (TGFs) such as TGF-« and TGF-B; insulin-like growth factor-I and -1I; erythropoietin (EPO); osteoinductive factors; interferons such as interferon -«, -B, and -y; colony stimulating factors (CSFs) such as macrophage-CSF (M-CSF), granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-

CSF); interleukins (ILs) such as IL-1, IL- 1a, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-11, IL-12; a tumor necrosis factor suchas TNF-a or TNF-8; and other polypeptide factors including LIF and kit ligand (KL). As used herein, the term cytokine includes proteins from natural sources or from recombinant cell culture and biologically active equivalents of the native sequence cytokines.

The term “prodrug” as used in this application refers to a precursor or derivative form of a pharmaceutically active substance that is less cytotoxic to tumor cells compared to the parent drug and is capable of being enzymatically activated or converted into the more active parent form. See, e.g., Wilman, “Prodrugs in

Cancer Chemotherapy”, Biochemical Society Transactions, 14:375-382, 615th Meeting, Belfast (1986), and Stella et al., “Prodrugs: A Chemical Approach to Targeted Drug Delivery”, Directed Drug Delivery, Borchardt et al., (ed.), pp. 147-267 Humana Press (1985). The prodrugs of this invention include, but are not limited to, phosphate- containing prodrugs, thiophosphate-containing prodrugs, sulfate-containing prodrugs, peptide-containing prodrugs,

D-amino acid-modified prodrugs, glysocylated prodrugs, B-lactam-containing prodrugs, optionally substituted phenoxyacetamide-containing prodrugs or optionally substituted phenylacetamide-containing prodrugs, 5- : fluorocytosine and other 5-fluorouridine prodrugs which can be converted into the more active cytotoxic free drug.

Examples of cytotoxic drugs that can be derivatized into a prodrugs form for use in this invention include, but are not limited to, those chemotherapeutic agents described above.

An “effective amount” of a polypeptide disclosed herein or an antagonist thereof, in reference to inhibition of neoplastic cell growth, tumor growth or cancer cell growth, is an amount capable of inhibiting, to some extent, the growth of target cells. The term includes an amount capable of invoking a growth inhibitory. cytostatic and/or cytotoxic effect and/or apoptosis of the target cells. An “effective amount” of a PRO201, PRO292, PRO327,

PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide antagonist for purposes of inhibiting neoplastic cell growth, tumor growth or cancer cell growth, may be determined empirically and in a routine manner.

A “therapeutically effective amount”, in reference to the treatment of tumor, refers to an amount capable of invoking one or more of the following effects: (1) inhibition, to some extent, of tumor growth, including, slowing down and complete growth arrest; (2) reduction in the number of tumor cells; (3) reduction in tumor size; (4) inhibition (i.e., reduction, slowing down or complete stopping) of tumor cell infiltration into peripheral organs; (5) inhibition (i.e., reduction, slowing down or complete stopping) of metastasis; (6) enhancement of anti-tumor immune response, which may, but does not have to, result in the regression or rejection of the tumor; and/or (7) relief, to some extent, of one or more symptoms associated with the disorder. A “therapeutically effective amount” of a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017,

PRO1112, PRO509, PRO853 or PRO8S2 polypeptide antagonist for purposes of treatment of tumor may be determined empirically and in a routine manner.

A “growth inhibitory amount” of a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO8S53 or PRO8S? antagonist is an arnount capable of inhibiting the growth of a cell, especially tumor, e.g., cancer cell, either in vitro or in vivo. A “growth inhibitory amount” of a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,PRO357,PRO715,PROI017,

PRO1112, PRO509, PRO853 or PRO882 antagonist for purposes of inhibiting neoplastic cell growth may be determined empirically and in a routine manner.

A “cytotoxic amount” of aPRO201, PRO292, PRO327, PRO1265, PRO344, PRO343,PR0347,PR0O357,

PRO715, PRO1017, PRO1112, PRO509, PROS8S53 or PRO882 antagonist is an amount capable of causing the destruction of a cell, especially tumor, e.g., cancer cell, either in vitro or in vivo. A “cytotoxic amount” of a

PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PROI112,

PRO509, PRO853 or PRO882 antagonist for purposes of inhibiting neoplastic cell growth may be determined empirically and in a routine manner.

The terms “PRO201", “PRO292", “PRO327", “PRO1265", “PRO344", “PRO343 ", “PRO347", “PRO357", “PRO715", “PRO1017", “PRO1112", “PRO509", “PRO8S53" or “PROSE?” polypeptide or protein when used herein encompass native sequence PRO201, PRO292, PRO327,PRO1265,PRO344, PRO343,PR0O347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptides and PRO201, PR0O292, . PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO] 017,PRO1112, PROS509, PRO853 or ; 20 PROB882 polypeptide variants (which are further defined herein). The PRO201, PRO292, PRO327, PRO1265, } - PRO344,PRO343, PRO347,PRO357,PRO715,PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide may be isolated from a variety of sources, such as from human tissue types or from another source, or prepared by - recombinant and/or synthetic methods.

A "native sequence PRO201", “native sequence PRO292", “native sequence PRO327", “native sequence

PROI1265", “native sequence PRO344", “native sequence PRO343", “native sequence PRO347", “native sequence

PRO357", “native sequence PRO715", “native sequence PRO1017", “native sequence PRO1112", “native sequence

PROS509", “native sequence PRO853" or “native sequence PRO882" comprises a polypeptide having the same amino acid sequence as the PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357,

PRO715, PRO1017, PRO1112, PRO509, PROB53 or PRO882 polypeptide as derived from nature. Such native sequence PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO71S, PRO1017,

PRO1112, PROS509, PRO853 or PRO882 polypeptide can be isolated from nature or can be produced by recombinant and/or synthetic means. The term "native sequence” PRO201, PRO292, PRO327,PRO1265,PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PROS 82 specifically encompasses naturally-occurring truncated or secreted forms (e.g., an extracellular domain sequence), naturally- occurring variant forms (e.g., alternatively spliced forms) and naturally-occurring allelic variants of the PRO201,

PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO5(09,

PRO853 and PRO882 polypeptides. In one embodiment of the invention, the native sequence PRO201, PRO292,

PRO327,PRO1265, PRO344, PRO343, PRO347,PR0O357, PRO715, PRO1017, PRO11 12, PRO509, PROS853 or

PRO882 polypeptide is a mature or full-length native sequence PRO201, PRO292, PRO327, PRO 1265, PRO344,

PRO343,PR0O347, PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide as shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:6), Figure 6 (SEQ ID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQ ID NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:48), or Figure 28 (SEQ ID NO:53), respectively. Also, while the PRO201, PRO292, PRO327,

PRO1265,PRO344, PRO343,PRO347,PRO357, PRO715, PRO1017,PRO1112, PRO509, PRO853 and PRO882 polypeptides disclosed in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:6), Figure 6 (SEQ ID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NQ:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQ ID NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQIDNO:46), Figure 26 (SEQ ID NO:48), or Figure 28 (SEQ ID NO:53), respectively, are shown to begin with the methionine residue designated therein as amino acid position 1, it is conceivable and possible that another methionine residue located either upstream or downstream from amino acid position 1 in Figure 2 (SEQ ID NO:2),

Figure 4 (SEQ ID NO:6), Figure 6 (SEQ ID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure (SEQ ID NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:438), or

Figure 28 (SEQ ID NO:53), respectively, may be employed as the starting amino acid residue for the PRO201,

PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PROI1112, PRO509,

PRO853 or PRO882 polypeptide. ]

The “extracellular domain” or “ECD” of a polypeptide disclosed herein refers to a form of the polypeptide 20 which is essentially free of the transmembrane and cytoplasmic domains. Ordinarily, a polypeptide ECD will have less than about 1% of such transmembrane and/or cytoplasmic domains and preferably, will have less than about ) 0.5% of such domains. It will be understood that any transmembrane domain(s) identified for the 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 and as shown in the appended figures. As such, in one embodiment of the present invention, the extracellular domain of a polypeptide of the present invention romprices amino acide 1 to X of the matare amina arid cequence wherein X ic any amino acid within 5 amino acids on either side of the extracellular domain/transmembrane domain boundary.

The approximate location of the “signal peptides” of the various PRO polypeptides disclosed herein are shown inthe accompanying figures. Itis 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. "PRO201 polypeptide variant”, “PR0O292 polypeptide variant”, “PRO327 polypeptide variant”, “PRO1265 v » WO 00/37640 PCT/US99/300(95 polypeptide variant”, “PRO344 polypeptide variant”, “PRO343 polypeptide variant”, “PRO347 polypeptide variant”, “PRQO357 polypeptide variant”, “PRO715 polypeptide variant”, “PRO1017 polypeptide variant”, “PRO1112 polypeptide variant”, “PRO509 polypeptide variant”, “PRO853 polypeptide variant” or ‘‘PR0882 polypeptide variant” means an active PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PR0347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide as defined above or below having at least about 80% amino acid sequence identity with a full-length native sequence PRO201, PR0292,

PRO327,PRO1265, PRO344, PRO343,PR0O347, PRO357, PRO715,PRO1017, PRO1112, PRO509, PROS 3 or

PRO882 polypeptide sequence as disclosed herein, a PRO201, PR0292, PRO327, PRO1265, PRO344, PR0343,

PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO201, PRO292, PRO327, PROIJ265,

PRO344,PR0O343,PR0O347,PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide, with or without the signal peptide, as disclosed herein or any other fragment of a full-length PRO201, PR0292,

PRO327,PRO1265, PRO344, PRO343,PR0O347, PRO357, PRO715,PRO1017,PRO1112, PRO509, PRO853 or

PROS882 polypeptide sequence as disclosed herein. Such PRO201, PRO292, PRO327, PRO1265, PR0344,

PRO343, PRO347,PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide variants include, for instance, PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PR(715,

PRO1017, PRO1112, PRO509, PRO853 or PRO882 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 PR0201,

PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PR0509,

PROS853 or PROS882 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 leastabout 86% amino acid sequence identity, more preferably at least about 87% amino acid sequence identity, more preferably atleast 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 atleast 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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO7135, PROIO017,

PRO1112, PRO509, PRO853 or PRO882 polypeptide sequence as disclosed herein, aPRO201, PRO292, PR0327,

PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO201, PR0292,

PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO3SS3 or

PRO882 polypeptide, with or without the signal peptide, as disclosed herein or any other fragment of a full-length

PRO201, PR0O292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PROI1 112,

PROS09, PRO853 or PRO882 polypeptide sequence as disclosed herein. Ordinarily, PRO201, PRO292, PR0327,

PRO1265, PRO344, PR0O343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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.

As shown below, Table 1 provides the complete source code for the ALIGN-2 sequence comparison computer program. This source code may be routinely compiled for use on a UNIX operating system to provide the ALIGN-2 sequence comparison computer program.

In addition, Tables 2A-2D show hypothetical exemplifications for using the below described method to determine % amino acid sequence identity (Tables 2A-2B) and % nucleic acid sequence identity (Tables 2C-2D) using the ALIGN-2 sequence comparison computer program, wherein “PRO” represents the amino acid sequence of a hypothetical PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide of interest, “Comparison Protein” represents the amino acid sequence of a polypeptide against which the “PRO” polypeptide of interest is being compared, “PRO-

DNA” represents a hypothetical PRO201-, PRO292-, PR0O327-, PRO1265-, PRO344-, PRO343-, PRO347-,

PRO357-, PRO715-, PRO1017-, PRO1112-, PRO509-, PRO853- or PRO882-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, “X”, “Y”, and “Z” each represent different hypothetical amino acid residues and “N”, “L” and “V” each represent different hypothetical nucleotides. ’

+ » WO 00/37640 PCT/US99/30095

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 -8 /* value of a match with a stop */ int _day[26][26]) = { /* ABCDEFGHIJKLMNOPQRSTUVWXY 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}, /1*G*/ {1,0,-3, 1,0,-5, 5,-2,-3, 0,-2,-4,-3, 0,_M,-1,-1,-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}, /* 1% {-1,-2,-2,-2,-2, 1,-3,-2, 5, 0,-2, 2, 2,-2, M,-2,-2,-2,-1, 0, 0, 4,-5, 0,-1,-2},

I*1* {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,-1, 0, 2,-2, 0,-1,-2}, /*M */ {-1,-2,-5,-3,-2,0,-3,-2, 2,0, 0, 4, 6,-2, M,-2,-1, 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}, /*0* {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*/ {1,-1,-3,-1,-1,-5,-1, 0,-2, 0,-1,-3,-2,-1,_M, 6, 0, 0, 1, 0, 0,-1,-6, 0,-5, 0}, . 1*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,-1,4,-3, 2,-2, 0, 3,-3, 0, 0, M, 0, 1, 6, 0,-1, 0,-2, 2, 0,-4, 0}, 1% 8S */ {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}, 1*U */ {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}, : /*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,-7,-7, 0,-7,-3,-5, 0,-3,-2,-4,-4, M,-6,-5, 2,-2,-5, 0,-6,17, 0, 0,-6}, /*X */ {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}, 1*Y */ {-3,-3, 0,-4,-4, 7,-5, 0,-1, 0,-4,-1,-2,-2, M,-5,-4,-4,-3,-3, 0,-2, 0, 0,10,-4}, 1*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} b

Page 1 of day.h

[* */ #include <stdio.h> #include <ctype.h> #define MAXIMP 16 /* max jumps in a diag */ #define MAXGAP 24 /* don't continue to penalize gaps larger than this */ #define IMPS 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 DINSI 1 /* penalty per base */ #define PINSO 8 /* penalty for a gap */ #define PINSI 4 /* penalty per residue */ struct jmp { short n[MAXJIMP]; /* size of jmp (neg for dely) */ unsigned short x[MAXIMP]; /* base no. of jmp in seq x */

IS /* limits seq to 2716 -1 */ struct diag { int Score; /* score at last jmp */ long offset; /* offset of prev block */ short ijmp; /* current jmp index */ struct jmp ips /* list of jmps */ 8 struct path { : int spc; /* number of leading spaces */ short n[JMPS]; /* size of jmp (gap) */ int x[JMPS]}; /* foc of jmp (last elem before gap) */ bh ; char *ofile; /* output file name */ char *namex[2]; /* seq names: getseqs() */ char *prog; /* prog name for err msgs */ char *seqx [2]; /* segs: getseqs() */ int dmax; /* best diag: nw() */ int dmax0; /* final diag */ int dna; /* set if dna: main() */ int endgaps; /* set if penalizing end gaps */ int SPY SPY 1% total ganc in seqc */ int lenQ, 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 ppi2l; /* holds path for segs */ char *calloc(), *maltloc(), *index(), *strcpy(; char *getseq(), *g_calloc();

Page 1 of nw.h

3 “ WO 00/37640 PCT/US99/30095 /* 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 3 static ~~ _pbval[26] = {

L2|(1<<(D-'A"N|(1<<(N'-'A"), 4, 8, 16, 32, 64, 128, 256, OXFFFFFFF, 1< <10, 1< <1], 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, 1<<25|(1< <(E-A)|(1<<(Q'-'A"Y) 3 main(ac, av) main int ac; char *av[l; . { 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(1); 3 namex[0} = av{l]; namex[1] = av[2]; seqx[0] = getseq(namex [0], &len0); seqx[1] = getseq(namex[1], &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 */ readjmps(); /* get the actual jmps */ print(); /* print stats, alignment */ cleanup(0); /* unlink any tmp files */ }

Page 1 of nw.c

/* 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 *toa gap inseqy. */ 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 row0, row] */ int mis; {* score for each type */ int ins0, insl; /* insertion penalties */ register id; /* diagonal index */ register ij; /* jmp index */ register *colQ, *coll; /* score for curr, last row */ register XX, YY; /* index into seqs */ dx = (struct diag *)g_calloc("to get diags"”, len0+lenl +1, 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)); cold = (int *)g_calloc("to get col”, lenl +1, sizeof(int)); coll = (int *)g_calloc("to get coll”, lenl +1, sizeof(int)); insO = (dna)? DINSO : PINSO; . ins] = (dna)? DINS1 : PINS1; smax = -10000; if (endgaps) { - for (col0{0} = dely[0] = -insO, yy = 1; yy <= lenl; yy++) { colOfyy] = dely[yy] = colO[yy-1] - insl; ndely[yy] = yy; 3 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 < = len0; px+ +, xx+ +) { /* initialize first entry in col */ if (endgaps) { if(xx == 1) col1[0] = delx = -(insO+insl); else col1{0} = delx = col0[0] - insl; ndelx = xx; } else { col1(0} = 0; delx = -ins0; ndelx = 0; }

Page 2 of nw.c

- ...IW for (py = seqx[1], yy = 1; yy <=lenl; py++, yy++) { mis = colO[yy-1]; if (dna) mis += (xbm[*px-'A’'J&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 | | ndely[yy] < MAXGAP) { if (colOfyy] - insO > = dely[yy]) { delylyy] = colO{yy] - (insO-+ins1); ndelylyy} = 1; } else { dely[yy] -= insti; ndely{yy]+ +; } } else § if (colOfyy] - (insO+insl) > = dely[yy]) { dely(yy] = colO[yy] - (insO+ins1); ndely[yy] = 1; } else ndely[yy]+ +; } ) /* update penalty for del in y seq; * favor new del over ongong del */ if (endgaps || ndelx < MAXGAP) { ’ if (collfyy-1] - insO > = delx) { delx = coll[yy-1] - (insO+insl); ndelx = 1; } else { delx -= insl; ndelx+ +; } } else { if (coll{yy-1] - (insO+insl) > = delx) { delx = collfyy-1] - (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 ee IW id = xx-yy + lenl - 1; if (mis > = delx && mis > = delylyy}) collyy] = mis; else if (delx > = dely[yy]) { coll[yy] = delx; ij = dx[id].ijmp; if (dx[id].jp.n[0] && (‘dna {| (ndelx >= MAXIMP && xx > dx[id].jp.x[{j]+MX) || mis > dx[id].score+DINS0)) { dxfid].ijmp + +; i if (+ +ij >= MAXIMP) { writejmps(id); ij = dx[id].ijmp = 0; dx[id].offset = offset; offset + = sizeof(struct jmp) + sizeof(offset); } } dx[id}.jp.nlij] = ndelx; dx[id].jp.x[ij} = xx; dx[id].score = delx; } else { colifyy] = delylyyl: ij = dx[id).ijmp; if (dx[id].jp.n[0] && (!dna || (ndely[yy] > = MAXIMP && xx > dx[id].jp.x[ij] + MX) || mis > dx[id].score+DINSO)) { dx[id].ijmp+ +; if (+ +ij >= MAXIMP) { writejmps(id); ’ ij = dx[id].ijmp = 0; dx[id}.offset = offset; offset += sizeof(struct jmp) -+ sizeof(offset); } } dx[id].jp-nlij} = -ndelylyyl; dx[id].jp-x[ij] = xx; dx[id}.score = delylyyl; } if (xx == len0 && yy < lenl) { /* last col */ if (endgaps)

So1{Y] -= isu inst ~(leni=gy), if (coll [yy] > smax) { smax = collyyl; dmax = id; } } } if (endgaps && xx < len0) coll[yy-1} -= insO+insl*(len0-xx); if (coll[yy-1] > smax) { smax = colllyy-1}; dmax = id; } tmp = col0; col0 = coll; coil = tmp; 3 (void) free((char *)ndely); (void) free((char *)dely); (void) free((char *)col0); (void) free((char *)coll); } Page 4 of nw.c s iN WO 00/37640 PCT/US99/30095 /* * * print() -- only routine visible outside this module * * static: * getmat() -- trace back best path, count matches: print() * pr_align() -- print alignment of described in array p[]: print() * dumpblock() -- dump a block of lines with numbers, stars: pr_align(} * nums() —- put out a number line: dumpblock() * putline() -- put out a line (name, [num], seq, [num]): dumpblock() * stars() - -put a line of stars: dumpblock() * stripname() -- strip any path and prefix from a seqname */ #include "nw.h" #define SPC 3 #define P_LINE 256 /* maximum output line */ #defineP SPC 3 /* space between name or num and seq */ extern _day[26]{26]; int olen; /* set output line length */

FILE *fX; /* output file */ print() print { ] int Ix, ly, firstgap, lastgap; /* overlap */ if ((fx = fopen(ofile, "w")) == 0) { fprintf(stderr,” %s: can't write %s\n", prog, ofile); . cleanup(1); } fprintf(fx, " < first sequence: %s (length = %d)\n", namex[0], len0); fprintf(fx, " < second sequence: %s (length = %d)\n", namex[1], lenl); olen = 60;

Ix = len0Q; ly = lenl; firstgap = lastgap = O; if (dmax < lenl - 1) { /* leading gap in x */ ppl0].spc = firstgap = lenl - dmax - 1; ly -= pp[0}.spc; } else if (dmax > lenl - 1) { /* leading gap iny */ pp{1]).spc = firstgap = dmax - (lenl - 1);

Ix -= ppl1].spc; } } if (dmax0 < len0 - 1) { /* trailing gap in x */ lastgap = len0 - dmax0 -1;

Ix -= lastgap; } else if (dmax0 > lenO - 1) { /* trailing gap in y */ lastgap = dmax0 - (lenO - 1); ly -= lastgap; } getmat(lx, ly, firstgap, lastgap); pr_align(); }

Page 1 of nwprint.c

* trace back the best path, count matches */ static getmat(lx, ly, firstgap, lastgap) : getmat int Ix, ly; /* "core" (minus endgaps) */ int firstgap, lastgap; /* leading trailing overlap */ { int nm, i0, il, siz0, siz}; char outx{32]; double pct; register 10, nl; register char *p0, *pl; /* get total matches, score */ i0 = il = siz0 = sizl = 0; pO = seqx[Q] + pp[l].spc: pl = seqx(1] + ppl0).spc; n0 = pp[l).spc + 1. nl = pp[0].spc + I; nm = 0; while ( *p0 && *pl) { if (siz0) { pi+-+; nl++; siz0--; B ) } else if (sizl) { pO+ +; n0+ +; . sizl--; 3 else { if (xbm[*p0-'A’]&xbm{*pl-'A’]) nm+ +; if (n0+ + == pp[0].x[i0]) siz0 = pp[0].n[i0+ +]; if (n1++ == pp[1].x[il]) sizl = pp[l].n[il+ +]; po+ +; pi++; } } /* pct homology: * if penalizing endgaps, base is the shorter seq * else, knock off overhangs and take shorter core */ if (endgaps)

Ix = (len0 < len)? lenO : lenl; else

Ix = (Ix < ly)? Ix: ly; pct = 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", Ix, pct);

Page 2 of nwprint.c

’ a WO 00/37640 PCT/US99/30095 fprintf(fx, " < gaps in first sequence: %d", gapx); ees getmat if (gapx) { (void) sprintf(outx, " (%d %s%s)", ngapx, (dna)? "base": "residue", (ngapx == 1)? "":"s"); fprintf(fx," %s", outx); fprintf(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, DINSO, DINS1); else fprintf(fx, "\n< score: %d (Dayhoff PAM 250 matrix, gap penalty = %d + %d per residue)\n", smax, PINSO, 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 Imax; /* lengths of stripped file names */ static ij(2]; /* jmp index for a path */ static nc(2]; /* number at start of current line */ static ni[2]; /* 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 out[2][P_LINE}; /* output line */ static char star[P_LINE]; /* 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 > imax)

Imax = nn; ncli] = 1; nifi] = 1; siz[i} = ijli] = 0; psi] = seqx[i]; poli] = out(i]; }

Page 3 of nwprint.c for (nn = nm = 0, more = 1; more; ) { ...pr_align for i = more = 0;1 < 2; i++) { /* * do we have more of this sequence? */ if ("*psli]) continue; more + +; if (pplil.spc) { /* leading space */ *pofi]++ ="'"; ppli}.spe--; } else if (siz[i)) { /* ina gap */ *polil++ = '-%; sizfi}--; } else { /* we're putting a seq element */ *poli] = *pslil; if (islower(*pslil)) *ps[i] = toupper(*psil); polil ++; psli} + +; 1* ; * are we at next gap for this seq? */ if (nili] == pplil.x[iji]) { 1* ; * we need to merge all gaps * at this location */ siz(i] = pplil-nfijlil ++); while (ni{i] == pp[i].x(iji]]) siz[i] += pplil.nfi{i] + +1; } nili}+ +; } if (+ +nn == olen || imore && nn) { dumpblock(); for i =0;i<2;i++) poli] = outfil; nn = 0; } } 4

I* * dump a block of lines, including numbers, stars: pr_align() */

Static dumpblock() dumpblock { register i; for (i=0;i <2;i++) *pofi}- = "\0';

Page 4 of nwprint.c

...dumpblock (void) putc("\n', fx); for (i =0;i <2;i++){ if (*out[i] && (*out[i} I=" "|| *(pofil) != ' ")) { if ==0) nums(i); if (i == 0 && *out[1]) } stars(); putline(i); if (i == 0 && *out[1]) fprintf(fx, star); if(i==1) nums(i); } } } /* * put out a number line: dumpblock() */ static nums(ix) nums int ix; /* index in out[] holding seq line */ { char nline[P_LINE]; register i, Is . register char *pn, *px, *py; for (pn = nline, i = 0; i < Imax+P_SPC; i++, pn++) pn ="; . for (i = nc[ix], py = out[ix]; *py; py ++, pn++) { if (*py == ""|]| *py ==") ] *pn = '"; else { if (i%10==01||({==1&&nc[ix] |= 1)){ j=<O?-i:1; for (px = pn; j; j /= 10, px--) *px = j%10 + '0'; if <0) *px = wy } else *pn ="; i++; 3 } *pn = "\0'; nclix] = i; for (pn = nline; *pn; pn+ +) (veid) putc(*pn, fx); (void) putc('\n', fx); } 1* * put out a line (name, [num], seq, {num]): dumpblock() */ static putline(ix) putline int ix; {

Page 5 of nwprint.c

...putline int i; register char *pXx; for (px = namex[ix], i = 0; *px && *px != "i"; px+ +, i++) (void) putc(*px, fx); for (; i < Imax+P_SPC; i+ +) (void) putc(' *, fx); /* these count from 1: * nif] 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 (segs always in out{0], out[1]): dumpblock() */ static stars() stars { int i; register char *p0, *pl, cx, *px; . if (*out[0] || (*out[0} ==" ' && *(po[0]) == "") t*out[1] |} (*out[1] ==" "' && *(po[l1]) == '')) return; . px = star; for (i = Imax+P_SPC; i; i--)

FpX++ ="; for (p0 = out[0], pl = out[l]; *p0 && *pl; p0+ +, pl ++) { if (isalpha(*p0) && isalpha(*pl)) { if (xbm[*p0-'A']&xbm[*p1-'A']) { cx = nm+ +; } else if (!dna && _day[*p0-'A’']{*pl-'A'] > 0) cx ="."; else cx="" } else cx ="" *px++ = cx; } *px++ = "\n'; *px = "\0';

H

Page 6 of nwprint.c

/* * 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 =90; for (px = pn; *px; px+ +) if px =="/") py =px + I; if (py) (void) strcpy (pn, py); return(strlen(pn)); }

Page 7 of nwprint.c _33-

/* * cleanup() -- cleanup any tmp file * getseq() -- read in seq, set dna, len, maxlen * g_calloc() -- calloc() with error checkin * readjmps() -- get the good jmps, from tmp file if necessary * writejmps() -- 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 cleanup(); /* cleanup tmp file */ long Iseek(); /* * remove any tmp file if we blow */ cleanup(i) cleanup int i; { if (f)) (void) unlink(jname); exit(i); } /* . * read, return ptr to seq, set dna, len, maxien * skip lines starting with 3’, '<*, 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, tien;

FILE *fp; if (fp = fopen(file,"r")) == 0) { fprintf(stderr,” %s: can't read %s\n", prog, file); exit(l); } tlen = natgc = 0; while (fgets(line, 1024, fp)) { if (*line =="; || *line == '<' || *line ==>") continue; for (px = line; *px !'= "\n'; px+ +) if (isupper(*px) || islower(*px)) tlen+ +; } if ((pseq = malloc((unsigned)(tlen+6))) == 0) { fprintf(stderr,” %s: mailoc() failed to get %d bytes for %s\n", prog, tlen+6, file); exit(1); } pseq[0] = pseq[1] = pseq[2] = pseq[3] = "\0';

Page 1 of nwsubr.c

..getseq py = pseq + 4; *len = tlen; rewind(fp); while (fgets(line, 1024, fp)) { if (*line == ';" || *line == "<' || *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+ +; } 3 *py+ + = "\0'; *py = "\0'; (void) fclose(fp); dna = natgc > (tlen/3); return(pseq +4); } char * g_calloc(msg, nx, sz) g_calloc 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) { fprintf(stderr, "%s: g_calloc() failed %s (n= %d, sz= %d)\n", prog, msg, nx, sz); exit(1);

H

} return(px); } /* * get final jmps from dx[] or tmp file, set pp[], reset dmax: main() */ readjmps() readjmps { int fd =-1; int siz, 10, il; register i, j, xx; if (f)) { (void) fclose(fj); if (fd = open(jname, O RDONLY, 0)) < 0) { fprintf(stderr, " %s: can't open() %s\n", prog, jname); cleanup(1); } } for (i = i0 = il = 0, dmax0 = dmax, xx = len0; ; i++) { while (1) { for (j = dx[dmax].ijmp; j > = 0 && dx[dmax].jp.x[j] > = xx; j--)

Page 2 of nwsubr.c

...readjmps if (j < 0 && dx[dmax].offset && fj) { (void) Iseek(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 = MAXIMP-1; } else break; ¥ if i >= JMPS) { fprintf(stderr, " %s: too many gaps in alignment\n", prog); cleanup(l); 3 ifG>=01 siz = dx{dmax].jp.n{j]; xx = dx[dmax}.jp.x[j}; dmax + = siz; if (siz < 0) { /* gap in second seq */ ppll].nfil] = -siz;

XX + = siz; /*id = xx -yy + lenl - 1 */ ppl11.x[i1] = xx - dmax + lenl - 1; gapy ++; ngapy -= siz; /* ignore MAXGAP when doing endgaps */ siz = (-siz < MAXGAP || endgaps)? -siz : MAXGAP; il++; 3 else if (siz > 0) { /* gap in first seq */ ppl0].n[i0] = siz; } pp(0).x[i0] = xx; gapx+ +; ngapx + = siz; /* ignore MAXGAP when doing endgaps */ siz = (siz < MAXGAP || endgaps)? siz : MAXGAP; 10+ +; } } else break;

H

/* reverse the order of jmps */ for (j = 0, i0—; j < i0; j++, i0--) { i = ppl0].n(j]; pplOl.nfjl = pp[0].n[i0); pp{Q).n{i0} = i; y i = ppl0].x(j]; ppi0).x[j]1 = ppl0].x[i0]; pp{0].x[i0] = i; for j = 0, il; j < il; j++, il) { i = pp(1).n(j); pp(1].nj] = pp(1}.nfi1}; pp[1).n[il] = i; , i = pp[1}.x[]; ppl1].x[] = ppl1].x{il]; pp(1}.x{il} = i; if (fd >= 0) (void) close(fd); if (f) { (void) unlink(jname); fi=0; offset = 0; } } Page 3 of nwsubr.c

* * write a filled jmp struct offset of the prev one (if any): nw() */ writejmps(ix) writejmps int ix; { char *mktemp(); if (ff) { if (mktemp(jname) < 0) { fprintf(stderr, " %s: can't mkiemp() %s\n", prog, jname); cleanup(l); } if ((fj = fopen(jname, "w™)) == 0) { fprintf(stderr, "%s: can't write %s\n", prog, jname); exit(l); } } (void) fwrite((char *)&dx[ix].jp, sizeof(struct jmp), 1, fj); (void) fwrite((char *)&dx[ix].offset, sizeof(dx[ix].offset), 1, fj); }

Page 4 of nwsubr.c

Table 2A

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) = divided by 15 = 33.3%

’ , | WO 00/37640 PCT/US99/30095

Table 2B

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) = divided by 10 = 50%

Table 2C

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%

- | . WO 00/37640 PCT/US99/30095

Table 2D

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% .

"Percent (%) amino acid sequence identity" with respect to the PRO201, PRO292, PRO327, PRO1265,

PRO344,PRO343,PRO347,PRO357,PRO715,PRO1017,PRO1112,PRO509, PRO853 and PRO882 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 a PRO201, PR0292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 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, ALIGN-2 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 obtained as described below by using the sequence comparison computer program ALIGN-2, wherein the complete source code for the ALIGN-2 program is provided in Table 1.

The ALIGN-2 sequence comparison computer program was authored by Genentech, Inc., and the source code shown in Table 1 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. 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.

For purposes herein, 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 ic tha number of aminn arid recidnec crored ac identical matchec hy 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, Tables 2A-2B demonstrate how to calculate the % amino acid sequence identity of the amino acid sequence designated “Comparison Protein” to the amino acid sequence designated “PRO”.

Unless specifically stated otherwise, all % amino acid sequence identity values used herein are obtained as described above using the ALIGN-2 sequence comparison computer program. However, % 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-BLAST? sequence comparison program may be downloaded from http://www.ncbi.nim.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, dropofffor final gapped alignment = 25 and scoring matrix = BLOSUMG62.

In situations where NCBI-BLAST?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 alignmentprogram

NCBI-BLAST? in that program's alignment of A and B, and where Y is the total number of amino acidresidues 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.

In addition, % amino acid sequence identity may also be determined 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 scoringmatrix = : BLOSUMS62. For purposes herein, a % amino acid sequence identity value is determined by dividing (a) the : number of matching identical amino acids residues between the amino acid sequence of the PRO polypeptide of - 20 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 maybe 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 amino acid sequence A which has or having at least 80% amino acid sequence identity to the amino acid sequence B”, the amino acidsequence

Adis the comparison amino acid sequence of interest and the amino acid sequence B is the amino acid sequence of the PRO polypeptide of interest. "PRO201 variant polypeptide”, “PR0O292 variant polypeptide”, “PRO327 variant polypeptide”, ‘PRO1265 variant polypeptide”, “PRO344 variant polypeptide”, “PRO343 variant polypeptide”, “PRO34] variant polypeptide”, “PRO357 variant polypeptide”, “PRO715 variant polypeptide”, “PRO1017 variant polypeptide”, “PROI1112 variant polypeptide”, “PRO509 variant polypeptide”, “PRO853 variant polypeptide” and “PRO882 variant polypeptide” or "PRO201 variant nucleic acid sequence”, “PR0O292 variant nucleic acid sequence”, “PRO327 variant nucleic acid sequence”, “PRO1265 variant nucleic acid sequence”, “PRO344 variant nicleic acid sequence”, “PR0O343 variant nucleic acid sequence”, “PR0O347 variant nucleic acid sequence”, “PRO357 variant nucleic acid sequence”, “PRO715 variant nucleic acid sequence”, “PRO1017 variant nucleic acid sequence”, “PROI112 variant nucleic acid sequence”, “PRO509 variant nucleic acid sequence”, “PROB8S53 variant nucleic acid sequence” and “PRO882 variant nucleic acid sequence” means a nucleic acid molecule which encodes an active

PRO509, PRO853 and PRO882 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 PRO201, PRO292,

PRO327,PRO1265,PR0O344,PR0O343, PR0O347,PR0O357,PRO715,PRO1017,PRO1112, PRO509, PRO853 and

PROSS82 polypeptide sequence as disclosed herein, a full-length native sequence PRO201, PRO292, PRO327,

PRO1265,PR0344,PR0O343,PR0O347, PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 and PRO882 polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of aPRQ201, PRO292,

PRO327,PRO1265,PR0O344,PR0O343,PRO347,PRO357, PRO715,PRO1017,PRO1112, PRO509, PRO853 and

PRO509, PRO853 and PROS882 polypeptide sequence as disclosed herein. Ordinarily, a PRO201, PRO292,

PRO327,PRO1265,PR0O344,PR0O343, PRO347,PR0O357,PRO715,PRO1017,PRO1112, PRO509, PRO853 and

PRO882 variant polynucleotide will have atleast 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 the nucleic acid sequence encoding a full-length native sequence PRO201, PRO292,

PRO327,PRO1265,PR0O344,PRO343, PRO347,PRO357, PRO715,PRO1017,PRO1112,PRO509, PRO853 and

PRNRR? pnlypeptide sequence ac dicclnced herein a full-length native sequence PROT PROZ92. PRO3YT,

PRO1265,PR0O344, PRO343,PR0O347, PRO357,PRO715,PRO1017,PRO1112,PRO509, PRO853 and PRO882 polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of aPRO201, PRO292,

PRO327,PROI265,PRO344,PR0O343, PRO347,PRO357,PRO715,PRO1017,PRO1112,PRO509, PRO853 and

PRO882 polypeptide, with or without the signal sequence, as disclosed herein or any other fragment of a full-length

PRO309, PRO853 and PROS882 polypeptide sequence as disclosed herein. Variants do not encompass the native nucleotide sequence.

Ordinarily, PRO201, PR0292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017, PRO1112, PRO509, PRO853 and PRO882 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 the PRO201, PRO292, PRO327, PRO1265,

PRO344,PR0O343,PR0O347, PRO357,PRO715,PRO1017,PRO1112,PR0O509, PRO853and PRO882 polypeptide- encoding nucleic acid sequences identified herein is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in a PRO201, PR0292, PRO327, PRO1265, PRO344, PRO343,

PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide-encoding nucleic acid sequence, 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, ALIGN-2 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, % nucleic acid sequence identity values are obtained as described below by using the sequence comparison computer program ALIGN-2, wherein the complete source code for the ALIGN-2 program is provided in Table 1. The ALIGN-2 sequence : comparison computer program was authored by Genentech, Inc., and the source code shown in Table 1 has been : filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under - 20 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. 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.

For purposes herein, 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 2C-2D 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".

Unless specifically stated otherwise, all % nucleic acid sequence identity values used herein are obtained as described above using the ALIGN-2 sequence comparison computer program. However, % 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-BLAST?2 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 =235, dropoff for final gapped alignment = 25 and scoring matrix = BLOSUM62.

In situations where NCBI-BLAST?2 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-

BLAST? 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 addition, % nucleic acid sequence identity values may also be generated 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 = BLOSUMSG62. For purposes herein, 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 pslypeptids encoding nucleic acid molecule of interest is heing 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.

In other embodiments, PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357,

PRO715,PRO1017,PRO1112,PRO509, PRO853 and PRO882 variant polynucleotides are nucleic acid molecules that encode an active PRO201, PR0O292, PR0O327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide and which are capable of hybridizing, preferably under stringent hybridization and wash conditions, to nucleotide sequences encoding the full-length PRO201,

PRO853 or PRO882 polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:6), Figure 6 (SEQID

NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID

NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQ ID NO:42), Figure 22 (SEQID

NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:48), or Figure 28 (SEQ ID NO:53), respectively.

PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347; PRO357, PRO715, PRO1017, PRO1112,

PRO509, PRO853 or PRO882 variant polypeptides may be those that are encoded by a PRO201, PR0O292,

PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,PRO1017, PRO1112, PRO509, PRO853 or

PRO882 variant polynucleotide.

The term "positives", in the context of the amino acid sequence identity comparisons performed as described 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 3 below) of the amino acid residue of interest.

For purposes herein, 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 in that program’s alignment of A and B, and where Y is the total number of amino acid residues inB. 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. Preferably, the isolated polypeptide is free of association with all components with which it is naturally associated. 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 sifu within recombinant cells, since at least one component of the

PRO509, PRO853 or PRO882 natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step.

An "isolated" nucleic acid molecule encoding a PRO201, PR0O292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide or an “isolated” nucleic acid encoding an anti-PRO201, anti-PR0O292, anti-PRO327, anti-PRO 1265, anti-PRO344, anti-

PRO343, anti-PR0O347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody, 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 PRO201-, PRO292-,

PRO327-, PRO1265-, PRO344-, PRO343-, PRO347-, PRO357-, PRO715-, PRO1017-, PRO1112-, PRO509-,

PROS853- or PRO882-encoding nucleic acid or the anti-PRO201-, anti-PR0O292-, anti-PRO327-, anti-PRO1265-, anti-PRO344-, anti-PRO343-, anti-PRO347-, anti-PRO357-, anti-PRO715-, anti-PRO1017-, anti-PRO1112-, anti-

PROS509-,anti- PRO853- or anti-PRO882-encoding nucleic acid. Preferably, the isolated nucleic acid is free of association with all components with which it is naturally associated. An isolated PRO201-, PRO292-, PRO327-,

PRO1265-, PRO344-, PRO343-, PRO347-, PRO357-, PRO715-, PRO1017-, PRO1112-, PRO509-, PRO853- or

PRO882-encoding nucleic acid molecule or an anti-PRO201-, anti-PR0O292-, anti-PR0O327-, anti-PRO1265-, anti-

PRO344-, anti-PRO343-, anti-PRO347-, anti-PRO357-, anti-PRO715-, anti-PRO1017-, anti-PRO1112-, anti-

PRO509-, anti-PRO853- or anti-PRO882-encoding nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated nucleic acid molecules therefore are distinguished from the PRO201-,

PRO292-, PRO327-, PRO1265-, PRO344-, PRO343-, PRO347-, PRO357-, PRO715-, PRO1017-, PRO1112-,

PROS509-, PRO8S3- or PRO882-encoding nucleic acid molecule or the anti-PRO201 -, anti-PR0292-, anti-PRO327-, anti-PRO1265-, anti-PR0O344-, anti-PRO343-, anti-PRO347-, anti-PRO357-, anti-PRO715-, anti-PRO1017-, anti-

PRO1112-, anti-PRO509-, anti-PRO853- or anti-PRO882-encoding nucleic acid molecule as it exists in natural cells. However, an isolated nucleic acid molecule encoding a PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343,PR0O347,PR0O357,PRO715,PRO1017,PRO1112,PRO509, PRO853 or PRO882 polypeptide or an anti-

PRO201, anti-PRO292, anti-PRO327, anti-PRO1265, anti-PRO344, anti-PRO343, anti-PR0O347, anti-PRO357, anti-PRO7135, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody includes :

PRO201-, PRO292-, PRO327-, PRO1265-, PRO344-, PRO343-, PRO347-, PRO357-, PRO715-, PRO1017-,

PRO1112-, PRO509-, PRO853- or PRO882-nucleic acid molecules and anti-PRO201-, anti-PR0O292-, anti-

PRO327-, anti-PRO1265-, anti-PRO344-, anti-PRO343-, anti-PRO347-, anti-PRO357-, anti-PRO715-, anti-

PROI1017-, anti-PRO1112-, anti-PRO509-, anti-PRO853- or anti-PRO882-encoding nucleic acid molecules contained in cells that ordinarily express PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO257.PROTIS, PROOF, DDA1112, PDASN0, DROYS2 or PROLRD nolypeptides oreyprecc anti-PROIN anti.

PRO292, anti-PRO327, anti-PRO1265, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibodies 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-

PRO201, anti-PR0O292, anti-PRO327, anti-PRO1265, anti-PRO344, anti-PR0O343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 monoclonal antibodies (including antagonist, and neutralizing antibodies),anti-PRO201, anti-PRO292, anti-PR0O327, anti-PRO1265, anti- PRO344, anti-PRO343, anti-PRO347, anti-PR0O357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody compositions with polyepitopic specificity, single chain anti-PRO201, anti-

PRO292, anti-PRO327, anti-PRO1265, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PR0O509, anti-PRO853 or anti-PRO882 antibodies, and fragments of anti-

PRO201, anti-PRO292, anti-PR0O327, anti-PRO1265, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PROS09, anti-PRO853 or anti-PRO882 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 < 20 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, itfollows 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/S0mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42°C; or (3) employ 50% formamide, S 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 ug/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 than 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), SO 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 35°C-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 PRO201,

PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509. PRO853 or PRO8S2 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 itis 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). “Active” or "activity" for the purposes herein refers to form(s) of PRO201, PRO292, PRO327, PRO1265,

PRO344, PRO343,PR0O347, PRO357, PRO715,PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptides which retain a biological and/or an immunological activity/property of a native or naturally-occurring PRO201,

PROS8S53 or PROSS2 polypeptide, wherein “biological” activity refers to a function (either inhibitory or stimulatory) caused by a native or naturally-occurring PRO201, PR0O292, PRO327, PRO1265, PRO344, PRO343, PRO347, :

PRO357,PRO715,PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide other than the ability to induce the production of an antibody against an antigenic epitope possessed bya a native or naturally-occurring PRO201,

PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PROS509,

PROSS3 or PRO882 polypeptide and an “immunological” activity refers to the ability to induce the production of an antibody against an antigenic epitope possessed by a native or natural y-occurring PRO201, PRO292, PRO327,

BRU12b5, PRU344, PRU343, FRO347, FRO357; PRG715,PRO1017, PROT? PROS09. PRO8S3 or PROB82 polypeptide. “Biological activity” in the context of an antibody or another antagonist molecule that can be identified by the screening assays disclosed herein (e.g., an organic or inorganic small molecule, peptide, etc.) is used to refer to the ability of such molecules to bind or complex with the polypeptides encoded by the amplified genes identified herein, or otherwise interfere with the interaction of the encoded polypeptides with other cellular proteins or otherwise interfere with the transcription or translation of a PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide. A preferred biological activity is growth inhibition of a target tumor cell. Another preferred biological activity is cytotoxic activity resulting in the death of the target tumor cell.

The term “biological activity” in the context of a PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide means

’ + WO 00/37640 PCT/US99/30095 the ability of aPRO201, PRO292, PRO327,PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,PRO1017,

PRO1112, PRO509, PRO853 or PRO882 polypeptide to induce neoplastic cell growth or uncontrolled cell growth.

The phrase “immunological activity” means immunological cross-reactivity with at least one epitope of aPRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357,PRO715,PRO1017, PRO1112, 5S PROS509, PRO8S3 or PRO882 polypeptide. “Immunological cross-reactivity” as used herein means that the candidate polypeptide is capable of competitively inhibiting the qualitative biological activity of a PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide having this activity with polyclonal antisera raised against the known active PRO201, PRO292, PRO327, PRO1265,

PRO344,PR0O343,PRO347, PRO357, PRO715,PRO1017,PRO1112,PRO509, PRO853 or PRO882 polypeptide.

Such antisera are prepared in conventional fashion by injecting goats or rabbits, for example, subcutaneously with the known active analogue in complete Freund's adjuvant, followed by booster intraperitoneal or subcutaneous injection in incomplete Freunds. The immunological cross-reactivity preferably is “specific”, which means that the binding affinity of the immunologically cross-reactive molecule (e.g., antibody) identified, to the corresponding

PRO509, PRO853 or PRO882 polypeptide is significantly higher (preferably at least about 2-times, more preferably at least about 4-times, even more preferably at least about 8-times, most preferably at least about 10-times higher) than the binding affinity of that molecule to any other known native polypeptide.

The term "antagonist" is used in the broadest sense, and includes any molecule that partially ot fully blocks, inhibits, or neutralizes a biological activity of a native PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, ’ PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide disclosed herein or the transcription or translation thereof. Suitable antagonist molecules specifically include antagonist antibodies or antibody fragments, fragments, peptides, small organic molecules, anti-sense nucleic acids, etc. Included are methods for identifying antagonists of a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide with a candidate antagonist molecule and measuring a detectable change in one or more biological activities normally associated with the

PRQS509, PRO853 or PRO882 polypeptide.

A “small molecule” is defined herein to have a molecular weight below about 500 Daltons. “Antibodies” (Abs) and "immunoglobulins" (Igs) are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to a specific antigen, immunoglobulins include both antibodies and other antibody-like molecules which lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas. The term “antibody” is used in the broadest sense and specifically covers, without limitation, intact monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies) formed from at least two intact antibodies, and antibody fragments so long as they exhibit the desired biological activity. "Native antibodies" and "native immunoglobulins" are usually heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each light chain is linked to a heavy chain by one covalent disulfide bond, while the number of disulfide linkages varies among the heavy chains of different immunoglobulin isotypes. Each heavy and light chain also has regularly spaced intrachain disulfide bridges. Each heavy chain has at one end a variable domain (Vy) followed by a number of constant domains. Each light chain has a variable domain at one end (V) and a constant domain at its other end; the constant domainof the light chain is aligned with the first constant domain of the heavy chain, and the li ght-chain variable domain is aligned with the variable domain of the heavy chain. Particular amino acid residues are believed to form an interface between the light- and heavy-chain variable domains.

The term "variable" refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies. It is concentrated in three segments called complementarity-determining regions (CDRs) or hypervariable regions both in the light-chain and the heavy-chain variable domains. The more highly conserved portions of variable domains are called the framework (FR) regions. The variable domains of native heavy and light chains each comprise four

FR regions, largely adopting a B-sheet configuration, connected by three CDRs, which form loops connecting, and in some cases forming part of, the B-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Kabat et al., NIH Publ. N0.91-3242, Vol. I, pages 647-669 (1991). The constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity.

The term “hypervariable region” when used herein refers to the amino acid residues of an antibody which are responsible for antigen-binding. The hypervariable region comprises amino acid residues from a - “complementarity determining region” or “CDR” (i.e., residues 24-34 (L1), 50-56 (L2) and 89-97 (L3) in the light chain variable domain and 31-35 (H1), 50-65 (H2) and 95-102 (H3) in the heavy chain variable domain; Kabat et al., Sequences of Proteins of Immunological Interest, Sth Ed. Public Health Service, National Institute of Health,

Bethesda, MD. [1991)) and/or those residues froma “hypervariable loop” (i.e., residues 26-32 (L1), 50-52 (L2)and 91-96 (L3) in the light chain variable domain and 26-32 (HI), 53-55 (H2) and 96-101 (H3) in the heavy chain vatigbie Gutait , Ciuiiia and Lesk, J, Meal: Bisl,, 10£:001-017 [10R7]} “Framework” or “FR” residues are those variable domain residues other than the hypervariable region residues as herein defined. "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"),, and Fv fragments; diabodies; linear antibodies (Zapata et al., Protein Eng. , 8(10):1057-1062 {1995]); sin gle-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, whose name reflects its ability to crystallize readily. Pepsin treatment yields an F(ab’), 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-covalentassociation.

Itis in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the V,,-V, 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 CH1 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"), 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 (x) and lambda (A), 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 canbe 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.,1gG1, 1gG2,1gG3,1gG4, IgA, and IgA2.

The heavy-chain constant domains that correspond to the different classes of immunoglobulins are called «, 6, €, vy, and p, respectively. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known.

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. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to conventional (polyclonal) antibody preparations which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they are synthesized by the hybridoma culture, uncontaminated by other immunoglobulins. The modifier "monoclonal" indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler et al., Nature, 256:495 [1975], or may be made by recombinant DNA methods (see, e¢.g., U.S. Patent No. 4,816,567). The "monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described in Clackson er al., Nature, 352:624-628 [1991] and Marks et al., J. Mol. Biol., 222:581-597 (1991), for example.

The monoclonal antibodies herein specifically include "chimeric" antibodies (immunoglobulins) in which aportion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Patent No. 4,816,567; Morrison et al., Proc. Natl. Acad. Sci. USA, 81:6851-6855 "Humanized" forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab’, F(ab"), or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. For the most part, humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a CDR of the recipient are replaced by residues froma 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 FR residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies may comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. These modifications are made to further refine and maximize antibody performance. 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 sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see, Jones et al., Nature, 321:522-525 (1986); Reichmann ez al., Nature, 332:323-329 [1988]; and Presta, Curr. Op. Struct. Biol., 2:593-596 (1992). The humanized antibody includes a

PRIMATIZED™ antibody wherein the antigen-binding region of the antibody is derived froman antibody produced by immunizing macaque monkeys with the antigen of interest. "Single-chain Fv" or "sFv" antibody fragments comprise the V,, and V, domains of antibody, wherein these domains are present in a single polypeptide chain. Preferably, the Fv polypeptide further comprises a polypeptide : linker between the V,, and V, 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 (Vy) connected to a light-chain variable domain (V) in the same polypeptide chain { Vy; - VJ. BY usittg a luker that is toc chert 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 froma 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. Radionuclides that can serve as detectable labels include, for example, 1-131, 1-123, 1-125, Y-90, Re-188, Re-186, At-211, Cu-67, Bi-212, and Pd-109. The label may also be a non-detectable entity such as a toxin.

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 itis 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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PRO1017, PRO1112, PROS509, PRO853 or PRO882 polypeptide or antibody thereto and, optionally, a chemotherapeutic agent) to a mammal. The components of the liposome are commonly arranged in a bilayer formation, similar to the lipid arrangement of biological membranes.

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 areceptor or a ligand. The immunoglobulin constant domain sequence in the immunoadhesin may be obtained from any immunoglobulin, such as IgG-1,1gG-2, 1gG-3, or IgG-4 subtypes, IgA (including IgA-1 and IgA-2), IgE, IgD or IgM.

IL Compositions and Methods of the Invention

A. Full-length PRO201, PRO292, PRO327, PRO1265. PRO344. PRO343, PRO347. PRO357. PRO71S,

PROI1017,PRO1112 PROS509, PRO853 and PRO882 polypeptides

The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PROI1017, PRO1112, PRO509, PRO853 and PROS882. In particular, cDNA encoding

PRO201, PR0O292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PROI1112,

PROS509, PRO853 and PRO882 polypeptides has 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 proteins encoded by the herein disclosed nucleic acid sequences as well as all further native homologues and variants included in the foregoing definition of

PROS509, PRO853 and PRO882 will be referred to as “PR0O201, PRO292, PRO327, PRO1265, PRO344, PRO343,

PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882", regardless of their origin or mode of preparation.

As disclosed in the Examples below, cDNA clones have been deposited with the ATCC. The actual nucleotide sequence of the 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 sequences can be determined from the nucleotide sequences using routine skill. For the PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptides and encoding nucleic acid described herein, Applicants have identified what are believed to be the reading frames best identifiable with the sequence information available at the time.

B. PRO201, PRO292. PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO71S, PRO1017,

PROI1112, PRO509, PRO853 and PROS882 Variants

In addition to the full-length native sequence PRO201, PR0292, PRO327,PRO1265, PRO344, PRO343,

PRO347, PRO357, PROT15,PRO1017. PRO1112, PRO509, PRO853 and PRO882 polypeptides described herein, it is contemplated that PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO7135,

PRO1017, PRO1112, PRO509, PRO853 and PROS882 variants can be prepared. PRO201, PRO292, PRO327,

PRO1265,PRO344, PRO343, PRO347,PR0O357,PRO715,PRO1017,PRO11 12, PRO509, PRO853 and PRO882 variants can be prepared by introducing appropriate nucleotide changes into the PRO201, PRO292, PRO327,

PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882

DNA, and/or by synthesis of the desired PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PRO1017, PRO1112, PROS09, PRO853 or PRO882 polypeptide. Those skilled in the art will appreciate that amino acid changes may alter post-translational processes of the PRO201, PRO292, PRO327,

PRU 263, PROS, FROJ40, TRG347, PRO257,PROTIS PROINI7. PRO1112, PRO509, PRO853 or PROSS2, such as changing the number or position of glycosylation sites or altering the membrane anchoring characteristics.

Variations in the native full-length sequence PRO201, PRO292, PRO327, PRO1265, PRO344,PRO343,

PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 or in various domains of the PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112,

PROS09, PRO853 or PRO882 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 PRO201, PRO292,

PRO327, PRO1265, PRO344, PRO343, PRO347, PR0O357, PRO715, PRO1017,PRO11 12, PRO509, PRO853 or

PROS8S2 that results in a change in the amino acid sequence of the PRO201, PRO292, PRO327, PRO1265,

PRO344, PRO343, PRO347,PRO357,PRO715,PRO1017, PRO1112, PROS09, PROS853 or PRO882 as compared with the native sequence PRO201, PRO292, PRO327, PRO1265,PRO344, PRO343,PR0O347,PRO357, PRO715,

PRO1017, PRO1112, PRO509, PRO853 or PRO882. 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 PRO201, PRO292, PRO327, PRO1265,

PRO344,PR0O343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882. Guidance in determining which amino acid residue may be inserted, substituted or deleted without adversely affecting the

S desired activity may be found by comparing the sequence of the PRO201, PRO292, PR0327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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.

PRO201, PR0O292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017,

PRO1112, PRO509, PRO853 and PRO882 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 PRO201, PRO292,PR0327, PRO1265,PRO344, PRO343, PRO347,PRO357, PRO715, PRO1017,

PRO1112, PRO509, PRO853 or PRO882 polypeptide.

PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, - PRO1112, PRO509, PRO853 or PRO882 fragments may be prepared by any of a number of conventional techniques. Desired peptide fragments may be chemically synthesized. An alternative approach involves generating

PRO509, PRO853 or PRO882 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, PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide fragments share at least one biological and/or immunological activity with the native PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide.

In particular embodiments, conservative substitutions of interest are shown in Table 3 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 3, or as further described below in reference to amino acid classes, are introduced and the products screened.

Table 3

Original Exemplary Preferred

Residue Substitutions Substitutions

Ala (A) val; leu; ile val

Arg(R) lys; gln; asn lys

Asn (N) gin; his; lys; arg gin

Asp (D) glu glu

Cys (C) ser ser

Gln (Q) asn asn

Glu (E) asp asp

Gly (G) pro; ala ala

His (H) asn; gln; lys; arg arg

Ile (1) 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) trp; phe; thr; ser phe

Vval(V) ile; leu; met; phe; . ala; norleucine leu

Substantial modifications in function or immunological identity of the polypeptide are accomplished by ] selecting substitutions that differ significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, 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 40 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 ef al., Nucl.

Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)], cassette mutagenesis [Wells ef al.,

Gene, 34:315 (1985)}, restriction selection mutagenesis [Wells eral. Philos. Trans. R. Soc. London SerA, 317:415

(1986)] or other known techniques can be performed on the cloned DNA to produce the PRO201, PRO292,

PRO327, PRO1265, PRO344, PRO343, PRO347,PRO357, PRO715,PRO1017,PRO1112,PRO509, PRO853 or

PROS882 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. Bjol., 150:1 (1976)]. If alanine substitution does not yield adequate amounts of variant, an isoteric amino acid can be used.

C. Modifications of PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357,

PRO715, PRO1017, PRO1112, PRO509, PRO853 and PRO8Z2

Covalent modifications of PRO201, PRO292, PRO327,PRO1265,PR0344,PR0O343, PRO347,PRO357,

PRO715,PRO1017, PRO1112, PRO509, PRO853 and PRO882 are included within the scope of this invention.

One type of covalent modification includes reacting targeted amino acid residues of a PRO201, PRO292, PRO327,

PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 oo polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C- terminal residues of the PRO201, PRO292, PRO327, PRO1265, PRO344, PR0O343, PR0O347, PRO357, PRO715, - 20 PROI1017,PRO1112, PRO509, PRO853 or PRO882. Derivatization with bifunctional agents is useful, for instance, for crosslinking PRO201, PR0O292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017, PRO1112, PRO509, PRO853 or PRO882 to a water-insoluble support matrix or surface for use in the method for purifying anti-PRO201, anti-PRO292, anti-PRO327, anti-PRO1 265, anti-PRO344, anti-PR0O343, anti-

PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO8S2 antibodies, and vice-versa. Commonly used crosslinking agents include, e.g., 1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylic acid, homobifunctional irnidoesters, including disuccinimidyl esters such as 3,3"-dithiobis(succinimidylpropionate), bifunctional maleimides such as bis-N-maleimido-1,8-octane and agents such as methyl-3-[(p-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 a-amino groups of lysine, arginine, and histidine side chains [T.E. Creighton, Proteins: Structure 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 PRO201, PRO292, PRO327, PRO1 265, PRO344, PR0O343,

PRO347,PRO357,PRO715,PRO1017, PRO1112, PRO509, PRO853 or PRO882 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 PRO201, PR0O292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PROT715,

PRO1017, PRO1112, PRO509, PRO853 or PRO882 (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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO832. 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 PRO201, PRO292, PR0O327, PRO1265,PR0O344, PRO343,PR0O347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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 PRO201, PR0292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 (for O-linked glycosylation sites). The PRO201, PR0O292, PRO327,PRO1265, PRO344, PRO343,PRO347,PRO357, PRO715,

PRO1017, PRO1112, PRO509, PRO853 or PRO882 amino acid sequence may optionally be altered through changes atthe DNA level, particularly by mutating the DNA encoding the PRO201, PRO292,PR0O327, PRO1265,

PRO344, PRO343,PR0347, PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 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 PRO201, PRO292, PRO327,

PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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. Bigchem., : pp- 259-306 (1981).

Removal of carbohydrate moieties present on the PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide may be accomplished chemically or enzymatically or by mutational substitution of codons encoding for amino acid residues that serve as targets for glycosylation. Chemical deglycosylation techniques are known in the art and described, for itistative, by Hakiuwddin, ei ul, Areh: Bisshens. Biophys, 289:52 (1087) and hy Fdge of 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. Enzymol., 138:350 (1987).

Another type of covalent modification of PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343,

PRO347,PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 comprises linking the PRO201,

PRO853 or PRO882 polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylene, 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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,PRO357, PRO715, PROI1017,

PRO1112, PRO509, PRO853 or PRO882 of the present invention may also be modified in a way to forma chimeric molecule comprising PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

: , | WO 00/37640 PCT/US99/30095

PRO1017, PRO1112, PRO509, PRO853 or PRO882 fused to another, heterologous polypeptide or amino acid sequence.

In one embodiment, such a chimeric molecule comprises a fusion of the PRO201, PRO292, PRO327,

PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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 PRO201, PR0292, PR0327, PRO1265, PRO344,

PRO343,PR0O347,PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882. The presence of such epitope-tagged forms of the PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357,

PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 can be detected using an antibody against the tag polypeptide. Also, provision of the epitope tag enables the PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347,PR0O357, PRO715,PRO1017, PRO1112, PRO509, PRO853 or PRO882 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 12CAS5 [Field eral, 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 er al., Science, 255:192-194 (1992)]; an «a-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 PRO201, PRO292,

PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017,PRO1112, PRO509, PRO853 or

PRO882 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 substitution of a soluble (transmembrane domain deleted or inactivated) form of a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017,

PRO1112, PRO509, PRO853 or PRO882 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 IgG1 molecule. For the production of immunoglobulin fusions see also, US

Patent No. 5,428,130 issued June 27, 1995.

D. Preparation of PRO201, PRO292. PRO327. PRO1265, PRO344, PRO343, PRO347, PRO357,

PRO715, PRO1017, PRO1112, PRO509, PRO853 and PROS? Polypeptides

The description below relates primarily to production of PRO201, PRO292, PR0327, PRO1265,PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 by culturing cells transformed or transfected with a vector containing PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343,

PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 nucleic acid. It is, of course,

contemplated that alternative methods, which are well known in the art, may be employed to prepare PRO201,

PRO292, PRO327, PR01265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509,

PROS853 or PRO882. For instance, the PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347,

PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 sequence, or portions thereof, may be produced by direct peptide synthesis using solid-phase techniques [see, e.g., Stewart ef 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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343,

PRO347,PRO357, PRO715,PRO1017, PRO1112, PRO509, PRO853 or PRO882 may be chemically synthesized separately and combined using chemical or enzymatic methods to produce the full-length PRO201, PRO292,

PRO8S82. a. Isolation of DNA Encoding a PRO201, PRO292, PRO327. PRO1265, PRO344, PRO343,

PRO347, PRO357. PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 Polypeptide

DNA encoding PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017, PRO11 12, PRO509, PRO853 or PRO882 may be obtained from a cDNA library prepared from tissue believed to possess the PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PRO1017, PRO1112,PRO509, PRO853 or PRO882 mRNA and to express it at a detectable level. Accordingly, human PRO201, PR0O292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, :

PRO1112, PRO509, PRO853 or PRO882 DNA can be conveniently obtained from a cDNA library prepared from human tissue, such as described in the Examples. PRO201-, PRO292-, PRO327-, PRO1265-, PRO344-, PRO343-,

PRO347-, PRO357-,PRO715-, PRO1017-, PRO1112-, PRO509-, PRO853- or PRO882-encoding gene may also be obtained from a genomic library or by oligonucleotide synthesis.

Libraries can be screened with probes (such as antibodies to the PRO201, PRO292, PRO327, PRO1265,

FROS3%4, FROJ43; PROI47, PRG357; PRO71S,PRO1I01T, PROT) PRNSNG PRORS3 or PRO882 polypeptide, or oligonucleotides of at least about 20-80 bases) designed to identify the gene of interest or the protein encoded byit. Screening the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor

Laboratory Press, 1989). An alternative means to isolate the gene encoding PRO201,PR0O292, PRO327,PRO1265,

PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 is to use

PCR methodology [Sambrook ez 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 er al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA. b. Selection and Transformation of Host Celis

Host cells are transfected or transformed with expression or cloning vectors described herein for PRO201,

PRO853 or PRO882 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 Sambrook etal. supra. - 20 Methods of eukaryotic cell transfection and prokaryotic cell transformation are known to the ordinarily skilled artisan, for example, CaCl,, CaPO,, 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 er 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., I. Bact., 130:946 (1977) and Hsiao ez 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, polyornithine, may also be used. For various techniques for transforming mammalian cells, see, Keown er 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 E. coli strain 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 1 A2, which has the complete genotype torA ; 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 E15 (argF-lac)]169 degP ompT kan’; E. coli W3110 strain 37D6, which has the complete genotype ronA ptr3 phoA E15 (argF-lac)l69 degP ompT rbs7 ilvG kan"; E. coli W3110 strain 40B4, which is strain 37D6 with a non-kanamycin resistant deg P deletion mutation; and an E. 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 PRO201-, PRO292-, PRO327-, PRO1265-, PRO344-, PRO343-, PRO347-, PRO357-,

PRO715-,PRO1017-, PRO1112-, PRO509-, PRO853- or PRO882-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 er 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; Vanden Berg et al.,

Bio/Technology, 8:135 (1990), K . thermotolerans, and K. marxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070: Sreekrishna ef 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 sushas Schwanniomycoc arcidontalic (FP 304 538 nublished 31 October 1990); and filamentous fungi suchas, e.g.,

Neurospora, Penicillium, Tolypocladium (WO 91/00357 published 10 January 1991), and Aspergillus hosts such as A. nidulans (Ballance et al., Biochem. Biophys. Res. Commun., 112:284-289 [1983]; Tilburn et al., Gene, 26:205-221[1983); Yelton etal., Proc. Natl. Acad. Sci. USA, 81:1470-1474 [1984]) and A. 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 Rhodororula. 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 PRO201, PRO292, PRO327, PRO1265, PRO344,

PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 are derived from multicellular organisms. Examples of invertebrate cells include insect cells such as Drosophila S2 and Spodoptera

S19, 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., J. 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 tumor (MMT 060562, ATCC CCL51). The selection of the appropriate host cell is deemed to be within the skill in the art. c. Selection and Use of a Replicable Vector

The nucleic acid (e.g., cDNA or genomic DNA) encoding PRO201, PRO292, PRO327, PRO1265,

PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343,PRO347, PRO357, PRO715, PRO1017,

PRO1112, PRO509, PRO853 or PRO882 may be produced recombinantly not only directly, but also as a fusion © 20 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 PRO201-, PRO292-, PRO327-, PRO1265-, PRO344-, PRO343-,

PRO347-, PRO357-, PRO715-, PRO1017-, PRO1112-, PRO509-, PRO853- or PRO882-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, 1pp, 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 a-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 2. 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 cellscompetent to take up the PRO201-, PRO292-, PRO327-,PRO1265-, PRO344-, PRO343-, PRO347-,PRO357-,

PRO715-, PRO1017-, PRO1112-, PRO509-, PRO853- or PRO882-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 ez 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 PRO201-, PRO292-,

PROB853-or PRO882-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 B-lactamase and lactose promoter systems [Chang et al., Nature, 275:615 (1978); Goeddel er 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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, -

PRO1017, PRO1112, PROS09, PRO853 or PROSS2. :

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]. 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 icamerace, 2.phnephnglycerate mntace 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.

PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017,

PROI1112, PRO509, PRO853 or PRO882 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

. | WO 00/37640 PCT/US99/30095 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 PRO201, PRO292, PR0O327, PRO1265, PRO344, PRO343,

PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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, e-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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017,

PRO1112, PRO509, PRO853 or PRO882 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 PRO201, PRO292, PRO327,

PRO1265,PR0O344, PRO343, PRO347, PRO357, PRO715,PRO1017, PRO1112, PRO509, PRO853 or PROS82.

Still other methods, vectors, and host cells suitable for adaptation to the synthesis of PRO201, PRO292,

PRO327,PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or . PRO882 in recombinant vertebrate cell culture are described in Gething ez al., Nature, 293:620-625 (1981); Mantei et al., Nature, 281:40-46 (1979); EP 117,060; and EP 117,058. d. 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 PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343,

PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide or against a synthetic peptide based on the DNA sequences provided herein or againstan exogenous sequence fused to PRO201,

PRO853 or PRO882 DNA and encoding a specific antibody epitope. e. Purification of Polypeptide

Forms of PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715,

PROI1017, PRO1112, PRO509, PRO853 or PRO882 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 PRO201, PRO292, PRO327, PRO1265,

PRO344, PR0O343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 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 PRO201,PR0O292, PRO327,PRO1265,PR0O344, PRO343, PRO347,PRO357,

PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 fromrecombinant 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 PRO201, PRO292, PRO327,PRO1265, PRO344, PRO343, PRO347, PRO357,

PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882. 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 step(s) selected will depend, for example, on the nature of the production process used and the particular PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017,

PRO1112, PRO509, PRO853 or PRO882 produced.

E. Amplification of Genes Encoding the PRO201, PRO292 PRO327, PRO1265, PRO344. PRO343, PRO347.PRO357.PROTIS. PRO1017.PDO1112 DDOSO0 DRAORS2 ~r PROLRY) Polunentidec in Timor Ticcnes and Cell Lines

The present invention is based on the identification and characterization of genes that are amplified in certain cancer cells.

The genome of prokaryotic and eukaryotic organisms is subjected to two seemingly conflicting requirements. One is the preservation and propagation of DNA as the genetic information in its original form, to guarantee stable inheritance through multiple generations. On the other hand, cells or organisms must be able to adapt to lasting environmental changes. The adaptive mechanisms can include qualitative or quantitative modifications of the genetic material. Qualitative modifications include DNA mutations, in which coding sequences are altered resulting in a structurally and/or functionally different protein. Gene amplification is a quantitative modification, whereby the actual number of complete coding sequence, i.e., a gene, increases, leading to an increased number of available templates for transcription, an increased number of translatable transcripts, and,

ultimately, to an increased abundance of the protein encoded by the amplified gene.

The phenomenon of gene amplification and its underlying mechanisms have been investigated in vitro in several prokaryotic and eukaryotic culture systems. The best-characterized example of gene amplification involves the culture of eukaryotic cells in medium containing variable concentrations of the cytotoxic drug methotrexate (MTX). MTX is a folic acid analogue and interferes with DNA synthesis by blocking the enzyme dihydrofolate reductase (DHFR). During the initial exposure to low concentrations of MTX most cells (>99.9%) will die. A small number of cells survive, and are capable of growing in increasing concentrations of MTX by producing large amounts of DHFR-RNA and protein. The basis of this overproduction is the amplification of the single DHFR gene. The additional copies of the gene are found as extrachromosomal copies in the form of small, supernumerary chromosomes (double minutes) or as integrated chromosomal copies.

Gene amplification is most commonly encountered in the development of resistance to cytotoxic drugs (antibiotics for bacteria and chemotherapeutic agents for eukaryotic cells) and neoplastic transformation.

Transformation of a eukaryotic cell as a spontaneous event or due to a viral or chemical/environmental insult is typically associated with changes in the genetic material of that cell. One of the most common genetic changes observed in human malignancies are mutations of the p53 protein. p53 controls the transition of cells from the stationary (G1) to the replicative (S) phase and prevents this transition in the presence of DNA damage. In other words, one of the main consequences of disabling p53 mutations is the accumulation and propagation of DNA damage, i.e., genetic changes. Common types of genetic changes in neoplastic cells are, in addition to point mutations, amplifications and gross, structural alterations, such as translocations.

The amplification of DNA sequences may indicate a specific functional requirement as illustrated in the : DHFR experimental system. Therefore, the amplification of certain oncogenes in malignancies points toward a causative role of these genes in the process of malignant transformation and maintenance of the transformed phenotype. This hypothesis has gained support in recent studies. For example, the bcl-2 protein was found to be amplified in certain types of non-Hodgkin's lymphoma. This protein inhibits apoptosis and leads to the progressive accumulation of neoplastic cells. Members of the gene family of growth factor receptors have been found to be amplified in various types of cancers suggesting that overexpression of these receptors may make neoplastic cells less susceptible to limiting amounts of available growth factor. Examples include the amplification of the androgen receptor in recurrent prostate cancer during androgen deprivation therapy and the amplification of the growth factor receptor homologue ERB2 in breast cancer. Lastly, genes involved in intracellular signaling and control of cell cycle progression can undergo amplification during malignant transformation. This is illustrated by the amplification of the bel-I and ras genes in various epithelial and lymphoid neoplasms.

These earlier studies illustrate the feasibility of identifying amplified DNA sequences in neoplasms, because this approach can identify genes important for malignant transformation. The case of ERB2 also demonstrates the feasibility from a therapeutic standpoint, since transforming proteins may represent novel and specific targets for tumor therapy.

Several different techniques can be used to demonstrate amplified genomic sequences. Classical cytogenetic analysis of chromosome spreads prepared from cancer cells is adequate to identify gross structural . alterations, such as translocations, deletions and inversions. Amplified genomic regions can only be visualized, if they involve large regions with high copy numbers or are present as extrachromosomal material. While cytogenetics was the first technique to demonstrate the consistent association of specific chromosomal changes with particular neoplasms, it is inadequate for the identification and isolation of manageable DNA sequences. The more recently developed technique of comparative genomic hybridization (CGH) has illustrated the widespread phenomenon of genomic amplification in neoplasms. Tumor and normal DNA are hybridized simultaneously onto metaphases of normal cells and the entire genome can be screened by image analysis for DNA sequences that are present in the tumor at an increased frequency. (WO 93/18,186; Gray et al., Radiation Res., 137:275-289[1994)). As ascreening method, this type of analysis has revealed a large number of recurring amplicons (a stretch of amplified DNA) in a variety of human neoplasms. Although CGH is more sensitive than classical cytogenetic analysis in identifying amplified stretches of DNA, it does not allow a rapid identification and isolation of coding sequences within the amplicon by standard molecular genetic techniques. ’

The most sensitive methods to detect gene amplification are polymerase chain reaction (PCR)-based assays.

These assays utilize very small amount of tumor DNA as starting material, are exquisitely sensitive, provide DNA that is amenable to further analysis, such as sequencing and are suitable for high-volume throughput analysis.

The above-mentioned assays are not mutually exclusive, but are frequently used in combination to identify amplifications in neoplasms. While cytogenetic analysis and CGH represent screenin g methods to survey the entire genome for amplified regions, PCR-based assays are most suitable for the final identification of coding sequences, i.e., genes in amplified regions.

According to the present invention, such genes have been identified by quantitative PCR (S. Gelmini et al, Clin. Chem., 43:752 [1997)), by comparing DNA from a variety of primary tumors, including breast, lung, colon, prostate, brain, liver, kidney, pancreas, spleen, thymus, testis, ovary, uterus, etc., tumor, or tumor cell lines, - with pooled DNA from healthy donors. Quantitative PCR was performed using a TagMan instrument (ABI).

Gene-specific primers and fluorogenic probes were designed based upon the coding sequences of the DNAs.

Human lung carcinoma cell lines include A549 (SRCC768), Calu-1 (SRCC769), Calu-6 (SRCC770), H157 (SRCC771), H441 (SRCC772), H460 (SRCC773), SKMES-1 (SRCC774), SW900 (SRCC775), H522 (SRCC832),and H810 (SRCC833), all available from ATCC. Primary human lung tumor cells usually derive from adenoearéinoimas; sguamens 22! carcinamac large cell carcinomas. non-small cell carcinomas, small cell carcinomas, and broncho alveolar carcinomas, and include, for example, SRCC724 (adenocarcinoma, abbreviated as “AdenoCa”)(LT1), SRCC725 (squamous cell carcinoma, abbreviated as “SqCCa)(L.T1a), SRCC726 (adenocarcinoma)(LT2), SRCC727 (adenocarcinoma)(LT3), SRCC728 (adenocarcinoma)(LT4), SRCC729 (squamous cell carcinoma)(LT6), SRCC730 (adeno/squamous cell carcinoma)(LT7), SRCC73] (adenocarcinoma)(LT9), SRCC732 (squamous cell carcinoma)(LT10), SRCC733 (squamous cell carcinoma)(LT11), SRCC734 (adenocarcinoma)(LT12), SRCC735 (adeno/squamous cell carcinoma)(LT13),

SRCC736 (squamous cell carcinoma)(LT15), SRCC737 (squamous cell carcinoma)(L.T16), SRCC738 (squamous cellcarcinoma)(LT17), SRCC739 (squamous cell carcinoma)(LT18), SRCC740 (squamous cell carcinoma)(LT19),

SRCC741 (lung cell carcinoma, abbreviated as “LCCa”)(L.T21), SRCC811 (adenocarcinoma)(LT22), SRCC825 (adenocarcinoma)(LT8), SRCC886 (adenocarcinoma)(LT25), SRCC887 (squamous cell carcinoma) (LT26),

SRCC888 (adeno-BAC carcinoma) (LT27), SRCC889 (squamous cell carcinoma) (L.T28), SRCC890 (squamous cell carcinoma) (LT29), SRCC891 (adenocarcinoma) (LT30), SRCC892 (squamous cell carcinoma) (LT31),

SRCC894 (adenocarcinoma) (LT33). Also included are human lung tumors designated SRCC1125 [HF-000631],

SRCC1127 [HF-000641], SRCC1129 [HF-000643), SRCC1133 [HF-000840], SRCC1135 [HF-000842],

SRCC1227 [HF-001291], SRCC1229 [HF-001293], SRCC1230 [HF-001294], SRCC1231 [HF-001295],

SRCC1232 [HF-001296), SRCC1233 [HF-001297], SRCC1235 [HF-001299], and SRCC1236 [HF-001300].

Colon cancer cell lines include, for example, ATCC cell lines SW480 (adenocarcinoma, SRCC776),

SW620 (lymph node metastasis of colon adenocarcinoma, SRCC777), Colo320 (carcinoma, SRCC778), HT29 (adenocarcinoma, SRCC779), HM7 (a high mucin producing variant of ATCC colon adenocarcinoma cell line,

SRCC780, obtained from Dr. Robert Warren, UCSF), CaWiDr (adenocarcinoma, SRCC781), HCT116 (carcinoma,

SRCC782), SKCO1 (adenocarcinoma, SRCC783), SW403 (adenocarcinoma, SRCC784), LS174T (carcinoma,

SRCC785), Colo205 (carcinoma, SRCC828), HCT15 (carcinoma, SRCC829), HCC2998 (carcinoma, SRCC830), and KM12 (carcinoma, SRCC831). Primary colon tumors include colon adenocarcinomas designated CT2 (SRCC742), CT3 (SRCC743) ,CT8 (SRCC744), CT10 (SRCC745), CT12 (SRCC746), CT14 (SRCC747), CT15 (SRCC748), CT16 (SRCC749), CT17 (SRCC750), CT1 (SRCC751), CT4 (SRCC752), CT5 (SRCC753), CT6 (SRCC754), CT7 (SRCC755), CT9 (SRCC756), CT11 (SRCC757), CT18 (SRCC758), CT19 (adenocarcinoma,

SRCC906), CT20 (adenocarcinoma, SRCC907), CT21 (adenocarcinoma, SRCC908), CT22 (adenocarcinoma,

SRCC909), CT23 (adenocarcinoma, SRCC910), CT24 (adenocarcinoma, SRCC911), CT25 (adenocarcinoma,

SRCC912), CT26 (adenocarcinoma, SRCC913), CT27 (adenocarcinoma, SRCC914),CT28 (adenocarcinoma, ) SRCC915), CT29 (adenocarcinoma, SRCC916), CT30 (adenocarcinoma, SRCC917), CT31 (adenocarcinoma,

SRCC918), CT32 (adenocarcinoma, SRCC919), CT33 (adenocarcinoma, SRCC920), CT35 (adenocarcinoma, : SRCC921), and CT36 (adenocarcinoma, SRCC922). Also included are human colon tumor centers designated

SRCC1051 [HF-000499], SRCC1052 [HF-000539], SRCC1053 [HF-000575}, SRCC1054 [HF-000698],

SRCC1142 [HF-000762], SRCC1144 [HF-000789]), SRCC1146 [HF-000795] and SRCC1148[HF-000811].

Human breast carcinoma cell lines include, for example, HBL 100 (SRCC759), MB435s (SRCC760), T47D (SRCC761), MB468(SRCC762), MB175 (SRCC763), MB361 (SRCC764), BT20(SRCC765), MCF7 (SRCC766), and SKBR3 (SRCC767), and human breast tumor center designated SRCC1057 [HF-000545]. Also included are human breast tumors designated SRCC1094, SRCC1095, SRCC1096, SRCC1097, SRCC1098, SRCC1099,

SRCC1100, SRCC1101, and human breast-met-lung-NS tumor designated SRCC893 [LT 32].

Human kidney tumor centers include SRCC989 [HF-000611] and SRCC1014 [HF-000613].

Human testis tumor center includes SRCC1001 [HF-000733] and testis tumor margin SRCC999 [HF- 000716].

Human parathyroid tumor includes SRCC1002 [HF-000831] and SRCC1003 [HF-000832].

F. Tissue Distribution

The results of the gene amplification assays herein can be verified by further studies, such as, by determining mRNA expression in various human tissues.

As noted before, gene amplification and/or gene expression in various tissues may be measured 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 siti 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.

Gene expression in various tissues, alternatively, may be measured by immunological methods, such as immunohistochemical staining of 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 PRO201,PR0292, PR0O327,PRO1265,PR0O344, PRO343,PRO347, PRO357,

PRO715,PRO1017, PRO1112, PRO509, PRO853 or PRO8S2 polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence fused to sequence PRO201, PRO292, PRO327,

PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO8S2

DNA and encoding a specific antibody epitope. General techniques for generating antibodies, and special protocols for Northern blotting and in situ hybridization are provided hereinbelow.

G. Chromosome Mapping

If the amplification of a given gene is functionally relevant, then that gene should be amplified more than neighboring genomic regions which are not important for tumor survival. To test this, the gene can be mapped to a particular chromosome, e.g., by radiation-hybrid analysis. The amplification level is then determined at the location identified, and at the neighboring genomic region. Selective or preferential amplification at the genomic region to which the gene has been mapped is consistent with the possibility that the gene amplification observed . promotes tumor growth or survival. Chromosome mapping includes both framework and epicenter mapping. For further details see, e.g., Stewart ef al., Genome Research, 7:422-433 (1997).

H. Antibody Binding Studies

The results of the gene amplification study can be further verified by antibody binding studies, in which theabilityof anti-PROINT anti-PRO292. anti-PRO327, anti-PRO1265, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO 1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibodies to inhibit the expression of PR0O201, PR0292, PR0O327, PRO1265, PRO344, PRO343, PRO347, PRO357,

PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptides on tumor (cancer) cells is tested.

Exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heteroconjugate antibodies, the preparation of which will be described hereinbelow.

Antibody binding studies may be carried out in any known assay method, such as competitive binding assays, direct and indirect sandwich assays, and immunoprecipitation assays. Zola, Monoclonal Antibodies: A

Manual of Techniques, pp.147-158 (CRC Press, Inc., 1987).

Competitive binding assays rely on the ability of a labeled standard to compete with the test sample analyte for binding with a limited amount of antibody. The amount of target protein (encoded by a gene amplified in a tumor cell) in the test sample is inversely proportional to the amount of standard that becomes bound to the antibodies. To facilitate determining the amount of standard that becomes bound, the antibodies preferably are insolubilized before or after the competition, so that the standard and analyte that are bound to the antibodies may conveniently be separated from the standard and analyte which remain unbound.

Sandwich assays involve the use of two antibodies, each capable of binding to a different immunogenic portion, or epitope, of the protein to be detected. In a sandwich assay, the test sample analyte is bound by a first antibody which is immobilized on a solid support, and thereafter a second antibody binds to the analyte, thus forming an insoluble three-part complex. See, e.g., U.S. Patent No. 4,376,110. The second antibody may itself be labeled with a detectable moiety (direct sandwich assays) or may be measured using an anti-immunoglobulin antibody that is labeled with a detectable moiety (indirect sandwich assay). For example, one type of sandwich assay is an ELISA assay, in which case the detectable moiety is an enzyme.

For immunohistochemistry, the tumor sample may be fresh or frozen or may be embedded in paraffin and fixed with a preservative such as formalin, for example.

I Cell-Based Tumor Assays

Cell-based assays and animal models for tumors (e.g., cancers) can be used to verify the findings of the gene amplification assay, and further understand the relationship between the genes identified herein and the development and pathogenesis of neoplastic cell growth. The role of gene products identified herein in the development and pathology of tumor or cancer can be tested by using primary tumor cells or cells lines that have ) been identified to amplify the genes herein. Such cells include, for example, the breast, colon and lung cancer cells and cell lines listed above. - 20 In a different approach, cells of a cell type known to be involved in a particular tumor are transfected with the cDNAs herein, and the ability of these cDNAs to induce excessive growth is analyzed. Suitable cells include, for example, stable tumor cells lines such as, the B104-1-1 cell line (stable NIH-3T3 cell line transfected with the neu protooncogene) and ras-transfected NIH-3T3 cells, which can be transfected with the desired gene, and monitored for tumorogenic growth. Such transfected cell lines can then be used to test the ability of poly- or monoclonal antibodies or antibody compositions to inhibit tumorogenic cell growth by exerting cytostatic or cytotoxic activity on the growth of the transformed cells, or by mediating antibody-dependent cellular cytotoxicity (ADCQ). Cells transfected with the coding sequences of the genes identified herein can further be used to identify drug candidates for the treatment of cancer.

In addition, primary cultures derived from tumors in transgenic animals (as described below) can be used inthe cell-based assays herein, although stable cell lines are preferred. Techniques to derive continuous cell lines from transgenic animals are well known in the art (see, e.g., Small er al., Mol. Cell. Biol., 5:642-648 [1985]).

J. Animal Models

A variety of well known animal models can be used to further understand the role of the genes identified herein in the development and pathogenesis of tumors, and to test the efficacy of candidate therapeutic agents, including antibodies, and other antagonists of the native polypeptides, including small molecule antagonists. The in vivo nature of such models makes them particularly predictive of responses in human patients. Animal models

Claims

WHAT IS CLAIMED IS:

1. An isolated antibody that binds to a PRO201, PR0292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide.

2. The antibody of Claim 1 which specifically binds to said polypeptide.

3. The antibody of Claim 1 which induces the death of a cell that expresses said polypeptide.

4. The antibody of Claim 3, wherein said cell is a cancer cell that overexpresses said polypeptide as compared to a normal cell of the same tissue type.

5. The antibody of Claim 1 which is a monoclonal antibody.

6. The antibody of Claim 5 which comprises a non-human complementarity determining region (CDR) or a human framework region (FR).

7. The antibody of Claim 1 which is labeled.

8. The antibody of Claim 1 which is an antibody fragment or a single-chain antibody. :

9. A composition of matter which comprises an antibody of Claim 1 in admixture with a } pharmaceutically acceptable carrier.

10. The composition of matter of Claim 9 which comprises a therapeutically effective amount of said antibody. iL The composition of matter of Claim 9 which further comprises a cytotoxic or a chemotherapeutic agent.

12. An isolated nucleic acid molecule that encodes the antibody of Claim 1.

13. A vector comprising the nucleic acid molecule of Claim 12.

14. A host cell comprising the vector of Claim 13.

15. A method for producing an antibody that binds to a PRO201, PRO292, PRO327, PROI1265, PRO344, PRO343,PRO347,PRO357, PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide, said method comprising culturing the host cell of Claim 14 under conditions sufficient to allow expression of said i WO 00/37640 PCT/US99/30095 antibody and recovering said antibody from the cell culture.

16. An antagonist of a PRO201, PRO292, PRO327,PRO1265, PRO344, PRO343, PRO347,PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PROS882 polypeptide.

17. The antagonist of Claim 16, wherein said antagonist inhibits tumor cell growth.

18. Anisolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO201, PRO292, PRO327, PRO1265, PRO344, PR0O343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide, or the complement thereof.

19. The isolated nucleic acid molecule of Claim 18, wherein said hybridization is under stringent hybridization and wash conditions.

20. A method for determining the presence of a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO201, anti-PRO292, anti-PRO327, anti-PRO 1265, anti-PRO344, anti-PR0O343, anti-PRO347, anti-PRO357, anti-PRO715, ’ anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody and determining binding of said antibody to said polypeptide in said sample.

21. The method of Claim 20, wherein said sample comprises a cell suspected of containing a PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PROS09, PROS853 or PRO882 polypeptide.

22. The method of Claim 21, wherein said cell is a cancer cell.

23. A method of diagnosing tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO201, PRO292, PR0327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of tumor in the mammal from which the test tissue cells were obtained.

24. A method of diagnosing tumor in a mammal, said method comprising (a) contacting an anti- PRO201, anti-PRO292, anti-PRO327, anti-PRO1265, anti-PRO344, anti-PR0O343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO8S53 or anti-PRO832 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said oo WO 00/37640 | PCT/US9Y30095 antibody'and aPRO201,PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357,PRO7135,PROI017, . - PRO1112, PROS09, PRO8S3 or PRO882 polypeptide in the test sample, wherein the formation of a complex is Co : indicative of the presence of a tumor in said mammal. . :

25. The method of Claim 24, wherein said antibody is detectably labeled. : 5 26. The method of Claim 24, wherein said test sample of tissue cells is obtained from an individual suspected of having neoplastic cell growth or proliferation. 0

27. A cancer diagnostic kit comprising an anti-PRO201, anti-PR0O292, anti-PRO327, anti-PRO1265, . . anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO7135, anti-PRO1017, anti-PROI112, anti- PROS509, anti-PRO8S3 or anti-PRO882 antibody and a carrier in suitable packaging.

28. The kit of Claim 27 which further comprises instructions for using said antibody to detect the Co + presence ofa PRO20t, PRO292, PRO327, PRO1265, PRO344, PR0O343, PRO347, PRO357, PRO715,PROI017, = "PRO1112, PROS509, PRO8S53 or PRO882 polypeptide in a sample suspected of containing the same.

29. The use of an agent that inhibits a biological activity of a PRO201, PRO292, PRO327, ] o PROI1265, PRO344, PRO343, PRO347, PRO715, PRO1017, PRO1112, PRO509, PRO853, or PRO882 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

30. The use of Claim 29, wherein said tumor cells overexpress said polypeptide as compared to Co normal cells of the same tissue type. :

31. The use of Claim 29, wherein said agent is an ant-PRO201 , anti-PRO292, anti-PRO327, anti-

20 . PROI126S, anti-PRO344, anti-PRO343, anti-PRO347,anti-PRO357,anti-PRO71S, anti-PRO1017, anti-PRO1 112, anti-PRO509, anti-PRO833 or anti-PRO8S2 antibody.

32. The use of Claim 31, wherein said anti-PRO201, anti-PRO292, anti-PRO327, anti-PRO1255, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO71S, ant-PRO1017, anti-PROI112, anti- PRO3509, anti-PRO8S3 or anti-PRO882 antibody induces cell death.

33. The use of Claim 29, wherein said tumor cells are further exposed to radiation treatment, a cytotoxic agent or a chemotherapeutic agent.

34. The use of an agent that inhibits the expression of a PRO201, PRO292, PRO327, = ~ PROI265, PRO344, PRO343, PRO347, PRO71S, PROI1017, PRO1112, PROS509, PRO853, or PRO882 Co -178- AMENDED SHEET 22/05/2002

= .polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein oo o growth of said tumor cells is thereby inhibited. i ’

35. ‘The use of Claim 34, wherein said mor cells overexpress said polypeptide as compared to normal cells of the same tissue type. - br} : 36. The use of Claim 34, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO201, PRO292, PRO327, PRO1263, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PROS09, PROSS3 oc PRO882 polypeptide or the complement thereof. Co 37. The use of Claim 36, Wherein said tumor cells are fucther exposed ta radiation treatment, a cytotoxic agent ora chematherapeutic agent. | | -

38. An article of manufacture, comprising: : : ) a container; Co : a label on the container; and } : oo : a compasition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the * 15 composition is effective for treating conditions characterized by overexpression of a PRO201, PRO292, PRO327,- _ PRO1265, PRO344, PR0O343, PRO347, PRO357, PRO71S, PRO101 7,PROI1112, PRO509, PRO8S53 or PRO8S2 : ] polypeptide in said tumor cells as compared to in normal cells of the same tissue type. }

39. The article of manufacture of Claim 38, wherein said active agent inhibits a biological activity of RE and/or the expression of said PRO201, PRO292, PRO327, PRO 12635, PRO344, PRO343, PRO347, PRO3S57, ~20 PRO715,PRO10I7, PROL112. PROS09, PRO8BS3 or PRO8S2 polypeptide.

40. The article of manufacture of Claim 39, wherein said active agent is an anti-PRO201, anti-PR0O292, anti-PRO327, anti-PRO126S, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO3S57, anti-PRO713, anti- PRO1017, anti-PRO1112, anti-PRO509, anti-PROS53 or anti-PROKS?2 antibody.

41. The article of manufacture of Claim 39, wherein said active agent is an antisense oligonucleatide.

41. A method of identifying a compound that inhibits a biological or immunological activity of a : PRO201, PRO292, PRO327, PRO(265, PRO344, PRO343, PRO347, PRO357, PROTILS, PRO1017, PROI1 12, PROS09, PRO853 or PRO882 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient © allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited. -179- : AMENDED SHEET 22/05/2002

43. The method of Claim 42, wherein said candidate compound is an anti-PRO201, anti-PR0O292, anti- PRO327, anti-PRO1265, anti-PRO344, anti-PRO343, anti-PRO347, anti-PRO357, anti-PRO715, anti-PRO1017, anti-PRO1112, anti-PRO509, anti-PRO853 or anti-PRO882 antibody.

44. The method of Claim 42, wherein said candidate compound or said PRO201, PRO292, PRO327, PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide is immobilized on a solid support.

45. The method of Claim 44, wherein the non-immobilized component is detectably labeled.

46. A method of identifying a compound that inhibits an activity of a PRO201, PRO292, PRO327, PRO1265, PRO344, PR0O343, PRO347,PRO357, PRO715, PRO1017, PRO1112, PRO509, PRO853 or PRO882 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist.

47. A method for identifying a compound that inhibits the expression of a PRO201, PR0O292, PRO327, - PRO1265, PRO344, PRO343, PRO347, PRO357, PRO715, PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

48. The method of Claim 47, wherein said candidate compound is an antisense oligonucleotide.

49. Isolated nucleic acid having at least 80% nucleic acid sequence identity to a nucleotide sequence that encodes 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:6), Figure 6 (SEQ ID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQ ID NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:48), and Figure 28 (SEQ ID NO:53).

50. Isolated nucleic acid having at least 80% nucleic acid sequence identity to a nucleotide sequence selected from the group consisting of the nucleotide sequence shown in Figure 1 (SEQ ID NO:1), Figure 3 (SEQ ID NO:5), Figure 5 (SEQ ID NO:7), Figure 7 (SEQ ID NO:12), Figure 9 (SEQ ID NO:14), Figure 11 (SEQ ID NO:22), Figure 13 (SEQ ID NO:27), Figure 15 (SEQ ID NO:32), Figure 17 (SEQ ID NO:39), Figure 19 (SEQ ID NO:4)), Figure 21 (SEQ ID NO:43), Figure 23 (SEQ ID NO:45), Figure 25 (SEQ ID NO:47), and Figure 27 (SEQ ID NO:52).

co \

51. Isolated nucleic acid having at least 80% nucleic acid sequence identity to a nucleotide sequence selected from the group consisting of the full-length coding sequence of the nucleotide sequence shown in Figure 1 (SEQ ID NO:1), Figure 3 (SEQ ID NO:5), Figure 5 (SEQ ID NO:7), Figure 7 (SEQ ID NO:12), Figure 9 (SEQ ID NO:14), Figure 11 (SEQ ID NO:22), Figure 13 (SEQ ID NO:27), Figure 15 (SEQ ID NO:32), Figure 17 (SEQ ID NO:39), Figure 19 (SEQ ID NO:41), Figure 21 (SEQ ID NO:43), Figure 23 (SEQ ID NO:45), Figure 25 (SEQ ID NO:47), and Figure 27 (SEQ ID NO:52).

52. Isolated nucleic acid having at least 80% nucleic acid sequence identity to the full-length coding sequence of the DNA deposited under ATCC accession number 209567, 209530, 203452, 209492, 209481, 209532, 209527, 209570, 209883, 209951 or 209812.

53. A vector comprising the nucleic acid of any one of Claims 49 to 52.

54. The vector of Claim 53 operably linked to control sequences recognized by a host cell transformed with the vector.

55. A host cell comprising the vector of Claim 53. : 56. The host cell of Claim 55, wherein said cell is a CHO cell.

57. The host cell of Claim 55, wherein said cell is an E. coli.

58. The host cell of Claim 55, wherein said cell is a yeast cell.

59. The host cell of Claim 55, wherein said cell is a Baculovirus-infected insect cell.

60. A process for producing a PRO201,PR0O292, PRO327, PRO1265, PRO344,PR0O343, PRO347, PRO357,PRO715,PRO1017,PRO1112, PRO509, PRO853 or PRO882 polypeptide comprising culturing the host cell of Claim 55 under conditions suitable for expression of said polypeptide and recovering said polypeptide from the cell culture.

61. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence selected from the group consisting of the amino acid sequence shown in Figure 2 (SEQ 1D NO:2), Figure 4 (SEQ ID NO:6), Figure 6 (SEQ ID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQ ID NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:43), and Figure 28 (SEQ ID NO:53).

ks

62. Anisolated polypeptide scoring at least 80% positives when compared 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:6), Figure 6 (SEQ ID NQ:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQ ID NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:48), and Figure 28 (SEQ ID NO:53).

63. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209567, 209530, 203452, 209492, 209481, 209532, 209527, 209570, 209883, 209951 or 209812.

64. A chimeric molecule comprising a polypeptide according to any one of Claims 61 to 63 fused to a heterologous amino acid sequence.

65. The chimeric molecule of Claim 64, wherein said heterologous amino acid sequence is an epitope tag sequence.

66. The chimeric molecule of Claim 64, wherein said heterologous amino acid sequence is a Fc region of an immunoglobulin. :

67. An antibody which specifically binds to a polypeptide according to any one of Claims 61 to 63.

68. The antibody of Claim 67, wherein said antibody is amonoclonal antibody, a humanized antibody or a single-chain antibody.

69. Isolated nucleic acid having at least 80% nucleic acid sequence identity to: 2U 4) a nucicoiide sequence encoding the nolvpeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:6), Figure 6 (SEQ ID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQ ID NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ 1D NO:48), or Figure 28 (SEQ ID NO:53), 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:6), Figure 6 (SEQ ID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO: 15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQ ID NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:48), or Figure 28 (SEQ ID NQ:53), with its associated signal peptide; or (©) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:6), Figure 6 (SEQ ID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ

: \ ID NO:15), Figure 12 (SEQ 1D N0O:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQ ID NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:48), or Figure 28 (SEQ ID NO:53), lacking its associated signal peptide.

70. 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:6), Figure 6 (SEQID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQ ID NO:42), Figure 22 (SEQID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:48), or Figure 28 (SEQ ID NO:53), lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ1D NO:6), Figure 6 (SEQ ID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQID NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:48), or Figure 28 (SEQ ID NO:53), with its associated signal peptide; or (¢) anextracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQID NO:6), Figure 6 (SEQ ID NO:8), Figure 8 (SEQ ID NO:13), Figure 10 (SEQ ID NO:15), Figure 12 (SEQ ID NO:23), Figure 14 (SEQ ID NO:28), Figure 16 (SEQ ID NO:33), Figure 18 (SEQ ID NO:40), Figure 20 (SEQID ’ NO:42), Figure 22 (SEQ ID NO:44), Figure 24 (SEQ ID NO:46), Figure 26 (SEQ ID NO:48), or Figure 28 (SEQ ID NO:53), lacking its associated signal peptide.

) 71. The isolated antibody of Claim 1 that binds to a PRO201 polypeptide.

72. The isolated antibody of Claim 1 that binds to a PRO292 polypeptide.

73. The isolated antibody of Claim 1 that binds to a PRO327 polypeptide.

74. The isolated antibody of Claim 1 that binds to a PRO1265 polypeptide.

75. The isolated antibody of Claim 1 that binds to a PRO344 polypeptide.

76. The isolated antibody of Claim 1 that binds to a PRO343 polypeptide.

77. The isolated antibody of Claim 1 that binds to a PRO347 polypeptide.

78. The isolated antibody of Claim 1 that binds to a PRO357 polypeptide.

79. The isolated antibody of Claim 1 that binds to a PRO715 polypeptide.

80. The isolated antibody of Claim 1 that binds to a PRO1017 polypeptide.

81. The isolated antibody of Claim 1 that binds to a PRO1112 polypeptide.

82. The isolated antibody of Claim 1 that binds to a PROS09 polypeptide.

83. The isolated antibody of Claim 1 that binds to a PRO853 polypeptide.

84. The isolated antibody of Claim 1 that binds to a PRO882 polypeptide.

85. The isolated antibody of any one of Claims 71 to 84 which specifically binds to said polypeptide.

86. The isolated antibody of any one of Claims 71 to 84 which induces the death of a cell that expresses said polypeptide.

87. The isolated antibody of Claim 86, wherein said cell is a cancer cell that overexpresses said polypeptide as compared to a normal cell of the same tissue type. 184 AMENDED SHEET 22/05/2002

88. The isolated antibody of any one of Claims 71 to 84 which is a monoclonal antibody.

89. The isolated antibody of Claim 88, wherein said antibody contains a non-human complementarity determining region (CDR) residues and human framework region (FR) residues.

90. The isolated antibody of any one of Claims 71 to 84 which is labeled.

91. The isolated antibody of any one of Claims 71 to 84 which is an antibody fragment or a single- chain antibody.

92. A composition of matter which comprises an isolated antibody of any one of Claims 71 to 84 inadmixture with a pharmaceutically acceptable carrier.

93. The composition of matter of Claim 92 which comprises a therapeutically effective amount of said antibody.

94. The composition of matter of Claim 92 which further comprises a cytotoxic or a chemotherapeutic agent.

95. An isolated nucleic acid molecule that encodes the antibody of Claim 71.

96. An isolated nucleic acid molecule that encodes the antibody of Claim 72.

97. An isolated nucleic acid molecule that encodes the antibody of Claim 73.

98. An isolated nucleic acid molecule that encodes the antibody of Claim 74.

99. An isolated nucleic acid molecule that encodes the antibody of Claim 75.

100. An isolated nucleic acid molecule that encodes the antibody of Claim 76.

101. An isolated nucleic acid molecule that encodes the antibody of Claim 77.

102. An isolated nucleic acid molecule that encodes the antibody of Claim 78.

. 185 AMENDED SHEET 22/05/2002

) 103. An isolated nucleic acid molecule that encodes the antibody of Claim 79.

104. An isolated nucleic acid molecule that encodes the antibody of Claim 80.

105. An isolated nucleic acid molecule that encodes the antibody of Claim 81.

106. An isolated nucleic acid molecule that encodes the antibody of Claim 82.

107. An isolated nucleic acid molecule that encodes the antibody of Claim 83.

108. An isolated nucleic acid molecule that encodes the antibody of Claim 84.

109. A vector comprising the isolated nucleic acid molecule of Claim 95.

110. A vector comprising the isolated nucleic acid molecule of Claim 96.

111. A vector comprising the isolated nucleic acid molecule of Claim 97.

112. A vector comprising the isolated nucleic acid molecule of Claim 98.

113. A vector comprising the isolated nucleic acid molecule of Claim 99.

114. A vector comprising the isolated nucleic acid molecule of Claim 100.

115. A vector comprising the isolated nucleic acid molecule of Claim 101.

116. A vector comprising the isolated nucleic acid molecule of Claim 102.

117. A vector comprising the isolated nucleic acid molecule of Claim 103.

118. A vector comprising the isolated nucleic acid molecule of Claim 104.

119. A vector comprising the isolated nucleic acid molecule of Claim 105.

120. A vector comprising the isolated nucleic acid molecule of Claim 106. 186 AMENDED SHEET 22/05/2002

) : 121. A vector comprising the isolated nucleic acid molecule of Claim 107.

122. A vector comprising the isolated nucleic acid molecule of Claim 108.

123. A host cell comprising the vector of Claim 109.

124. A host cell comprising the vector of Claim 110.

125. A host cell comprising the vector of Claim 111.

126. A host cell comprising the vector of Claim 112.

127. A host cell comprising the vector of Claim 113.

128. A host cell comprising the vector of Claim 114.

129. A host cell comprising the vector of Claim 115.

130. A host cell comprising the vector of Claim 116.

131. A host cell comprising the vector of Claim 117.

132. A host cell comprising the vector of Claim 118.

133. A host cell comprising the vector of Claim 119. : :

134. A host cell comprising the vector of Claim 120.

135. A host cell comprising the vector of Claim 121.

136. A host cell comprising the vector of Claim 122.

137. A method of producing an antibody that binds to a PRO201 polypeptide, said method comprising culturing the host cell of Claim 123 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture. 187 AMENDED SHEET 22/05/2002

) 138. A method of producing an antibody that binds to a PRO292 polypeptide, said method comprising culturing the host cell of Claim 124 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

139. A method of producing an antibody that binds to a PRO327 polypeptide, said method comprising culturing the host cell of Claim 125 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

140. A method of producing an antibody that binds to a PRO1265 polypeptide, said method comprising culturing the host cell of Claim 126 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

141. A method of producing an antibody that binds to a PRO344 polypeptide, said method comprising culturing the host cell of Claim 127 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

142. A method of producing an antibody that binds to a PRO343 polypeptide, said method comprising : culturing the host cell of Claim 128 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

143. A method of producing an antibody that binds to a PRO347 polypeptide, said method comprising culturing the host cell of Claim 129 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

144. A method of producing an antibody that binds to a PRO357 polypeptide, said method comprising culturing the host cell of Claim 130 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

145. A method of producing an antibody that binds to a PRO715 polypeptide, said method comprising culturing the host cell of Claim 131 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

146. A method of producing an antibody that binds to a PRO1017 polypeptide, said method comprising culturing the host cell of Claim 132 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture. 188 AMENDED SHEET 22/05/2002

) 147. A method of producing an antibody that binds to a PRO1112 polypeptide, said method comprising culturing the host cell of Claim 133 under conditions sufficient to allow expression of said antibody and recovering said antibody from the celf culture.

148. A method of producing an antibody that binds to a PRO509 polypeptide, said method comprising culturing the host cell of Claim 134 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

149. A method of producing an antibody that binds to a PRO853 polypeptide, said method comprising culturing the host cell of Claim 135 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

150. A method of producing an antibody that binds to a PRO882 polypeptide, said method comprising culturing the host cell of Claim 136 under conditions sufficient to allow expression of said antibody and recovering said antibody from the cell culture.

151. An antagonist of a PRO201 polypeptide.

152. An antagonist of a PRO292 polypeptide.

153. An antagonist of a PRO327 polypeptide.

154. An antagonist of a PRO1265 polypeptide.

155. An antagonist of a PRO344 polypeptide.

156. An antagonist of a PRO343 polypeptide.

157. An antagonist of a PRO347 polypeptide.

158. An antagonist of a PRO357 polypeptide.

159. An antagonist of a PRO715 polypeptide.

160. An antagonist of a PRO1017 polypeptide. 189 AMENDED SHEET 22/05/2002

A ’ 161. An antagonist of a PRO1112 polypeptide.

162. An antagonist of a PRO509 polypeptide.

163. An antagonist of a PRO853 polypeptide.

164. An antagonist of a PRO882 polypeptide.

165. The antagonist of any one of Claims 151 to 164, wherein said antagonist inhibits tumor cell growth.

166. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO201 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

167. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO292 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

168. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO327 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

169. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO1265 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

170. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO344 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

171. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO343 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions. 190 AMENDED SHEET 22/05/2002

ES

172. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO347 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

173. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO357 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

174. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO715 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

175. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO1017 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and ~ wash conditions.

176. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO1112 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

177. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PROS509 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

178. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO853 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

179. An isolated nucleic acid molecule that hybridizes to a nucleic acid sequence that encodes a PRO882 polypeptide, or the complement thereof, wherein said hybridization is under stringent hybridization and wash conditions.

180. A method for determining the presence of a PRO201 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO201 antibody and determining binding of said antibody to said polypeptide in said sample. 191 AMENDED SHEET 22/05/2002

Sr : 181. A method for determining the presence of a PRO292 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PR0O292 antibody and determining binding of said antibody to said polypeptide in said sample.

182. A method for determining the presence of a PRO327 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO327 antibody and determining binding of said antibody to said polypeptide in said sample.

183. A method for determining the presence of a PRO1265 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO1265 antibody and determining binding of said antibody to said polypeptide in said sample.

184. A method for determining the presence of a PRO344 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO344 antibody and determining binding of said antibody to said polypeptide in said sample.

185. A method for determining the presence of a PRO343 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO343 antibody and determining binding of said antibody to said polypeptide in said sample.

186. A method for determining the presence of a PRO347 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO347 antibody and determining binding of said antibody to said polypeptide in said sample.

187. A method for determining the presence of a PRO357 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO357 antibody and determining binding of said antibody to said polypeptide in said sample.

188. A method for determining the presence of a PRO715 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO715 antibody and determining binding of said antibody to said polypeptide in said sample.

189. A method for determining the presence of a PRO1017 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO1017 antibody and determining binding of said antibody to said polypeptide in said sample. 192 AMENDED SHEET 22/05/2002

190. A method for determining the presence of a PRO1112 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO1112 antibody and determining binding of said antibody to said polypeptide in said sample.

191. A method for determining the presence of a PRO509 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO509 antibody and determining binding of said antibody to said polypeptide in said sample.

192. A method for determining the presence of a PRO853 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO853 antibody and determining binding of said antibody to said polypeptide in said sample.

193. A method for determining the presence of a PRO882 polypeptide in a sample suspected of containing said polypeptide, said method comprising exposing the sample to an anti-PRO882 antibody and determining binding of said antibody to said polypeptide in said sample.

194. The method of Claim 180, wherein said sample comprises a cell suspected of containing a PRO201 polypeptide.

195. The method of Claim 181, wherein said sample comprises a cell suspected of containing a PRO292 polypeptide.

196. The method of Claim 182, wherein said sample comprises a cell suspected of containing a PRO327 polypeptide.

197. The method of Claim 183, wherein said sample comprises a cell suspected of containing a PRO1265 polypeptide.

198. The method of Claim 184, wherein said sample comprises a cell suspected of containing a PRO344 polypeptide.

199. The method of Claim 185, wherein said sample comprises a cell suspected of containing a PRO343 polypeptide.

200. The method of Claim 186, wherein said sample comprises a cell suspected of containing a PRO347 polypeptide. 193 AMENDED SHEET 22/05/2002

201. The method of Claim 187, wherein said sample comprises a cell suspected of containing a PRO357 polypeptide.

202. The method of Claim 188, wherein said sample comprises a cell suspected of containing a PRO715 polypeptide. :

203. The method of Claim 189, wherein said sample comprises a cell suspected of containing a PRO1017 polypeptide.

204. The method of Claim 190, wherein said sample comprises a cell suspected of containing a PRO1112 polypeptide.

205. The method of Claim 191, wherein said sample comprises a cell suspected of containing a PROS09 polypeptide.

206. The method of Claim 192, wherein said sample comprises a cell suspected of containing a PRO853 polypeptide.

207. The method of Claim 193, wherein said sample comprises a cell suspected of containing a PRO8&82 polypeptide.

208. The method of any one of Claims 194 to 207, wherein said cell is a cancer cell.

209. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO201 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in ~~ the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

210. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO292 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained. 194 AMENDED SHEET 22/05/2002

) 211. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO327 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

212. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO1265 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

213. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO344 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

214. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO343 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

215. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO347 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

216. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO357 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained. 195 AMENDED SHEET 22/05/2002

* 217. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO715 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

218. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO1017 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

219. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO1112 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

220. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PROS509 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

221. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO853 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained.

222. A method of diagnosing a tumor in a mammal, said method comprising detecting the level of expression of a gene encoding a PRO882 polypeptide (a) in a test sample of tissue cells obtained from the mammal, -and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher expression level in the test sample, as compared to the control sample, is indicative of the presence of said tumor in the mammal from which the test tissue cells were obtained. 196 AMENDED SHEET 22/05/2002

223. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO201 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO201 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

224. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO292 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO292 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

225. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO327 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO327 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

226. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO1265 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO1265 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

227. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO344 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO344 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

228. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti PRO343 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO343 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

229. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO347 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO347 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal. 197 AMENDED SHEET 22/05/2002

230. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO357 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO357 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

231. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO715 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO715 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

232. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO1017 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO1017 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

233. A method of diagnosing a tumor in a mammal, said method comprising (2) contacting an anti- PRO1112 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO1112 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

234. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO509 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO509 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

235. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO853 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO853 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal.

236. A method of diagnosing a tumor in a mammal, said method comprising (a) contacting an anti- PRO882 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO882 polypeptide in the test sample, wherein the formation of a complex is indicative of the presence of said tumor in said mammal. 198 AMENDED SHEET 22/05/2002

) 237. The method of any one of Claims 223 to 236, wherein said antibody is detectably labeled.

238. The method of any one of Claims 223 to 236, wherein said test sample of tissue cells is obtained from an individual suspected of having neoplastic cell growth or proliferation.

239. A cancer diagnostic kit comprising an anti-PR0O201 antibody and a carrier in suitable packaging.

240. A cancer diagnostic kit comprising an anti-PR0O292 antibody and a carrier in suitable packaging.

241. A cancer diagnostic kit comprising an anti-PRO327 antibody and a carrier in suitable packaging.

242. A cancer diagnostic kit comprising an anti-PRO1265 antibody and a carrier in suitable packaging.

243. A cancer diagnostic kit comprising an anti-PRO344 antibody and a carrier in suitable packaging.

244. A cancer diagnostic kit comprising an anti-PR0O343 antibody and a carrier in suitable packaging.

245. A cancer diagnostic kit comprising an anti-PRO347 antibody and a carrier in suitable packaging.

246. A cancer diagnostic kit comprising an anti-PRO357 antibody and a carrier in suitable packaging.

247. A cancer diagnostic kit comprising an anti-PRO715 antibody and a carrier in suitable packaging.

248. A cancer diagnostic kit comprising an anti-PRO1017 antibody and a carrier in suitable packaging. 249, A cancer diagnostic kit comprising an anti-PRO1112 antibody and a carrier in suitable packaging.

250. A cancer diagnostic kit comprising an anti-PROS509 antibody and a carrier in suitable packaging.

251. A cancer diagnostic kit comprising an anti-PRO853 antibody and a carrier in suitable packaging.

252. A cancer diagnostic kit comprising an anti-PRO882 antibody and a carrier in suitable packaging.

253. The cancer diagnostic kit of Claim 239 which further comprises instructions for using said antibody to detect the presence of a PRO201 polypeptide in a sample suspected of containing the same. 199 AMENDED SHEET 22/05/2002

254. The cancer diagnostic kit of Claim 240 which further comprises instructions for using said antibody to detect the presence of a PRO292 polypeptide in a sample suspected of containing the same.

255. The cancer diagnostic kit of Claim 241 which further comprises instructions for using said antibody to detect the presence of a PRO327 polypeptide in a sample suspected of containing the same.

256. The cancer diagnostic kit of Claim 242 which further comprises instructions for using said antibody to detect the presence of a PRO1265 polypeptide in a sample suspected of containing the same.

257. The cancer diagnostic kit of Claim 243 which further comprises instructions for using said antibody to detect the presence of a PRO344 polypeptide in a sample suspected of containing the same.

258. The cancer diagnostic kit of Claim 244 which further comprises instructions for using said antibody to detect the presence of a PRO343 polypeptide in a sample suspected of containing the same.

259. The cancer diagnostic kit of Claim 245 which further comprises instructions for using said antibody to detect the presence of a PRO347 polypeptide in a sample suspected of containing the same.

260. The cancer diagnostic kit of Claim 246 which further comprises instructions for using said antibody to detect the presence of a PRO357 polypeptide in a sample suspected of containing the same.

261. The cancer diagnostic kit of Claim 247 which further comprises instructions for using said antibody to detect the presence of a PRO715 polypeptide in a sample suspected of containing the same.

262. The cancer diagnostic kit of Claim 248 which further comprises instructions for using said antibody to detect the presence of a PRO1017 polypeptide in a sample suspected of containing the same.

263. The cancer diagnostic kit of Claim 249 which further comprises instructions for using said antibody to detect the presence of a PRO1112 polypeptide in a sample suspected of containing the same.

264. The cancer diagnostic kit of Claim 250 which further comprises instructions for using said antibody to detect the presence of a PROS509 polypeptide in a sample suspected of containing the same.

265. The cancer diagnostic kit of Claim 251 which further comprises instructions for using said antibody to detect the presence of a PRO8S53 polypeptide in a sample suspected of containing the same. 200 AMENDED SHEET 22/05/2002

) 266. The cancer diagnostic kit of Claim 252 which further comprises instructions for using said antibody to detect the presence of a PRO882 polypeptide in a sample suspected of containing the same.

267. The use of an agent that inhibits a biological activity of a PRO201 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

268. The use of an agent that inhibits a biological activity of a PRO292 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

269. The use of an agent that inhibits a biological activity of a PRO327 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

270. The use of an agent that inhibits a biological activity of a PRO1265 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

271. The use of an agent that inhibits a biological activity of a PRO344 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

272. The use of an agent that inhibits a biological activity of a PRO343 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

273. The use of an agent that inhibits a biological activity of a PRO347 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said 201 AMENDED SHEET 22/05/2002

) tumor cells is thereby inhibited.

274. The use of an agent that inhibits a biological activity of a PRO357 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

275. The use of an agent that inhibits a biological activity of a PRO715 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

276. The use of an agent that inhibits a biological activity of a PRO1017 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

277. The use of an agent that inhibits a biological activity of a PRO1112 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

278. The use of an agent that inhibits a biological activity of a PRO509 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

279. The use of an agent that inhibits a biological activity of a PRO853 polypeptide in a method of ’ making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

280. The use of an agent that inhibits a biological activity of a PRO882 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited. 202 AMENDED SHEET 22/05/2002

281. The use of any one of Claims 267 to 280, wherein said tumor cells overexpress said polypeptide as compared to normal cells of the same tissue type.

282. The use of Claim 267, wherein said agent is an anti-PRO201 antibody.

283. The use of Claim 268, wherein said agent is an anti-PRO292 antibody.

284. The use of Claim 269, wherein said agent is an anti*PR0O327 antibody.

285. The use of Claim 270, wherein said agent is an anti-PRO1265 antibody.

286. The use of Claim 271, wherein said agent is an anti-PRO344 antibody.

287. The use of Claim 272, wherein said agent is an anti-PRO343 antibody.

288. The use of Claim 273, wherein said agent is an anti-PRO347 antibody.

289. The use of Claim 274, wherein said agent is an anti-PRO357 antibody.

290. The use of Claim 275, wherein said agent is an anti-PRO715 antibody.

291. The use of Claim 276, wherein said agent is an anti-PRO1017 antibody.

292. The use of Claim 277, wherein said agent is an anti-PRO1112 antibody.

293. The use of Claim 278, wherein said agent is an anti-PRO509 antibody.

294. The use of Claim 279, wherein said agent is an anti-PRO853 antibody.

295. The use of Claim 280, wherein said agent is an anti-PRO882 antibody.

296. The use of Claim 282, wherein said anti-PRO201 antibody induces cell death.

297. The use of Claim 283, wherein said anti-PR0O292 antibody induces cell death. 203 AMENDED SHEET 22/05/2002

’ 298. The use of Claim 284, wherein said anti-PR0O327 antibody induces cell death.

299. The use of Claim 285, wherein said anti-PRO12635 antibody induces cell death.

300. The use of Claim 286, wherein said anti-PR0O344 antibody induces cell death.

301. The use of Claim 287, wherein said anti-PRO343 antibody induces cell death.

302. The use of Claim 288, wherein said anti-PRO347 antibody induces cell death.

303. The use of Claim 289, wherein said anti-PRO357 antibody induces cell death.

304. The use of Claim 290, wherein said anti-PRO715 antibody induces cell death.

305. The use of Claim 291, wherein said anti-PRO1017 antibody induces cell death.

306. The use of Claim 292, wherein said anti-PRO1112 antibody induces cell death.

307. The use of Claim 293, wherein said anti-PRO509 antibody induces cell death.

308. The use of Claim 294, wherein said anti-PRO853 antibody induces cell death.

309. The use of Claim 295, wherein said anti-PRO882 antibody induces cell death.

310. The use of any one of Claims 267 to 280, wherein said tumor cells are further exposed to radiation treatment, a cytotoxic agent or a chemotherapeutic agent.

311. The use of an agent that inhibits the expression of a PRO201 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

312. The use of an agent that inhibits the expression of a PRO292 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of szid tumor cells is thereby inhibited. 204 AMENDED SHEET 22/05/2002

313. The use of an agent that inhibits the expression of a PRO327 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of’ said tumor cells is thereby inhibited.

314. The use of an agent that inhibits the expression of a PRO1265 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

315. The use of an agent that inhibits the expression of a PRO344 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

316. The use of an agent that inhibits the expression of a PRO343 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

317. The use of an agent that inhibits the expression of a PRO347 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

318. The use of an agent that inhibits the expression of a PRO357 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

319. The use of an agent that inhibits the expression of a PRO715 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited. 205 AMENDED SHEET 22/05/2002 i 320. The use of an agent that inhibits the expression of a PRO1017 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

321. The use of an agent that inhibits the expression of a PRO1112 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

322. The use of an agent that inhibits the expression of a PRO509 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

323. The use of an agent that inhibits the expression of a PRO853 polypeptide in 2 method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

324. The use of an agent that inhibits the expression of a PRO882 polypeptide in a method of making a medicament for use in a method for inhibiting the growth of tumor cells, said method comprising exposing tumor cells that express the polypeptide to an effective amount of said agent, wherein growth of said tumor cells is thereby inhibited.

325. The use of any one of Claims 311 to 324, wherein said tumor cells overexpress said polypeptide as compared to normal cells of the tissue type.

326. The use of Claim 311, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO201 polypeptide, or the complement thereof.

327. The use of Claim 312, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO292 polypeptide, or the complement thereof.

328. The use of Claim 313, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO327 polypeptide, or the complement thereof. 206 AMENDED SHEET 22/05/2002

329. The use of Claim 314, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO1265 polypeptide, or the complement thereof.

330. The use of Claim 315, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO344 polypeptide, or the complement thereof.

331. The use of Claim 316, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO343 polypeptide, or the complement thereof.

332. The use of Claim 317, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO347 polypeptide, or the complement thereof.

333. The use of Claim 318, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO357 polypeptide, or the complement thereof.

334. The use of Claim 319, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO715 polypeptide, or the complement thereof.

335. The use of Claim 320, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO1017 polypeptide, or the complement thereof.

336. The use of Claim 321, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO1112 polypeptide, or the complement thereof.

337. The use of Claim 322, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PROS509 polypeptide, or the complement thereof.

338. The use of Claim 323, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO853 polypeptide, or the complement thereof.

339. The use of Claim 324, wherein said agent is an antisense oligonucleotide that hybridizes to a nucleic acid which encodes the PRO882 polypeptide, or the complement thereof.

340. The use of any one of Claims 311 to 324, wherein said tumor cells are further exposed to radiation treatment, a cytotoxic agent or a chemotherapeutic agent. 207 AMENDED SHEET 22/05/2002

341. An article of manufacture comprising: : a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO201 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

342. An article of manufacture comprising: a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO292 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

343. An article of manufacture comprising: a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO327 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

344. An article of manufacture comprising: a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO1265 polypeptide in said tumor cells as compared to in normal cells of the same tissue type. 345, An article of manufacture comprising: a container; a label on the container; and 208 AMENDED SHEET 22/05/2002

) a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the : composition is effective for treating conditions characterized by overexpression of a PRO344 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

346. An article of manufacture comprising: a container; -a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO343 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

347. An article of manufacture comprising: a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO347 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

348. An article of manufacture comprising: a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO357 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

349. An article of manufacture comprising: a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO715 polypeptide in said tumor cells as compared to in normal cells of the same tissue type. 209 AMENDED SHEET 22/05/2002

: 350. An article of manufacture comprising: a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO1017 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

351. An article of manufacture comprising: a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO1112 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

352. An article of manufacture comprising: a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO509 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

353. An article of manufacture comprising: . a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PROS853 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

354. An article of manufacture comprising: a container; a label on the container; and a composition comprising an active agent contained within the container, wherein the composition 210 AMENDED SHEET 22/05/2002 is effective for inhibiting the growth of tumor cells and wherein the label on the container indicates that the composition is effective for treating conditions characterized by overexpression of a PRO882 polypeptide in said tumor cells as compared to in normal cells of the same tissue type.

355. The article of manufacture of Claim 341, wherein said active agent inhibits a biological activity of and/or expression of said PRO201 polypeptide.

356. The article of manufacture of Claim 342, wherein said active agent inhibits a biological activity - of and/or expression of said PRO292 polypeptide.

357. The article of manufacture of Claim 343, wherein said active agent inhibits a biological activity of and/or expression of said PRO327 polypeptide.

358. The article of manufacture of Claim 344, wherein said active agent inhibits a biological activity of and/or expression of said PRO1265 polypeptide. . 359. The article of manufacture of Claim 345, wherein said active agent inhibits a biological activity of and/or expression of said PRO344 polypeptide.

360. The article of manufacture of Claim 346, wherein said active agent inhibits a biological activity of and/or expression of said PRO343 polypeptide.

361. The article of manufacture of Claim 347, wherein said active agent inhibits a biological activity of and/or expression of said PRO347 polypeptide.

362. The article of manufacture of Claim 348, wherein said active agent inhibits a biological activity of and/or expression of said PRO357 polypeptide.

363. The article of manufacture of Claim 349, wherein said active agent inhibits a biological activity of and/or expression of said PRO715 polypeptide.

364. The article of manufacture of Claim 350, wherein said active agent inhibits a biological activity of and/or expression of said PRO1017 polypeptide.

365. The article of manufacture of Claim 351, wherein said active agent inhibits a biological activity of and/or expression of said PRO1112 polypeptide. 211 AMENDED SHEET 22/05/2002

: 366. The article of manufacture of Claim 352, wherein said active agent inhibits a biological activity : of and/or expression of said PRO509 polypeptide.

367. The article of manufacture of Claim 353, wherein said active agent inhibits a biological activity of and/or expression of said PRO853 polypeptide. ]

368. The article of manufacture of Claim 354, wherein said active agent inhibits a biological activity of and/or expression of said PRO882 polypeptide.

369. The article of manufacture of Claim 355, wherein said active agent is an anti-PRO201 antibody.

370. The article of manufacture of Claim 356, wherein said active agent is an anti-PRO292 antibody.

371. The article of manufacture of Claim 357, wherein said active agent is an anti-PRO327 antibody.

372. The article of manufacture of Claim 358, wherein said active agent is an anti-PRO1265 antibody.

373. The article of manufacture of Claim 359, wherein said active agent is an anti-PR0O344 antibody.

374. The article of manufacture of Claim 360, wherein said active agent is an anti-PRO343 antibody.

375. The article of manufacture of Claim 361, wherein said active agent is an anti-PRO347 antibody.

376. The article of manufacture of Claim 362, wherein said active agent is an anti-PRO357 antibody.

377. The article of manufacture of Claim 363, wherein said active agent is an anti-PRO715 antibody.

378. The article of manufacture of Claim 364 wherein said active agent is an anti-PRO1017 antibody.

379. The article of manufacture of Claim 365, wherein said active agent is an anti-PRO1112 antibody.

380. The article of manufacture of Claim 366, wherein said active agent is an anti-PRO509 antibody.

381. The article of manufacture of Claim 367, wherein said active agent is an anti-PRO853 antibody.

382. The article of manufacture of Claim 368, wherein said active agent is an anti-PRO882 antibody. 212 AMENDED SHEET 22/05/2002 :

+

383. The article of manufacture of any one of Claims 355 to 368, wherein said active agent is an antisense oligonucleotide.

384. A method of identifying a compound that inhibits a biological or immunological activity of a PRO201 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

385. A method of identifying a compound that inhibits a biological or immunological activity of a PRO292 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

386. A method of identifying a compound that inhibits a biological or immunological activity of a PRO327 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological i or immunological activity of said polypeptide is inhibited.

387. A method of identifying a compound that inhibits a biological or immunological activity of a PRO1265 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

388. A method of identifying a compound that inhibits a biological or immunological activity of a PRO344 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

389. A method of identifying a compound that inhibits a biological or immunological activity of a PRO343 polypeptide, said method comprising contacting a candidate compound with said polypeptide under : conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited. 213 AMENDED SHEET 22/05/2002

»

390. A method of identifying a compound that inhibits a biological or immunological activity of a PRO347 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

391. A method of identifying a compound that inhibits a biological or immunological activity of a PRO357 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

392. A method of identifying a compound that inhibits a biological or immunological activity of a PRO715 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

393. A method of identifying a compound that inhibits a biological or immunological activity of a PRO1017 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

394. A method of identifying a compound that inhibits a biological or immunological activity of a PRO1112 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

395. A method of identifying a compound that inhibits a biological or immunological activity of a PROS09 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

396. A method of identifying a compound that inhibits a biological or immunological activity of a PRO853 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited. 214 AMENDED SHEET 22/05/2002

»

397. A method of identifying a compound that inhibits a biological or immunological activity of a PRO882 polypeptide, said method comprising contacting a candidate compound with said polypeptide under conditions and for a time sufficient to allow the two components to interact and determining whether a biological or immunological activity of said polypeptide is inhibited.

398. The method of Claim 384, wherein said candidate compound is an anti-PRO201 antibody.

399. The method of Claim 385, wherein said candidate compound is an anti-PRO292 antibody.

400. The method of Claim 386, wherein said candidate compound is an anti-PRO327 antibody.

401. The method of Claim 387, wherein said candidate compound is an anti-PRO1265 antibody.

402. The method of Claim 388, wherein said candidate compound is an anti-PRO344 antibody.

403. The method of Claim 389, wherein said candidate compound is an anti-PR0O343 antibody.

404. The method of Claim 390, wherein said candidate compound is an anti-PRO347 antibody.

405. The method of Claim 391, wherein said candidate compound is an anti-PRO357 antibody.

406. The method of Claim 392, wherein said candidate compound is an anti-PRO715 antibody.

407. The method of Claim 393, wherein said candidate compound is an anti-PRO1017 antibody.

408. The method of Claim 394, wherein said candidate compound is an anti-PRO1112 antibody.

409. The method of Claim 395, wherein said candidate compound is an anti-PRO509 antibody.

410. The method of Claim 396, wherein said candidate compound is an anti-PRO853 antibody.

411. The method of Claim 397, wherein said candidate compound is an anti-PRO882 antibody.

412. The method of Claim 384, wherein said candidate compound or said PRO20! polypeptide is immobilized on a solid support. 215 AMENDED SHEET 22/05/2002

413. The method of Claim 385, wherein said candidate compound or said PRO292 polypeptide is immobilized on a solid support.

414. The method of Claim 386, wherein said candidate compound or said PRO327 polypeptide is immobilized on a solid support.

415. The method of Claim 387, wherein said candidate compound or said PRO1265 polypeptide is immobilized on a solid support.

416. The method of Claim 388, wherein said candidate compound or said PRO344 polypeptide is immobilized on a solid support.

417. The method of Claim 389, wherein said candidate compound or said PRO343 polypeptide is immobilized on a solid support.

418. The method of Claim 390, wherein said candidate compound or said PRO347 polypeptide is immobilized on a solid support.

419. The method of Claim 391, wherein said candidate compound or said PRO357 polypeptide is immobilized on a solid support.

420. The method of Claim 392, wherein said candidate compound or said PRO715 polypeptide is immobilized on a solid support.

421. The method of Claim 393, wherein said candidate compound or said PRO1017 polypeptide is immobilized on a solid support.

422. The method of Claim 394, wherein said candidate compound or said PRO1112 polypeptide is immobilized on a solid support.

423. The method of Claim 395, wherein said candidate compound or said PRO509 polypeptide is immobilized on a solid support.

424. The method of Claim 396, wherein said candidate compound or said PRO853 polypeptide is immobilized on a solid support. 216 AMENDED SHEET 22/05/2002

425. The method of Claim 397, wherein said candidate compound or said PRO882 polypeptide is immobilized on a solid support.

426. The method of any one of Claims 412 to 425, wherein the non-immobilized component is detectably labeled.

427. A method of identifying a compound that inhibits an activity of a PRO201 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist. © 428. A method of identifying a compound that inhibits an activity of a PRO292 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist.

429. A method of identifying a compound that inhibits an activity of a PRO327 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist.

430. A method of identifying a compound that inhibits an activity of a PRO1265 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist. 217 AMENDED SHEET 22/05/2002

431. A method of identifying a compound that inhibits an activity of a PRO344 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist.

432. A method of identifying a compound that inhibits an activity of a PRO343 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist.

433. A method of identifying a compound that inhibits an activity of a PRO347 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist.

434. A method of identifying a compound that inhibits an activity of a PRO357 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist.

435. A method of identifying a compound that inhibits an activity of a PRO715 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist. 218 AMENDED SHEET 22/05/2002

436. A method of identifying a compound that inhibits an activity of a PRO1017 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist.

437. A method of identifying a compound that inhibits an activity of a PRO1112 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist.

438. A method of identifying a compound that inhibits an activity of a PRO509 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist. 439, A method of identifying a compound that inhibits an activity of a PRO853 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist; wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist.

440. A method of identifying a compound that inhibits an activity of a PRO882 polypeptide, said method comprising the steps of (a) contacting cells and a candidate compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist, wherein the lack of induction of said cellular response is indicative of said compound being an effective antagonist. 219 CL AMENDED SHEET 22/05/2002

) 441. A method for identifying a compound that inhibits the expression of a PRO201 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

442. A method for identifying a compound that inhibits the expression of a PRO292 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

443. A method for identifying a compound that inhibits the expression of a PRO327 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

444. A method for identifying a compound that inhibits the expression of a PRO1265 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

445. A method for identifying a compound that inhibits the expression of a PRO344 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

446. A method for identifying a compound that inhibits the expression of a PRO343 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

447. A method for identifying a compound that inhibits the expression of a PRO347 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

448. A method for identifying a compound that inhibits the expression of a PRO357 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited. 449, A method for identifying a compound that inhibits the expression of a PRO715 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited. 220 AMENDED SHEET 22/05/2002

[

450. A method for identifying a compound that inhibits the expression of a PRO1017 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

451. A method for identifying a compound that inhibits the expression of a PRO1112 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

452. A method for identifying a compound that inhibits the expression of a PRO509 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

453. A method for identifying a compound that inhibits the expression of a PRO853 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

454. A method for identifying a compound that inhibits the expression of a PRO882 polypeptide in cells that express said polypeptide, wherein said method comprises contacting said cells with a candidate compound and determining whether expression of said polypeptide is inhibited.

455. The method of any one of Claims 441 to 454, wherein said candidate compound is an antisense oligonucleotide.

456. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 2 (SEQ ID NO:2).

457. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 4 (SEQ ID NO:6).

458. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 6 (SEQ ID NO:8).

459. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 8 (SEQ ID NO: 13). 221 AMENDED SHEET 22/05/2002

460. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 10 (SEQ ID NO:15).

461. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 12 (SEQ ID NO:23).

462. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 14 (SEQ ID NO:28).

463. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 16 (SEQ ID NO:33). 464, An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 18 (SEQ ID NO:40). .

46S. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 20 (SEQ ID NO:42).

466. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 22 (SEQ ID NO:44).

467. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 24 (SEQ ID NO:46).

468. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 26 (SEQ ID NO:48).

469. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding the polypeptide shown in Figure 28 (SEQ ID NO:53).

470. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 1 (SEQ ID NO:1).

471. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 3 (SEQ ID NO:5). 222 AMENDED SHEET 22/05/2002

}

472. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 5 (SEQ ID NO:7).

473. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 7 (SEQ ID NO:12).

474. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 9 (SEQ ID NO:14).

475. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 11 (SEQ ID NO:22).

476. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 13 (SEQ ID NO:27). 4717. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 15 (SEQ ID NO:32).

478. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 17 (SEQ ID NO:39).

479. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 19 (SEQ ID NO:41).

480. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 21 (SEQ ID NO:43).

481. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 23 (SEQ ID NO:45).

482. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 25 (SEQ ID NO:47).

483. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to a nucleotide sequence shown in Figure 27 (SEQ ID NO:52). 223 AMENDED SHEET 22/05/2002

‘A EY

484. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 1 (SEQ ID NO:1).

485. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 3 (SEQ ID NO:5).

486. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 5 (SEQ ID NO:7).

487. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 7 (SEQ ID NO: 12).

488. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 9 (SEQ ID NO:14).

489. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 11 (SEQ ID NO:22).

490. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 13 (SEQ ID NO:27).

491. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 15 (SEQ ID NO:32). 492, An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 17 (SEQ ID NO:39).

493. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 19 (SEQ ID NO:41).

494. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 21 (SEQ ID NO:43).

495. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 23 (SEQ ID NO:45). 224 AMENDED SHEET 22/05/2002

-

496. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 25 (SEQ ID NO:47).

497. An isolated nucleic acid molecule having at least 830% nucleic acid sequence identity to the full- length coding sequence of the nucleotide sequence shown in Figure 27 (SEQ ID NO:52).

498. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 209567.

499. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 209530.

500. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 203452.

501. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 209492.

502. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 209481.

503. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 209532.

504. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 209527.

505. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 209570.

506. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 209883.

507. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 209951. 225 AMENDED SHEET 22/05/2002

N

508. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to the full- length coding sequence of the DNA deposited under ATCC accession number 209812.

509. A vector comprising the nucleic acid of any one of Claims 456 to 508.

510. A host cell comprising the vector of Claim 509. S511. The host cell of Claim 510, wherein said cell is a CHO cell, an E.coli, a yeast cell or a Baculovirus-infected insect cell.

S12. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 2 (SEQ ID NO:2).

513. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 4 (SEQ ID NO:6).

514. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 6 (SEQ ID NO:8).

515. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 8 (SEQ ID NO:13).

516. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 10 (SEQ ID NO:15).

517. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 12 (SEQ ID NO:23).

518. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 14 (SEQ ID NO:28).

519. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 16 (SEQ ID NO:33).

520. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 18 (SEQ ID NO:40). 226 AMENDED SHEET 22/05/2002

A

521. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 20 (SEQ ID NO:42).

522. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 22 (SEQ ID NO:44).

523. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 24 (SEQ ID NO:46).

524. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 26 (SEQ [D NO:48).

525. An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence shown in Figure 28 (SEQ ID NO:53).

526. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209567.

527. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209530.

528. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 203452.

529. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209492.

530. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209481. : 531. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209532.

532. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209527. 227 AMENDED SHEET 22/05/2002

A

533. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209570.

534. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209883.

535. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid } sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209951.

536. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209812.

537. A chimeric molecule comprising a polypeptide according to any one of Claims 512 to 536 fused to a heterologous amino acid sequence.

538. The chimeric molecule of Claim 537, wherein said heterologous amino acid sequence is an epitope tag sequence.

539. The chimeric molecule of Claim 537, wherein said heterologous amino acid sequence is a Fc region of an immunoglobulin.

540. An antibody which specifically binds to a polypeptide according to any one of Claims 512 to 536.

541. The antibody of Claim 540, wherein said antibody is a monoclonal antibody, a humanized antibody or a single-chain antibody.

542. An jsolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 2 (SEQ ID NO:2) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2) 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) lacking its associated signal peptide. 228 AMENDED SHEET 22/05/2002

543. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 4 (SEQ ID NO:6) lacking its associated signal peptide; ‘ (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 4 (SEQ ID NO:6) with its associated signal peptide; or (c) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 4 (SEQ ID NO:6) lacking its associated signal peptide.

544. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 6 (SEQ ID NO:8) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 6 (SEQ ID NO:8) with its associated signal peptide; or : (c) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 6 (SEQ ID NO:8) lacking its associated signal peptide.

545. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 8 (SEQ ID NO:13) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 8 (SEQ ID NO:13) with its associated signal peptide; or (c) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 8 (SEQ ID NO:13) lacking its associated signal peptide.

546. An isolated nucleic acid molecufe having at least 80% nucleic acid sequence identity to: . (a) a nucleotide sequence encoding the polypeptide shown in Figure 10 (SEQ ID NO:15) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 10 (SEQ ID NO:15) with its associated signal peptide; or (c) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 10 (SEQ ID NO:15) lacking its associated signal peptide.

547. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 12 (SEQ ID NO:23) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in 229 AMENDED SHEET 22/05/2002

Figure 12 (SEQ ID NO:23) with its associated signal peptide; or (¢) anucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 12 (SEQ ID NO:23) lacking its associated signal peptide.

548. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 14 (SEQ ID NO:28) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 14 (SEQ ID NO:8) with its associated signal peptide; or (c) anucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 14 (SEQ ID NO:28) lacking its associated signal peptide.

549. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 16 (SEQ ID NO:33) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 16 (SEQ ID NO:33) with its associated signal peptide; or (c) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 16 (SEQ ID NO:33) lacking its associated signal peptide.

550. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 18 (SEQ ID NO:40) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 18 (SEQ ID NO:40) with its associated signal peptide; or (c) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 18 (SEQ ID NO:40) lacking its associated signal peptide.

551. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 20 (SEQ ID NO:42) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 20 (SEQ ID NO:42) with its associated signal peptide; or (c) anucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 20 (SEQ ID NO:42) lacking its associated signal peptide. 230 AMENDED SHEET 22/05/2002

552. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 22 (SEQ ID NQ:44) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 22 (SEQ ID NO:44) with its associated signal peptide; or (¢) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 22 (SEQ ID NO:44) lacking its associated signal peptide.

553. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 24 (SEQ ID NO:46) lacking its associated signal peptide; {b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 24 (SEQ ID NO:46) with its associated signal peptide; or : (¢) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 24 (SEQ ID NO:46) lacking its associated signal peptide.

554. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 26 (SEQ ID NO:48)lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 26 (SEQ ID NO:48) with its associated signal peptide; or (c) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 26 (SEQ ID NO:48) lacking its associated signal peptide. © 555. An isolated nucleic acid molecule having at least 80% nucleic acid sequence identity to: (a) a nucleotide sequence encoding the polypeptide shown in Figure 28 (SEQ ID NO:53) lacking its associated signal peptide; (b) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 28 (SEQ ID NO:53) with its associated signal peptide; or (¢) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 28 (SEQ ID NQO:53) lacking its associated signal peptide.

556. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 2 (SEQ ID NO:2) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2) with its 231 AMENDED SHEET 22/05/2002 a © associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 2 (SEQ IDNO:2) lacking its associated signal peptide.

557. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 4 (SEQ ID NO:6) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 4 (SEQ ID NO:6) with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 4 (SEQ IDNO:6) lacking its associated signal peptide.

558. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 6 (SEQ ID NO:8) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 6 (SEQ ID NO:8) with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 6 (SEQ IDNO:8) lacking its associated signal peptide.

559. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 8 (SEQ ID NO:13) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 8 (SEQ ID NO:13) with its associated signal peptide; or (c} an extracellular domain of the polypeptide shown in Figure 8 (SEQ IDNO: 13) lacking its associated signal peptide.

560. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 10 (SEQ ID NO:15) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 10 (SEQ ID NO:15) with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 10 (SEQ IDNO: 15) lacking its associated signal peptide.

561. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 12 (SEQ ID NO:23) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 12 (SEQ ID NO:23) with its associated signal peptide; or 232 AMENDED SHEET 22/05/2002

« (c) an extracellular domain of the polypeptide shown in Figure 12 (SEQ IDNO:23) lacking its associated signal peptide.

562. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 14 (SEQ ID NO:28) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 14 (SEQ ID NO:28) with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 14 (SEQ IDNO:28) lacking its associated signal peptide.

563. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 16 (SEQ ID NO:33) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 16 (SEQ ID NO:33) with its associated signal peptide; or : (c) an extracellular domain of the polypeptide shown in Figure 16 (SEQ IDNO:33) lacking its associated signal peptide.

564. An isolated polypeptide having at least 80% amino acid sequence identity to: : (a) the polypeptide shown in Figure 18 (SEQ ID NO:40) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 18 (SEQ ID NO:40) with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 18 (SEQ IDNO:40) lacking its : associated signal peptide.

565. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 20 (SEQ ID NO:42) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 20 (SEQ ID NO:42) with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 20 (SEQ IDNO:42) lacking its associated signal peptide.

566. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 22 (SEQ ID NO:44) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 22 (SEQ ID NO:44) with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 22 (SEQ IDNO:44) lacking its 233 AMENDED SHEET 22/05/2002 v WO 00/37640 PCT/US99/30095 associated signal peptide.

567. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 24 (SEQ ID NO:46) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 24 (SEQ ID NO:46) with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 24 (SEQ IDNO:46) lacking its associated signal peptide.

568. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 26 (SEQ ID NO:48) lacking its associated signal peptide; {(b) an extracellular domain of the polypeptide shown in Figure 26 (SEQ ID NO:48) with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 26 (SEQ IDNO:48) lacking its associated signal peptide. . 569. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 28 (SEQ ID NO:53) lacking its associated signal peptide; (b) an extracellular domain of the polypeptide shown in Figure 28 (SEQ ID NO:53) with its associated signal peptide; or (c) an extracellular domain of the polypeptide shown in Figure 28 (SEQ IDNO:53) lacking its associated signal peptide. 234 AMENDED SHEET 22/05/2002