JP2006223304A - Secreted and transmembrane polypeptide and nucleic acid encoding same - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide novel polypeptides for stimulating the proliferation or differentiation of chondrocytes or for adjusting the proliferation of human microvascular endothelial cells, and to provide nucleic acid molecules encoding the polypeptides. <P>SOLUTION: The present invention is directed to novel polypeptides containing specific amino acid sequences, and to isolated nucleic acid molecules having nucleic acid sequence homology of at least 80% based on nucleic acid sequences encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention. <P>COPYRIGHT: (C)2006,JPO&NCIPI

Description

Detailed Description of the Invention

(Field of Invention)
The present invention relates generally to the identification and isolation of novel DNA and the recombinant production of novel polypeptides.

(Background of the invention)
Extracellular proteins play a particularly important role in the formation, differentiation and maintenance of multicellular organisms. Many individual cell fates, such as proliferation, migration, differentiation or interaction with other cells, are typically governed by information received from other cells and / or the immediate environment. This information is often transmitted by secreted polypeptides (e.g., mitogens, survival factors, cytotoxic factors, differentiation factors, neuropeptides, and hormones) that are in turn taken by various cell receptors or membrane-bound proteins. Is interpreted. These secreted polypeptides or signal molecules usually pass through the cell secretory pathway to reach their site of action in the extracellular environment.
Secreted proteins have a variety of industrial applications, including pharmaceuticals, diagnostics, biosensors and bioreactors. Most protein drugs currently available, such as thrombolytic agents, interferons, interleukins, erythropoietin, colony stimulating factor, and various other cytokines are secreted proteins. In addition, these receptors that are membrane proteins have potential as therapeutic or diagnostic agents. Efforts have been made by both industry and academia to identify new native secreted proteins. Much effort has been devoted to screening mammalian recombinant DNA libraries to identify novel secretory protein coding sequences. Examples of screening methods and techniques are described in the literature [see, eg, Klein et al., Proc. Natl. Acad. Sci. 93; 7108-7113 (1996); US Pat. No. 5,536,637] .

Membrane-bound proteins and receptors play an important role in the formation, differentiation and maintenance of multicellular organisms. The fate of many individual cells, such as proliferation, migration, differentiation or interaction with other cells, is typically governed by information received from other cells and / or the immediate environment. This information is often transmitted by secreted polypeptides (e.g., mitogens, survival factors, cytotoxic factors, differentiation factors, neuropeptides, and hormones) that are then received by various cell receptors or membrane-bound proteins. Interpreted. Such membrane-bound proteins and cell receptors include, but are not limited to, cytokine receptors, receptor kinases, receptor phosphatases, receptors involved in cell-cell interactions, and cell adhesions such as selectins and integrins. Contains molecules. For example, the transmission of signals that regulate cell growth and differentiation is regulated in part by phosphorylation of various cellular proteins. Protein tyrosine kinases, enzymes that catalyze the process, also act as growth factor receptors. Specific examples include fibroblast growth factor and nerve growth factor receptor.
Membrane-bound proteins and receptor molecules have a variety of industrial applications, including pharmaceutical and diagnostic agents. For example, receptor immunoadhesins can be used as therapeutic agents that block receptor-ligand interactions. Membrane-bound proteins can also be used to screen for peptide or small molecule inhibitors with potential for related receptor / ligand interactions.
Efforts have been made by both industry and academia to identify new natural receptors or membrane-bound proteins. Much effort has been devoted to screening mammalian recombinant DNA libraries to identify novel receptor or membrane-bound protein coding sequences.

(Summary of Invention)
In one embodiment, the present invention provides an isolated nucleic acid molecule comprising a nucleotide sequence encoding a PRO polypeptide.
In one aspect, an isolated nucleic acid molecule comprises (a) a full-length amino acid sequence disclosed herein, an amino acid sequence that lacks a signal peptide disclosed herein, a transmembrane disclosed herein with or without a signal peptide. A DNA molecule encoding a PRO polypeptide having the extracellular domain of a protein or any other specifically defined fragment of the full-length amino acid sequence disclosed herein, or (b) the complement of a DNA molecule of (a) In contrast, at least about 80% nucleic acid sequence identity, alternatively at least about 81% nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84 % Nucleic acid sequence identity, or at least about 85% nucleic acid sequence identity, or at least about 86% nucleic acid sequence identity Or at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, or at least about 91%. Nucleic acid sequence identity, or at least about 92% nucleic acid sequence identity, or at least about 93% nucleic acid sequence identity, or at least about 94% nucleic acid sequence identity, or at least about 95% nucleic acid sequence identity, or Nucleotide sequences having at least about 96% nucleic acid sequence identity, alternatively at least about 97% nucleic acid sequence identity, alternatively at least about 98% nucleic acid sequence identity, or at least about 99% nucleic acid sequence identity.

  In another aspect, the isolated nucleic acid molecule comprises: (a) a coding sequence for a full-length PRO polypeptide cDNA disclosed herein, a coding sequence for a PRO polypeptide DNA that lacks a signal peptide disclosed herein, a signal peptide A DNA molecule comprising the coding sequence of the extracellular domain of a transmembrane PRO polypeptide disclosed herein with or without any other specifically defined fragment of the full-length amino acid sequence disclosed herein, or (B) at least about 80% nucleic acid sequence identity, or at least about 81% nucleic acid sequence identity, or at least about 82% nucleic acid sequence identity to the complement of the DNA molecule of (a), or at least About 83% nucleic acid sequence identity, or at least about 84% nucleic acid sequence identity, or at least about 85% nucleic acid sequence Identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, or at least about 90% nucleic acid sequence identity, or at least about 91% nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, or at least about 94% nucleic acid sequence identity Or at least about 95% nucleic acid sequence identity, alternatively at least about 96% nucleic acid sequence identity, alternatively at least about 97% nucleic acid sequence identity, alternatively at least about 98% nucleic acid sequence identity, or at least about 99 % Nucleotide sequence having a nucleic acid sequence identity.

  In a further aspect, the present invention provides (a) a DNA molecule encoding the same mature polypeptide encoded by any human protein cDNA deposited with the ATTC disclosed herein, or (b) a DNA molecule of (a) At least about 80% nucleic acid sequence identity, or at least about 81% nucleic acid sequence identity, or at least about 82% nucleic acid sequence identity, or at least about 83% nucleic acid sequence identity to the complement of Alternatively, at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% Nucleic acid sequence identity, or at least about 89% nucleic acid sequence identity, or at least about 90% Nucleic acid sequence identity, or at least about 91% nucleic acid sequence identity, or at least about 92% nucleic acid sequence identity, or at least about 93% nucleic acid sequence identity, or at least about 94% nucleic acid sequence identity, or At least about 95% nucleic acid sequence identity, alternatively at least about 96% nucleic acid sequence identity, alternatively at least about 97% nucleic acid sequence identity, alternatively at least about 98% nucleic acid sequence identity, or at least about 99% nucleic acid It relates to an isolated nucleic acid molecule comprising a nucleotide sequence having sequence identity.

  Another aspect of the present invention provides a nucleotide sequence encoding a PRO polypeptide, either having a transmembrane domain deleted or a transmembrane domain inactivated, or a nucleotide sequence complementary to such an encoded nucleotide sequence. An isolated nucleic acid molecule comprising such a transmembrane domain of such a polypeptide is disclosed herein. Accordingly, the soluble extracellular domains of the PRO polypeptides described herein are contemplated.

  Another embodiment is directed to a fragment of a PRO polypeptide coding sequence, or a complement thereof, eg, a hybridization probe of an encoded fragment of a PRO polypeptide that optionally encodes a polypeptide comprising a binding site for an anti-PRO antibody Or as an antisense oligonucleotide probe. Such nucleic acid fragments are usually at least about 20 nucleotides long, alternatively at least about 30 nucleotides long, alternatively at least about 40 nucleotides long, alternatively at least about 50 nucleotides long, alternatively at least about 60 nucleotides long, alternatively at least about 70 nucleotides long, Or at least about 80 nucleotides long, alternatively at least about 90 nucleotides long, alternatively at least about 100 nucleotides long, alternatively at least about 110 nucleotides long, alternatively at least about 120 nucleotides long, alternatively at least about 130 nucleotides long, alternatively at least about 140 nucleotides long, or At least about 150 nucleotides long, alternatively at least about 160 nucleotides long, alternatively at least about 170 nucleotides Tide length, alternatively at least about 180 nucleotides, alternatively at least about 190 nucleotides, alternatively at least about 200 nucleotides, alternatively at least about 250 nucleotides, alternatively at least about 300 nucleotides, alternatively at least about 350 nucleotides, alternatively at least about 400 nucleotides Long, alternatively at least about 450 nucleotides long, alternatively at least about 500 nucleotides long, alternatively at least about 600 nucleotides long, alternatively at least about 700 nucleotides long, alternatively at least about 800 nucleotides long, alternatively at least about 900 nucleotides long, alternatively at least about 1000 nucleotides long Where the word “about” is the plus or minus of the length of reference It is meant to refer to nucleotide sequence length 0%. A novel fragment of a PRO polypeptide-encoding nucleotide sequence aligns the PRO polypeptide-encoding nucleotide sequence with other known nucleotide sequences using any of a number of well-known sequence alignment programs, By determining whether a PRO polypeptide-encoding nucleotide sequence fragment is novel, it may be identified by routine techniques. All such PRO polypeptide-encoding nucleotide sequences are contemplated herein. Also contemplated are PRO polypeptide fragments encoded by these nucleotide molecule fragments, preferably PRO polypeptide fragments comprising a binding site for an anti-PRO antibody.

In another embodiment, the present invention provides an isolated PRO polypeptide encoded by any of the isolated nucleic acid sequences identified above.
In one aspect, the invention provides for a full-length amino acid sequence disclosed herein, an amino acid sequence lacking a signal peptide disclosed herein, a cell of a transmembrane protein with or without a signal peptide disclosed herein. At least about 80% amino acid sequence identity, or at least about 81% amino acid sequence identity to a PRO polypeptide having an outer domain or other specifically identified fragment of the full-length amino acid sequence disclosed herein Or at least about 82% amino acid sequence identity, alternatively at least about 83% amino acid sequence identity, alternatively at least about 84% amino acid sequence identity, alternatively at least about 85% amino acid sequence identity, alternatively at least about 86% Amino acid sequence identity, or at least about 87% amino acid sequence Identity, or at least about 88% amino acid sequence identity, alternatively at least about 89% amino acid sequence identity, alternatively at least about 90% amino acid sequence identity, alternatively at least about 91% amino acid sequence identity, or at least about 92% amino acid sequence identity, or at least about 93% amino acid sequence identity, alternatively at least about 94% amino acid sequence identity, alternatively at least about 95% amino acid sequence identity, or at least about 96% amino acid sequence identity Or an isolated PRO polynucleotide comprising an amino acid sequence having at least about 97% amino acid sequence identity, alternatively at least about 98% amino acid sequence identity, and alternatively at least about 99% amino acid sequence identity Relates to peptides.

  In a further aspect, the present invention provides at least about 80% amino acid sequence identity to the amino acid sequence encoded by any human protein cDNA deposited with the ATCC disclosed herein, or at least about 81% amino acid sequence. Identity, alternatively at least about 82% amino acid sequence identity, alternatively at least about 83% amino acid sequence identity, alternatively at least about 84% amino acid sequence identity, alternatively at least about 85% amino acid sequence identity, or at least about 86% amino acid sequence identity, or at least about 87% amino acid sequence identity, alternatively at least about 88% amino acid sequence identity, alternatively at least about 89% amino acid sequence identity, or at least about 90% amino acid sequence identity Sex or little At least about 91% amino acid sequence identity, or at least about 92% amino acid sequence identity, alternatively at least about 93% amino acid sequence identity, alternatively at least about 94% amino acid sequence identity, or at least about 95% amino acid. Sequence identity, alternatively at least about 96% amino acid sequence identity, alternatively at least about 97% amino acid sequence identity, alternatively at least about 98% amino acid sequence identity, and alternatively at least about 99% amino acid sequence identity. It relates to an isolated PRO polypeptide comprising an amino acid sequence having.

In a particular aspect, the invention provides an isolated PRO polypeptide that does not have an N-terminal signal sequence and / or an initiation methionine and is encoded by a nucleotide sequence that encodes an amino acid sequence as described above. Methods for producing these are also described herein, which involve culturing host cells containing a vector containing a suitable encoding nucleic acid molecule under conditions suitable for the expression of the PRO polypeptide, from the culture medium. Recovering.
Other aspects of the invention provide isolated PRO polypeptides that are either transmembrane domain deleted or transmembrane domain inactivated. A method for producing this is also described herein, wherein the method comprises culturing a host cell comprising a vector containing a suitable encoding nucleic acid molecule under conditions suitable for expression of the PRO polypeptide, and extracting the PRO polypeptide from the cell culture medium. Including recovery.

In yet other embodiments, the invention relates to agonists and antagonists of the native PRO polypeptides identified herein. In a particular embodiment, the agonist or antagonist is an anti-PRO antibody or a small molecule.
In a further embodiment, the present invention relates to a method for identifying an agonist or antagonist of a PRO polypeptide, which comprises contacting the PRO polypeptide with a candidate molecule and monitoring biological activity mediated by said PRO polypeptide. including. Preferably, the PRO polypeptide is a native PRO polypeptide.
In yet a further embodiment, the invention relates to a composition comprising a PRO polypeptide, or an agonist or antagonist of a PRO polypeptide described herein, or an anti-PRO antibody in combination with a carrier. In some cases, the carrier is a pharmaceutically acceptable carrier.

Another embodiment of the present invention is for the treatment of a condition responsive to a PRO polypeptide, an agonist or antagonist thereof or an anti-PRO antibody of a PRO polypeptide, or an agonist or antagonist thereof, or an anti-PRO antibody as described above. Directed to use for the preparation of useful medicaments.
In a further embodiment of the invention, the invention provides a vector comprising DNA encoding any of the polypeptides described herein. A host cell comprising any such vector is also provided. As an example, the host cell may be a CHO cell, E. coli, or yeast. Further provided is a method for producing any of the polypeptides described herein, comprising culturing host cells under conditions suitable for expression of the desired polypeptide and recovering the desired polypeptide from the cell culture medium. Including.

In other embodiments, the invention provides chimeric molecules comprising any of the polypeptides described herein fused to a heterologous polypeptide or amino acid sequence. Examples of such chimeric molecules include any polypeptide described herein fused to an epitope tag sequence or an Fc region of an immunoglobulin.
In other embodiments, the present invention provides antibodies that specifically bind to any of the above or below described polypeptides. In some cases, the antibody is a monoclonal antibody, a humanized antibody, an antibody fragment or a single chain antibody.
In yet another embodiment, the present invention provides oligonucleotide probes useful for the isolation of genomic and cDNA nucleotide sequences or antisense probes, which probes are derived from any of the nucleotide sequences described above or below. sell.
In yet another embodiment, the invention relates to methods of using the PRO polypeptides of the invention for various uses based on the functional biological assay data shown in the examples below.

Detailed Description of Preferred Embodiments
I. Definitions The terms “PRO polypeptide” and “PRO” as used herein refer to various polypeptides when immediately followed by a numerical sign, with the full sign (ie, PRO / number) being It refers to the specific polypeptide sequence described herein. The terms “PRO / number polypeptide” and “PRO / number” as used herein, where “number” is the actual numerical sign used herein are native sequence polypeptides and variants (herein more detailed). Defined). The PRO polypeptides described herein may be isolated from a variety of sources, such as human tissue types or other sources, and may be prepared by recombinant or synthetic methods. The term “PRO polypeptide” refers to each individual PRO / number polypeptide disclosed herein. All disclosures in this specification that refer to “PRO polypeptides” refer to each polypeptide individually or in combination. For example, descriptions of prepared, purified, induced, antibody formation, administration, containing composition, disease treatment, etc. are relevant to each polypeptide of the present invention. The term “PRO polypeptide” also includes variants of the PRO / number polypeptides disclosed herein.

  A “native sequence PRO polypeptide” includes a polypeptide having the same amino acid sequence as the corresponding PRO polypeptide from nature. Such native sequence PRO polypeptides can be isolated from nature or can be produced by recombinant or synthetic means. The term “native sequence PRO polypeptide” specifically includes naturally occurring truncated or secreted forms (eg, extracellular domain sequences), naturally occurring mutated forms (eg, alternatively spliced) of a particular PRO polypeptide. Form) and naturally occurring allelic variants of the polypeptide. In various embodiments of the invention, the native sequence PRO polypeptide disclosed herein is a mature or full length native sequence polypeptide containing the full length amino acid sequence shown in the associated figures. Start and stop codons are shown in the figure in bold typeface and underline. However, while the PRO polypeptide disclosed in the relevant figure is shown at amino acid position 1 in the figure to begin with a methionine residue, other polypeptides located either upstream or downstream of amino acid position 1 in the figure It is possible and possible that a methionine residue is used as the starting amino acid residue of a PRO polypeptide.

  The PRO polypeptide “extracellular domain” or “ECD” means a form of a PRO polypeptide that is substantially free of transmembrane and cytoplasmic domains. Usually, PRO polypeptide ECD has less than 1% of their transmembrane and / or cytoplasmic domains, preferably less than 0.5% of such domains. It will be understood that any transmembrane domain identified for a PRO polypeptide of the invention is identified according to criteria routinely used in the art to identify that type of hydrophobic domain. . Although the exact boundaries of the transmembrane domain can vary, it is likely not to exceed about 5 amino acids from either end of the originally identified domain. Thus, the PRO polypeptide extracellular domain may optionally comprise no more than about 5 amino acids from either end of the transmembrane domain identified in the Examples or specifications and has a signal peptide for attachment. Such polypeptides without or with such nucleic acids and nucleic acids encoding them are contemplated in the present invention.

  Appropriate positions for the “signal peptides” of the various PRO polypeptides disclosed herein are set forth herein and in the accompanying drawings. However, as noted, the C-terminal boundary of the signal peptide can vary, but is most likely less than about 5 amino acids on either side of the signal peptide C-terminal boundary as defined herein. High, the C-terminal boundary of a signal peptide can be identified according to criteria routinely used to identify such types of amino acid sequence components (eg, Nielsen et al., Prot. Eng. 10: 1-6). (1997) and von Heinje et al., Nucl. Acids. Res. 14: 4683-4690 (1986)). Furthermore, in some cases, it is also observed that cleavage of the signal peptide from the secreted polypeptide is not completely uniform, resulting in one or more secreted species. These mature polypeptides, and polynucleotides encoding them, which are cleaved within less than about 5 amino acids on either side of the C-terminal boundary of the signal peptide as defined herein, are contemplated in the present invention. The

  A “PRO polypeptide variant”, as defined above or below, is a full-length native sequence PRO polypeptide disclosed herein, a full-length native sequence PRO polypeptide sequence that lacks a signal peptide disclosed herein. Means an active PRO polypeptide having at least about 80% amino acid sequence identity with the extracellular domain of a PRO disclosed herein with or without a signal peptide or other fragments of the full-length PRO polypeptide disclosed herein . Such PRO polypeptide variants include, for example, PRO polypeptides in which one or more amino acid residues have been added or deleted at the N- or C-terminus of the full-length natural amino acid sequence. Typically, a PRO polypeptide variant is disclosed herein with or without a full-length native amino acid sequence disclosed herein, a full-length native sequence PRO polypeptide sequence that lacks a signal peptide disclosed herein. At least about 80% amino acid sequence identity, or at least about 81% amino acid sequence identity, or at least about at least about the extracellular domain of PRO or other specifically identified fragments of the full-length PRO polypeptide disclosed herein. 82% amino acid sequence identity, or at least about 83% amino acid sequence identity, alternatively at least about 84% amino acid sequence identity, alternatively at least about 85% amino acid sequence identity, or at least about 86% amino acid sequence identity Or at least about 87% amino acid sequence Or at least about 88% amino acid sequence identity, alternatively at least about 89% amino acid sequence identity, alternatively at least about 90% amino acid sequence identity, alternatively at least about 91% amino acid sequence identity, or at least about 92 % Amino acid sequence identity, or at least about 93% amino acid sequence identity, alternatively at least about 94% amino acid sequence identity, alternatively at least about 95% amino acid sequence identity, or at least about 96% amino acid sequence identity Or at least about 97% amino acid sequence identity, alternatively at least about 98% amino acid sequence identity, and alternatively at least about 99% amino acid sequence identity. Typically, the PRO variant polypeptide is at least about 10 amino acids long, alternatively at least about 20 amino acids long, alternatively at least about 30 amino acids long, alternatively at least about 40 amino acids long, alternatively at least about 50 amino acids long, alternatively at least about 60 amino acids long. Or at least about 70 amino acids long, alternatively at least about 80 amino acids long, alternatively at least about 90 amino acids long, alternatively at least about 100 amino acids long, alternatively at least about 150 amino acids long, alternatively at least about 200 amino acids long, alternatively at least about 300 amino acids long, Or more.

  The “percent (%) amino acid sequence identity” identified herein for a PRO polypeptide as defined herein introduces gaps if necessary to align the sequences and obtain maximum percent sequence identity. And is defined as the percentage of amino acid residues in the candidate sequence that are identical to the amino acid residues of the PRO polypeptide, assuming that any conservative substitutions are not considered part of the sequence identity. Alignments for the purpose of determining percent amino acid sequence identity are publicly available such as various methods within the skill of the art, such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software This can be achieved by using computer software. One skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms necessary to achieve maximal alignment over the full length of the sequences being compared. However, for purposes herein,% amino acid sequence identity values can be obtained by using the sequence comparison program ALIGN-2, for which the complete source code for the ALIGN-2 program is provided in Table 1 below. can get. The ALIGN-2 sequence comparison computer program was created by Genentech, Inc., and the source code shown in Table 1 below was submitted to the US Copyright Office, Washington DC, 20559 along with the user documentation, with US copyright registration number TXU510087 Registered below. ALIGN-2 is preferably available from Genentech, South San Francisco, California, and may be compiled from the source code provided in Table 1 below. The ALIGN-2 program is compiled for use on a UNIX® operating system, preferably Digital UNIX® V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary.

In situations where ALIGN-2 is used for amino acid sequence comparison,% amino acid sequence identity of a given amino acid sequence A with or against a given amino acid sequence B (or with a given amino acid sequence B, or In contrast, a given amino acid sequence A, which has or contains some% amino acid sequence identity) is calculated as follows:
100 times the fraction X / Y, where X is the number of amino acid residues with a score matched by A and B alignment of the sequence alignment program ALIGN-2, and Y is the total amino acid residue of B Is a number. It will be understood that if the length of amino acid sequence A is different from the length of amino acid sequence B, then the% amino acid sequence identity of A to B is different from the% amino acid sequence identity of B to A. As an example of calculating% amino acid sequence identity using this method, “PRO” represents the amino acid sequence of the hypothetical PRO polypeptide of interest, and “comparison protein” of interest is compared to the “comparison” protein of interest. And "X", "Y" and "Z" each represent a different hypothetical amino acid residue, and Tables 2 and 3 show the amino acid sequence "PRO" The calculation method of% amino acid sequence identity with respect to the amino acid sequence called "is shown.

  Unless otherwise indicated, all% amino acid sequence identity values herein are obtained using the ALIGN-2 sequence comparison computer program as described above. However,% amino acid sequence identity values may be determined using the WU-BLAST-2 computer program (Altschul et al., Methods in Enzymology 266: 460-480 (1996)). In addition, most WU-BLAST-2 search parameters are set to initial values. Parameters that are not set to initial values, ie adjustable parameters, are set to the following values: overlap span = 1, overlap fraction = 0.125, word threshold (T) = 11, and scoring matrix = BLOSUM62. When WU-BLAST2 is used, the% amino acid sequence identity value is: (a) the amino acid sequence of the subject PRO polypeptide having a sequence derived from a native PRO polypeptide and the subject comparative amino acid The number of identical identical amino acid residues determined by WU-BLAST-2 between sequences (ie, sequences that may be PRO polypeptide variants against which the PRO polypeptide of interest is compared), ( b) determined by the quotient divided by the total number of residues of the subject PRO polypeptide. For example, in the expression “polypeptide comprising amino acid sequence A having or having at least 80% amino acid sequence identity to amino acid sequence B”, amino acid sequence A is a comparative amino acid sequence of interest, Amino acid sequence B is the amino acid sequence of the subject PRO polypeptide.

  The% amino acid sequence identity may 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 can be downloaded from http://www.ncbi.nlm.nih.gov or otherwise obtained from the National Institutes of Health, Bethesda, Maryland. NCBI-BLAST2 uses several search parameters, all of which are set to initial values, eg unmask = allowable, chain = all, predicted occurrence = 10, minimum low composite length = 15/5 Multipath e-value = 0.01, multipath constant = 25, final gap alignment dropoff = 25, and scoring matrix = BLOSUM62.

In situations where NCBI-BLAST2 is used for amino acid sequence comparison,% amino acid sequence identity of a given amino acid sequence A with or against a given amino acid sequence B (or with a given amino acid sequence B, or A given amino acid sequence A, which has or contains some% amino acid sequence identity, on the other hand) is calculated as follows:
100 times the fraction X / Y, where X is the number of amino acid residues with a score matched by A and B alignment of the sequence alignment program NCBI-BLAST2, and Y is the total amino acid residue of B Is a number. It will be understood that if the length of amino acid sequence A is different from the length of amino acid sequence B, then the% amino acid sequence identity of A to B is different from the% amino acid sequence identity of B to A.

  A “PRO variant polynucleotide” or “PRO variant nucleic acid sequence” is a nucleic acid molecule that encodes an active PRO polypeptide, as defined below, and a full-length native sequence PRO polypeptide sequence disclosed herein. A full-length native sequence PRO polypeptide sequence lacking the signal peptide disclosed herein, an extracellular domain of a PRO polypeptide disclosed herein with or without a signal peptide, or a full-length PRO polypeptide sequence disclosed herein. At least about 80% nucleic acid sequence identity with a nucleic acid sequence encoding any other fragment, preferably at least about 81% nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, or at least about 83% Or at least about 84% nucleic acid sequence identity, or At least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid Sequence identity, or at least about 90% nucleic acid sequence identity, alternatively at least about 91% nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, or at least About 94% nucleic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about 96% nucleic acid sequence identity, alternatively at least about 97% nucleic acid sequence identity, alternatively at least about 98% nucleic acid sequence Have identity and / or at least about 99% nucleic acid sequence identity There. Variants do not contain the native nucleotide sequence.

  Typically, the PRO variant polynucleotide is at least about 30 nucleotides in length, alternatively at least about 60 nucleotides in length, alternatively at least about 90 nucleotides in length, alternatively at least about 120 nucleotides in length, alternatively at least about 150 nucleotides in length, alternatively at least about 180 nucleotides in length. Or at least about 210 nucleotides long, alternatively at least about 240 nucleotides long, alternatively at least about 270 nucleotides long, alternatively at least about 300 nucleotides long, alternatively at least about 450 nucleotides long, alternatively at least about 600 nucleotides long, alternatively at least about 900 nucleotides long, Or more.

  “Percent (%) nucleic acid sequence identity” relative to the PRO-encoding nucleic acid sequence identified herein introduces a gap if necessary to align the sequences and obtain maximum percent sequence identity, and Defined as the percent of nucleotides in the candidate sequence that are identical. Alignments for the purpose of determining percent nucleic acid sequence identity can be obtained from various methods within the knowledge of those skilled in the art, such as publicly available computers such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. This can be achieved by using software. For purposes herein,% amino acid sequence identity values are obtained by using the sequence comparison program ALIGN-2, for which the complete source code for the ALIGN-2 program is provided in Table 1 below. . The ALIGN-2 sequence comparison computer program was created by Genentech, and the source code shown in Table 1 below was submitted to the US Copyright Office, Washington DC, 20559 along with the user documentation, with US copyright registration number TXU510087. Registered below. ALIGN-2 is preferably available from Genentech, South San Francisco, California, and may be compiled from the source code provided in Table 1 below. The ALIGN-2 program is compiled for use on a UNIX® operating system, preferably Digital UNIX® V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary.

In situations where ALIGN-2 is used for nucleic acid sequence comparison, the% nucleic acid sequence identity of, or relative to, a given nucleic acid sequence C (or a given amino acid sequence D, or In contrast, a given nucleic acid sequence C having or containing a certain percentage of nucleic acid sequence identity) may be calculated as follows:
100 times the fraction W / Z, where W is the number of nucleic acid residues with a score matched by C and D alignments of the sequence alignment program ALIGN-2, and Z is the total nucleic acid residues of D Is a number. It will be understood that if the length of the nucleic acid sequence C is different from the length of the amino acid sequence D, then the% nucleic acid sequence identity of C to D is different from the% nucleic acid sequence identity of D to C. As an example of calculating% nucleic acid sequence identity using this method, “PRO-DNA” represents a hypothetical PRO-encoding nucleic acid sequence of interest and “Comparative DNA” is a “PRO-DNA” nucleic acid molecule of interest. Represents the nucleic acid sequences being compared, and each of “N”, “L” and “V” represents a different hypothetical amino acid residue, and Tables 4 and 5 are nucleic acid sequences referred to as “comparison DNA” 2 shows a method for calculating% nucleic acid sequence identity to a nucleic acid sequence referred to as “PRO-DNA”.

  Unless otherwise indicated, all% nucleic acid sequence identity values herein are obtained using the ALIGN-2 sequence comparison computer program as set forth in the immediately preceding paragraph. However,% nucleic acid sequence identity values may be determined using the WU-BLAST-2 computer program (Altschul et al., Methods in Enzymology 266: 460-480 (1996)). In addition, most WU-BLAST-2 search parameters are set to initial values. Parameters that are not set to initial values, ie adjustable parameters, are set to the following values: overlap span = 1, overlap fraction = 0.125, word threshold (T) = 11, and scoring matrix = BLOSUM62. When WU-BLAST-2 is used, the% nucleic acid sequence identity value is: (a) the nucleic acid sequence of the subject PRO polypeptide-encoding nucleic acid molecule having a sequence derived from a native sequence PRO polypeptide-encoding nucleic acid And a comparative nucleic acid sequence of interest (ie, a sequence that may be a PRO polypeptide variant to which the subject PRO polypeptide-encoding nucleic acid molecule is compared) determined by WU-BLAST-2 Determined by the quotient of the number of identical identical nucleic acid residues divided by (b) the total number of nucleotides of the subject PRO polypeptide-encoding nucleic acid molecule. For example, in the expression “polypeptide comprising nucleic acid sequence A having or having at least 80% nucleic acid sequence identity to nucleic acid sequence B”, nucleic acid sequence A is the target nucleic acid sequence, Nucleic acid sequence B is the nucleic acid sequence of the PRO polypeptide-encoding nucleic acid molecule of interest.

  The% 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 can be downloaded from http://www.ncbi.nlm.nih.gov or otherwise obtained from the National Institutes of Health, Bethesda, Maryland. NCBI-BLAST2 uses several search parameters, all of which are set to initial values, eg unmask = allowable, chain = all, predicted occurrence = 10, minimum low composite length = 15/5 Multipath e-value = 0.01, multipath constant = 25, final gap alignment dropoff = 25, and scoring matrix = BLOSUM62.

In situations where NCBI-BLAST2 is used for nucleic acid sequence comparison, the% nucleic acid sequence identity of, or relative to, a given nucleic acid sequence C (or a given nucleic acid sequence D, or In contrast, a given nucleic acid sequence C, which has or contains a certain percentage of nucleic acid sequence identity), is calculated as follows:
100 times the fraction W / Z, where W is the number of nucleic acid residues with a score matched by C and D alignment of the sequence alignment program NCBI-BLAST2, and Z is the total nucleic acid residues of D Is a number. It will be appreciated that if the length of the nucleic acid sequence C is different from the length of the nucleic acid sequence D, then the% nucleic acid sequence identity of C to D is different from the% nucleic acid sequence identity of D to C.

In other embodiments, the PRO variant polypeptide nucleotide encodes an active PRO polypeptide, preferably high under the stringent hybridization and wash conditions, to the nucleotide sequence encoding the full-length PRO polypeptide disclosed herein. A nucleic acid molecule that hybridizes. The PRO variant polypeptide may be one encoded by a PRO variant polynucleotide.
“Isolated”, when used to describe the various polypeptides disclosed herein, means a polypeptide that has been identified and separated and / or recovered from a component of its natural environment. Contaminant components of the natural environment are substances that typically interfere with the diagnostic or therapeutic use of the polypeptide, including enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In a preferred embodiment, the polypeptide is (1) sufficient to obtain an N-terminal or internal amino acid sequence of at least 15 residues by using a spinning cup sequenator, or (2) Coomassie blue or It is preferably purified to homogeneity by SDS-PAGE under non-reducing or reducing conditions using silver staining. Isolated polypeptide includes protein in situ within recombinant cells, since at least one component of the PRO polypeptide natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step.

An “isolated” PRO polypeptide-encoding nucleic acid is a nucleic acid molecule that has been identified and separated from at least one contaminating nucleic acid molecule normally associated with the natural source of the nucleic acid encoding the PRO polypeptide. An isolated PRO polypeptide-encoding nucleic acid molecule is other than in the form or setting in which it is found in nature. Thus, an isolated PRO polypeptide-encoding nucleic acid molecule is distinguished from a PRO polypeptide-encoding nucleic acid molecule that is present in natural cells. However, an isolated PRO polypeptide-encoding nucleic acid molecule includes, for example, a PRO polypeptide nucleic acid molecule contained in a cell that normally expresses the PRO polypeptide at a chromosomal location different from that of natural cells. .
The expression “control sequence” refers to a DNA sequence necessary to express an operably linked coding sequence in a particular host organism. For example, suitable control sequences for prokaryotes include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals and enhancers.

A nucleic acid is “operably linked” when it is in a functional relationship with another nucleic acid sequence. For example, a presequence or secretory leader DNA is operably linked to the polypeptide DNA if expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is responsible for the transcription of the sequence. If it does, it is operably linked to the coding sequence; or the ribosome binding site is operably linked to the coding sequence if it is in a position that facilitates translation. In general, “operably linked” means that the bound DNA sequences are in close proximity and, in the case of a secretory leader, in close proximity and in the reading phase. However, enhancers do not necessarily have to be close together. Binding is achieved by ligation at convenient restriction sites. If such sites do not exist, synthetic oligonucleotide adapters or linkers are used according to conventional techniques.
The term “antibody” is used in the broadest sense and includes, for example, a single anti-PRO polypeptide monoclonal antibody (including agonists, antagonists, and neutralizing antibodies), anti-PRO antibody compositions with multiple epitope specificity, one Including single chain anti-PRO antibodies and fragments of anti-PRO antibodies (see below). The term “monoclonal antibody” as used herein is identical except for a substantially homogeneous population of antibodies, ie, naturally occurring mutations in which the individual antibodies that make up may be present in minor amounts. Refers to antibodies obtained from a population.

  The “stringency” of a hybridization reaction is readily determined by those skilled in the art and is generally an empirical calculation that depends on probe length, wash temperature, and salt concentration. In general, the longer the probe, the higher the temperature for proper annealing, and the shorter the probe, the lower the temperature. Hybridization generally depends on the ability of denatured DNA to reanneal when the complementary strand is present in an environment close to but below its melting point. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature that can be used. As a result, higher relative temperatures make the reaction conditions more stringent, while lower temperatures reduce stringency. Furthermore, stringency is inversely proportional to salt concentration. For further details and explanation of the stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).

  As defined herein, “stringent conditions” or “highly stringent conditions” are: (1) 0.015 M sodium chloride / 0.0015 M at low ionic strength and high temperature, eg, 50 ° C., for washing. Using sodium citrate / 0.1% sodium dodecyl sulfate; (2) denaturing agents such as formamide during hybridization, eg 50% (v / v) formamide and 0.1% bovine serum albumin at 42 ° C. /0.1% Ficoll / 0.1% polyvinylpyrrolidone / 50 mM sodium phosphate buffer pH 6.5 and 750 mM sodium chloride, 75 mM sodium citrate; (3) 50% formamide at 42 ° C. 5 × SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM LiS Sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 × Denhardt's solution, sonicated salmon sperm DNA (50 μg / ml), 0.1% SDS, and 10% dextran sulfate at 42 ° C. Identified by washing with 0.2x SSC (sodium chloride / sodium citrate) and 50% formamide at 55 ° C followed by a high stringency wash consisting of 0.1x SSC with EDTA at 55 ° C.

“Moderate stringency conditions” were identified as described in Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Press, 1989) Use of conditions (eg, temperature, ionic strength and% SDS) Moderate stringency conditions include 20% formamide, 5 × SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7. 6) Conditions such as overnight incubation at 37 ° C. in a solution containing 5 × denhard solution, 10% dextran sulfate, and 20 mg / mL denatured sheared salmon sperm DNA, then washing the filter at 37-50 ° C. in 1 × SSC. Those skilled in the art will know how to adjust the temperature, ion, etc. as necessary to accommodate factors such as probe length. It recognizes whether or not to adjust the strength and the like.
The term “epitope tag” as used herein refers to a PRO polypeptide fused to a “tag polypeptide”, or a chimeric polypeptide comprising their domain sequence. A tag polypeptide has a sufficient number of residues to provide an epitope from which the antibody can be produced, or an epitope that can be identified by some other reagent, but its length is the length of the PRO polypeptide of interest. Short enough not to inhibit the activity of the peptide. Also, the tag polypeptide is preferably fairly unique so that the antibody does not substantially cross-react with other epitopes. Suitable tag polypeptides generally have at least 6 amino acid residues, usually about 8 to about 50 amino acid residues (preferably about 10 to about 20 residues).

The term “immunoadhesin” as used herein refers to an antibody-like molecule that binds the binding specificity of a heterologous protein (“adhesin”) to an immunoglobulin constant domain. Structurally, an immunoadhesin comprises a fusion of an immunoglobulin constant domain sequence with the desired binding specificity and other than the antigen recognition and binding site of an antibody (ie, “heterologous”) and an immunoglobulin constant domain sequence. . The adhesin portion of an immunoadhesin molecule is typically a contiguous amino acid sequence that includes at least a receptor or ligand binding site. The immunoglobulin constant domain sequence of the immunoadhesin can be any of IgG-1, IgG-2, IgG-3 or IgG-4 subtype, IgA (including IgA-1 and IgA-2), IgE, IgD or IgM It can be obtained from the immunoglobulins.
As used herein, “active” and “activity” means a form of PRO that retains the biological and / or immunological activity of a natural or naturally occurring PRO polypeptide, and “biological” By activity is meant a biological function (inhibitory or stimulatory) caused by a natural or naturally occurring PRO, excluding the ability to generate antibodies against the antigenic epitope of the natural or naturally occurring PRO. Thus, “immunological” activity means the ability to generate antibodies against an antigenic epitope of a natural or naturally occurring PRO.

  The term “antagonist” is used in the broadest sense and refers to any molecule that prevents, inhibits, or neutralizes the biological activity of a native PRO polypeptide disclosed herein. Similarly, the term “agonist” is used in the broadest sense and refers to any molecule that mimics the biological activity of a native PRO polypeptide disclosed herein. Suitable agonist or antagonist molecules include in particular agonist or antagonist antibodies or antibody fragments, fragments of native PRO polypeptides or amino acid sequence variants, peptides, small organic molecules, and the like. A method of identifying an agonist or antagonist of a PRO polypeptide comprises contacting the PRO polypeptide with a candidate antagonist or agonist and measuring a change in one or more biological activities normally associated with the PRO polypeptide. May be included.

“Treatment” as used herein refers to both curative treatment, prophylactic and preventative therapies, in which a patient is prevented or reduced (reduced) in a targeted pathological condition or disease. Those in need of treatment include those already afflicted with the disease as well as those susceptible to or afflicted with the disease.
“Chronic” administration means that the drug is administered in a continuous manner as opposed to an acute manner, and the initial therapeutic effect (activity) is maintained over a long period of time. An “intermittent” administration is a treatment that is not made continuously without interruption, but rather is essentially periodic.
“Mammals” for treatment subjects are classified as mammals, including humans, domestic and agricultural animals, zoos, sports, or pet animals such as dogs, cats, cows, horses, sheep, pigs, rabbits, and the like. Means any animal. Preferably the mammal is a human.
Administration “in combination with” one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.

  As used herein, a “carrier” includes a pharmaceutically acceptable carrier, excipient, or stabilizer and is non-toxic to cells or mammals exposed to them at the dosages and concentrations used. . Often the physiologically acceptable carrier is an aqueous pH buffered solution. Examples of physiologically acceptable carriers include phosphate, citrate, and other organic acid salt buffers; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; Eg serum albumin, gelatin or immunoglobulin; hydrophobic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides and other carbohydrates including glucose, mannose or dextran; EDTA Chelating agents such as; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and / or nonionic surfactants such as TWEEN (trade name), polyethylene glycol (PEG), and PLURONICS (product) Name).

“Antibody fragments” comprise a portion of an intact antibody, preferably the antigen binding or variable region of the intact antibody. Examples of antibody fragments are Fab, Fab ′, F (ab ′) ₂ , and Fv fragments; diabodies; linear antibodies (Zapata et al., Protein Eng. 8 (10): 1057-1062 [1995]. ); Single chain antibody molecules; and multispecific antibodies formed from antibody fragments.
Papain digestion of antibodies produces two identical antibody-binding fragments called “Fab” fragments, each of which has a single antigen-binding site, the rest reflecting the ability to crystallize easily. It is named a fragment. Pepsin treatment yields an F (ab ′) ₂ fragment that has two antigen-binding sites and can cross-link 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 chain and one light chain variable region in tight, non-covalent association. In this arrangement, the three CDRs of each domain interact to determine the antigen binding site on the surface of the mer with V _H -V _L. Correctly, the six CDRs provide antigen binding specificity for the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for the antigen) has a lower affinity than the entire binding site, but has the ability to recognize and bind to the antigen. .

The Fab fragment also contains the constant domain of the light chain and the first constant domain (CH1) 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. Here, Fab′-SH represents Fab ′ in which the cysteine residue of the constant domain has a free thiol group. F (ab ′) ₂ antibody fragments are initially produced as pairs of Fab ′ fragments, with a hinge cysteine between them. Other chemical couplings of antibody fragments are also known.
“Light chains” of antibodies (immunoglobulins) from any vertebrate species are classified into one of two distinctly different types called kappa and lambda, based on the amino acid sequence of their constant domains.
Depending on the amino acid sequence of the constant domain of their heavy chains, immunoglobulins can be classified into different classes. There are five main classes of immunoglobulins: IgA, IgD, IgE, IgG and IgM, some of which are further classified into subclasses (isotypes) such as IgG1, IgG2, IgG3, IgG4, IgA and IgA2.

“Single-chain Fv” or “sFv” antibody fragments comprise antibody fragments comprising the V _H and V _L domains of antibody, wherein these domains are present in a single polypeptide chain. Preferably, the Fv polypeptide further comprises a polypeptide linker between the _VH and _VL domains that allows 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, Springer-Verlag, New York, pp. 269-315 (1994).
The term “diabodies” refers to a small antibody fragment with two antigen binding sites that binds to the light chain variable domain (V _L ) within the same polypeptide chain (V _H -V _L ). Heavy chain variable domain (V _H ). By using a linker that is too short to pair between two domains of the same chain, the domain is forced to pair with the complementary domains of the other chain to produce two antigen binding sites. Diabodies are well described, for example, by EP 404,097; WO 93/11161; and Hollinger et al., Proc. Natl. Acad. Sci. USA, 90: 6444-6448 (1993).

An “isolated” antibody is one that has been identified and separated and / or recovered from a component of its natural environment. Contaminating components of the natural environment are substances that interfere with the use of the antibody in diagnosis or therapy, including enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In a preferred embodiment, the antibody is (1) more than 95% antibody as measured by the Raleigh method, most preferably more than 99% by weight, and (2) at least 15 residues by using a spinning cup sequenator. Sufficient to obtain the N-terminal or internal amino acid sequence of (3), or (3) purified to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or preferably silver staining. 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.
An antibody that “specifically binds” or “specifically” to a specific polypeptide or an epitope on a specific polypeptide is a specific polypeptide that does not substantially bind to another polypeptide or polypeptide epitope. Or an epitope on a specific polypeptide.

The term “label” as used herein refers to a detectable compound or composition that is conjugated directly or indirectly to the antibody, such that a “labeled” antibody is produced. The label may itself be detectable (eg, a radioactive label or a fluorescent label) or, in the case of an enzyme label, may catalyze chemical conversion of the detectable substrate compound or composition.
“Solid phase” means a non-aqueous matrix to which an antibody of the invention can be attached. Examples of solid phases contemplated herein include those formed, in part or in whole, from glass (eg, controlled pore glass), polysaccharides (eg, agarose), polyacrylamide, polystyrene, polyvinyl alcohol and silicone. In certain embodiments, depending on the content, the solid phase can constitute the well of an assay plate; in others it can be a purification column (eg, an affinity chromatography column). The term also encompasses a discontinuous solid phase of discrete particles, such as those described in US Pat. No. 4,275,149.
“Liposomes” are small vesicles composed of various types of lipids, phospholipids and / or surfactants, and are useful for transporting drugs (such as PRO polypeptides or antibodies thereof) to mammals. The components of the liposome are usually arranged in a bilayer format similar to the lipid arrangement of biological membranes.
“Small molecule” is defined herein as having a molecular weight of less than about 500 Daltons.
An “effective amount” of a polypeptide disclosed herein, or an agonist or antagonist thereof, is an amount sufficient to carry out a specifically mentioned purpose. An “effective amount” can be determined by empirical and routine methods in connection with the stated purpose.

II. Compositions and Methods of the Invention Full Length PRO Polypeptides The present invention provides newly identified and isolated nucleic acid sequences that encode polypeptides referred to in this application as PRO polypeptides. In particular, cDNAs encoding various PRO polypeptides have been identified and isolated, as described in further detail in the Examples below. Note that proteins produced in separate rounds of expression are given different PRO numbers, but the UNQ numbers are unique to all given DNA and encoded proteins and do not change. However, for simplicity, the proteins encoded by the full-length natural nucleic acid molecules disclosed herein, as well as additional natural homologues and variants included in the PRO definition above, are used herein for their origin or preparation. Regardless of format, it is called “PRO / number”.
As disclosed in the examples below, various cDNA clones have been deposited with the ATCC. The exact nucleotide sequence of these clones can be readily determined by sequencing the deposited clones using routine methods in the art. The predicted amino acid sequence can be determined from the nucleotide sequence using routine skill. For the PRO polypeptides and encoding nucleic acids described herein, Applicants have identified what is believed to be the reading frame that best matches the currently available sequence information.

B. PRO polypeptide variants In addition to the full-length native sequence PRO polypeptides described herein, it is contemplated that PRO variants can also be prepared. PRO variants can be prepared by introducing appropriate nucleotide changes into the PRO polypeptide DNA or by synthesizing the desired PRO polypeptide. One skilled in the art will appreciate that amino acid changes such as changes in the number or position of glycosylation sites or changes in membrane anchoring properties can alter the post-translational process of the PRO polypeptide.

  Mutations in the various domains of the native full-length sequence PRO or the PRO polypeptides described herein can be performed using any technique for conservative and non-conservative mutations described, for example, in US Pat. No. 5,364,934 and This can be done using guidelines. A mutation may be a substitution, deletion or insertion of one or more codons encoding a PRO polypeptide that results in a change in the amino acid sequence of the PRO polypeptide as compared to the native sequence PRO. In some cases, the mutation is a substitution of at least one amino acid by any other amino acid in one or more domains of the PRO polypeptide. Guidance on which amino acid residues are inserted, substituted or deleted without adversely affecting the desired activity can be obtained by comparing the sequence of the PRO polypeptide with that of a known protein molecule of homology. Is found by minimizing amino acid sequence changes made within the high region of. Amino acid substitutions can be the result of substitution of one amino acid with another amino acid having similar structural and / or chemical properties, eg, substitution of leucine with serine, ie, a conservative amino acid substitution. Insertions and deletions can optionally be in the range of 1 to 5 amino acids. Acceptable mutations are determined by systematically making amino acid insertions, deletions or substitutions in the sequence and testing the resulting mutants for activity in any of the in vitro assays described in the Examples below. Is done.

PRO polypeptide fragments are provided herein. Such fragments may be cleaved at the N-terminus or C-terminus, for example, or lack internal residues when compared to a full-length native protein. Certain fragments lack amino acid residues that are not essential for a desired biological activity of the PRO polypeptide.
PRO fragments may be prepared by any of a number of conventional techniques. Desired peptide fragments may be chemically synthesized. An alternative method is enzymatic digestion, for example by treating the protein with an enzyme known to cleave the protein at a site determined by a particular amino acid residue, or by digesting the DNA with an appropriate restriction enzyme. Production of the PRO fragment by isolating the desired fragment. Yet another suitable technique involves isolating and amplifying a DNA fragment encoding the desired polypeptide fragment by polymerase chain reaction (PCR). Oligonucleotides that determine the desired ends of the DNA fragments are used in PCR 5 ′ and 3 ′ primers. Preferably, the PRO polypeptide fragment shares at least one biological and / or immunological activity with the native PRO polypeptide disclosed herein.
In a particular embodiment, the conservative substitutions of interest are shown in Table 6 starting with the preferred substitution. If such a substitution results in a change in biological activity, a more substitutional change is introduced and the product screened, as named in Table 6 as an exemplary substitution or as further described in the amino acid classification below. Is done.

Substitutional modifications of the function and immunological identity of the polypeptide can include (a) the structure of the polypeptide backbone of the substitution region, eg a sheet or helical arrangement, (b) the charge or hydrophobicity of the target site, or (c) the side This is achieved by selecting substituents that differ substantially in their effect while maintaining chain bulk. Naturally occurring residues can be grouped based on common side chain properties:
(1) Hydrophobicity: norleucine, met, ala, val, leu, ile;
(2) Neutral hydrophilicity: cys, ser, thr;
(3) Acidity: asp, glu;
(4) Basicity: asn, gln, his, lys, arg;
(5) Residues affecting chain orientation: gly, pro; and (6) Aromatics: trp, tyr, phe.

Non-conservative substitutions will require exchanging one member of these classes for another. Residues so substituted can also be introduced at conservative substitution sites, preferably at remaining (non-conserved) sites.
Mutations can be performed using oligonucleotide-mediated (site-specific) mutagenesis, alanine scanning, and PCR mutagenesis [Carter et al., Nucl. Acids Res., 13: 4331 (1986); Zoller et al., Nucl. Acids Res., 10: 6487 (1987)], cassette mutagenesis [Wells et al., Gene, 34: 315 (1985)], limited selective mutagenesis [Wells et al., Philos. Trans. R. Soc. London SerA, 317: 415 (1986)] or other methods known in the art can be used, or other known techniques can be performed on the cloned DNA to generate PRO mutant DNA.

  Scanning amino acid analysis can also be used to identify one or more amino acids along adjacent sequences. Preferred scanning amino acids are relatively small and neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is a typically preferred scanning amino acid in this group because it eliminates side chains beyond the beta carbon and is unlikely to change the backbone structure of the mutant [Cunningham and Wells, Science, 244: 1081-1085 (1989)]. Alanine is also typically preferred because it is the most common amino acid. Furthermore, it is often found in both buried and exposed positions [Creighton, The Proteins, (W.H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150: 1 (1976)]. If alanine substitution does not result in a sufficient amount of mutants, isoteric amino acids can be used.

C. Modification of PRO Covalent modifications of PRO polypeptides are included within the scope of the present invention. One type of covalent modification is by reacting a PRO polypeptide target amino acid residue with an organic derivatization reagent capable of reacting with a selected side chain or N- or C-terminal residue of the PRO polypeptide. is there. Derivatization with bifunctional reagents is useful, for example, to cross-link PRO to a surface for use in a water-insoluble support matrix or anti-PRO antibody purification method or vice versa. Commonly used crosslinking agents include, for example, 1,1-bis (diazoacetyl) -2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, such as esters with 4-azidosalicylic acid, 3,3′-dithiobis (succinyl). Homobifunctional imide esters including disuccinimidyl esters such as cinimidyl propionate), bifunctional maleimides such as bis-N-maleimide-1,8-octane, and methyl-3-[(p-azide) Phenyl) -dithio] propioimidate and other reagents.

Other modifications include deamination of glutaminyl and asparaginyl residues to the corresponding glutamyl and aspartyl residues, hydroxylation of proline and lysine, phosphorylation of the hydroxyl group of seryl or threonyl residues, lysine, arginine, and histidine, respectively. Methylation of α-amino group of side chain [TE Creighton, Proteins: Structure and Molecular Properties, WH Freeman & Co., San Francisco, pp. 79-86 (1983)], acetylation of N-terminal amine, and optional Includes amidation of the C-terminal carboxyl group.
Another type of covalent modification of a PRO polypeptide included within the scope of the present invention involves altering the native glycosylation pattern of the polypeptide. By “altering the native glycosylation pattern” is intended herein the deletion of one or more carbohydrate moieties found in the native sequence PRO (removal of existing glycosylation sites or chemical and / or enzymatic). By means of any deletion of glycosylation by means) and / or the addition of one or more glycosylation sites not present in the native sequence PRO. In addition, this clause includes qualitative changes in glycosylation of natural proteins, including changes in the nature and properties of the various carbohydrate moieties present.

Addition of glycosylation sites to the PRO polypeptide may involve amino acid sequence alterations. This change may be made, for example, by addition or substitution of one or more serine or threonine residues to the native sequence PRO (O-linked glycosylation site). The PRO amino acid sequence is optionally altered through changes at the DNA level, particularly by mutating the DNA encoding the PRO polypeptide at a preselected base to produce a codon that is translated into the desired amino acid. Also good.
Another means of increasing the number of carbohydrate moieties on the PRO polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Such methods are described in the art, for example, in WO 87/05330 issued September 11, 1987, and in Aplin and Wriston, CRC Crit. Rev. Biochem., Pp. 259-306 (1981). Has been.

Removal of carbohydrate moieties present on the PRO polypeptide can be accomplished chemically or enzymatically, or by mutational substitution of codons encoding amino acid residues presented as targets for glucosylation. Chemical deglycosylation techniques are known in the art, for example by Hakimuddin et al., Arch. Biochem. Biophys., 259: 52 (1987) and Edge et al., Anal. Biochem., 118: 131 (1981 ). Enzymatic cleavage of the carbohydrate moiety on the polypeptide is accomplished by using various endo and exoglycosidases as described in Thotakura et al., Meth. Enzymol. 138: 350 (1987).
Another type of covalent modification of the PRO of the present invention is described in U.S. Pat. No. 4, to a non-proteinaceous polymer of PRO polypeptide, such as polyethylene glycol, polypropylene glycol, or polyoxyalkylene. 640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337. Including the combination.
The PRO polypeptides of the present invention may also be modified by methods that form chimeric molecules comprising PRO polypeptides fused to other heterologous polypeptides or amino acid sequences.

  In one embodiment, such a chimeric molecule comprises a fusion of a tag polypeptide and a PRO polypeptide that provides an epitope to which an anti-tag antibody can selectively bind. The epitope tag is generally located at the amino or carboxyl terminus of the PRO polypeptide. The presence of such an epitope tag form of a PRO polypeptide can be detected using an antibody against the tag polypeptide. Providing the epitope tag also allows the PRO polypeptide to be readily purified by affinity purification using an anti-tag antibody or other 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; flu HA tag polypeptide and its antibody 12CA5 [Field et al., Mol. Cell. Biol., 8: 2159. -2165 (1988)]; c-myc tag and 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto [Evan et al., Molecular and Cellular Biology, 5: 3610-3616 (1985)]; and herpes simplex virus sugars A protein D (gD) tag and its antibody [Paborsky et al., Protein Engineering, 3 (6): 547-553 (1990)]. Other tag polypeptides include flag peptides [Hopp et al., BioTechnology, 6: 1204-1210 (1988)]; KT3 epitope peptides [Martin et al., Science, 255: 192-194 (1992)]; α-tubulin epitope peptides [Skinner et al., J. Biol. Chem., 266: 15163-15166 (1991)]; and 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 PRO immunoglobulin or a fusion with a specific region of an immunoglobulin. For the bivalent form of the chimeric molecule (also referred to as “immunoadhesin”), such a fusion may be the Fc region of an IgG molecule. The Ig fusion preferably comprises a solubilized (transmembrane domain deleted or inactivated) form of the PRO polypeptide in place of at least one variable region within the Ig molecule. In particularly preferred embodiments, the immunoglobulin fusion comprises the hinge, CH2 and CH3, or hinge, CH1, CH2 and CH3 regions of an IgG1 molecule. For the production of immunoglobulin fusions, see US Pat. No. 5,428,130 issued June 27, 1995.

D. PRO Preparation The following description relates primarily to a method for producing PRO by culturing cells transformed or transfected with a vector containing PRO nucleic acid. Of course, it is believed that the PRO can be prepared using other methods well known in the art. For example, PRO sequences, or portions thereof, may be produced by direct peptide synthesis using solid phase techniques [eg, Stewart et al., Solid-Phase Peptide Synthesis, WH Freeman Co., San Francisco, California (1969). Merrifield, J. Am. Chem. Soc., 85: 2149-2154 (1963)]. In vitro protein synthesis may be performed by manual techniques or by automation. Automated synthesis may be performed, for example, using an Applied Biosystems Peptide Synthesizer (Foster City, CA) according to the manufacturer's instructions. The various portions of the PRO may be chemically synthesized separately and combined using chemical or enzymatic methods to produce the full-length PRO.

1. Isolation of PRO-encoding DNA PRO-encoding DNA can be obtained from a cDNA library prepared from tissues that carry PRO mRNA and are believed to express it at detectable levels. Accordingly, human PRODNA can be conveniently obtained from a cDNA library prepared from human tissue, as described in the Examples. The PRO-encoded gene can also be obtained from a genomic library or by a known synthesis method (for example, automated nucleic acid synthesis).
Libraries can be screened with probes (such as antibodies to PRO or oligonucleotides of at least about 20-80 bases) designed to identify the gene of interest or the protein encoded by that gene. Screening of cDNA or genomic libraries with selected probes is performed using standard procedures described in, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989). be able to. Another method for isolating the gene encoding the desired PRO polypeptide is to use PCR [Sambrook et al., Supra; Dieffenbach et al., PCR Primer: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995). ].

The following examples describe cDNA library screening techniques. The oligonucleotide sequence selected as the probe must be long enough and clear enough to minimize false positives. 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 such as ³² P-labeled ATP, biotinylation or enzyme labeling. Hybridization conditions, including moderate stringency and high stringency, are shown in Sambrook et al., Supra.
Sequences identified in such library screening methods can be compared and aligned with well-known sequences deposited in the public databases of Genbank et al., Or in private sequence databases and made available to the public. Sequence identity within the determined region of the molecule or over the full length (either at the amino acid or nucleic acid level) can be determined using methods known in the art and described herein. it can.
Nucleic acids with protein coding sequences use the deduced amino acid sequences disclosed herein for the first time, and if necessary, Sambrook et al., Supra, which detects intermediates and precursors of mRNA not reverse transcribed into cDNA Obtained by screening selected cDNA or genomic libraries using conventional primer extension methods as described in.

2. Host Cell Selection and Transformation Host cells are transfected or transformed with the expression or cloning vectors for PRO production described herein to induce promoters, select transformants, or encode the desired sequence. In order to amplify the gene to be cultured, it is cultured in a conventional nutrient medium appropriately modified. Culture conditions such as medium, temperature, pH, etc. can be selected by those skilled in the art without undue experimentation. In general, principles, protocols, and practical techniques for maximizing cell culture productivity can be found in Mammalian Cell Biotechnology: a Practical Approach, edited by M. Butler (IRL Press, 1991) and Sambrook et al., Supra. it can.

How prokaryotic cell transfection and eukaryotic cell transfection, for example, CaCl _2, CaPO _4, liposome-mediated and electroporation are known to those skilled in the art. Depending on the host cell used, transformation is done using standard methods appropriate to that cell. Calcium treatment or electroporation with calcium chloride as described in Sambrook et al., Supra, is generally used for prokaryotes. Infection with Agrobacterium tumefaciens is characterized by the characteristics of certain plant cells, as described in Shaw et al., Gene, 23: 315 (1983) and WO 89/05859 published June 29, 1989. Used for conversion. For mammalian cells without such cell walls, the calcium phosphate precipitation method of Graham and van der Eb, Virology, 52: 456-457 (1978) is preferred. General aspects of mammalian cell host system transformations are described in US Pat. No. 4,399,216. Transformation into yeast is typically performed by Van Solingen et al., J. Bact., 130: 946 (1977) and Hsiao et al., Proc. Natl. Acad. Sci. USA, 76: 3829 (1979). Implemented according to the method. However, other methods of introducing DNA into cells, such as nuclear microinjection, electroporation, intact cells, or bacterial protoplast fusion using polycations such as polybrene, polyornithine, etc. can also be used. See Keown et al., Methods in Enzymology, 185: 527-537 (1990) and Mansour et al., Nature, 336: 348-352 (1988) for various techniques for transforming mammalian cells.

Suitable host cells for cloning or expressing the DNA in the vectors described herein are prokaryotic, yeast, or higher eukaryotic cells. Suitable prokaryotes include, but are not limited to, eubacteria such as Gram negative or Gram positive organisms such as Enterobacteriaceae such as E. coli. Various E. coli strains are available to the public, for example, E. coli K12 strain MM294 (ATCC 31,446); E. coli X1776 (ATCC 31,537); E. coli strains W3110 (ATCC 27,325) and K5772 (ATCC 53,635). Other preferred prokaryotic host cells are E. coli, such as E. coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, such as Salmonella typhimurium, Serratia, such as Serratia marcesans ( Serratia marcescans), and Shigella, and Neisseria gonorrhoeae, such as B. subtilis and B. licheniformis (for example, described in DD 266,710 issued April 12, 1989) Bacillus licheniformis 41P), Pseudomonas, including Enterobacteriaceae such as Pseudomonas 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 the issuance of recombinant DNA production. Preferably, the host cell secretes a minimal amount of proteolytic enzyme. For example, strain W3110 may be modified to have a genetic mutation in a gene encoding a foreign protein in the cell, examples of such hosts include E. coli W3110 strain 1A2 with the complete genotype tonA; E. coli W3110 strain 9E4 with the complete genotype tonA ptr3; E. coli W3110 strain 27C7 (ATCC 55,244) with the complete genotype tonA prt3 phoA E15 (argF-lac) 169 degP ompT kan ^r ; E15 (algF-lac) 169 degP ompT rbs7 E. coli W3110 strain 37D6 with ilvG kan ^r ; E. coli W3110 strain 40B4 which is a 37D6 strain with a non-kanamycin resistant degP deletion mutation; and August 1990 Issued 7 days Includes E. coli strains with mutated periplasmic protease disclosed in US Pat. No. 4,946,783. Alternatively, in vitro methods of cloning such as PCR or other nucleic acid polymerase reactions are preferred.

  In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for PRO polypeptide-encoding vectors. Saccharomyces cerevisia is a commonly used lower eukaryotic host microorganism. In addition, Schizosaccharomyces prombe (Beach and Nurse, Nature, 290: 140 [1981]; EP 139,383 issued May 2, 1985); Kluveromyces hosts (US Pat. No. 4 , 943,529; Fleer et al., Bio / Technology, 9: 968-975 (1991)), for example, K. lactis (MW98-8C, CBS683, CBS4574; Louvencourt et al., J. Bacteriol. 154). (2): 737-742 [1983]), K. fragilis (ATCC 12,424), K. bulgaricus (ATCC 16,045), Kruberomyces wickeramii ( K. wickeramii) (ATCC 24,178), K. waltii (ATCC 56,500), K. drosophilarum (ATCC 36,906; Van den Berg et al., Bio / Technology, 8: 135 (1990)), K. thermotolerans and K. marxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070; Sreekrishna et al., J. Basic Microbiol) , 28: 265-278 [1988]); Candida; Trichoderma reesia (EP 244, 234); Akapan mold (Case et al., Proc. Natl. Acad. Sci. USA, 76: 5259-5263 [1979]) Schwanniomyces, for example Schwanniomyces occidentalis (EP 394,538, published October 31, 1990); and filamentous fungi, such as Neurospora, Penicillium, Tripocladium ( Tolypocladium) (WO 91/00357 published 10 January 1991); and Aspergillus hosts, such as Aspergillus nida Lance (Ballance et al., Biochem. Biophys. Res. Commun., 112: 284-289 [1983]; Tilburn et al., Gene, 26: 205-221 [1983]; Yelton et al., Proc. Natl. Acad. Sci. USA, 81: 1470-1474 [1984]) and Aspergillus niger (Kelly and Hynes, EMBO J., 4: 475-479 [1985]). Preferred methylotrophic (C1 compound assimilation, Methylotropic) yeasts herein are not limited to these, but include Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Contains yeast that can grow on methanol selected from the genus consisting of Rhodotorula. A list of specific species, illustrative of this yeast classification, is described in C. Anthony, The Biochemistry of Methylotrophs, 269 (1982).

  Suitable host cells for the expression of glycosylated PRO are derived from multicellular organisms. Examples of invertebrate cells include insect cells such as Drosophila S2 and Spodospera Sf9, and plant cells. Examples of useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More detailed examples include monkey kidney CV1 strain transformed with SV40 (COS-7, ATCC CRL 1651); human embryonic kidney strain (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 hepatocytes (Hep G2, HB 8065); and mouse breast tumor cells ( MMT 060562, ATCC CCL51). The selection of an appropriate host cell is within the common general knowledge of this field.

3. Selection and use of replicable vectors Nucleic acid (eg, cDNA or genomic DNA) encoding a PRO polypeptide is inserted into a replicable vector for cloning (amplification of DNA) or expression. Various vectors are publicly available. The vector can be, for example, in the form of a plasmid, cosmid, virus particle, or phage. The appropriate nucleic acid sequence is inserted into the vector by a variety of techniques. In general, DNA is inserted into an appropriate restriction endonuclease site using techniques well known in the art. Vector components generally include, but are not limited to, one or more signal sequences, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Standard ligation techniques known to those skilled in the art are used to make a suitable vector containing one or more of these components.

  PRO polypeptides are not only produced directly by recombinant techniques, but also fused to heterologous polypeptides, which are signal sequences or mature proteins or other polypeptides having a specific cleavage site at the N-terminus of the polypeptide. It is also produced as a peptide. In general, the signal sequence is a component of the vector or a part of the PRO-encoding DNA that is inserted into the vector. The signal sequence may be, for example, a prokaryotic signal sequence selected from the group of alkaline phosphatase, penicillinase, lpp or a thermostable enterotoxin II leader. For yeast secretion, signal sequences include yeast invertase leader, alpha factor leader (Saccharomyces and Kluyveromyces α factor leader, the latter described in US Pat. No. 5,010,182. Or an acid phosphatase leader, a C. albicans glucoamylase leader (EP362179, issued April 4, 1990), or a signal described in WO90 / 13646 published on November 15, 1990. It can be. In mammalian cell expression, mammalian signal sequences may be used for direct secretion of proteins such as signal sequences from the same or related species of secreted polypeptides 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 many bacteria, yeasts and viruses. The origin of replication derived from plasmid pBR322 is suitable for most gram-negative bacteria, the 2μ plasmid origin is suitable for yeast, and the various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are suckling. Useful for cloning vectors in animal cells.
Expression and cloning vectors typically contain a selection gene, also termed a selectable marker. Typical selection genes are (a) conferring resistance to antibiotics or other toxins such as ampicillin, neomycin, methotrexate or tetracycline, (b) compensate for auxotrophic defects, or (c) the genetic code for eg Basili It encodes a protein that supplies important nutrients not available from complex media, such as D-alanine racemase.

Examples of markers that can be appropriately selected for mammalian cells are those that can identify cellular components that can take up a PRO-encoding nucleic acid, such as DHFR or thymidine kinase. Suitable host cells using wild type DHFR are defective in DHFR activity prepared and grown as described by Urlaub et al. In Proc. Natl. Acad. Sci. USA, 77: 4216 (1980). This is a CHO cell line. A suitable selection gene for use in yeast is the trp1 gene present in the yeast plasmid YRp7 [Stinchcomb et al., Nature, 282: 39 (1979); Kingsman et al., Gene, 7: 141 (1979); Tschemper et al., Gene, 10: 157 (1980)]. The trp1 gene provides a selectable marker for mutant strains of yeast lacking the ability to grow in tryptophan, such as, for example, ATCC No. 44076 or PEP4-1 [Jones, Genetics, 85:12 (1977)].
Expression and cloning vectors usually contain a promoter that is operably linked to the PRO-encoding nucleic acid sequence and controls mRNA synthesis. Suitable promoters that are recognized by a variety of possible host cells are known. Suitable promoters for use in prokaryotic hosts are the β-lactamase and lactose promoter systems [Chang et al., Nature, 275: 615 (1978); Goeddel et al., Nature, 281: 544 (1979)], alkaline phosphatase, 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). )]including. Promoters used in bacterial systems also have a Shine-Dalgarno (SD) sequence operably linked to the DNA encoding the PRO polypeptide.

Examples of suitable promoter sequences for use with yeast hosts include 3-phosphoglycerate kinase [Hitzeman et al., J. Biol. Chem., 255: 2073 (1980)] or other glycolytic enzymes [Hess et al., J. Biol. Adv. Enzyme Reg., 7: 149 (1968); Holland, Biochemistry, 17: 4900 (1987)], eg enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, Glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, trioselate isomerase, phosphoglucose isomerase, and glucokinase are included.
Other yeast promoters are inducible promoters that have the additional effect that transcription is controlled by growth conditions, such as alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degrading enzymes related to nitrogen metabolism, metallothionein, glycerin There are promoter regions of aldehyde-3-phosphate dehydrogenase and the enzymes that govern the utilization of maltose and galactose. Vectors and promoters that are preferably used for expression in yeast are further described in EP 73,657.

PRO polypeptide transcription from vectors in mammalian host cells can be performed, for example, by polyoma virus, infectious epithelioma virus (UK 2,211,504 published July 5, 1989), adenovirus (eg, adenovirus 2), bovine Promoters derived from the genomes of viruses such as papilloma virus, avian sarcoma virus, cytomegalovirus, retrovirus, hepatitis B virus and simian virus 40 (SV40), heterologous mammalian promoters such as actin promoter or immunoglobulin promoter , And by promoters derived from heat shock promoters, such promoters are controlled as long as they are compatible with the host cell system.
Transcription of the DNA encoding the desired PRO polypeptide by higher eukaryotes can be enhanced by inserting an enhancer sequence into the vector. Enhancers are cis-acting elements of DNA, usually about 10 to 300 base pairs, that act on a promoter to enhance its transcription. Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, α-fetoprotein and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the late SV40 enhancer (100-270 base pairs) of the origin of replication, the cytomegalovirus early promoter enhancer, the polyoma enhancer and the adenovirus enhancer late of the origin of replication. Enhancers can be spliced into the vector at the 5 'or 3' position of the PRO coding sequence, but are preferably located 5 'from the promoter.

Expression vectors used for eukaryotic host cells (nucleated cells derived from yeast, fungi, insects, plants, animals, humans, or other multicellular organisms) are sequences required for termination of transcription and stabilization of mRNA. Including. Such sequences can be obtained from the normally 5 ', sometimes 3' untranslated region of eukaryotic or viral DNA or cDNA. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding the PRO polypeptide.
Other methods, vectors and host cells suitable for adapting to the synthesis of PRO polypeptides in recombinant vertebrate cell culture are described in Gething et al., Nature, 293: 620-625 (1981); Mantei et al., Nature, 281: 40-46 (1979); EP 117,060; and EP 117,058.

4). Gene amplification / expression detection Gene amplification and / or expression is based on the sequences provided herein, using appropriately labeled probes, eg, conventional Southern blotting, Northern to quantify mRNA transcription It can be measured directly in a sample by blotting [Thomas, Proc. Natl. Acad. Sci. USA, 77: 5201-5205 (1980)], dot blotting (DNA analysis), or in situ hybridization. it can. Alternatively, antibodies capable of recognizing specific double strands, including DNA double strands, RNA duplexes and DNA-RNA hybrid duplexes or DNA-protein duplexes, can also be used. The antibody can then be labeled and an assay can be performed, where the duplex is bound to the surface, so that the antibody bound to the duplex at the time of formation on the surface of the duplex is bound. The presence can be detected.
Alternatively, gene expression can be measured by immunological methods that directly quantify gene product expression, such as immunohistochemical staining of cells or tissue sections and cell culture or body fluid assays. Antibodies useful for immunohistochemical staining and / or assay of sample fluids can be monoclonal or polyclonal and can be prepared in any mammal. Conveniently, the antibody is directed against a native sequence PRO polypeptide or against a synthetic peptide based on the DNA sequence provided herein, or an exogenous sequence fused to PRO DNA and encoding a specific antibody epitope. Can be prepared.

5. Purification of polypeptides PRO polypeptide forms can be recovered from culture media or lysates of host cells. If membrane-bound, it can be detached from the membrane using an appropriate wash solution (eg Triton-X100) or enzymatic cleavage. Cells used for the expression of PRO polypeptides can be disrupted by various chemical or physical means such as freeze-thaw cycles, sonication, mechanical disruption, or cytolytic agents.
It may be desirable to purify the PRO polypeptide from recombinant cell proteins or polypeptides. Purified by the following procedure, which is an example of a suitable purification procedure: fractionation on an ion exchange column; ethanol precipitation; reverse phase HPLC; chromatography on silica or a cation exchange resin such as DEAE; chromatofocusing; PAGE; ammonium sulfate precipitation; gel filtration using, for example, Sephadex G-75; protein A sepharose column to remove contaminants such as IgG; and metal chelation column to bind the epitope tag form of the PRO polypeptide. It is possible to use many protein purification methods 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). it can. The purification process chosen depends, for example, on the production method used and in particular on the nature of the particular PRO produced.

E. PRO Applications Nucleic acid sequences encoding PRO (or their complements) are widely used in the field of molecular biology, including use as hybridization probes, in chromosome and gene mapping, and in the production of antisense RNA and DNA. Has a use. PRO nucleic acids are also useful for preparing PRO polypeptides by the recombinant techniques described herein.

The full-length native sequence PRO gene or a portion thereof may be isolated from the full-length PRO cDNA or other genes having the desired sequence identity to the PRO sequences disclosed herein (eg, naturally occurring variants of PRO or other Can be used as hybridization probes for cDNA libraries for the isolation of PROs from those species. In some cases, the length of the probe is from about 20 to about 50 bases. Hybridization probes may be derived at least in part from novel regions of the full-length native nucleotide sequence, which regions include the promoter, enhancer component and intron of the native sequence PRO without undue experimentation. It can be derived from a genomic sequence. For example, the screening method involves synthesizing a selected probe of about 40 bases by isolating the coding region of the PRO polypeptide gene using a known DNA sequence. Hybridization probes can be labeled with a variety of labels including radioactive nucleotides such as ³² P or ³⁵ S, or enzyme labels such as alkaline phosphatase attached to the probe via an avidin / biotin binding system. A labeled probe having a sequence complementary to the PRO polypeptide gene of the present invention screens a library of human cDNA, genomic DNA or mRNA and determines which members of the library hybridize to the probe. Can be used to do. Hybridization techniques are described in further detail in the examples below.

Any EST disclosed in this application can be used in the manner described herein, as well as a probe.
Other useful fragments of PRO nucleic acids include antisense or sense oligonucleotides that comprise a single stranded nucleic acid sequence (either RNA or DNA) that can bind to a target PRO mRNA (sense) or PRO DNA (antisense) sequence. The antisense or sense oligonucleotide, according to the invention, comprises a fragment of the coding region of PRO DNA. Such fragments generally comprise at least about 14 nucleotides, preferably from about 14 to 30 nucleotides. The possibility of controlling antisense or sense oligonucleotides based on a cDNA sequence encoding a given protein is described, for example, by Stein and Cohen (Cancer Res. 48: 2659: 1988) and van der Krol et al. (BioTechniques 6: 958, 1988).

Binding of the antisense or sense oligonucleotide to the target nucleic acid sequence results in the formation of a duplex, which can be one of several methods including promoting duplex degradation, premature termination of transcription or translation, or Other methods block transcription or translation of the target sequence. Thus, antisense oligonucleotides are used to block the expression of PRO proteins. Antisense or sense oligonucleotides further include oligonucleotides having modified sugar-phosphodiester backbones (or other sugar linkages, such as those described in WO 91/06629), where such sugar linkages are endogenous nuclease resistant. . Oligonucleotides with such resistant sugar linkages are stable in vivo (ie, able to withstand enzymatic degradation), but retain sequence specificity that allows them to bind to the target nucleotide sequence.
Other examples of sense or antisense oligonucleotides include organic moieties, such as those described in WO 90/10048, and other moieties that improve the affinity of the oligonucleotide for the target nucleic acid sequence, such as poly- (L -Oligonucleotides covalently linked to (lysine). Furthermore, an intercalating agent such as ellipticine, an alkylating agent or a metal product may be bound to the sense or antisense oligonucleotide to modify the binding specificity of the antisense or sense oligonucleotide to the target nucleotide sequence.

The antisense or sense oligonucleotide comprises the target nucleic acid sequence by any gene transformation method including, for example, CaPO ₄ -mediated DNA transfection, electroporation, or by using a gene transformation vector such as Epstein-Barr virus. Introduced into cells. In a preferred method, the antisense or sense oligonucleotide is inserted into a suitable retroviral vector. A cell containing the target nucleic acid sequence is contacted with the recombinant retroviral vector in vivo or ex vivo. Suitable retroviral vectors include, but are not limited to, those derived from the murine retrovirus M-MuLV, N2 (retrovirus derived from M-MuLV), or double named DCT5A, DCT5B and DCT5C. A copy vector (see WO90 / 13641) is included.
Sense or antisense oligonucleotides may also be introduced into cells containing the target sequence by formation of a complex with a ligand binding molecule, as described in WO 91/04753. Suitable ligand binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to cell surface receptors. Preferably, complex formation of the ligand binding molecule substantially reduces the ability of the ligand binding molecule to bind to its corresponding molecule or receptor or to prevent entry of a sense or antisense oligonucleotide or complex thereof into the cell. Does not interfere.

Alternatively, sense or antisense oligonucleotides may be introduced into cells containing the target nucleic acid sequence by formation of oligonucleotide-lipid complexes, as described in WO 90/10448. The sense or antisense oligonucleotide-lipid complex is preferably degraded intracellularly by endogenous lipase.
Antisense RNA or DNA molecules are generally at least about 5 bases long, about 10 bases long, about 15 bases long, about 20 bases long, about 25 bases long, about 30 bases long, about 35 bases long, about 40 bases long, about 45 base length, about 50 base length, about 55 base length, about 60 base length, about 65 base length, about 70 base length, about 75 base length, about 80 base length, about 85 base length, about 90 base length, about It is 95 bases long, about 100 bases long or longer.
Probes can also be used in PCR techniques to create a pool of sequences for identification of closely related PRO coding sequences.
The nucleotide sequence encoding PRO can also be used to create hybridization probes for mapping the gene encoding the PRO and for gene analysis of individuals with genetic disorders. The nucleotide sequences provided herein can be mapped to specific regions of chromosomes and chromosomes using well-known techniques such as in situ hybridization, binding analysis to known chromosomal markers, and hybridization screening in libraries. .

  If the coding sequence of the PRO encodes a protein that binds to another protein (eg, when PRO is a receptor), PRO can be used in an assay to identify its ligand. By such methods, inhibitors of receptor / ligand binding interactions can be identified. Proteins involved in such binding interactions can also be used to screen for peptides or small molecule inhibitors or agonists of binding interactions. Receptor PRO can also be used to isolate related ligands. Screening assays are designed for the discovery of lead compounds that resemble the biological activity of native PRO or its receptor. Such screening assays are also used for high-throughput screening of chemical libraries, making them particularly suitable for the identification of small molecule candidate drugs. Small molecules considered include synthetic organic or inorganic compounds. The assays are performed in a variety of formats including protein-protein binding assays, biological screening assays, immunoassays and cell-based assays that are well known and characterized in the art.

  Also, nucleic acids encoding PRO or any modified form thereof can be used to produce either transgenic or “knockout” animals, which are useful for the development and screening of therapeutically useful reagents. . A transgenic animal (eg, a mouse or rat) is an animal having cells that contain the transgene introduced into the animal or its ancestors before birth, eg, at the embryonic stage. A transgene is DNA that is integrated into the genome of a cell in which a transgenic animal develops. In one embodiment, the cDNA encoding the PRO is a genomic DNA encoding the PRO based on the genomic sequence and established techniques used to generate a transgenic animal comprising cells expressing the DNA encoding the PRO. Can be used to clone. Methods for producing transgenic animals, particularly specific animals such as mice or rats, are routine in the art and are described, for example, in US Pat. Nos. 4,736,866 and 4,870,009. ing. Typically, specific cells are targeted for introduction of the PRO transgene with a tissue-specific enhancer. Transgenic animals containing a copy of a PRO-encoding transgene introduced into the germ line of the animal at the embryonic stage can be used to examine the effects of increased expression of DNA encoding PRO. Such animals can be used, for example, as tester animals for reagents that would confer protection against pathological conditions associated with their overexpression. In this aspect of the invention, if an animal is treated with a reagent and the incidence of the pathological condition is low compared to an untreated animal with the transgene, it indicates the possibility of therapeutic treatment for the pathological condition. It is.

  Alternatively, a non-human homologue of PRO is a defect that encodes PRO by homologous recombination between the altered genomic DNA encoding PRO introduced into an animal embryonic cell and the endogenous gene encoding PRO. Alternatively, it can be used to create PRO “knock-out” animals with altered genes. For example, a cDNA encoding PRO can be used to clone genomic DNA encoding PRO according to established techniques. A portion of the genomic DNA encoding PRO can be deleted or replaced with other genes such as a gene encoding a selectable marker used to monitor integration. Typically, the vector contains several kilobases of intact flanking DNA (both 5 'and 3' ends) [eg, Thomas and Capecchi, Cell, 51: 503 (1987) for homologous recombination vectors]. checking]. Vectors were introduced into embryonic stem cells (eg, by electroporation) and cells were selected in which the introduced DNA was recombined homologously with endogenous DNA [eg, Li et al., Cell, 69: 915 (1992 )reference]. The selected cells are then injected into the blastocyst of the animal (eg mouse or rat) to form an aggregate chimera [eg Bradley, Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, EJ Robertson, ed. , Oxford, 1987), pp. 113-152]. The chimeric embryo is then transplanted into an appropriate pseudopregnant female nanny to create a “knockout” animal over time. Offspring with DNA homologously recombined into embryonic cells are identified by standard techniques and can be used to breed animals that contain DNA in which all cells of the animal are homologously recombined . Knockout animals are characterized by their ability to defend against certain pathological conditions and progression of those pathological conditions due to PRO polypeptide deficiency.

  A nucleic acid encoding a PRO polypeptide can also be used for gene therapy. In gene therapy applications, genes are introduced to achieve in vivo synthesis of a therapeutically effective amount of a gene product, eg, to replace a defective gene. “Gene therapy” includes both conventional gene therapy where a continuous effect is achieved by a single treatment and administration of a gene therapy drug including single or repeated administration of therapeutically effective DNA or mRNA. . Antisense RNA and DNA can be used as therapeutic agents to block in vivo expression of certain genes. It has already been shown that short antisense oligonucleotides can be transferred into cells that act as inhibitors, despite low intracellular concentrations due to limited uptake by the cell membrane (Zamecnik et al., Proc. Natl Acad. Sci. USA 83: 4143-4146 [1986]). Oligonucleotides may be modified to facilitate uptake by replacing their negatively charged phosphodiester groups with uncharged groups.

  There are a variety of techniques for introducing nucleic acids into viable cells. These techniques vary depending on whether the nucleic acid is transferred to the cultured cells in vitro or in vivo in the intended host cell. Suitable methods for transferring nucleic acids into mammalian cells in vitro include liposomes, electroporation, microinjection, cell fusion, DEAE-dextran, calcium phosphate precipitation, and the like. Currently preferred in vivo gene transfer techniques are transfection with viral (typically retroviral) vectors and viral coat protein-liposome mediated transfection (Dzau et al., Trends in Biotechnology 11, 205-210 (1993)). In some situations, it may be desirable to provide a source of nucleic acid with an agent that targets the target cell, such as a cell surface membrane protein or an antibody specific for the target cell, a ligand for a receptor on the target cell. When using liposomes, proteins that bind to cell surface membrane proteins with endocytosis, eg, capsid proteins or fragments thereof that are tropic for a particular cell type, antibodies to proteins that undergo internalization in the cycle, intracellular localization Proteins that target and improve intracellular half-life are used to promote targeting and / or uptake. Receptor-mediated endocytosis is described, for example, by Wu et al., J. Biol. Chem. 262, 4429-4432 (1987); and Wagner et al., Proc. Natl. Acad. Sci. USA 87, 3410-3414 (1990). Has been. For review of gene generation and gene therapy protocols, see Anderson et al., Science 256, 808-813 (1992).

The PRO polypeptides described herein may be used as molecular weight markers for protein electrophoresis purposes, and isolated nucleic acid sequences may be used for recombinant expression of these markers.
Nucleic acid molecules encoding the PRO polypeptides or fragments thereof described herein are useful for chromosome identification. In this respect, the identification of novel chromosomal markers is necessary because chromosomal marking reagents based on actual sequences are hardly available. Each PRO nucleic acid molecule of the present invention can be used as a chromosomal marker.
Also, the PRO polypeptides and nucleic acid molecules of the present invention can be used for tissue typing, and the PRO polypeptides of the present invention are preferably compared in diseased tissue compared to normal tissue of the same type in one tissue compared to the other. Different expression. PRO nucleic acid molecules will find use for generating probes for PCR, Northern analysis, Southern analysis and Western analysis.

  The PRO polypeptides described herein may be used as therapeutic agents. The PRO polypeptides of the present invention are formulated according to known methods for preparing pharmaceutically useful compositions, whereby the PRO product is mixed with a pharmaceutically acceptable carrier medium. The therapeutic formulation is in the form of a lyophilized formulation or an aqueous solution by mixing any pharmaceutically acceptable carrier, excipient or stabilizer with an active ingredient having the desired degree of purification ( Remington's Pharmaceutical Sciences, 16th edition, A. Osol, Ed., [1980]), prepared and stored. Acceptable carriers, excipients or stabilizers are nontoxic to recipients at the dosages and concentrations used and are buffers such as phosphate, citrate and other organic acids; antioxidants including ascorbic acid Agent; low molecular weight (less than 10 residues) polypeptide; protein such as serum albumin, gelatin or immunoglobulin; hydrophilic polymer such as polyvinylpyrrolidone; amino acid such as glycine, glutamine, asparagine, arginine or lysine; glucose, Monosaccharides such as mannose or dextrin, disaccharides or other carbohydrates, chelating agents such as EDTA, sugars such as mannitol or sorbitol, salt-forming counterions such as sodium; and / or TWEEN (trade name), PLURONICS (trade name) Or a nonionic surfactant such as PEG.

The formulation used for in vivo administration must be sterile. This is easily accomplished by filtration through sterile filter membranes before or after lyophilization and reconstitution.
Here, the pharmaceutical composition of the present invention is generally placed in a container having a sterile access port, for example, an intravenous bag or vial having a stopper pierceable by a hypodermic needle.
The route of administration is by well known methods such as injection or infusion by intravenous, intraperitoneal, intracerebral, intramuscular, intraocular, intraarterial or intralesional route, local administration, or sustained release system.
The dosage of the pharmaceutical composition of the present invention and the desired drug concentration will vary depending on the particular application intended. The determination of an appropriate dose or route of administration is within the ordinary skill of a physician. Animal experiments provide reliable guidance on determining effective doses for human therapy. Effective species interspecific scaling is described in Toxicokinetics and New Drug Development, Yacobi et al., Ed., Pergamon Press, New York 1989, pp. 42-96, Mordenti, J. and Chappell, W. "The use of interspecies scaling in toxicokinetics" Can be implemented according to the principles described in.

When in vivo administration of a PRO polypeptide or agonist or antagonist thereof is used, the normal dosage is about 10 ng / kg to 100 mg / kg, preferably about 1 μg per day per mammal body weight, depending on the route of administration. / Kg / day to 10 mg / kg / day. Specific dosage and delivery method guidelines are given in the literature; see, eg, US Pat. Nos. 4,657,760, 5,206,344, or 5,225,212. It is expected that different formulations will be effective for different therapeutic compounds and different diseases, for example, administration targeting one organ or tissue will require delivery in a different manner than other organs or tissues Is done.
Where sustained release of the PRO polypeptide is desired in a formulation with release characteristics suitable for the treatment of any disease or condition that requires administration of the PRO polypeptide, microencapsulation of the PRO polypeptide is contemplated. Microencapsulation of recombinant proteins for sustained release has been successfully performed with human growth hormone (rhGH), interferon- (rhIFN-), interleukin-2, and MN rgp120. Johnson et al., Nat. Med., 2: 795-799 (1996); Yasuda, Biomed. Ther., 27: 1221-1223 (1993); Hora et al., Bio / Technology, 8: 755-758 (1990); Cleland , “Design and Production of Single Immunization Vaccines Using Polyactide Polyglycolide Microsphere Systems” Vaccine Design: The Subunit and Adjuvant Approach, edited by Powell and Newman, (Plenum Press: New York, 1995), p.439-462; WO97 / 03692, WO96 / 40072, WO 96/07399; and US Pat. No. 5,654,010.

Sustained release formulations of these proteins have been developed based on their biocompatibility and a wide range of biodegradation properties using poly-lactic-coglycolic acid (PLGA) polymers. The degradation products of PLGA, lactic acid and glycolic acid, are cleared immediately in the human body. Furthermore, the degradability of the polymer can be adjusted from months to years depending on the molecular weight and composition. Lewis, “Controlled release of bioactive agents from lactide / glycolide polymer”: M. Chasin and R. Langer (eds.), Biodegradable Polymers as Drug Delivery Systems (Marcel Dekker: New York, 1990), pp. 1-41.
The invention also encompasses methods of screening compounds to identify those that are similar to PRO polypeptides (agonists) or that inhibit the effects of PRO polypeptides (antagonists). A screening assay for an antagonist candidate drug is a compound that binds or complexes with the PRO polypeptide encoded by the gene identified herein, or that otherwise inhibits the interaction of the encoded polypeptide with other cellular proteins Designed to identify Such screening assays include those applicable to high-throughput screening of chemical libraries that make it particularly suitable for the identification of small molecule drug candidates.
The assay is performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays, and cell-based assays, known in the art.
All assays for antagonists require that they contact the candidate drug with the PRO polypeptide encoded by the nucleic acid identified here under conditions and for a time sufficient for these two components to interact. Is common.

  In binding assays, the interaction is binding and the complex formed is isolated or detected in the reaction mixture. In a particular embodiment, the PRO polypeptide or candidate drug encoded by the gene identified herein is immobilized to a solid phase, such as a microtiter plate, by covalent or non-covalent bonding. Non-covalent binding is generally achieved by coating a solid surface with a solution of PRO polypeptide and drying. Alternatively, an immobilized antibody specific for the immobilized PRO polypeptide, such as a monoclonal antibody, can be used to anchor it to a solid surface. The assay is performed by adding a non-immobilized component, which may be labeled with a detectable label, to a coated surface containing an immobilized component, such as an anchoring component. When the reaction is completed, unreacted components are removed, for example, by washing, and the complex adhered to the solid surface is detected. If the first non-immobilized component has a detectable label, detection of the label immobilized on the surface indicates that complex formation has occurred. If the initial non-immobilized component does not have a label, complex formation can be detected, for example, by a labeled antibody that specifically binds to the immobilized complex.

  If a candidate compound interacts but does not bind to a specific PRO polypeptide encoded by the gene identified herein, the interaction with that polypeptide is a well-known method for detecting protein-protein interactions. Can be assayed. Such assays include traditional techniques such as cross-linking, co-immunoprecipitation, and co-purification through a gradient or chromatographic column. Furthermore, protein-protein interactions are described in Fields and co-workers [Fiels and Song, as disclosed in Chevray and Nathans [Proc. Natl. Acad. Sci. USA 89, 5789-5793 (1991)]. Nature (London) 340, 245-246 (1989); Chien et al., Proc. Natl. Acad. Sci. USA 88, 9578-9582 (1991)]. Can do. Many transcriptional activators such as yeast GAL4 consist of two physically distinct modular domains, one that acts as a DNA binding domain and the other that functions as a transcriptional activation domain. The yeast expression system described in the previous literature (commonly referred to as the “2-hybrid system”) takes advantage of this property, as well as using two hybrid proteins, while the target protein is the DNA binding domain of GAL4. On the other hand, a candidate activation protein is fused to the activation domain. Expression of the GAL1-lacZ reporter gene under the control of a GAL4-activated promoter depends on reconstitution of GAL4 activity through protein-protein interactions. Colonies containing interacting polypeptides are detected with a chromogenic substance for β-galactosidase. A complete kit (MATCHMAKER®) for identifying protein-protein interactions between two specific proteins using the two-hybrid technology is commercially available from Clontech. This system can also be extended to the mapping of protein domains involved in specific protein interactions as well as the identification of amino acid residues important for these interactions.

  Compounds that inhibit the interaction of the gene encoding the PRO polypeptide identified herein with intracellular or extracellular components can be tested as follows: Usually, the reaction mixture is the gene product and extracellular or intracellular. The ingredients are prepared to include conditions and over time that allow the interaction and binding of these two products. In order to test the ability of a candidate compound to inhibit binding, the reaction is performed in the absence and presence of the test compound. In addition, a placebo may be added to the third reaction mixture to provide a positive control. The binding (complex formation) between the test compound and the intracellular or extracellular component present in the mixture is monitored as described above. Formation of the complex in the control reaction, but not the reaction mixture containing the test compound, indicates that the test compound inhibits the interaction between the test compound and its binding partner.

  To assay for an antagonist, a PRO polypeptide may be added to a cell along with a compound that is screened for a particular activity, and the ability of a compound to inhibit a subject activity in the presence of the PRO polypeptide is determined by the compound's ability to produce the PRO polypeptide. It is shown that it is an antagonist. Alternatively, antagonists may be detected by binding a potential antagonist having a PRO polypeptide and a membrane-bound PRO polypeptide receptor or recombinant receptor under conditions suitable for competitive inhibition assays. PRO polypeptides can be labeled, such as by radioactivity, and the number of PRO polypeptides bound to the receptor can be used to determine the effectiveness of a potential antagonist. The gene encoding the receptor can be identified by a number of methods known to those skilled in the art, such as ligand panning and FACS sorting. Coligan et al., Current Protocols in Immun., 1 (2): Chapter 5 (1991). Preferably, expression cloning is used, polyadenylated RNA is prepared from cells reactive to the PRO polypeptide, cDNA libraries generated from this RNA are distributed into pools, COS cells or other non-PRO polypeptide reactive Used for transfection of cells. Transfected cells that are grown on glass slides are exposed with labeled PRO polypeptide. The PRO polypeptide can be labeled by a variety of means including iodination or inclusion of a recognition site for a site-specific protein kinase. After fixation and incubation, the slides are subjected to autoradiographic analysis. Positive pools are identified, and subpools are prepared and re-transfected using an interactive subpooling and rescreening process, ultimately generating a single clone encoding the putative receptor.

As an alternative method of receptor identification, the labeled PRO polypeptide can be photoaffinity bound to a cell membrane or extract preparation that expresses the receptor molecule. The cross-linked material is dissolved by PAGE and exposed to X-ray film. The labeled complex containing the receptor can be excited, broken down into peptide fragments, and subjected to protein microsequencing. The amino acid sequence obtained from microsequencing is used in the design of a set of degenerate oligonucleotide probes that screen cDNA libraries that identify genes encoding putative receptors.
In other assays for antagonists, mammalian cells or membrane preparations expressing the receptor are incubated with labeled PRO polypeptide in the presence of the candidate compound. The ability of the compound to promote or block this interaction is then measured.
More specific examples of potential antagonists include oligonucleotides that bind to fusions of immunoglobulins and PRO polypeptides, particularly but not limited to polypeptide- and monoclonal antibodies and antibody fragments, single chain antibodies, anti-chains, It includes idiotype antibodies, and chimeric or humanized forms of these antibodies or fragments, as well as antibodies, including human antibodies and antibody fragments. Alternatively, a potential antagonist may be a closely related protein, eg, a variant form of a PRO polypeptide that recognizes but does not have an effect on the receptor and thus competitively inhibits the action of the PRO polypeptide.

  Other potential PRO polypeptide antagonists are antisense RNA or DNA constructs prepared using antisense technology, for example, antisense RNA or DNA hybridizes to target mRNA and interferes with protein translation It acts to directly block the translation of mRNA. Antisense technology can be used to control gene expression through triple helix formation or antisense DNA or RNA, both of which are based on the binding of polypeptide nucleotides to DNA or RNA. For example, the 5 'coding portion of the polypeptide nucleotide sequence encoding the mature PRO polypeptide herein is used in the design of antisense RNA oligonucleotides of about 10 to 40 base pairs in length. DNA oligonucleotides are designed to be complementary to regions of the gene involved in transcription (Triple Helix-Lee et al., Nucl, Acid Res., 6: 3073 (1979); Cooney et al., Science, 241: 456 (1988); Dervan et al., Science, 251: 1360 (1991)), thereby preventing transcription and production of PRO polypeptides. Antisense RNA oligonucleotides hybridize to mRNA in vivo to block translation of mRNA molecules into PRO polypeptides (Antisense-Okano, Neurochem., 56: 560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression ( SRS Press: Boca Raton, FL, 1988)). The oligonucleotides described above can also be transported into cells to express antisense RNA or DNA in vivo to inhibit PRO polypeptide production. When antisense DNA is used, oligodeoxyribonucleotides derived from the translation initiation site, eg, between the −10 and +10 positions of the target gene nucleotide sequence, are preferred.

Potential antagonists include small molecules that bind to the active site, receptor binding site, or growth factor or other relevant binding site of a PRO polypeptide, thereby blocking the normal biological activity of the PRO polypeptide. Examples of small molecules include, but are not limited to, small peptides or peptide-like molecules, preferably soluble peptides, and synthetic non-peptide organic or inorganic compounds.
Ribozymes are enzymatic RNA molecules that can catalyze the specific cleavage of RNA. Ribozymes act by sequence-specific hybridization to complementary target RNA, followed by nucleotide strand breaks. Specific ribozyme cleavage sites within a potential RNA target can be identified by known techniques. For further details see, for example, Rossi, Current Biology 4: 469-471 (1994) and PCT Publication No. WO 97/33551 (published 18 September 1997).

Nucleic acid molecules in triple helix formation used for transcription inhibition are single-stranded and composed of deoxynucleotides. The basic composition of these oligonucleotides is designed to promote triple helix formation via Hoogstin base pairing rules, which generally requires a resizable extension of purine or pyrimidine on one strand of the duplex . For further details see, for example, PCT Publication No. WO 97/33551, supra.
These small molecules can be identified by any one or more of the screening assays discussed above and / or by any other screening technique well known to those skilled in the art.
Also, the diagnostic and therapeutic uses of the molecules disclosed herein are based on the positive function assay hits disclosed and described below.

F. Anti-PRO Antibody The present invention further provides an anti-PRO antibody. Examples of antibodies include polyclonal, monoclonal, humanized, bispecific and heteroconjugate antibodies.

1. Polyclonal antibodies Anti-PRO antibodies include polyclonal antibodies. Methods for preparing polyclonal antibodies are known to those skilled in the art. Polyclonal antibodies in mammals can be generated by one or more injections of, for example, an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and / or adjuvant is injected into the mammal by multiple subcutaneous or intraperitoneal injections. The immunizing agent can comprise a PRO polypeptide or a fusion protein thereof. It is useful to conjugate the immunizing agent to a protein that is known to be immunogenic in the immunized mammal. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. Examples of adjuvants that can be used include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl lipid A, synthetic trehalose dicorynomycolate). The immunization protocol will be selected by one skilled in the art without undue experimentation.

2. Monoclonal antibody Alternatively, the anti-PRO antibody may be a monoclonal antibody. Monoclonal antibodies can be prepared using the hybridoma method as described in Kohler and Milstein, Nature, 256: 495 (1975). In hybridoma methods, mice, hamsters or other suitable host animals are typically immunized with an immunizing agent to generate antibodies that specifically bind to the immunizing agent or to induce lymphocytes that can be generated. . Alternatively, lymphocytes can be immunized in vitro.

  The immunizing agent typically comprises a subject PRO polypeptide or a fusion protein thereof. In general, peripheral blood lymphocytes ("PBLs") are used when human-derived cells are desired, or spleen cells or lymph node cells are used when non-human mammalian sources are desired. Subsequently, lymphocytes are fused with immortalized cell lines using an appropriate fusion agent such as polyethylene glycol to form hybridoma cells [Goding, Monoclonal Antibodies: Principles and Practice, Academic Press, (1986) pp. 59- 103]. Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells from rodents, cows and humans. Usually, rat or mouse myeloma cell lines are used. The hybridoma cells are preferably cultured in a suitable medium containing one or more substances that inhibit the survival or growth of unfused, immortalized cells. For example, if the parent cell lacks the enzyme hypoxanthine guanine phosphoribosyltransferase (HGPRT or HPRT), the hybridoma's medium typically contains hypoxatin, aminopetitin and thymidine (“HAT medium”). This substance prevents the growth of HGPRT-deficient cells.

Preferred immortalized cell lines are those that fuse efficiently, support stable high levels of antibody expression by selected antibody-producing cells, and are sensitive to a medium such as HAT medium. A more preferred immortalized cell line is the mouse myeloma line, which is available, for example, from the Salk Institute Cell Distribution Center in San Diego, California and the American Type Culture Collection in Rockville, Maryland. Human myeloma and mouse-human heteromyeloma cell lines for generating human monoclonal antibodies have also been disclosed [Kozbor, J. Immunol., 133: 3001 (1984), Brodeur et al., Monoclonal Antibody Production Techniques and Applications. , Marcel Dekker, Inc., New York, (1987) pp. 51-63].
The culture medium in which the hybridoma cells are cultured is then assayed for the presence of monoclonal antibodies against PRO. Preferably, the binding specificity of monoclonal antibodies produced by hybridoma cells is measured by immunoprecipitation or in vitro binding assays such as radioimmunoassay (RIA) or enzyme-linked immunoassay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can be measured, for example, by the Scatchard analysis method by Munson and Pollard, Anal. Biochem., 107: 220 (1980).

After the desired hybridoma cells are identified, clones can be subcloned by limiting dilution and grown by standard methods [Goding, supra]. Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle Medium and RPMI-1640 medium. Alternatively, the hybridoma cells can be grown as ascites in vivo in a mammal.
Monoclonal antibodies secreted by the subclone can be isolated from the culture medium or ascites fluid by conventional immunoglobulin purification methods such as protein A-Sepharose method, hydroxylapatite chromatography method, gel electrophoresis method, dialysis method or affinity chromatography. Separated or purified.

  Monoclonal antibodies can also be made by recombinant DNA methods, such as those described in US Pat. No. 4,816,567. The DNA encoding the monoclonal antibody of the present invention can be easily obtained using a conventional method (for example, using an oligonucleotide probe capable of specifically binding to the gene encoding the heavy and light chains of the mouse antibody). Can be isolated and sequenced. The hybridoma cells of the present invention are a preferred source of such DNA. Once isolated, the DNA can be placed into an expression vector that is transfected into a host cell, such as a monkey COS cell, a Chinese hamster ovary (CHO) cell, or a myeloma cell that does not produce immunoglobulin protein. The monoclonal antibody can be synthesized in a recombinant host cell. Alternatively, the DNA may be substituted, for example, by replacing the coding sequences of human heavy and light chain constant domains in place of homologous mouse sequences [US Pat. No. 4,816,567; Morrison et al., Supra], or immunoglobulin coding. The sequence can be modified by covalently linking part or all of the coding sequence of the non-immunoglobulin polypeptide. Such non-immunoglobulin polypeptides can be substituted for the constant domains of the antibodies of the invention, or can be substituted for the variable domains of one antigen binding site of the antibodies of the invention, producing chimeric bivalent antibodies.

The antibody may be a monovalent antibody. Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chains and modified heavy chains. The heavy chain is generally cleaved at any point in the Fc region so as to prevent heavy chain crosslinking. Alternatively, the relevant cysteine residues are substituted or deleted with other amino acid residues to prevent crosslinking.
In vitro methods are also suitable for preparing monovalent antibodies. Generation of fragments, particularly Fab fragments, by antibody digestion can be accomplished using conventional techniques known in the art.

3. Human and humanized antibodies The anti-PRO antibodies of the present invention further include humanized antibodies or human antibodies. Humanized forms of non-human (eg mouse) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (eg Fv, Fab, Fab ′, F (ab ′) ₂ or other antigen binding subsequences of antibodies). And contains the minimum sequence derived from non-human immunoglobulin. A humanized antibody is a CDR residue of a non-human species (donor antibody) in which the complementarity determining region (CDR) of the recipient has the desired specificity, affinity and ability, such as mouse, rat or rabbit. Human immunoglobulin (recipient antibody) substituted by In some examples, human immunoglobulin Fv framework residues are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, a humanized antibody has at least one, typically all or almost all CDR regions corresponding to those of non-human immunoglobulin and all or almost all FR regions of human immunoglobulin consensus sequences, typically Contains substantially all of the two variable domains. Humanized antibodies optimally comprise an immunoglobulin constant region (Fc), typically at least a portion of a human immunoglobulin constant region [Jones et al., Nature, 321: 522-525 (1986); Riechmann et al., Nature, 332: 323-329 (1988); and Presta, Curr. Op Struct. Biol., 2: 593-596 (1992)].

  Methods for humanizing non-human antibodies are well known in the art. Generally, one or more amino acid residues derived from non-human are introduced into a humanized antibody. These non-human amino acid residues are often referred to as “import” residues, which are typically taken from an “import” variable domain. Humanization basically involves the replacement of the relevant sequence of a human antibody with a rodent CDR or CDR sequence by Winter and co-workers [Jones et al., Nature, 321: 522-525 (1986); Riechmann Et al., Nature, 332: 323-327 (1988); Verhoeyen et al., Science, 239: 1534-1536 (1988)] by replacing the rodent CDR or CDR sequence with the corresponding sequence of a human antibody. To be implemented. Thus, such “humanized” antibodies are chimeric antibodies (US Pat. No. 4,816,567) wherein substantially less than an intact human variable domain has been substituted with the corresponding sequence from a non-human species. is there. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.

  Human antibodies also include phage display libraries [Hoogenboom and Winter, J. Mol. Biol., 227: 381 (1991); Marks et al., J. Mol. Biol., 222: 581 (1991)]. It can also be created using various known methods. The methods of Cole et al. And Boerner et al. Can also be used to prepare human monoclonal antibodies [Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss. P. 77 (1985) and Boerner et al., J. Immunol. , 147 (1): 86-95 (1991)]. Similarly, human antibodies can be produced by introducing human immunoglobulin loci into transgenic animals, eg, mice in which endogenous immunoglobulin genes have been partially or completely inactivated. Upon administration, human antibody production is observed that is very similar to that found in humans in all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; No. 5,661,016 and the following scientific literature: Marks et al., Bio / Technology 10, 779-783 (1992); Lonberg et al., Nature 368 856-859 (1994); Morrison, Nature 368, 812- 13 (1994); Fishwild et al., Nature Biotechnology 14, 845-51 (1996); Neuberger, Nature Biotechnology 14, 826 (1996); Lonberg and Huszar, Intern. Rev. Immunol. 13 65-93 (1995). ing.

  The antibody is also affinity matured using known selection and / or mutagenesis methods as described above. Preferred affinity matured antibodies are 5 times, more preferably 10 times, even more preferably 20 or 30 times higher than the starting antibody from which the mature antibody is prepared (generally mouse, humanized or human) Has affinity.

4). Bispecific antibodies Bispecific antibodies are monoclonal antibodies, preferably human or humanized antibodies, that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for PRO and the other is for any other antigen, preferably a cell surface protein or receptor or receptor subunit.
Methods for making bispecific antibodies are well known in the art. Traditionally, recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy / light chain pairs with different specificities of the two heavy chains [Milstein and Cuello, Nature, 305: 537-539 (1983)]. Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of 10 different antibody molecules, only one of which has the correct bispecific structure. Purification of the correct molecule is usually achieved by an affinity chromatography step. Similar procedures are disclosed in WO 93/08829 published May 13, 1993 and Traunecker et al., EMBO J., 10: 3655-3659 (1991).

Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. Desirably, at least one fusion has a first heavy chain constant region (CH1) containing the site necessary for light chain binding. The DNA encoding the immunoglobulin heavy chain fusion and, if desired, the immunoglobulin light chain are inserted into separate expression vectors and cotransfected into a suitable host organism. For further details of generating bispecific antibodies see, for example, Suresh et al., Methods in Enzymology, 121: 210 (1986).
According to another method described in WO 96/27011, the interface between a pair of antibody molecules can be manipulated to maximize the proportion of heterodimers recovered from recombinant cell culture. A suitable interface includes at least a portion of the CH3 region of an antibody constant domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (eg tyrosine or tryptophan). A complementary “cavity” of the same or similar size as the large side chain is created at the interface of the second antibody molecule by replacing the large amino acid side chain with a small one (eg, alanine or threonine). This provides a mechanism to increase the yield of heterodimers over other unwanted end products such as homodimers.

Bispecific antibodies can be prepared as full length antibodies or antibody fragments (eg F (ab ′) ₂ bispecific antibodies). Techniques for producing bispecific antibodies from antibody fragments have also been described in the literature. For example, bispecific antibodies can be prepared using chemical linkage. Brennan et al., Science, 229: 81 (1985) describes a procedure in which intact antibodies are proteolytically cleaved to produce F (ab ′) ₂ fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The produced Fab ′ fragment is then converted to a thionitrobenzoate (TNB) derivative. One of the Fab′-TNB derivatives is then reconverted to Fab′-thiol by reduction with mercaptoethylamine and mixed with an equimolar amount of other Fab′-TNB derivatives to form bispecific antibodies. The produced bispecific antibody can be used as a drug for selective immobilization of an enzyme.
Fab ′ fragments can be recovered directly from E. coli, which can be chemically coupled to form bispecific antibodies. Shalaby et al., J. Exp. Med., 175: 217-225 (1992) describes the production of _two fully humanized bispecific antibody F (ab ') molecules. Each Fab ′ fragment is secreted separately from E. coli and undergoes directed chemical coupling in vitro to form bispecific antibodies. The bispecific antibody thus formed is capable of binding to normal human T cells and cells overexpressing ErbB2 receptor, and induces cytolytic activity of human cytotoxic lymphocytes against human breast tumor targets. Become.

Various methods for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al., J. Immunol. 148 (5): 1547-1553 (1992). Leucine zipper peptides from Fos and Jun proteins are linked to the Fab ′ portions of two different antibodies by gene fusion. Antibody homodimers are reduced at the hinge region to form monomers and then reoxidized to form antibody heterodimers. This method can also be used for the production of antibody homodimers. The “diabody” technique described by Hollinger et al., Proc. Natl. Acad. Sci. USA, 90: 6444-6448 (1993) provided an alternative mechanism for generating bispecific antibody fragments. A fragment consists of a heavy chain variable domain (V _H ) linked to a light chain variable domain (V _L ) by a linker that is short enough to allow pairing between two domains on the same chain. Thus, the V _H and V _L domains of one fragment are forced to pair with the complementary V _L and V _H domains of another fragment to form two antigen binding sites. Other strategies for producing bispecific antibody fragments by use of single chain Fv (sFv) dimers have also been reported. See Gruber et al., J. Immunol. 152: 5368 (1994).
More than bivalent antibodies are also contemplated. For example, trispecific antibodies can be prepared. Tutt et al. J. Immunol. 147: 60 (1991).

  Exemplary bispecific antibodies can bind to two different epitopes of the PRO polypeptide provided herein. Alternatively, the arm of the anti-PRO polypeptide may be a trigger molecule on leukocytes such as a T cell receptor molecule (eg, CD2, CD3, CD28, or B7) or the like, so as to focus the cytoprotective mechanism on specific PRO polypeptide expressing cells It can bind to an arm that binds to an Fc receptor for IgG (FcγR) such as FcγRI (CD64), FcγRII (CD32) and FcγRIII (CD16). Bispecific antibodies can also be used to localize cytotoxic drugs to cells expressing a particular PRO polypeptide. These antibodies have a PRO binding arm and an arm that binds to a cytotoxic or radiochelating agent such as EOTUBE, DPTA, DOTA, or TETA. Other bispecific antibodies of interest bind to the PRO polypeptide and further bind to tissue factor (TF).

5. Heteroconjugate antibodies Heteroconjugate antibodies are also within the scope of the present invention. Heteroconjugate antibodies consist of two covalently bound antibodies. Such antibodies are used, for example, to target immune system cells to unwanted cells [US Pat. No. 4,676,980] and for the treatment of HIV infection [WO91 / 00360; WO92 / 003733; EP03089 ]Proposed. This antibody could be prepared in vitro using known methods in synthetic protein chemistry, including those related to crosslinkers. For example, immunotoxins can be made using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in US Pat. No. 4,676,980.

6). Processing of Effector Function It is desirable to modify the antibody of the present invention with respect to the effector function, for example to improve the effectiveness of the antibody in treating cancer. For example, a cysteine residue may be introduced into the Fc region, thereby forming an interchain disulfide bond in this region. Allogeneic dimeric antibodies so produced may have improved internalization capability and / or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp. Med. 176: 1191-1195 (1992) and Shopes, BJ Immunol. 148: 2918-2922 (1992). In addition, homodimeric antibodies with improved antitumor activity can be prepared using heterobifunctional cross-linking as described in Wolff et al., Cancer research 53: 2560-2565 (1993). Alternatively, the antibody can be engineered to have two Fc regions, thereby improving complement lysis and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design 3: 219-230 (1989).

7). Immunoconjugates The invention also relates to chemotherapeutic agents, cytotoxic agents such as toxins (eg, enzymatically active toxins from bacteria, fungi, plants or animals, or fragments thereof), or radioisotopes (ie, radioconjugates). And an immune complex comprising an antibody conjugated with.
Chemotherapeutic agents useful for the generation of such immune complexes have been described above. Enzyme-active toxins and fragments thereof that can be used include diphtheria A chain, non-binding active fragment of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A Chain, alpha-sarcin, Aleurites fordii protein, dianthin protein, Phytolaca americana protein (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, Curcin, crotin, sapaonaria oficinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin and trichothecene ( tricothecene). A variety of radioactive nucleotides are available for the production of radioconjugated antibodies. Examples include ²¹² Bi, ¹³¹ I, ¹³¹ In, ⁹⁰ Y, and ¹⁸⁶ Re.

The conjugates of antibodies and cytotoxic agents can be used for various bifunctional protein coupling agents such as N-succinimidyl-3- (2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), imidoester bifunctionality. Derivatives (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azide compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium Using derivatives (such as bis- (p-diazoniumbenzoyl) -ethylenediamine), diisocyanates (such as triene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene) Can be created. For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science 238: 1098 (1987). Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylenetriaminepentaacetic acid (MX-DTPA) is an example of a chelating agent for conjugation of radionucleotide to an antibody. See WO94 / 11026.
In other embodiments, the antibody may be conjugated to a “receptor” (such as streptavidin) for use in tumor pre-targeting, and the antibody-receptor complex is administered to the patient, followed by a clarifier. Used to remove unbound complexes from the circulation, followed by administration of a “ligand” (eg, avidin) conjugated to a cytotoxic agent (eg, a radionucleotide, etc.).

8). Immunoliposomes The antibodies disclosed herein may also be prepared as immunoliposomes. Liposomes containing antibodies are described in Epstein et al., Proc. Natl. Acad. Sci. USA, 82: 3688 (1985); Hwang et al., Proc. Natl. Acad. Sci. USA, 77: 4030 (1980); Prepared by methods known in the art, such as described in US Pat. Nos. 4,485,045 and 4,544,545. Liposomes with improved circulation time are disclosed in US Pat. No. 5,013,556.
Particularly useful liposomes are generated by the reverse phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol and PEG-derivatized phosphatidylethanolamine (PEG-PE). Liposomes are extruded through a filter of a predetermined size to produce liposomes having a desired diameter. Fab ′ fragments of antibodies of the invention can be conjugated to liposomes via a disulfide exchange reaction as described in Martin et al., J. Biol. Chem. 257: 286-288 (1982). A chemotherapeutic agent (such as doxorubicin) is optionally contained within the liposome. See Gabizon et al., J. National Cancer Inst. 81 (19) 1484 (1989).

9. Antibody Pharmaceutical Compositions Antibodies that specifically bind to the PRO polypeptides identified herein, as well as other molecules identified by the screening assays disclosed above, may be used in pharmaceutical compositions for the treatment of various diseases. It can be administered in the form.
When the PRO polypeptide is intracellular and the whole antibody is used as an inhibitor, an uptake antibody is preferred. However, lipofection or liposomes can also be used to introduce antibodies, or antibody fragments, into cells. Where antibody fragments are used, the smallest inhibitory fragment that specifically binds to the binding domain of the target protein is preferred. For example, peptide molecules that retain the ability to bind to a target protein sequence can be designed based on the variable region sequence of the antibody. Such peptides can be synthesized chemically or can be produced by recombinant DNA techniques. See, for example, Marasco et al., Proc. Natl. Acad. Sci. USA 90, 7889-7893 (1993). The formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other. Alternatively or in addition, the composition may comprise a cytotoxic agent, cytokine or growth inhibitor. These molecules are suitably present in combination in amounts that are effective for the purpose intended.

The active ingredients can also be used in colloidal drug delivery systems (eg, in microcapsules prepared by coacervation techniques or by interfacial polymerization, eg, hydroxymethylcellulose or gelatin-microcapsules and poly (methyl methacrylate) microcapsules, respectively. , Liposomes, albumin globules, microemulsions, nanoparticles and nanocapsules) or microemulsions. These techniques are disclosed in Remington's Pharmaceutical Science, supra.
The formulation used for in vivo administration must be sterile. This is easily accomplished by filtration through sterile filtration membranes.
Sustained release formulations may be prepared. Suitable examples of sustained release formulations include a semi-permeable matrix of solid hydrophobic polymer containing antibodies, which matrix is in the form of a molded article, such as a film or microcapsule. Examples of sustained release matrices are polyester hydrogels (eg poly (2-hydroxyethyl-methacrylate) or poly (vinyl alcohol)), polyactides (US Pat. No. 3,773,919), L-glutamic acid and γ-ethyl. Degradable lactic acid-glycolic acid copolymers such as L-glutamate, non-degradable ethylene-vinyl acetate, LUPRON DEPOT (trade name) (injectable globules of lactic acid-glycolic acid copolymer and leuprolide acetate), poly- (D) Contains -3-hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid can release molecules for over 100 days, certain hydrogels release proteins in a shorter time. When encapsulated antibodies remain in the body for a long time, they denature or aggregate upon exposure to moisture at 37 ° C, resulting in reduced biological activity and possible changes in immunogenicity. . Reasonable methods can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is found to be intermolecular S—S bond formation through thio-disulfide exchange, stabilization may include modification of sulfhydryl residues, lyophilization from acidic solutions, control of water content, appropriate Addition of various additives and the development of specific polymer matrix compositions.

G. Use of anti-PRO antibody The anti-PRO antibody of the present invention has various utilities. For example, anti-PRO antibodies are used in PRO diagnostic assays, such as detecting its expression in specific cells, tissues, or serum. Competitive binding assays, direct or indirect sandwich assays, and immunoprecipitation assays performed in heterogeneous or homogeneous phases [Zola, Monoclonal Antibodies: A Manual of Techniques, CRC Press, Inc. (1987) pp. 147-158] Various diagnostic assay techniques known in the art are used. Antibodies used in diagnostic assays are labeled with a detectable moiety. The detectable site must generate a detectable signal, either directly or indirectly. For example, the detectable site may be a radioisotope such as ³ H, ¹⁴ C, ³² P, ³⁵ S or ¹²⁵ I, a fluorescent or chemiluminescent compound such as fluorescein isothiocyanate, rhodamine or luciferin, or alkaline phosphatase, beta-galactosidase Or it may be an enzyme such as horseradish peroxidase. Any method known in the art can be used to conjugate the detectable site to the antibody, including Hunter et al., Nature 144: 945 (1962); David et al., Biochemistry, 13: 1014 (1974); Et al., J. Immunol. Meth., 40: 219 (1981); and Nygren, J. Histochem. And Cytochem., 30: 407 (1982).

Anti-PRO antibodies are also useful for affinity purification of PRO from recombinant cell culture or natural sources. In this method, the antibody against PRO is immobilized on a suitable support such as Sephadex resin or filter paper using methods well known in the art. The immobilized antibody is then contacted with a sample containing PRO to purify, and the support is then washed with a suitable solvent that removes substantially all of the material in the sample other than PRO bound to the immobilized antibody. Wash. Finally, the support is washed with another suitable solvent that will release PRO from the antibody.
The following examples are provided for purposes of illustration only and are not intended to limit the scope of the invention in any way.
All patents and references cited herein are hereby incorporated by reference in their entirety.

(Example)
All commercially available reagents referred to in the examples were used according to manufacturer's instructions unless otherwise indicated. The source of cells identified by the ATCC registration number throughout the following examples and specification is American Type Culture Collection, Manassas, Virginia.

Example 1: Extracellular domain homology screening to identify novel polypeptides and cDNAs encoding them
Extracellular domain (ECD) sequences from about 950 known secreted proteins from the Swiss-Prot public database (including secreted signal sequences, if necessary) were used to search the EST database. EST databases include public databases (eg, Dayhoff, GenBank) and proprietary databases (eg, LIFESEQ (trade name), Incyte Pharmaceuticals, Palo Alto, CA). The search was performed using the computer program BLAST or BLAST-2 (Altschul et al., Methods in Enzymology 266: 460-480 (1996)) as a comparison of the ECD protein sequence with a 6-frame translation of the EST sequence. Comparisons that do not encode known proteins and have a Blast score of 70 (possibly 90) or higher can be grouped with the program “phrap” (Phil Green, University of Washington, Seattle, WA) and consensus DNA sequences Built in.
Using this extracellular domain homology screen, consensus DNA sequences were constructed against other identified EST sequences using phrap. Furthermore, the resulting consensus DNA sequence is often extended using repeated cycles of BLAST or BLAST-2 and phrap (if not all) and the consensus sequence is as long as possible using the sources of EST sequences discussed above. Elongated.

Based on the consensus sequence obtained as described above, oligonucleotides are then synthesized, to identify a cDNA library containing the sequence of interest by PCR, and to isolate a clone of the full-length coding sequence of the PRO polypeptide. Used for use as a probe. Forward and reverse PCR primers generally range from 20 to 30 nucleotides and are often designed to give PCR products that are about 100-1000 bp long. The probe sequence is typically 40-55 bp long. In some cases, additional oligonucleotides are synthesized when the consensus sequence is greater than about 1-1.5 kbp. To screen several libraries for full-length clones, DNA from the libraries was screened by PCR with PCR primer pairs as in Ausubel et al., Current Protocols in Molecular Biology. The positive library was then used to isolate clones encoding the gene of interest using one of the probe oligonucleotides and primer pairs.
The cDNA library used for the isolation of cDNA clones was prepared by standard methods using commercially available reagents such as Invitrogen, San Diego, CA. The cDNA is primed with oligo dT with a NotI site, ligated to a SalI hemikinase adapter with blunt ends, cleaved with NotI, classified into the appropriate size by gel electrophoresis, and a suitable cloning vector (such as pRKB or pRKD). PRK5B is a precursor of pRK5D that does not contain an SfiI site; see Holmes et al., Science, 253: 1278-1280 (1991)) and cloned in the defined orientation at the unique XhoI and NotI sites.

Example 2: Isolation of cDNA clones by amylase screening Preparation of oligo dT prime cDNA library
MRNA was isolated from human tissues of interest using reagents and protocols from Invitrogen, San Diego, CA (Fast Track 2). This RNA was used to generate an oligo dT primed cDNA library with the vector pRK5D using the reagents and protocol of Life Technologies, Gaithersburg, MD (Super Script Plasmid system). In this method, double-stranded cDNA was classified into a size exceeding 1000 bp, and SalI / NotI-linked cDNA was cloned into an XhoI / NotI-cut vector. pRK5D is a cloning vector with an sp6 transcription start site followed by a SfiI restriction enzyme site located in front of the XhiI / NotI cDNA cloning site.

2. Preparation of Random Primed cDNA Library A secondary cDNA library was created to favorably express the 5 ′ end of the primary cDNA clone. Sp6RNA was generated from the primary library (above) and this RNA was then used to generate the vector pSST-AMY.com which utilizes reagents and protocols from Life Technologies (Super Script Plasmid system referenced above). Used to generate a random primed cDNA library at zero. In this method, double stranded cDNA was sized to 500-1000 bp, ligated to a NotI adapter with blunt ends, cut at the SfiI site, and cloned into the SfiI / NotI cut vector. pSST-AMY. 0 is a cloning vector which has a yeast alcohol dehydrogenase promoter before the cDNA cloning site and a mouse amylase sequence (a mature sequence without a secretion signal) followed by an alcohol dehydrogenase transcription termination region after the cloning site. Thus, cDNA cloned into this vector fused in frame with the amylase sequence leads to secretion of amylase from appropriately transfected yeast colonies.

3. Transformation and detection The DNA of the library described in paragraph 2 above was chilled on ice, to which electrocompetent DH10B bacteria (Life Technologies, 20 ml) were added. The bacteria and vector mixture was then electroporated as recommended by the manufacturer. SOC medium (Life Technologies, 1 ml) was then added and the mixture was incubated at 37 ° C. for 30 minutes. Transformants were then plated on 20 standard 150 mm LB plates containing ampicillin and incubated for 16 hours (37 ° C.). Positive colonies were scraped from the plate and DNA was isolated from the bacterial pellet using standard methods, such as a CsCl-gradient. The following yeast protocol was then applied to the purified DNA.
Yeast methods are divided into three categories: (1) transformation with yeast plasmid / cDNA binding vectors; (2) detection and isolation of yeast clones secreting amylase; and (3) direct from yeast colonies. PCR amplification of large inserts and purification of DNA for sequencing and further analysis.

The yeast strain used was HD56-5A (ATCC-90785). This strain has the following genotypes: MAT alpha, ura3-52, leu2-3, leu2-112, his3-11, his3-15, MAL ⁺ , SUC ⁺ , GAL ⁺ . Preferably, yeast mutants with incomplete post-translational pathways can be used. Such mutants have transpositional deficient alleles at sec71, sec72, and sec62, with truncated sec71 being most preferred. Alternatively, antagonists (including antisense nucleotides and / or ligands) that inhibit the normal manipulation of these genes, other proteins involved in this post-translational pathway (eg, SEC61p, SEC72p, SEC62p, SEC63p, TDJ1p, SSA1p − 4p) or complex formation of these proteins is also preferred and used in combination with amylase expressing yeast.
Transformation was performed based on the protocol outlined by Gietz et al., Nucl. Acid. Res., 20: 1425 (1992). The transformed cells were then seeded from agar into YEPD complex medium broth (100 ml) and grown overnight at 30 ° C. YEPD broth was prepared as described in Kaiser et al., Methods in Yeast Genetics, Cold Spring Harbor Press, Cold Spring Harbor, NY, p. 207 (1994). The overnight medium is then diluted to approximately 2 × 10 ⁶ cells / ml (approximately OD ₆₀₀ = 0.1) in fresh YEPD broth (500 ml) and 1 × 10 ⁷ cells / ml (approximately OD ₆₀₀ = 0.4−0.5). ).

The cells are then harvested, transferred to a GS3 rotor bottle in a Sorval GS3 rotor for 5 minutes at 5,000 rpm, the supernatant is discarded and then prepared for transformation by resuspension in sterile water and then 50 ml The Falcon tube was centrifuged again at 3,500 rpm in a Beckman GS-6KR centrifuge. The supernatant is discarded, and the cells are subsequently washed with LiAc / TE (10 ml, 10 mM Tris-HCl, 1 mM EDTA pH 7.5, 100 mM Li ₂ OOCCH ₃ ), and in LiAc / TE (2.5 ml). Resuspended.
Transformation is initiated by mixing the prepared cells (100 μl) with fresh denatured single-stranded salmon sperm DNA (Lofstrand Labs, Gaithersburg, MD) and transforming DNA (1 μg vol. <10 μl) in a microtube. did. The mixture was mixed briefly by vortexing, then 40% PEG / TE (600 μl, 40% polyethylene glycol-4000, 10 mM Tris-HCl, 1 mM EDTA, 100 mM LiOOCCH ₃ , pH 7.5) was added. The mixture was gently agitated and incubated at 30 ° C. with agitation for 30 minutes. The cells were then heat shocked at 42 ° C. for 15 minutes, the reaction vessel was centrifuged in a microtube at 12,000 rpm for 5-10 seconds, decanted and TE (500 μl, 10 mM Tris-HCl, 1 mM EDTA, Following resuspension to pH 7.5), it was centrifuged. The cells were then diluted in TE (1 ml) and aliquots (200 μl) were spread on selective media previously prepared in 150 mm growth plates (VWR).

Alternatively, instead of multiple small reactions, the amount of reagent was scaled up accordingly and transformation was performed in one large scale reaction.
The selection medium used was synthetic complete dextrose agar lacking uracil prepared as described in Kaiser et al., Methods in Yeast Genetics, Cold Spring Harbor Press, Cold Spring Harbor, NY, p. 208-210 (1994). SCD-Ura). Transformants were grown at 30 ° C. for 2-3 days.
Detection of colonies secreting amylase was performed by including red starch in the selective growth medium. Starch was coupled to a red dye (reactive Red-120, Sigma) according to the method described in Biely et al., Anal. Biochem., 172: 176-179 (1988). Bound starch was incorporated into SCD-Ura agar plates at a final concentration of 0.15% (w / v) and buffered to pH 7.0 with potassium phosphate (final concentration 50-100 mM).
In order to obtain a well-isolated and identifiable single colony, a positive colony was picked and streaked into fresh selection medium (150 mm plate). Detection of colonies that were positive for amylase secretion and well isolated were performed by direct incorporation of red starch into buffered SCD-Ura agar. Positive colonies were determined by their ability to form clear halos visible directly around positive colonies by degrading the colony starch.

4). Isolation of DNA by PCR amplification When a positive colony was isolated, a part thereof was picked with a toothpick and diluted with sterile water (30 μl) in a 96-well plate. At this point, positive colonies are either frozen and stored for subsequent analysis or are immediately amplified. An aliquot (5 μl) of cells was added to 0.5 μl Klentaq (Clontech, Palo Alto, Calif.); 4.0 μl 10 mM dNTP (Perkin Elmer-Cetus); 2.5 μl Kentaq buffer (Clontech); 0.25 μl positive Direction oligo 1; 0.25 μl reverse oligo 2; used as template for PCR reaction in 25 μl volume containing 12.5 μl distilled water.
The sequence of forward oligonucleotide 1 is:
5'-TGTAAAACGACGGCCAGTTAAATAGACCTGCAATTATTAATCT-3 '
(SEQ ID NO: 611)
The sequence of reverse oligonucleotide 2 is:
5'-CAGGAAACAGCTATGACCACCTGCACACCTGCAAATCCATT -3 '
(SEQ ID NO: 612)
Met.
PCR was then performed as follows:
a. Denaturation 92 ° C, 5 minutes b. Next 3 cycles Denaturation 92 ℃, 30 seconds
Annealing 59 ℃, 30 seconds
Elongation 72 ° C, 60 seconds c. Next 3 cycles Denaturation 92 ℃, 30 seconds
Annealing 57 ℃, 30 seconds
Elongation 72 ° C, 60 seconds d. Next 25 cycles Denaturation 92 ℃, 30 seconds
Annealing 55 ℃, 30 seconds
Elongation 72 ° C, 60 seconds e. Holding 4 ℃

Underlined regions anneal to the ADH promoter region and amylase region, respectively, and in the absence of insert, the vector pSST-AMY. Amplify the 0 307 bp region. Typically, the first 18 nucleotides at the 5 ′ end of these oligonucleotides contained the annealing site for the sequence primer. Therefore, the total product of the PCR reaction from the empty vector was 343 bp. However, the signal sequence fusion cDNA resulted in a fairly long nucleotide sequence.
Following PCR, an aliquot (5 μl) of the reaction is subjected to agarose gel electrophoresis using a Tris-borate-EDTA (TBE) buffer system in a 1% agarose gel as described in Sambrook et al., Supra. Considered by. Clones that produced a single strong PCR product greater than 400 bp were further analyzed by DNA sequence after purification on a 96 Qiaquick PCR clean column (Quagen Inc., Chatsworth, Calif.).

Example 3 Isolation of cDNA Clones Using Signal Algorithm Analysis Sequence discovery algorithms originally developed by Genentech, Inc. (South San Francisco, Calif.) Were developed using public (eg, GenBank) and / or individual (LIFESEQ® (Trademark), Incyte Pharmaceuticals, Inc., Palo Alto, Calif.), Various polypeptide-encoding nucleic acid sequences were identified by application to ESTs as well as those assembled and assembled from the database. This signal sequence algorithm calculates a secretion signal score based on the letters of the DNA nucleotide surrounding the first or second methionine codon (ATG) at the 5 ′ end of the sequence or sequence fragment under consideration. The nucleotide following the first ATG must encode at least 35 unambiguous amino acids without a stop codon. If the first ATG has an essential amino acid, the second is not considered. If none of the requirements is met, the candidate sequence is not scored. To determine whether an EST sequence contains a genuine signal sequence, the DNA surrounding the ATG codon and the corresponding amino acid sequence are one of seven sensors (evaluation parameters) known to be associated with the secretion signal. Scores were assigned using pairs. Using this algorithm, a number of polypeptide-encoding nucleic acid sequences have been identified.

Example 4: Isolation of cDNA clones encoding human PRO polypeptides Using the techniques described in Examples 1 to 3 above, as disclosed herein, a number of full-length cDNA clones were Identified as encoding a polypeptide. These cDNAs were deposited with the American Type Culture Collection, 10801 University Boulevard, Manassas, Virginia 20110-2209 USA (ATCC) according to the terms of the Budapest Treaty, as shown in Table 7 below.

Table 7
Material ATCC Deposit Number Deposit Date
DNA16422-1209 209929 June 2, 1998
DNA19902-1669 203454 November 3, 1998
DNA21624-1391 209917 Jun 2, 1998
DNA34387-1138 209260 September 16, 1997
DNA35880-1160 209379 Oct 16, 1997
DNA39984-1221 209435 November 7, 1997
DNA44189-1322 209699 March 26, 1998
DNA48303-2829 PTA-1342 Feb 8, 2000
DNA48320-1433 209904 May 27, 1998
DNA56049-2543 203662 9 February 1999
DNA57694-1341 203017 Jun 23, 1998
DNA59208-1373 209881 May 20, 1998
DNA59214-1449 203046 July 1, 1998
DNA59485-1336 203015 Jun 23, 1998
DNA64966-1575 203575 Jan 12, 1999
DNA 82403-2959 PTA-2317 1 August 2000
DNA83505-2606 PTA-132 May 25, 1999
DNA84927-2585 203865 March 23, 1999
DNA92264-2616 203969 Apr 27, 1999
DNA94713-2561 203835 March 9, 1999
DNA96869-2673 PTA-255 June 22, 1999
DNA96881-2699 PTA-553 August 17, 1999
DNA96889-2641 PTA-119 May 25, 1999
DNA96898-2640 PTA-122 May 25, 1999
DNA97003-2649 PTA-43 May 11, 1999
DNA98565-2701 PTA-481 August 3, 1999
DNA102846-2742 PTA-545 August 17, 1999
DNA102847-2726 PTA-517 Aug 10, 1999
DNA102880-2689 PTA-383 Jul 20, 1999
DNA105782-2683 PTA-387 20 July 1999
DNA108912-2680 PTA-124 May 25, 1999
DNA115253-2757 PTA-612 August 31, 1999
DNA119302-2737 PTA-520 Aug 10, 1999
DNA119536-2752 PTA-551 August 17, 1999
DNA119542-2754 PTA-619 August 31, 1999
DNA143498-2824 PTA-1263 February 2, 2000
DNA145583-2820 PTA-1179 Jan 11, 2000
DNA161000-2896 PTA-1731 Apr 18, 2000
DNA161005-2943 PTA-2243 June 27, 2000
DNA170245-3053 PTA-2952 Jan 23, 2001
DNA171771-2919 PTA-1902 May 23, 2000
DNA173157-2981 PTA-2388 August 8, 2000
DNA175734-2985 PTA-2455 September 12, 2000
DNA176108-3040 PTA-2824 December 19, 2000
DNA190710-3028 PTA-2822 December 19, 2000
DNA190803-3019 PTA-2785 12/12/2000
DNA191064-3069 PTA-3016 February 6, 2001
DNA194909-3013 PTA-2779 12/12/2000
DNA203532-3029 PTA-2823 December 19, 2000
DNA213858-3060 PTA-2958 Jan 23, 2001
DNA216676-3083 PTA-3157 March 6, 2001
DNA222653-3104 PTA-3330 April 24, 2001
DNA96897-2688 PTA-379 20 July 1999
DNA142917-3081 PTA-3155 March 6, 2001
DNA142930-2914 PTA-1901 May 23, 2000
DNA147253-2983 PTA-2405 22 August 2000
DNA149927-2887 PTA-1782 Apr 25, 2000

These deposits were made in accordance with the provisions of the Budapest Treaty and its regulations (Budapest Convention) on the international recognition of the deposit of microorganisms in the patent procedure. This assures that the viable culture of the deposit is maintained for 30 years from the date of deposit. Deposits may be obtained from the ATCC in accordance with the terms of the Budapest Treaty and in accordance with the agreement between Genentech and ATCC, regardless of which is the first issue of the relevant U.S. patent or any Ensures that the progeny of the deposited culture are made available permanently and unrestricted at the time of publication of the US or foreign patent application, and is subject to 35 USC 122 and the Patent Office Commissioner Regulation (specifically 37 CFR of reference number 886OG638). Guarantees that the offspring will be available to those who have been determined to have rights in accordance with (including Section 1.14).
The assignee of this application agrees that if the deposited culture dies or is lost or destroyed when cultured under appropriate conditions, the material will be immediately replaced with the same other upon notification. To do. The availability of deposited materials is not considered a license to practice the present invention in violation of rights granted under any governmental authority in accordance with patent law.

Example 5: Use of PRO as a hybridization probe The following method demonstrates the use of a nucleic acid sequence encoding PRO as a hybridization probe.
A DNA containing a full-length or mature PRO coding sequence disclosed herein is a probe for screening for homologous DNA (such as that encoding a naturally occurring variant of PRO) of a human tissue cDNA library or a human tissue genomic library. Used as
Hybridization and washing of the filter containing any library DNA is performed under the following high stringency conditions. Hybridization of the radiolabeled PRO induction probe to the filter was performed using 50% formamide, 5 × SSC, 0.1% SDS, 0.1% sodium pyrophosphate, 50 mM sodium phosphate, pH 6.8, 2 × denhardt solution, and 10% dextran. Carry out in a solution of sulfuric acid at 42 ° C. for 20 hours. Filter washing is performed at 42 ° C. in 0.1 × SSC and 0.1% aqueous SDS.
The DNA having the desired sequence identity with the DNA encoding the full length native sequence can then be identified using standard techniques known in the art.

Example 6: Expression of PRO in E. coli This example illustrates the preparation of a non-glycosylated form of PRO by recombinant expression in E. coli.
The DNA sequence encoding PRO is first amplified using selected PCR primers. This primer must contain a restriction enzyme site corresponding to the restriction enzyme site on the selected expression vector. A variety of expression vectors can be used. An example of a suitable vector is pBR322 (derived from E. coli; see Bolivar et al., Gene, 2:95 (1977)) containing genes for ampicillin and tetracycline resistance. The vector is digested with restriction enzymes and dephosphorylated. The PCR amplified sequence is then ligated to the vector. The vector preferably encodes an antibiotic resistance gene, a trp promoter, a polyHis leader (including the first six STII codons, a poly His sequence, and an enterokinase cleavage site), a PRO coding region, a lambda transcriptional concentrator and the argU gene. Contains an array.
This ligation mixture was then utilized to transform selected E. coli strains using the method described in Sambrook et al., Supra. Transformants are identified by their ability to grow on LB plates and then antibiotic resistant colonies are selected. Plasmid DNA can be isolated and confirmed by restriction analysis and DNA sequencing.
Selected clones can be grown overnight in liquid medium such as LB broth supplemented with antibiotics. This overnight culture may then be used to seed a larger scale culture. The cells are then grown to the desired optical density, during which the expression promoter begins to act.
After further culturing the cells for several hours, the cells can be collected by centrifugation. The cell pellet obtained by centrifugation can be solubilized using various agents known in the art, and then this lysed PRO protein is metal chelated under conditions that allow tight binding of the protein. It is possible to purify using a column.

PRO may be expressed in E. coli in poly-His tag form using the following procedure. DNA encoding PRO was first amplified using selected PCR primers. This primer provides a restriction enzyme site that corresponds to the restriction enzyme site of the selected expression vector, and efficient and reliable translation initiation, rapid purification on metal chelate columns, and proteolytic removal with enterokinase. Contains other useful sequences to give. The PCR amplified poly-His tag sequence was then ligated into an expression vector, which was used for transformation of an E. coli host based on strain 52 (W3110 fuhA (tonA) longalE rpoHts (htpRts) clpP (lacIq)). Transformants were first treated with 3-5 O.D. with shaking at 30 ° C in LB containing 50 mg / ml carbenicillin. D. Grow to 600. The culture was then added to CRAP medium (3.57 g (NH ₄ ) ₂ SO ₄ , 0.71 g sodium citrate · 2H ₂ O, 1.07 g KCl, 5.36 g Difco yeast extract, 5 in 500 mL water. Diluted 50-100 times in .36 g Sheffield hycase SF and 110 mM MPOS, pH 7.3, mixed with 0.55% (w / v) glucose and 7 mM MgSO ₄ ) at 30 ° C. Grow for about 20-30 hours by shaking. In order to confirm the expression by SDS-PAGE, a sample was taken out, and the bulk medium was centrifuged so that the cells became a pellet. The cell pellet was frozen until purification and refolding (refolding).
E. coli paste from 0.5-1 L fermentation (6-10 g pellet) was resuspended in 10 volumes (w / v) in 7 M guanidine, 20 mM Tris, pH 8 buffer. Solid sodium sulfate and sodium tetrathionate were added to final concentrations of 0.1 M and 0.02 M, respectively, and the solution was stirred at 4 ° C. overnight. This step results in a denatured protein in which all cysteine residues are blocked with sulfite. The solution was concentrated in a Beckman Ultracentifuge at 40,000 rpm for 30 minutes. The supernatant is diluted with 3-5 volumes of metal chelate column buffer (6M guanidine, 20 mM Tris, pH 7.4) and filtered through a 0.22 micron filter for clarity. The clear extract was loaded onto a 5 ml Qiagen Ni-NTA metal chelate column equilibrated with metal chelate column buffer. The column was washed with an addition buffer containing 50 mM imidazole (Calbiochem, Utrol grade), pH 7.4. The protein was eluted with a buffer containing 250 mM imidazole. Fractions containing the desired protein were pooled and stored at 4 ° C. The protein concentration was estimated by its absorption at 280 nm using the extinction coefficient calculated based on its amino acid sequence.

By gradually diluting the sample in freshly prepared regeneration buffer consisting of 20 mM Tris, pH 8.6, 0.3 M NaCl, 2.5 M urea, 5 mM cysteine, 20 mM glycine and 1 mM EDTA, The protein was regenerated. The refolding volume was selected so that the final protein concentration was 50-100 microgram / ml. The refolding solution was slowly stirred at 4 ° C. for 12-36 hours. The refolding reaction was stopped by adding TFA at a collection concentration of 0.4% (pH of about 3). Prior to further purification of the protein, the solution was filtered through a 0.22 micron filter and acetonitrile was added at a final concentration of 2-10%. The regenerated protein was chromatographed on a Poros R1 / H reverse phase column using a 0.1% TFA transfer buffer and elution with a 10-80% acetonitrile gradient. Aliquots of fractions with A280 absorption were analyzed on SDS polyacrylamide gels and fractions containing homologous regenerative proteins were pooled. In general, most correctly regenerated protein species are eluted at the lowest concentration of acetonitrile because these species are the most compact and their hydrophobic inner surface is shielded from interaction with the reverse phase resin. Aggregated species are usually eluted at higher acetonitrile concentrations. In addition to removing the incorrectly regenerated protein from the desired form, the reverse phase process also removes endotoxin from the sample.
Fractions containing the desired regenerated PRO polypeptide were pooled and the acetonitrile removed using a gentle stream of nitrogen directed at the solution. The protein was prepared to 20 mM Hepes, pH 6.8 containing 0.14 M sodium chloride and 4% mannitol by gel filtration and sterile filtration on G25 Superfine (Pharmacia) resin equilibrated with dialysis or preparation buffer.
Many of the PRO polypeptides disclosed herein were successfully expressed by the methods described above.

Example 7: Expression of PRO in mammalian cells This example illustrates the preparation of a potentially glycosylated form of PRO by recombinant expression in mammalian cells.
The vector pRK5 (see EP307,247 published on March 15, 1989) was used as an expression vector. In some cases, PRO DNA is bound to pRK5 with the selected restriction enzyme and PRO DNA is inserted using a ligation method such as that described in Sambrook et al. The resulting vector is called pRK5-PRO.

In one embodiment, the selected host cell can be a 293 cell. Human 293 cells (ATCC CCL 1573) were grown and confluent in tissue culture plates in media such as DMEM supplemented with fetal bovine serum and optionally nourishing ingredients and / or antibiotics. About 10 μg of pRK5-PRO DNA is mixed with about 1 μg of DNA encoding the VA RNA gene [Thimmappaya et al., Cell, 31: 543 (1982))] and 500 μl of 1 mM Tris-HCl, 0.1 mM EDTA, 0 .227M was dissolved in CaCl _2. To this mixture, drop-like 500 μl of 50 mM HEPES (pH 7.35), 280 mM NaCl, 1.5 mM NaPO ₄ was added, and a precipitate was formed at 25 ° C. for 10 minutes. The precipitate was suspended and added to 293 cells and allowed to settle for about 4 hours at 37 ° C. The medium was aspirated and 2 ml of 20% glycerol in PBS was added for 30 seconds. The 293 cells were then washed with serum free medium, fresh medium was added and the cells were incubated for about 5 days.

Approximately 24 hours after transfection, the medium was removed and replaced with medium (only) or medium containing 200 μCi / ml ³⁵ S-cysteine and 200 μCi / ml ³⁵ S-methionine. After 12 hours of incubation, the conditioned medium was collected, concentrated with a spin filter and added to a 15% SDS gel. The treated gel was dried and exposed to the film for a selected time revealing the presence of PRO polypeptide. The medium containing the transformed cells was further incubated (in serum-free medium) and the medium was tested with the selected bioassay.

In an alternative technique, PRO can be transiently introduced into 293 cells using the dextran sulfate method described in Somparyrac et al., Proc. Natl. Acad. Sci., 12: 7575 (1981). 293 cells are grown to maximum density in a spinner flask and 700 μg pRK5-PRO DNA is added. The cells were first concentrated from the spinner flask by centrifugation and washed with PBS. The DNA-dextran precipitate was incubated on the cell pellet for 4 hours. Cells were treated with 20% glycerol for 90 seconds, washed with tissue medium, and reintroduced into a spinner flask containing tissue medium, 5 μg / ml bovine insulin and 0.1 μg / ml bovine transferrin. After about 4 days, the conditioned medium was centrifuged and filtered to remove cells and cell debris. The sample containing the expressed PRO was then concentrated and purified by selected methods such as dialysis and / or column chromatography.
In other embodiments, PRO can be expressed in CHO cells. The pRK5-PRO can be transfected into CHO cells using known reagents such as CaPO ₄ or DEAE- dextran. As described above, the cell medium can be incubated and the medium can be replaced with culture medium (only) or medium containing a radioactive label such as ³⁵ S-methionine. After identifying the presence of the PRO polypeptide, the medium may be replaced with serum-free medium. Preferably, the medium is incubated for about 6 days and then the conditioned medium is collected. The medium containing the expressed PRO can then be concentrated and purified by any selected method.

In addition, the epitope tag PRO may be expressed in the host CHO cell. PRO may be subcloned from the pRK5 vector. The subclone insert can be PCR-fused into a frame with a selected epitope tag, such as a poly-his tag in a baculovirus expression vector. The poly-his tagged PRO insert can then be subcloned into an SV40 derived vector containing a selectable marker such as DHFR for selection of stable clones. Finally, CHO cells were transfected with the SV40 derived vector (as described above). To confirm expression, labeling may be performed as described above. The medium containing the expressed poly-his-tagged PRO can then be concentrated and purified by selected methods such as Ni ²⁺ -chelate affinity chromatography.
Moreover, PRO may be expressed in CHO and / or COS cells by a transient expression method, and in CHO cells by another stable expression method.
Stable expression in CHO cells is performed using the following method. Proteins may be IgG constructs (immunoadhesins) in which the coding sequence (eg, extracellular domain) of each protein's solubilized form is fused to a constant region sequence comprising the hinge, CH2, and CH2 domains of IgG1, and / or poly -Expressed as a His-tag form.

Following PCR amplification, the corresponding DNA is subcloned into a CHO expression vector using standard techniques such as those described in Ausubel et al., Current Protocols of Molecular Biology, Unit 3.16, John Wiley and Sons (1997). The CHO expression vector has restriction sites compatible with 5 ′ and 3 ′ of the DNA of interest, and is constructed so that the cDNA can be conveniently shuttled. The vectors used expression in CHO cells as described in Lucas et al., Nucl. Acids Res. 24: 9, 1774-1779 (1996), and used for expression of the cDNA of interest and dihydrofolate reductase (DHFR). The SV40 early promoter / enhancer is used for control. DHFR expression allows selection for stable maintenance of the plasmid following transfection.
Twelve micrograms of the desired plasmid DNA is introduced into about 10 million CHO cells of the commercially available transfection reagents Superfect® (Qiagen), Dosper® and Fugene® (Boehringer Mannheim). Cells are grown as described in Lucas et al. Above. Approximately 3 × 10 ⁷ cells are frozen in ampoules for further growth and production as described below.

An ampoule containing the plasmid DNA was placed in a water bath, thawed, and mixed by vortexing. The contents were pipetted into a centrifuge tube containing 10 mL of medium and centrifuged at 1000 rpm for 5 minutes. The supernatant is aspirated and the cells are suspended in 10 mL of selective medium (with 0.2 μm filtered PS20, 5% 0.2 μm diafiltered fetal calf serum). The cells are then divided into 100 mL spinners containing 90 mL selective medium. After 1-2 days, the cells are transferred to a 250 mL spinner filled with 150 mL selective growth medium and incubated at 37 ° C. After a further 2-3 days, 250 mL, 500 mL and 2000 mL spinners are seeded at 3 × 10 ⁵ cells / mL. The cell medium was replaced with fresh medium by centrifugation and resuspended in production medium. Any suitable CHO medium may be used, but in practice the production medium described in US Pat. No. 5,122,469 issued June 16, 1992 is used. A 3 L production spinner was seeded at 1.2 × 10 ⁶ cells / mL. On day 0, cell number and pH were measured. On the first day, the spinner was sampled and sprayed with filtered air. On the second day, sample the spinner, change the temperature to 33 ° C, 30 mL of 500 g / L glucose and 0.6 mL of 10% antifoam (eg 35% polydimethylsiloxane emulsion, Dow Corning 365 Medical Grade Emulsion) I took. Throughout production, the pH was adjusted and maintained near 7.2. After 10 days, or until the viability fell below 70%, cell culture medium was collected by centrifugation and filtered through a 0.22 μm filter. The filtrate is stored at 4 ° C. or immediately packed into a purification column.

For poly-His tag constructs, the protein is purified using a Ni-NTA column (Qiagen). Prior to purification, imidazole is added to the conditioned medium to a concentration of 5 mM. Conditioned media is pumped at 4 ° C. at a flow rate of 4-5 ml / min onto a 6 ml Ni-NTA column equilibrated with 20 mM Hepes, pH 7.4 buffer containing 0.3 M NaCl and 5 mM imidazole. After packing, the column is further washed with equilibration buffer and the protein is eluted with equilibration buffer containing 0.25 M imidazole. The highly purified protein is subsequently desalted using a 25 ml G25 Superfine (Pharmacia) column in a storage buffer containing 10 mM Hepes, 0.14 M NaCl and 4% mannitol, pH 6.8, − Store at 80 ° C.
Immunoadhesin (Fc-containing) constructs are purified from conditioned media as follows. Conditioned medium is pumped onto a 5 ml protein A column (Pharmacia) equilibrated with 20 mM sodium phosphate buffer, pH 6.8. After packing, the column was washed strongly with equilibration buffer and then eluted with 100 mM citric acid, pH 3.5. The eluted protein is immediately neutralized by collecting 1 ml fractions in a tube containing 275 μL of 1M Tris buffer, pH 9. The highly purified protein is subsequently desalted in the storage buffer described above for the poly-His tag protein. Uniformity is assessed by SDS-polyacrylamide gel and N-terminal amino acid sequencing by Edman degradation.
Many of the PRO polypeptides disclosed herein were successfully expressed as described above.

Example 8: Expression of PRO in yeast The following method describes recombinant expression of PRO in yeast.
First, a yeast expression vector is produced for intracellular production or secretion of PRO from the ADH2 / GAPDH promoter. DNA encoding PRO and a promoter are inserted into appropriate restriction enzyme sites of the selected plasmid to direct intracellular expression of PRO. For selection of plasmids encoding DNA encoding PRO for secretion, DNA encoding ADH2 / GAPDH promoter, native PRO signal peptide or other mammalian signal peptide, or, for example, yeast alpha factor or invertase secretion signal / reader The sequence and (if necessary) can be cloned with a linker sequence for expression of PRO.

Yeasts such as yeast strain AB110 can then be transformed with the expression plasmid and cultured in the selected fermentation medium. The transformed yeast supernatant can be analyzed by precipitation with 10% trichloroacetic acid and separation by SDS-PAGE, followed by staining of the gel with Coomassie blue staining.
The recombinant PRO can then be isolated and purified by removing the yeast cells from the fermentation medium by centrifugation and then concentrating the medium using a selected cartridge filter. The concentrate containing PRO may be further purified using a selected column chromatography resin.
Many of the PRO polypeptides disclosed herein were successfully expressed as described above.

Example 9: Expression of PRO in baculovirus infected insect cells The following method describes recombinant expression of PRO in baculovirus infected insect cells.
The PRO-encoding sequence was fused upstream of an epitope tag contained in a baculovirus expression vector. Such epitope tags include poly-his tags and immunoglobulin tags (such as the Fc region of IgG). A variety of plasmids can be used, including plasmids derived from commercially available plasmids such as pVL1393 (Novagen). Briefly, a predetermined portion of PRO or a PRO coding sequence, such as a sequence encoding the extracellular domain of a transmembrane protein or a sequence encoding a mature protein when the protein is extracellular, is located in the 5 ′ and 3 ′ regions. Amplified by PCR with complementary primers. The 5 ′ primer may include flanking (selected) restriction enzyme sites. The product is then digested with selected restriction enzymes and subcloned into an expression vector.
Recombinant baculoviruses were obtained by co-transfecting the above plasmid and BaculoGold (trade name) viral DNA (Pharmingen) into Spodoptera frugiperda (“Sf9”) cells (ATCC CRL 1711) using lipofectin (commercially available from GIBCO-BRL). Created by populating. After incubation at 28 ° C. for 4-5 days, the released virus was collected and used for further amplification. Viral infection and protein expression were performed as described in O'Reilley et al., Baculovirus expression vectors: A laboratory Manual, Oxford: Oxford University Press (1994).

The expressed poly-his tagged PRO is then purified as follows, for example, by Ni ²⁺ -chelate affinity chromatography. Extracts were prepared from virus-infected recombinant Sf9 cells as described in Rupert et al., Nature, 362: 175-179 (1993). Briefly, Sf9 cells were washed and sonicated buffer (25 mL Hepes, pH 7.9; 12.5 mM MgCl ₂ ; 0.1 mM EDTA; 10% glycerol; 0.1% NP-40; 0 .4M KCl) and sonicated twice on ice for 20 seconds. The sonicated product was clarified by centrifugation, and the supernatant was diluted 50-fold with a loading buffer (50 mM phosphate, 300 mM NaCl, 10% glycerol, pH 7.8) and filtered through a 0.45 μm filter. A Ni ²⁺ -NTA agarose column (commercially available from Qiagen) was prepared with a total volume of 5 mL, washed with 25 mL of water and equilibrated with 25 mL of loading buffer. The filtered cell extract was loaded onto the column at 0.5 mL per minute. The column was washed with loading buffer to A ₂₈₀ baseline where fraction collection began. The column was then washed with a secondary wash buffer (50 mM phosphate; 300 mM NaCl, 10% glycerol, pH 6.0), which elutes nonspecifically bound protein. After reaching A ₂₈₀ baseline again, the column was developed with a 0 to 500 mM imidazole gradient in the secondary wash buffer. 1 mL fractions were collected and analyzed by SDS-PAGE and silver staining or Western blot with Ni ²⁺ -NTA conjugated to alkaline phosphatase (Qiagen). Fractions containing the eluted His ₁₀ -tagged PRO were pooled and dialyzed against loading buffer.
Alternatively, purification of IgG tag (or Fc tag) PRO can be performed using known chromatographic techniques including, for example, protein A or protein G column chromatography.
Many of the PRO polypeptides disclosed herein were successfully expressed as described above.

Example 10: Preparation of antibodies that bind to PRO This example illustrates the preparation of monoclonal antibodies that can specifically bind to PRO.
Techniques for the production of monoclonal antibodies are known in the art and are described, for example, in Goding above. Immunogens that can be used include purified PRO, fusion proteins comprising PRO, cells expressing recombinant PRO on the cell surface. The selection of the immunogen can be made without undue experimentation by one skilled in the art.
Mice such as Balb / c are immunized with PRO immunogen emulsified in complete Freund's adjuvant and injected subcutaneously or intraperitoneally at 1-100 micrograms. Alternatively, the immunogen may be emulsified in MPL-TDM adjuvant (Ribi Immunochemical Research, Hamilton, Montana) and injected into the animal's hind footpad. Immunized mice are then boosted 10 to 12 days later with additional immunogen emulsified in the selected adjuvant. Thereafter, for several weeks, the mice are boosted with additional immunization injections. Serum samples from retroorbital hemorrhage may be taken periodically from mice for testing in an ELISA assay for detection of anti-PRO antibodies.

After a suitable antibody titer has been detected, animals “positive” for antibodies can be given a final infusion of PRO intravenous injection. Three to four days later, mice were sacrificed and spleen cells were removed. The spleen cells were then (using 35% polyethylene glycol), P3X63AgU. Fused to 1st selected mouse myeloma cell line. Hybridoma cells were generated by fusion and then plated on 96-well tissue culture plates containing HAT (hypoxanthine, aminopterin, and thymidine) medium to inhibit the growth of non-fused cells, myeloma hybrids, and spleen cell hybrids.
Hybridoma cells are screened by ELISA for reactivity to PRO. The determination of “positive” hybridoma cells that secrete the desired monoclonal antibody to PRO is within the common general knowledge.
Positive hybridoma cells are injected intraperitoneally into syngeneic Balb / c mice to produce ascites containing anti-PRO monoclonal antibodies. Alternatively, hybridoma cells can be grown in tissue culture flasks or roller bottles. Purification of monoclonal antibodies produced in ascites can be performed using ammonium sulfate precipitation followed by gel exclusion chromatography. Alternatively, affinity chromatography based on the affinity of antibody for protein A or protein G can also be used.

Example 11 Purification of PRO Polypeptides Using Specific Antibodies Natural or recombinant PRO polypeptides can be purified by various standard protein purification methods in the art. For example, pro-PRO polypeptide, mature polypeptide, or pre-PRO polypeptide is purified by immunoaffinity chromatography using an antibody specific for the PRO polypeptide of interest. In general, an immunoaffinity column is made by covalently binding an anti-PRO polypeptide antibody to an activated chromatography resin.
Polyclonal immunoglobulins are prepared from immune sera either by precipitation with ammonium sulfate or purification with immobilized protein A (Pharmacia LKB Biotechnology, Piscataway, NJ). Similarly, monoclonal antibodies are prepared from mouse ascites fluid by ammonium sulfate precipitation or chromatography with immobilized protein A. The partially purified immunoglobulin is covalently bound to a chromatographic resin such as CnBr-activated Sepharose (trade name) (Pharmacia LKB Biotechnology). The antibody is bound to the resin, the resin is blocked, and the derivative resin is washed according to the manufacturer's instructions.

Such immunoaffinity columns are utilized in the purification of PRO polypeptides by preparing fractions from cells containing solubilized forms of PRO polypeptides. This preparation is derived by solubilization of whole cells or cell component fractions obtained via addition of detergents or differential centrifugation by methods known in the art. Alternatively, solubilized PRO polypeptide comprising a signal sequence is secreted in useful amounts into the medium in which the cells are grown.
The solubilized PRO polypeptide-containing preparation is passed through an immunoaffinity column and the column is washed under conditions that allow preferred adsorption of the PRO polypeptide (eg, a high ionic strength buffer in the presence of a detergent). The column is then eluted under conditions that degrade antibody / PRO polypeptide binding (eg, a low pH such as about 2-3, a high concentration of urea or a chaotrope such as thiocyanate ion), and the PRO polypeptide is recovered. .

Example 12: Drug Screening The present invention is particularly useful for screening compounds by using PRO polypeptides or binding fragments thereof in various drug screening techniques. The PRO polypeptide or fragment used in such a test may be free in solution, immobilized on a solid support, supported on the cell surface, or located within the cell. One method of drug screening utilizes eukaryotic or prokaryotic host cells that are stably transfected with recombinant nucleic acids expressing the PRO polypeptide or fragment. Agents are screened against such transfected cells by competitive binding assays. Depending on either the viable or immobilized form, such cells can be used in standard binding assays. For example, the formation of a complex between the PRO polypeptide or fragment and the reagent being tested may be measured. Alternatively, the decrease in complex formation between the PRO polypeptide and its target cells caused by the reagent being tested can be tested.
Accordingly, the present invention provides methods for screening for drugs or any other reagent that can affect a PRO polypeptide related disease or disorder. These methods involve contacting the reagent with a PRO polypeptide or fragment, and (i) for the presence of a complex between the reagent and the PRO polypeptide or fragment, or (ii) between the PRO polypeptide or fragment and the cell. Testing for the presence of a complex between. In these competitive binding assays, the PRO polypeptide or fragment is typically labeled. After appropriate incubation, free PRO polypeptide or fragments are separated from those in bound form, and the amount of free or uncomplexed label determines whether a particular reagent binds to the PRO polypeptide or PRO polypeptide / cell complex. It is a measure of the ability to inhibit

Other techniques for drug screening provide high throughput screening for compounds with appropriate binding affinity for polypeptides and are described in detail in WO 84/03564 published September 13, 1984. ing. Briefly, a number of different small peptide test compounds are synthesized on a solid support such as plastic pins or some other surface. When applied to a PRO polypeptide, the peptide test compound reacts with the PRO polypeptide and is washed. Bound PRO polypeptide is detected by methods well known in the art. Purified PRO polypeptide can also be coated directly onto plates for use in the drug screening techniques described above. Furthermore, non-neutralizing antibodies can be used to capture the peptide and immobilize it on a solid support.
The present invention also contemplates competitive drug screening assays in which neutralizing antibodies capable of binding to the PRO polypeptide specifically compete with the test compound for the PRO polypeptide or fragment thereof. In this way, the antibody can be used to detect the presence of any peptide with one or more antigenic determinants in the PRO polypeptide.

Example 13 Rational Drug Design The purpose of rational drug design is the structure of a biologically active polypeptide of interest (eg, PRO polypeptide) or a small molecule with which they interact, such as an agonist, antagonist, or inhibitor Is to produce a similar analog. Any of these examples can be used to create a more active and stable form of a PRO polypeptide or a drug that promotes or inhibits the function of a PRO polypeptide in vivo (see Hodgson, Bio / Technology, 9: 19 -21 (1991)).

  In one method, the three-dimensional structure of a PRO polypeptide, or PRO polypeptide-inhibitor complex, is determined by x-ray crystallography, by computer modeling, most typically by a combination of the two methods. In order to elucidate the structure of the molecule and determine the active site, both the shape and charge of the PRO polypeptide must be confirmed. Less often, useful information regarding the structure of the PRO polypeptide may be obtained by modeling based on the structure of homologous proteins. In both cases, relevant structural information is used to design similar PRO polypeptide-like molecules or to identify effective inhibitors. Useful examples of rational drug design are molecules with improved activity or stability as shown in Braxton and Wells, Biochemistry, 31: 7796-7801 (1992), or Athauda et al., J. Biochem. , 113: 742-746 (1993), including molecules that act as inhibitors, agonists or antagonists of natural peptides.

It is also possible to isolate a target-specific antibody selected by the functional assay as described above and elucidate its crystal structure. This method in principle produces a pharmacore on which subsequent drug design can be based. By generating anti-idiotype antibodies (anti-ids) against functional pharmacologically active antibodies, protein crystallography can be bypassed. As a mirror image of the mirror image, the anti-ids binding site can be predicted to be an analog of the original receptor. Anti-ids can then be used to identify and isolate peptides from a bank of chemically or biologically produced peptides. The isolated peptide will function as a pharmacore.
In accordance with the present invention, sufficient quantities of PRO polypeptides are available to perform analytical experiments such as X-ray crystallography. In addition, the knowledge of PRO polypeptide amino acid sequences provided herein provides guidance for use in computer modeling techniques to replace or add to X-ray crystallography.

Example 14: Ability of PRO polypeptide to stimulate proteoglycan release from cartilage (Assay 97)
The ability of various PRO polypeptides to stimulate the release of proteoglycans from cartilage tissue was tested as follows.
The articular cartilage of a 4-6 month old pig was aseptically excised and the articular cartilage was removed by a freehand slice carefully avoiding the underlying bone. Finely chop cartilage and bulk in 95% air, 5% CO ₂ atmosphere in serum-free (SF) medium (DME / F12 1: 1) supplemented with 0.1% BSA and 100 U / ml penicillin and 100 μg / ml streptomycin. For 24 hours. After 3 washes, about 100 mg of articular cartilage was divided into micronics tubes and incubated for another 24 hours in the SF medium. Next, 1% of the PRO polypeptide was added alone or with 18 ng / ml of interleukin-1α, a proteoglycan release stimulator from known cartilage tissue. The supernatant was then collected and assayed for the amount of proteoglycan using a 1,9-dimethyl-methylene blue (DMB) colorimetric assay (Farndale and Battle, Biochem. Biophys. Acta 883: 173-177 (1985)). The positive results in this assay indicate that the test polypeptides find use in the treatment of, for example, exercise-related joint problems, articular cartilage disorders, osteoarthritis or rheumatoid arthritis.
When various PRO polypeptides were tested by the above assay, the polypeptides showed significant ability to stimulate proteoglycan release from cartilage tissue, fundamentally and 24 and 72 hours after stimulation with interleukin-1α. This indicates that these PRO polypeptides are useful for stimulating the release of proteoglycans from cartilage tissue. PRO polypeptides are therefore useful in the treatment of exercise-related joint problems, articular cartilage disorders, osteoarthritis or rheumatoid arthritis. In this assay, PRO6018 polypeptide was tested positive.

Example 15: Human microvascular endothelial cell proliferation (Assay 146)
This assay is intended to determine whether the PRO polypeptides of the present invention exhibit the ability to induce proliferation of human microvascular endothelial cells in the medium and thus function as an available growth factor.
On day 0, human microvascular endothelial cells were seeded in 96-well plates at 1000 cells / well in 100 microliters, complete medium [EGM-2 growth medium, + supplement: IGF-1; ascorbic acid; VEGF; hEGF; hFGF; Hydrocortisone, gentamicin (GA-1000), and fetal bovine serum (FBS, Clonetics)] were incubated overnight. On day 1, the complete medium was changed to basal medium [EBM-2 supplemented with 1% FBS] supplemented with 1%, 0.1% and 0.01% PRO polypeptide. On the seventh day, cell proliferation was assessed using ViaLight HS. Results are expressed as% of cell growth obtained with control buffer.
The following PRO polypeptides promoted human microvascular endothelial cell proliferation in this assay: PRO1313, PRO20080, and PRO21383.
In this assay, the following PRO polypeptides inhibited human microvascular endothelial cell proliferation: PRO6071, PRO4487, and PRO6006.

Example 16: Microarray analysis to detect over-expression of PRO polypeptides in cancerous tumors Nucleic acid microarrays, which in many cases contain thousands of gene sequences, are found in diseased tissues as compared to their normal counterparts. Useful for identifying differentially expressed genes. Using nucleic acid microassays, test and control mRNA samples from test and control tissue samples are reverse transcribed and labeled to generate cDNA probes. This cDNA probe is then hybridized with a number of nucleic acids immobilized on a solid support. This array is constructed so that the sequence and position of each member of the array is known. For example, a gene selected from genes known to be expressed at a certain disease stage may be aligned on a solid support. Hybridization of a labeled probe with a member of a particular array indicates that the sample from which the probe was derived expresses that gene. If the probe hybridization signal from the test (disease tissue) is greater than the probe hybridization signal from the control (normal tissue) sample, the gene or genes that are overexpressed in the disease tissue are identified. The implication of this result is that proteins that are overexpressed in diseased tissues are useful not only as diagnostic markers for the presence of disease symptoms but also as therapeutic targets for the treatment of disease symptoms. It is.
Nucleic acid hybridization and microarray technology methodologies are well known to those skilled in the art. In this example, the specific preparation of nucleic acids for hybridization and probes, slides, and hybridization conditions are all detailed in US Provisional Application No. 60 / 193,767, filed March 31, 2000. And is hereby incorporated by reference.

In this example, as an attempt to identify a PRO polypeptide overexpressed in cancerous tumors, derived from various human tissues for the expression of a PRO polypeptide-encoding gene associated with non-cancerous human tissues. Cancerous tumors that were identified were studied. Two sets of experimental data were generated. In one set, cancerous human colon tumor tissue from the same patient and matched non-cancerous human colon tumor tissue ("matched rectal control") are obtained and using the microarray technology described above, PRO poly Peptide expression was analyzed. In the second set of data, a “universal” epithelial control sample prepared by pooling non-cancerous human tissue from the epithelium, including the liver, kidney, and lung, with any of a variety of different human tumors Compared with. MRNA isolated from pooled tissue represents a mixture of expressed gene products in these different tissues. Microarray hybridization experiments with pooled control samples yielded a linear plot in the two-color analysis. The slope of this line generated in the two-color analysis was then used to normalize the ratio of (test: control detection) for each experiment. The standardized ratios of various experiments were then compared and used to identify gene expression accumulation. Thus, pooled “universal control” samples not only allow for effective and relative gene expression determination in simple two-sample comparisons, but also multiple sample comparisons over several experiments. Is also possible.
In this experiment, nucleic acid probes derived from the PRO polypeptide-encoding nucleic acid sequences described herein were used for the production of microarrays and the tumor tissue RNAs listed above were further used for hybridization. Standardized ratio: The value based on the experimental ratio was named “cut-off”. Only values above this cutoff were determined to be important. Table 8 below shows the results of these experiments and shows that the various PRO polypeptides of the present invention are significantly overexpressed in various human tumor tissues compared to non-cancerous human tissue controls. Yes. As described above, these data indicate that the PRO polypeptides of the present invention are not only as diagnostic markers indicating the presence of one or more cancerous tumors, but also as therapeutic targets for the treatment of these tumors. It also demonstrates that

Table 8
Where the molecule is overexpressed : compared to the following normal controls :
PRO240 Breast tumor General normal control
PRO240 Lung tumor General normal control

PRO256 Colorectal tumor General normal control
PRO256 Lung tumor General normal control
PRO256 Breast tumor General normal control

PRO306 Colorectal tumor General normal control
PRO306 Lung tumor General normal control

PRO540 Lung tumor General normal control
PRO540 Colorectal tumor General normal control

PRO773 Breast tumor General normal control
PRO773 Colorectal tumor General normal control

PRO698 Colorectal tumor General normal control
PRO698 Breast tumor General normal control
PRO698 Lung tumor General normal control
PRO698 Prostate tumor General normal control
PRO698 Rectal tumor General normal control

PRO3567 Colorectal tumor General normal control
PRO3567 Breast tumor General normal control
PRO3567 Lung tumor General normal control

PRO826 Colorectal tumor General normal control
PRO826 Lung tumor General normal control
PRO826 Breast tumor General normal control
PRO826 Rectal tumor General normal control
PRO826 Liver tumor General normal control

PRO1002 Colorectal tumor General normal control
PRO1002 Lung tumor General normal control

PRO1068 Colorectal tumor General normal control
PRO1068 Breast tumor General normal control

PRO1030 Colorectal tumor General normal control
PRO1030 Breast tumor General normal control
PRO1030 Lung tumor General normal control
PRO1030 Prostate tumor General normal control
PRO1030 Rectal tumor General normal control

PRO4397 Colorectal tumor General normal control
PRO4397 Breast tumor General normal control

PRO4344 Colorectal tumor General normal control
PRO4344 Lung tumor General normal control
PRO4344 Rectal tumor General normal control

PRO4407 Colorectal tumor General normal control
PRO4407 Breast tumor General normal control
PRO4407 Lung tumor General normal control
PRO4407 Liver tumor General normal control
PRO4407 Rectal tumor General normal control

PRO4316 Colorectal tumor General normal control
PRO4316 Prostate tumor General normal control

PRO5775 Colorectal tumor General normal control

PRO6016 Colorectal tumor General normal control

PRO4980 Breast tumor General normal control
PRO4980 Colorectal tumor General normal control
PRO4980 Lung tumor General normal control

PRO6018 Colorectal tumor General normal control

PRO7168 Colorectal tumor General normal control

PRO6000 Colorectal tumor General normal control

PRO6006 Colorectal tumor General normal control

PRO5800 Colon tumor General normal control
PRO5800 Breast tumor General normal control
PRO5800 Lung tumor General normal control
PRO5800 Rectal tumor General normal control

PRO7476 Colorectal tumor General normal control

PRO10268 Colorectal tumor General normal control

PRO6496 Colorectal tumor General normal control
PRO6496 Breast tumor General normal control
PRO6496 Lung tumor General normal control

PRO7422 Colorectal tumor General normal control

PRO7431 Colorectal tumor General normal control

PRO28633 Colorectal tumor General normal control
PRO28633 Lung tumor General normal control
PRO28633 Liver tumor General normal control

PRO21485 Colorectal tumor General normal control

PRO28700 Breast tumor General normal control
PRO28700 Lung tumor General normal control
PRO28700 Colorectal tumor General normal control

PRO34012 Colorectal tumor General normal control
PRO34012 Lung tumor General normal control

PRO34003 Colorectal tumor General normal control
PRO34003 Lung tumor General normal control

PRO34001 Colorectal tumor General normal control

PRO34009 Colorectal tumor General normal control
PRO34009 Breast tumor General normal control
PRO34009 Lung tumor General normal control
PRO34009 Rectal tumor General normal control

PRO34192 Colorectal tumor General normal control

PRO34564 Colorectal tumor General normal control

PRO35444 Colorectal tumor General normal control

PRO5998 Colorectal tumor General normal control
PRO5998 Lung tumor General normal control
PRO5998 Kidney tumor General normal control

PRO19651 Colorectal tumor General normal control

PRO20221 Liver tumor General normal control

PRO21434 Liver tumor General normal control

Example 17: Induction of fetal hemoglobin in an erythroblast cell line (assay 107)
This assay is useful for screening the ability of PRO polypeptides to induce the switch from adult hemoglobin to fetal hemoglobin in erythroblast cell lines. Molecules that have been tested positive in this assay are expected to be useful for therapeutic treatment of a variety of mammalian hemoglobin-related diseases, such as various thalassemias. This assay is performed as follows. Erythroid cells are seeded in standard growth medium at 1000 cells / well in a 96 well format. PRO polypeptide is added to the growth medium at a concentration of 0.2% or 2% and the cells are incubated at 37 ° C. for 5 days. As a positive control, cells are treated with 100 μM hemin and as a negative control, cells are not treated. After 5 days, cell lysates were prepared and analyzed for gamma globulin expression (fetal marker). Positive in this assay is that the gamma globulin level is at least twice that of the negative control.
This assay tested the PRO20080 polypeptide positive.

Example 18: Microarray analysis to detect overexpression of PRO polypeptides in HUVEC cells treated with growth factors This assay demonstrates that the PRO polypeptides of the present invention stimulate endothelial cell tube formation in HUVEC cells Designed to determine whether it exhibits the ability to induce angiogenesis.
Often, nucleic acid microarrays containing thousands of gene sequences are differentially expressed in tissues exposed to various stimuli (eg, growth factors) when compared to their normal tissues, ie, tissues that are not exposed to stimuli This is useful for identifying the genes that are present. When using nucleic acid microarrays, test and control mRNA samples from test and control tissue samples are reverse transcribed and labeled to generate cDNA probes. This cDNA probe is then hybridized with a number of nucleic acids immobilized on a solid support. This array is constructed so that the sequence and position of each member of the array is known. Hybridization of a labeled probe with a member of a particular array indicates that the sample from which the probe is derived expresses that gene. If the hybridization signal of the probe from the test (tissue exposed to the stimulus) is greater than the hybridization signal of the probe from the control (normal tissue, unexposed tissue) sample, excess in the tissue exposed to the stimulus The gene or genes that are expressed are identified. The implication of this result is that proteins that are overexpressed in tissues exposed to stimuli are involved in functional changes (eg, tube formation) in tissues exposed to stimuli.
Nucleic acid hybridization and microarray technology methodologies are well known to those skilled in the art. In this example, the specific preparation of nucleic acids for hybridization and probes, slides, and hybridization conditions are all detailed in US Provisional Application Serial No. 60 / 193,767, filed March 31, 2000. Which is incorporated herein by reference.

In this example, HUVEC cells growing in either collagen gel or fibrin gel were induced to form tubes by the addition of various growth factors. In particular, collagen gels have already been prepared as described in Yang et al., American J. Pathology, 1999, 155 (3): 887-895 and Xin et al., American J. Pathology, 2001, 158 (3): 1111-1120. It was. After gelation of HUVEC cells, 1X basal medium containing M199 and supplemented with 1% FBS, 1X ITS, 2 mM L-glutamine, 50 μg / ml ascorbic acid, 26.5 mM NaHCO ₃ , 100 U / ml penicillin and 100 U / ml streptomycin was added. Tube formation consists of phorbol myristate acetate (50 nM), vascular endothelial growth factor (40 ng / ml) and basic fibroblast growth factor (40 ng / ml) (&quot; PMA growth factor mixture &quot;), Alternatively, hepatocyte growth factor (40 ng / ml) and vascular endothelial growth factor (40 ng / ml) (HGF / VEGF mixture) were included in the indicated period. Fibrin gels were prepared by suspending Huvec (4 × 10 ⁵ cells / ml) in M199 containing 1% fetal calf serum (Hyclone) and human fibrinogen (2.5 mg / ml). Thrombin (50 U / ml) was then added to the fibrinogen suspension at a ratio of 1 part thrombin solution: 30 part fibrinogen suspension. The solution was then overlaid on a 10 cm tissue culture plate (total volume: 15 ml / plate) and then allowed to clot at 37 ° C. for 20 minutes. Thereafter, tissue culture medium (10 ml BM containing PMA (50 nM), bFGF (40 ng / ml) and VEGF (40 ng / ml)) was added, and the cells were air at 37 ° C., 5% CO ₂ . Incubated for the indicated period.
Total RNA was extracted from HUVEC cells incubated for 0, 4, 8, 24, 40 and 50 hours in a different matrix and medium combination followed by TRIzol extraction followed by a second extraction using RNAeasy Mini Kit (Qiagen) Extracted using. Total RNA was later used to prepare cRNA hybridized to the microarray.
In this experiment, nucleic acid probes derived from the PRO polypeptide-encoding nucleic acid sequences described herein were used for the production of microarrays, and RNA from the above HUVEC cells was used for hybridization therewith. The comparison between the two sets was done using a time 0 chip as the baseline. Three replicate samples were analyzed for each experimental condition and time. Therefore, there were 3 time 0 samples for each treatment and 3 replicates at each passage. Therefore, a 3 to 3 comparison for each time 0 was made at each time point. This resulted in 9 comparisons at each time point. Only genes with increased expression in all non-time 0 replicates in each different matrix and media combination were positive when compared to any of the three time 0s. This stringent data analysis method can tolerate false negatives, but minimizes false positives.
PRO281, PRO1560, PRO189, PRO4499, PRO6308, PRO6000, PRO10275, PRO21207, PRO20933, and PRO34274 were positive in this assay.

Example 19: Normal differential tissue expression distribution for tumors Oligonucleotide probes were constructed from the PRO polypeptide-encoding nucleotide sequences shown in the accompanying figures for use in quantitative PCR amplification reactions. This oligonucleotide probe was selected to yield an amplified fragment of approximately 200-600 base pairs from the 3 ′ end of the template corresponding to a standard PCR reaction. This oligonucleotide probe is used in standard quantitative PCR amplification reactions with cDNA libraries isolated from different human tumors and normal human tissue samples, and the PRO polypeptide coding in various tumors and normal tissues tested. In order to obtain a quantitative measurement of the expression level of the activated nucleic acid, it was analyzed by agarose gel electrophoresis. To confirm that equal amounts of nucleic acid were used in each reaction, β-actin was utilized as a control. Identification of differential expression of a PRO polypeptide-encoding nucleic acid in one or more tumor tissues compared to one or more of the same tissue types can be achieved by identifying a tumor in a subject suspected of having such a tumor. It provides a molecule that is therapeutically useful as a target for the treatment of, and at the same time, is diagnostically useful in ascertaining the presence or absence of a tumor that appears to have a tumor. These assays showed the following results:

(1) DNA161005-2943 molecule is very highly expressed in human umbilical vein endothelial cells (HUVEC), substantia nigra, hippocampus and dendrocytes; highly expressed in lymphoblasts; expressed in spleen, prostate, uterus and macrophages And weakly expressed in cartilage and heart. Of the panel of normal and tumor tissues tested, expressed in esophageal tumors and normal esophagus, normal stomach, stomach tumor, normal kidney, kidney tumor, normal lung, lung tumor, normal rectum, rectal tumor It is not expressed in normal liver and liver tumors.
(2) DNA170245-3053 molecule is highly expressed in cartilage, testis, adrenal gland, and uterus and not expressed in HUVEC, colon tumor, heart, placenta, bone marrow, spleen and aortic endothelial cells. In a panel of tumors and normal tissue samples tested, DNA170245-3053 molecules are expressed in normal esophagus and esophageal tumors, expressed in normal stomach and stomach tumors, but not in normal kidneys, but expressed in kidney tumors However, it has been found that it is not expressed in normal lung, but is expressed in lung tumors, not in normal rectum or rectal tumors, and not expressed in normal liver, but is expressed in liver tumors.

(3) The DNA173157-2981 molecule is significantly expressed in the following tissues: cartilage, testis, HUVEC, heart, placenta, bone marrow, adrenal gland, prostate, spleen, aortic endothelial cells, and uterus. When these assays were performed on a tumor tissue panel, DNA173157-2981 molecules were found to be significantly expressed in the following tissues: normal esophagus and esophageal tumors, normal stomach and stomach tumors, normal kidney and kidneys Tumors, normal lung and lung tumors, normal rectal and rectal tumors, normal liver and liver tumors, and colon tumors.
(4) The DNA175734-2985 molecule is significantly expressed in the adrenal gland and uterus. The DNA175734-2985 molecule is not significantly expressed in the following tissues: cartilage, testis, HUVEC, colon tumor, heart, placenta, bone marrow, prostate, spleen and aortic endothelial cells. Tumor panel screening revealed that DNA175734-2985 was significantly expressed in normal esophagus but not in esophageal tumors. Similarly, although highly expressed in normal rectum, DNA175734-2985 is expressed to a lesser extent in rectal tumors. DNA175734-2985 is equally expressed in normal stomach and stomach tumors, and in normal liver and liver tumors. Although not expressed in normal kidney, DNA175734-2985 is highly expressed in kidney tumors.

(5) DNA176108-3040 molecule is highly expressed in prostate and uterus, expressed in cartilage, testis, heart, placenta, bone marrow, adrenal gland and spleen, and not significantly expressed in HUVEC, colon tumors, and aortic endothelial cells . In a panel of tumors and normal tissue samples tested, DNA176108-3040 molecules are highly expressed in normal esophagus, but are expressed at lower levels in esophageal tumors, are highly expressed in normal stomach, and are low in gastric tumors. It was found to be expressed in kidney and kidney tumors, expressed in normal rectum and expressed at lower levels in rectal tumors, and expressed in normal liver and not in liver tumors.
(6) DNA191064-3069 molecule is significantly expressed in the following tissues: cartilage, testis, HUVEC, heart, placenta, bone marrow, adrenal gland, prostate, spleen, aortic endothelial cells and uterus: Absent. In a panel of tumor and normal tissue samples, DNA191064-3069 molecule is expressed in normal esophagus and esophageal tumor, expressed in normal stomach and stomach tumor, expressed in normal kidney and kidney tumor, normal lung and lung It was found to be expressed in tumors, in normal rectum and rectal tumors, and in normal liver and liver tumors.

(7) DNA194909-3013 molecule is highly expressed in placenta and expressed in cartilage, testis, HUVEC, colon tumor, heart, bone marrow, adrenal gland, prostate, spleen, aortic endothelial cells and uterus. In a panel of tumors and normal tissue samples tested, DNA194909-3013 molecule is expressed in normal esophagus and lower in esophageal tumors, not in normal stomach or stomach tumors, normal kidney and kidney It was found to be expressed in tumors, expressed in normal lung and lung tumors, expressed in normal rectum and rectal tumors, and not expressed in normal liver, but expressed in liver tumors.
(8) PRO34009 (DNA203532-3029) encoding the gene of the present invention was screened in normal tissues and the following primary tumors, and the results are reported below.
Tumor panel:
PRO34009 encoding the gene was expressed 39.3 times higher in lung tumors than in normal lung. It is 9.5 times higher in esophageal tumors than in normal esophagus. It is expressed 6.7 times higher in kidney tumors than in normal kidneys. Expressed 4.0 times higher in colon tumors than in normal colon. It is expressed 2.7 times higher in gastric tumors than in normal stomach. It is expressed at equivalent levels in normal rectal and rectal tumors, normal liver and liver tumors, normal uterus and uterine tumors.
Normal panel:
For normal tissue values, the most highly expressed normal tissue, in this case normal thymus, has a value of 1 and all other normal tissues have values lower than 1, and their expression relative to the thymus Based on expression, weakly expressed, not expressed. PRO34009 encoding the gene was expressed in normal thymus. Lymphoblast, spleen, heart, fetal limb, fetal lung, placenta, HUVEC, testis, fetal kidney, uterus, prostate, macrophage, nigra, hippocampus, liver, skin, esophagus, stomach, rectum, kidney, thyroid, skeletal muscle Or weakly expressed in fetal articular cartilage.
It is not expressed in bone marrow, fetal liver, large intestine, lung or dendrocyte.

(9) DNA213858-3060 molecule is not significantly expressed in cartilage, testis, HUVEC, colon tumor, heart, placenta, bone marrow, adrenal gland, prostate, spleen, aortic endothelial cell or uterus. In a panel of tumors and normal tissue samples tested, DNA213858-3060 molecule is expressed in normal esophagus and esophageal tumor, expressed in normal stomach and stomach tumor, expressed in normal kidney and kidney tumor, normal It was found to be expressed in normal lung and lung tumors, in normal rectum and rectal tumors, and in normal liver and liver tumors.
(10) The DNA216676-3083 molecule is significantly expressed in the following tissues: testis, heart, bone marrow, and uterus, and not in the following tissues: cartilage, HUVEC, colon tumor, placenta, adrenal gland, prostate, Spleen or aortic endothelial cells. In the panel of tumors and normal tissue samples tested, the DNA216676-3083 molecule is expressed in normal esophagus and esophageal tumors and not in normal stomach, but is expressed in gastric tumors, in normal kidney or kidney tumors It was found that it was not expressed, not in normal lung, but in lung tumors, not in normal rectum, but in rectum tumors, and not in normal liver or liver tumors.
(11) The DNA222653-3104 molecule is significantly expressed in the testis and not significantly expressed in cartilage, HUVEC, colon tumor, heart, placenta, bone marrow, adrenal gland, prostate, spleen, aortic endothelial cells and uterus. In a panel of tumors and normal tissue samples tested, DNA22653-3104 molecules were found in normal esophagus, esophageal tumor, normal stomach, stomach tumor, normal kidney, kidney tumor, normal lung, lung tumor, normal rectum Not expressed in rectal tumors, normal liver and liver tumors.

Example 20: Guinea Pig Vascular Leakage (Assay 51)
This assay is designed to determine whether a PRO polypeptide of the invention exhibits the ability to induce vascular permeability. PRO polypeptides rated positive in this assay are expected to be useful for the therapeutic treatment of conditions that benefit from hypertrophic vascular permeability, including those that benefit from enlarged local immune system cell infiltration, for example. .
350 g or more hairless guinea pigs were anesthetized by intramuscular administration of ketamine (75-80 mg / kg) and 5 mg / kg xylazine. A test sample containing the PRO polypeptide or a test sample containing physiological buffer without the test polypeptide was injected intradermally into the dorsal skin of the test animal at 100 μl per injection site. There were approximately 16-24 injection sites per animal. Then 1 ml of Evans Blue dye (1% in PBS) was injected intracardiac. The skin vascular permeability response to the compound (ie, spot at the injection site) was scored visually by measuring the diameter (mm) of the blue leakage from the injection site 1 and 6 hours after administration of the test animals. The blue diameter mm of the injection site was observed and recorded along with the severity of vascular leakage. Spots with a diameter of at least 5 mm are considered positive in the assay when testing purified protein, indicating the ability to induce vascular leakage or permeability. Responses with a diameter greater than 7 mm are considered positive for conditioned media samples. 0.1 μg / 100 μl of human VEGF was used as a positive control and induced a 15-23 mm diameter response.
This test tested the PRO19822 polypeptide as positive.

Example 21: Skin Vascular Permeability Assay (Assay 64)
This assay shows that certain polypeptides of the invention stimulate the immune system and induce inflammation by inducing mononuclear cells, eosinophils and PMN infiltration at the site of mammalian injection. Compounds that stimulate the immune response are therapeutically useful when the immune response is beneficial. This skin vascular permeability assay is performed as follows. 350 g or more hairless guinea pigs are anesthetized by intramuscular administration of ketamine (70-80 mg / kg) and 5 mg / kg xylazine (IM). The purified polypeptide of the invention or the conditional test sample is injected intradermally into the dorsal skin of the test animal at 100 μl per injection site. It is possible to have approximately 10-30, preferably 16-24, injection sites per animal. Then 1 μl of Evans Blue dye (1% buffered saline) is injected intracardiac. The spots at the injection site are then measured 1 and 6 hours after injection (mm diameter). The animals were sacrificed 6 hours after injection. Each skin injection site is biopsied and fixed with formalin. This skin is then conditioned for histopathological evaluation. Each site is evaluated for wet inflammatory cells on the skin. Sites of visible inflammatory cell wetting are scored as positive. Inflammatory cells can be neutrophils, eosinophils, mononuclear cells or lymphoid. At least the minimal perivascular wet at the site of injection is scored as positive and the non-wet at the site of injection is scored as negative.
In this assay, PRO19822 polypeptide was tested positive.

The nucleotide sequence of the native sequence PRO281 cDNA (SEQ ID NO: 1) is shown. SEQ ID NO: 1 is a clone designated herein as “DNA16422-1209”. 2 shows an amino acid sequence (SEQ ID NO: 2) derived from the coding sequence of SEQ ID NO: 1 shown in FIG. 1 shows the nucleotide sequence of the native sequence PRO1560 cDNA (SEQ ID NO: 3). SEQ ID NO: 3 is a clone designated herein as “DNA19902-1669”. 4 shows the amino acid sequence (SEQ ID NO: 4) derived from the coding sequence of SEQ ID NO: 3 shown in FIG. The nucleotide sequence (SEQ ID NO: 5) of the native sequence PRO189 cDNA is shown. SEQ ID NO: 5 is a clone designated herein as “DNA21624-1391”. The amino acid sequence (SEQ ID NO: 6) derived from the coding sequence of SEQ ID NO: 5 shown in FIG. 5 is shown. The nucleotide sequence of the native sequence PRO240 cDNA (SEQ ID NO: 7) is shown. SEQ ID NO: 7 is a clone designated herein as “DNA34387-1138”. SEQ ID NO: 7 shown in FIG. 7 shows the amino acid sequence derived from the coding sequence (SEQ ID NO: 8). The nucleotide sequence (SEQ ID NO: 9) of the native sequence PRO256 cDNA is shown. SEQ ID NO: 9 is a clone designated herein as “DNA35880-1160”. FIG. 10 shows an amino acid sequence (SEQ ID NO: 10) derived from the coding sequence of SEQ ID NO: 9 shown in FIG. The nucleotide sequence of the native sequence PRO306 cDNA (SEQ ID NO: 11) is shown. SEQ ID NO: 11 is a clone designated herein as “DNA39984-1221”. The amino acid sequence (SEQ ID NO: 12) derived from the coding sequence of SEQ ID NO: 11 shown in FIG. 11 is shown. 1 shows the nucleotide sequence of the native sequence PRO540 cDNA (SEQ ID NO: 13). SEQ ID NO: 13 is a clone designated herein as “DNA44189-1322”. An amino acid sequence (SEQ ID NO: 14) derived from the coding sequence of SEQ ID NO: 13 shown in FIG. 13 is shown. 1 shows the nucleotide sequence of the native sequence PRO773 cDNA (SEQ ID NO: 15). SEQ ID NO: 15 is a clone designated herein as “DNA48303-2829”. The amino acid sequence (SEQ ID NO: 16) derived from the coding sequence of SEQ ID NO: 15 shown in FIG. 15 is shown. The nucleotide sequence of the native sequence PRO698 cDNA (SEQ ID NO: 17) is shown. SEQ ID NO: 17 is a clone designated herein as “DNA48320-1433”. The amino acid sequence (SEQ ID NO: 18) derived from the coding sequence of SEQ ID NO: 17 shown in FIG. 1 shows the nucleotide sequence of the native sequence PRO3567 cDNA (SEQ ID NO: 19). SEQ ID NO: 19 is a clone designated herein as “DNA56049-2543”. The amino acid sequence (SEQ ID NO: 20) derived from the coding sequence of SEQ ID NO: 19 shown in FIG. The nucleotide sequence of the native sequence PRO826 cDNA (SEQ ID NO: 21) is shown. SEQ ID NO: 21 is a clone designated herein as “DNA57694-1341”. 21 shows the amino acid sequence (SEQ ID NO: 22) derived from the coding sequence of SEQ ID NO: 21 shown in FIG. The nucleotide sequence of the native sequence PRO1002 cDNA (SEQ ID NO: 23) is shown. SEQ ID NO: 23 is a clone designated herein as “DNA59208-1373”. 24 shows the amino acid sequence (SEQ ID NO: 24) derived from the coding sequence of SEQ ID NO: 23 shown in FIG. The nucleotide sequence of the native sequence PRO1068 cDNA (SEQ ID NO: 25) is shown. SEQ ID NO: 25 is a clone designated herein as “DNA59214-1449”. The amino acid sequence (SEQ ID NO: 26) derived from the coding sequence of SEQ ID NO: 25 shown in FIG. 25 is shown. The nucleotide sequence of the native sequence PRO1030 cDNA (SEQ ID NO: 27) is shown. SEQ ID NO: 27 is a clone designated herein as “DNA59485-1336”. 27 shows the amino acid sequence (SEQ ID NO: 28) derived from the coding sequence of SEQ ID NO: 27 shown in FIG. The nucleotide sequence of the native sequence PRO1313 cDNA (SEQ ID NO: 29) is shown. SEQ ID NO: 29 is a clone designated herein as “DNA64966-1575”. 30 shows the amino acid sequence (SEQ ID NO: 30) derived from the coding sequence SEQ ID NO: 29 shown in FIG. The nucleotide sequence of the native sequence PRO6071 cDNA (SEQ ID NO: 31) is shown. SEQ ID NO: 31 is a clone designated herein as “DNA82403-2959”. The amino acid sequence (sequence number: 32) derived from the coding sequence of sequence number: 31 shown in FIG. 31 is shown. The nucleotide sequence of the native sequence PRO4397 cDNA (SEQ ID NO: 33) is shown. SEQ ID NO: 33 is a clone designated herein as “DNA83505-2606”. The amino acid sequence (SEQ ID NO: 34) derived from the coding sequence of SEQ ID NO: 33 shown in FIG. 33 is shown. The nucleotide sequence of the native sequence PRO4344 cDNA (SEQ ID NO: 35) is shown. SEQ ID NO: 35 is a clone designated herein as “DNA84927-2585”. The amino acid sequence (SEQ ID NO: 36) derived from the coding sequence of SEQ ID NO: 35 shown in FIG. 35 is shown. The nucleotide sequence (SEQ ID NO: 37) of the native sequence PRO4407 cDNA is shown. SEQ ID NO: 37 is a clone designated herein as “DNA92264-2616”. 37 shows the amino acid sequence (SEQ ID NO: 38) derived from the coding sequence of SEQ ID NO: 37 shown in FIG. 1 shows the nucleotide sequence of the native sequence PRO4316 cDNA (SEQ ID NO: 39). SEQ ID NO: 39 is a clone designated herein as “DNA94713-2561”. The amino acid sequence (SEQ ID NO: 40) derived from the coding sequence of SEQ ID NO: 39 shown in FIG. 39 is shown. This shows the nucleotide sequence of the native sequence PRO5775 cDNA (SEQ ID NO: 41). SEQ ID NO: 41 is a clone designated herein as “DNA96869-2673”. 43 shows the amino acid sequence (SEQ ID NO: 42) derived from the coding sequence of SEQ ID NO: 41 shown in FIG. The nucleotide sequence of the native sequence PRO6016 cDNA (SEQ ID NO: 43) is shown. SEQ ID NO: 43 is a clone designated herein as “DNA96881-2699”. 43 shows the amino acid sequence (SEQ ID NO: 44) derived from the coding sequence of SEQ ID NO: 43 shown in FIG. The nucleotide sequence of the native sequence PRO4499 cDNA (SEQ ID NO: 45) is shown. SEQ ID NO: 45 is a clone designated herein as “DNA96889-2641”. 45 shows the amino acid sequence (SEQ ID NO: 46) derived from the coding sequence of SEQ ID NO: 45 shown in FIG. The nucleotide sequence of the native sequence PRO4487 cDNA (SEQ ID NO: 47) is shown. SEQ ID NO: 47 is a clone designated herein as “DNA96889-2640”. 47 shows the amino acid sequence (SEQ ID NO: 48) derived from the coding sequence of SEQ ID NO: 47 shown in FIG. The nucleotide sequence of the native sequence PRO4980 cDNA (SEQ ID NO: 49) is shown. SEQ ID NO: 49 is a clone designated herein as “DNA97003-2649”. 49 shows the amino acid sequence (SEQ ID NO: 50) derived from the coding sequence SEQ ID NO: 49 shown in FIG. The nucleotide sequence of the native sequence PRO6018 cDNA (SEQ ID NO: 51) is shown. SEQ ID NO: 51 is a clone designated herein as “DNA9855-2701”. An amino acid sequence (SEQ ID NO: 52) derived from the coding sequence of SEQ ID NO: 51 shown in FIG. 51 is shown. 1 shows the nucleotide sequence of the native sequence PRO7168 cDNA (SEQ ID NO: 53). SEQ ID NO: 53 is a clone designated herein as “DNA102844-2742”. An amino acid sequence (SEQ ID NO: 54) derived from the coding sequence of SEQ ID NO: 53 shown in FIG. 53 is shown. The nucleotide sequence of the native sequence PRO6308 cDNA (SEQ ID NO: 55) is shown. SEQ ID NO: 55 is a clone designated herein as “DNA102847-2726”. An amino acid sequence (SEQ ID NO: 56) derived from the coding sequence of SEQ ID NO: 55 shown in FIG. 55 is shown. The nucleotide sequence of the native sequence PRO6000 cDNA (SEQ ID NO: 57) is shown. SEQ ID NO: 57 is a clone designated herein as “DNA102880-2687”. 57 shows the amino acid sequence (SEQ ID NO: 58) derived from the coding sequence of SEQ ID NO: 57 shown in FIG. The nucleotide sequence of the native sequence PRO6006 cDNA (SEQ ID NO: 59) is shown. SEQ ID NO: 59 is a clone designated herein as “DNA105782-2669”. An amino acid sequence (SEQ ID NO: 60) derived from the coding sequence of SEQ ID NO: 59 shown in FIG. 1 shows the nucleotide sequence of the native sequence PRO5800 cDNA (SEQ ID NO: 61). SEQ ID NO: 61 is a clone designated herein as “DNA108912-2680”. An amino acid sequence (SEQ ID NO: 62) derived from the coding sequence of SEQ ID NO: 61 shown in FIG. 61 is shown. 1 shows the nucleotide sequence of the native sequence PRO7476 cDNA (SEQ ID NO: 63). SEQ ID NO: 63 is a clone designated herein as “DNA115253-2757”. An amino acid sequence (SEQ ID NO: 64) derived from the coding sequence of SEQ ID NO: 63 shown in FIG. 63 is shown. The nucleotide sequence of the native sequence PRO6496 cDNA (SEQ ID NO: 65) is shown. SEQ ID NO: 65 is a clone designated herein as “DNA119302-2737”. The amino acid sequence (SEQ ID NO: 66) derived from the coding sequence of SEQ ID NO: 65 shown in FIG. 65 is shown. The nucleotide sequence of the native sequence PRO7422 cDNA (SEQ ID NO: 67) is shown. SEQ ID NO: 67 is a clone designated herein as “DNA119536-2752”. The amino acid sequence (SEQ ID NO: 68) derived from the coding sequence of SEQ ID NO: 67 shown in FIG. 67 is shown. This shows the nucleotide sequence of the native sequence PRO7431 cDNA (SEQ ID NO: 69). SEQ ID NO: 69 is a clone designated herein as “DNA119542-2754”. The amino acid sequence (SEQ ID NO: 70) derived from the coding sequence of SEQ ID NO: 69 shown in FIG. 69 is shown. 1 shows the nucleotide sequence of the native sequence PRO10275 cDNA (SEQ ID NO: 71). SEQ ID NO: 71 is a clone designated herein as “DNA143498-2824”. An amino acid sequence (SEQ ID NO: 72) derived from the coding sequence of SEQ ID NO: 71 shown in FIG. 71 is shown. 1 shows the nucleotide sequence of the native sequence PRO10268 cDNA (SEQ ID NO: 73). SEQ ID NO: 73 is a clone designated herein as “DNA145583-2820”. An amino acid sequence (SEQ ID NO: 74) derived from the coding sequence of SEQ ID NO: 73 shown in FIG. 73 is shown. The nucleotide sequence of the native sequence PRO20080 cDNA (SEQ ID NO: 75) is shown. SEQ ID NO: 75 is a clone designated herein as “DNA161000-2896”. An amino acid sequence (SEQ ID NO: 76) derived from the coding sequence of SEQ ID NO: 75 shown in FIG. 75 is shown. This shows the nucleotide sequence of the native sequence PRO21207 cDNA (SEQ ID NO: 77). SEQ ID NO: 77 is a clone designated herein as “DNA161005-2943”. The amino acid sequence (SEQ ID NO: 78) derived from the coding sequence of SEQ ID NO: 77 shown in FIG. 77 is shown. 1 shows the nucleotide sequence of the native sequence PRO28663 cDNA (SEQ ID NO: 79). SEQ ID NO: 79 is a clone designated herein as “DNA170245-3053”. The amino acid sequence (SEQ ID NO: 80) derived from the coding sequence of SEQ ID NO: 79 shown in FIG. 79 is shown. This shows the nucleotide sequence of the native sequence PRO20933 cDNA (SEQ ID NO: 81). SEQ ID NO: 81 is a clone designated herein as “DNA1717771-2919”. An amino acid sequence (SEQ ID NO: 82) derived from the coding sequence of SEQ ID NO: 81 shown in FIG. 81 is shown. The nucleotide sequence of the native sequence PRO21383 cDNA (SEQ ID NO: 83) is shown. SEQ ID NO: 83 is a clone designated herein as “DNA173157-2981”. 83 shows an amino acid sequence (SEQ ID NO: 84) derived from the coding sequence of SEQ ID NO: 83 shown in FIG. 83. The nucleotide sequence of the native sequence PRO21485 cDNA (SEQ ID NO: 85) is shown. SEQ ID NO: 85 is a clone designated herein as “DNA175734-2985”. The amino acid sequence (SEQ ID NO: 86) derived from the coding sequence of SEQ ID NO: 85 shown in FIG. 85 is shown. The nucleotide sequence of the native sequence PRO28700 cDNA (SEQ ID NO: 87) is shown. SEQ ID NO: 87 is a clone designated herein as “DNA176108-3040”. This shows the amino acid sequence (SEQ ID NO: 88) derived from the coding sequence SEQ ID NO: 87 shown in FIG. The nucleotide sequence of the native sequence PRO34012 cDNA (SEQ ID NO: 89) is shown. SEQ ID NO: 89 is a clone designated herein as “DNA190710-3028”. The amino acid sequence (SEQ ID NO: 90) derived from the coding sequence of SEQ ID NO: 89 shown in FIG. 89 is shown. 1 shows the nucleotide sequence of the native sequence PRO34003 cDNA (SEQ ID NO: 91). SEQ ID NO: 91 is a clone designated herein as “DNA190803-3019”. An amino acid sequence (SEQ ID NO: 92) derived from the coding sequence of SEQ ID NO: 91 shown in FIG. 91 is shown. The nucleotide sequence of the native sequence PRO34274 cDNA (SEQ ID NO: 93) is shown. SEQ ID NO: 93 is a clone designated herein as “DNA191064-3069”. The amino acid sequence (SEQ ID NO: 94) derived from the coding sequence of SEQ ID NO: 93 shown in FIG. 93 is shown. The nucleotide sequence of the native sequence PRO34001 cDNA (SEQ ID NO: 95) is shown. SEQ ID NO: 95 is a clone designated herein as “DNA194909-3013”. 95 shows an amino acid sequence (SEQ ID NO: 96) derived from the coding sequence of SEQ ID NO: 95 shown in FIG. The nucleotide sequence of the native sequence PRO34009 cDNA (SEQ ID NO: 97) is shown. SEQ ID NO: 97 is a clone designated herein as “DNA203532-3029”. The amino acid sequence (SEQ ID NO: 98) derived from the coding sequence of SEQ ID NO: 97 shown in FIG. 97 is shown. The nucleotide sequence of the native sequence PRO34192 cDNA (SEQ ID NO: 99) is shown. SEQ ID NO: 99 is a clone designated herein as “DNA213858-3060”. 99 shows the amino acid sequence (SEQ ID NO: 100) derived from the coding sequence SEQ ID NO: 99 shown in FIG. The nucleotide sequence (SEQ ID NO: 101) of the native sequence PRO34564 cDNA is shown. SEQ ID NO: 101 is a clone designated herein as “DNA216676-3083”. An amino acid sequence (SEQ ID NO: 102) derived from the coding sequence of SEQ ID NO: 101 shown in FIG. 101 is shown. The nucleotide sequence (SEQ ID NO: 103) of the native sequence PRO35444 cDNA is shown. SEQ ID NO: 103 is a clone designated herein as “DNA2222653-3104”. An amino acid sequence (SEQ ID NO: 104) derived from the coding sequence of SEQ ID NO: 103 shown in FIG. 103 is shown. The nucleotide sequence of the native sequence PRO5998 cDNA (SEQ ID NO: 105) is shown. SEQ ID NO: 105 is a clone designated herein as “DNA96897-2688”. 105 shows the amino acid sequence (SEQ ID NO: 106) derived from the coding sequence of SEQ ID NO: 105 shown in FIG. 1 shows the nucleotide sequence of the native sequence PRO19651 cDNA (SEQ ID NO: 107). SEQ ID NO: 107 is a clone designated herein as “DNA142929-1781”. 107 shows an amino acid sequence (SEQ ID NO: 108) derived from the coding sequence of SEQ ID NO: 107 shown in FIG. 1 shows the nucleotide sequence of the native sequence PRO20221 cDNA (SEQ ID NO: 109). SEQ ID NO: 109 is a clone designated herein as “DNA142930-2914”. An amino acid sequence (SEQ ID NO: 110) derived from the coding sequence of SEQ ID NO: 109 shown in FIG. 109 is shown. The nucleotide sequence (SEQ ID NO: 111) of the native sequence PRO21434 cDNA is shown. SEQ ID NO: 111 is a clone designated herein as “DNA147253-2833”. An amino acid sequence (SEQ ID NO: 112) derived from the coding sequence of SEQ ID NO: 111 shown in FIG. 111 is shown. The nucleotide sequence of the native sequence PRO19822 cDNA (SEQ ID NO: 113) is shown. SEQ ID NO: 113 is a clone designated herein as “DNA149927-2887”. An amino acid sequence (SEQ ID NO: 114) derived from the coding sequence of SEQ ID NO: 113 shown in FIG. 113 is shown.

Claims (26)

SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 84, arrangement SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 100, SEQ ID NO: 102, SEQ ID NO: 104, sequence Having at least 80% nucleic acid sequence identity to a nucleotide sequence encoding an amino acid sequence selected from the group consisting of the amino acid sequences shown in SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 112, and SEQ ID NO: 114 Isolated nucleic acid. SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 83, sequence No: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97, SEQ ID NO: 99, SEQ ID NO: 101, SEQ ID NO: 103, sequence An isolated nucleic acid having at least 80% nucleic acid sequence identity to a nucleotide sequence selected from the group consisting of the nucleotide sequences set forth in SEQ ID NO: 105, SEQ ID NO: 109, SEQ ID NO: 111 and SEQ ID NO: 113 . SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 83, sequence No: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97, SEQ ID NO: 99, SEQ ID NO: 101, SEQ ID NO: 103, sequence 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 SEQ ID NO: 105, SEQ ID NO: 109, SEQ ID NO: 111 and SEQ ID NO: 113 Isolated nucleic acid. ATCC Registration Nos. -255, PTA-553, PTA-119, PTA-122, PTA-43, PTA-481, PTA-545, PTA-517, PTA-383, PTA-387, PTA-124, PTA-612, PTA-520 , PTA-551, PTA-619, PTA-1263, PTA-1179, PTA-1731, PTA-2243, PTA-2952, PTA-1902, PTA-2388 , PTA-2455, PTA-2824, PTA-2822, PTA-2785, PTA-3016, PTA-2779, PTA-2823, PTA-2958, PTA-3157, PTA-3330, PTA-379, PTA-1901, PTA An isolated nucleic acid having at least 80% nucleic acid sequence identity to the full-length coding sequence of the DNA deposited under 2405 and PTA-1782. A vector comprising the nucleic acid of claim 1. A host cell comprising the vector of claim 5. The host cell of claim 6, wherein the cell is a CHO cell. The host cell according to claim 6, wherein the cell is Escherichia coli. The host cell according to claim 6, wherein the cell is a yeast. A method for producing a PRO polypeptide comprising culturing the host cell of claim 6 under conditions suitable for expression of the PRO polypeptide, and recovering the PRO polypeptide from the cell culture medium. SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 84, arrangement SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 100, SEQ ID NO: 102, SEQ ID NO: 104, sequence An isolated poly having at least 80% amino acid sequence identity to an amino acid sequence selected from the group consisting of the amino acid sequences set forth in SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 112 and SEQ ID NO: 114 peptide. ATCC Registration Nos. -255, PTA-553, PTA-119, PTA-122, PTA-43, PTA-481, PTA-545, PTA-517, PTA-383, PTA-387, PTA-124, PTA-612, PTA-520 , PTA-551, PTA-619, PTA-1263, PTA-1179, PTA-1731, PTA-2243, PTA-2952, PTA-1902, PTA-2388 , PTA-2455, PTA-2824, PTA-2822, PTA-2785, PTA-3016, PTA-2779, PTA-2823, PTA-2958, PTA-3157, PTA-3330, PTA-379, PTA-1901, PTA An isolated polypeptide having at least 80% amino acid sequence identity to the amino acid sequence encoded by the full-length coding sequence of DNA deposited under 2405 and PTA-1782. A chimeric molecule comprising the polypeptide of claim 11 fused to a heterologous amino acid sequence. 14. The chimeric molecule of claim 13, wherein the heterologous amino acid sequence is an epitope tag sequence. 14. The chimeric molecule of claim 13, wherein the heterologous amino acid sequence is an immunoglobulin Fc region. An antibody that specifically binds to the polypeptide of claim 11. 17. The antibody of claim 16, wherein the antibody is a monoclonal antibody, a humanized antibody or a single chain antibody. (a) SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 16, lacking the signal peptide to be linked SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, sequence SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 56 SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, sequence No: 78, SEQ ID NO: 80, arrangement Sequence number: 82, sequence number: 84, sequence number: 86, sequence number: 88, sequence number: 90, sequence number: 92, sequence number: 94, sequence number: 96, sequence number: 98, sequence number: 100, SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 112 or nucleotide sequence encoding the polypeptide shown in SEQ ID NO: 114;
(b) SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, sequence having signal peptide to be linked SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, sequence SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 56 SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, sequence No: 78, SEQ ID NO: 80, Sequence number: 82, sequence number: 84, sequence number: 86, sequence number: 88, sequence number: 90, sequence number: 92, sequence number: 94, sequence number: 96, sequence number: 98, sequence number: 100, A nucleotide sequence encoding the extracellular domain of the polypeptide set forth in SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 112 or SEQ ID NO: 114; or
(c) SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 16, lacking the signal peptide to be linked SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, sequence SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 56 SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, sequence No: 78, SEQ ID NO: 80, arrangement SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 100, sequence SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 112 or nucleotide sequence encoding the extracellular domain of the polypeptide shown in SEQ ID NO: 114:
An isolated nucleic acid having at least 80% nucleic acid sequence identity to. (a) SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, sequence lacking the signal peptide to be linked SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, sequence SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 56 SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, sequence No: 78, SEQ ID NO: 80, arrangement SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 100, sequence SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 112, or the amino acid sequence of the polypeptide shown in SEQ ID NO: 114;
(b) SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, sequence having signal peptide to be linked SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, sequence SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 56 SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, sequence No: 78, SEQ ID NO: 80, Sequence number: 82, sequence number: 84, sequence number: 86, sequence number: 88, sequence number: 90, sequence number: 92, sequence number: 94, sequence number: 96, sequence number: 98, sequence number: 100, SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 112 or amino acid sequence of the extracellular domain of the polypeptide shown in SEQ ID NO: 114; or
(c) SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, sequence lacking the signal peptide to be linked SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, sequence SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 56 SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, sequence No: 78, SEQ ID NO: 80, arrangement Sequence number: 82, sequence number: 84, sequence number: 86, sequence number: 88, sequence number: 90, sequence number: 92, sequence number: 94, sequence number: 96, sequence number: 98, sequence number: 100, SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 112, or amino acid sequence of the extracellular domain of the polypeptide shown in SEQ ID NO: 114:
An isolated polypeptide having at least 80% amino acid sequence identity to. A method for promoting the proliferation or differentiation of chondrocytes, comprising bringing PRO6018 polypeptide into contact with the cells to promote the proliferation or differentiation of the cells. A method for promoting proliferation of human microvascular endothelial cells, comprising bringing PRO1313, PRO20080 or PRO21383 polypeptide into contact with said cells to promote proliferation of said cells. A method for inhibiting the growth of human microvascular endothelial cells, comprising contacting the cells with PRO6071, PRO4487 or PRO6006 polypeptide to inhibit the proliferation of the cells. A method for detecting the presence of a tumor in a mammal, comprising: (a) a test sample obtained from said mammal and (b) any PRO polypeptide shown in Table 8 in a control sample of normal cells of the same cell type. Comparing the expression level, wherein the presence of the tumor in the mammal is indicated by a high level of expression of the PRO polypeptide in the test sample relative to the control sample. 24. The method of claim 23, wherein the tumor is a lung tumor, a colon tumor, a breast tumor, a prostate tumor, a rectal tumor, a renal tumor or a liver tumor. A method for inducing endothelial cell tube formation, comprising administering to the endothelial cells PRO281, PRO1560, PRO189, PRO4499, PRO6308, PRO6000, PRO10275, PRO21207, PRO20933 or PRO34274 polypeptide, or an agonist thereof, A method comprising inducing formation. An oligonucleotide probe derived from any of the nucleotide sequences shown in the accompanying drawings.

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