JP4242371B2 - Compositions and methods for treating immune related diseases - Google Patents

Description

Detailed Description of the Invention

The present invention relates to compositions and methods useful for the diagnosis and treatment of immune related diseases.
(Background of the invention)
Immune-related and inflammatory diseases are important in normal physiology to respond to invasion or injury, initiate repair from invasion or injury, and provide innate and acquired defense against foreign organisms. A manifestation or result of a complex and often multiple interrelated biological pathways. A disease or condition is a condition where these normal physiological pathways are directly related to the intensity of the response, as a result of abnormal regulation or over-stimulation, as a response to self, or as a combination thereof, for further invasion or injury It occurs when it causes.
The occurrence of these diseases often involves multi-step pathways, often involving multiple different biological systems / pathways, but intervention at one or more important points of these pathways may improve or treat Can have. Therapeutic intervention can occur either by adverse process / pathway antagonism or by beneficial process / pathway stimulation.

Many immune related diseases are known and have been extensively studied. Such diseases include immune mediated inflammatory diseases, non-immune mediated inflammatory diseases, infectious diseases, immune deficiencies, abnormal growth and the like.
T lymphocytes (T cells) are an important component of mammalian immune responses. T cells recognize antigens that are bound to self-molecules encoded by genes within the major histocompatibility complex (MHC). Antigens can be displayed with MHC molecules on the surface of antigen presenting cells, virus infected cells, cancer cells, grafts, and the like. The T cell line eliminates these modified cells that threaten the health of the host mammal. T cells include helper T cells and cytotoxic T cells. Helper T cells proliferate extensively following recognition of antigen-MHC complexes on antigen presenting cells. Helper T cells also secrete various cytokines, namely lymphokines, which play a central role in the activation of B cells, cytotoxic T cells, and various other cells that contribute to the immune response.
The central events in both humoral and cell-mediated immune responses are helper T cell activation and clonal expansion. Helper T cell activation is initiated by the interaction of the T cell receptor (TCR) -CD3 complex with antigen-MHC on the surface of antigen presenting cells. This interaction mediates a biochemical event cascade that triggers resting helper T cells to enter the cell cycle (G0 to G1 transition), resulting in high affinity receptors for IL-2 and sometimes IL-4. To express. Activated T cells develop throughout the cycle, proliferate and differentiate into memory cells or effector cells.
In addition to signals mediated by TCR, T cell activation is further triggered by cytokines released by antigen presenting cells or by interaction of antigen presenting cells with membrane-bound molecules on T cells. Involved in stimulation. The cytokines IL-1 and IL-6 have been shown to provide costimulatory signals. In addition, T cells are activated by the interaction between B7 molecules expressed on the surface of antigen-presenting cells and CD28 and CTLA-4 molecules expressed on the surface of T cells. Activated T cells express an increased number of cell adhesion molecules such as ICAM-1, integrin, VLA-4, LFA-1, CD56 and the like.

T cell proliferation in a mixed lymphocyte culture or mixed lymphocyte reaction (MLR) is an established indicator of the ability of a compound to stimulate the immune system. In many immune responses, inflammatory cells infiltrate the site of injury or infection. The migrating cells can be neutrophils, eosinophils, monocytes or lymphocytes that can be quantified by histological examination of the affected tissue. Current Protocols in Immunology, John. E. Coligan, 1994, John Wiley & Sons, Inc.
Immune related diseases can be treated by suppressing the immune response. The use of neutralizing antibodies that inhibit molecules with immunostimulatory activity is useful for immune-mediated and inflammatory disease treatments. Molecules that inhibit immune responses can be used to inhibit immune responses (proteins directly or through the use of antibody agonists), thus improving immune related diseases.

(Summary of Invention)
A. Embodiments The present invention relates to compositions and methods useful for the diagnosis and treatment of immune related diseases in mammals, including humans. The present invention is based on the identification of proteins (including agonist and antagonist antibodies) that stimulate or inhibit immune responses in mammals. Immune related diseases can be treated by suppressing or enhancing the immune response. Molecules that enhance the immune response stimulate or enhance the immune response to the antigen. Where an enhanced immune response is beneficial, molecules that stimulate the immune response can be used for therapy. Alternatively, if sedation of the immune response is useful (eg inflammation), molecules that suppress the immune response (eg neutralizing antibodies) can be used therapeutically, such as sedating or reducing the immune response to the antigen. . Thus, PRO polypeptides, their agonists and antagonists are useful in the preparation of medicaments and drugs for the treatment of immune related and inflammatory diseases. In certain embodiments, such medicaments and drugs contain a therapeutically effective amount of a PRO polypeptide, agonist or antagonist thereof together with a pharmaceutically acceptable carrier. Preferably the mixture is sterilized.
In a further embodiment, the present invention provides a method for identifying an agonist or antagonist of a PRO polypeptide comprising contacting the PRO polypeptide with a candidate molecule and monitoring the biological activity mediated by said PRO polypeptide. About. Preferably, the PRO polypeptide is a native sequence PRO polypeptide. In certain aspects, the PRO agonist or antagonist is an anti-PRO antibody.

  In another embodiment, the invention relates to a composition comprising a PRO polypeptide or an agonist or antagonist antibody that binds to a polypeptide mixed with a carrier or excipient. In one aspect, the composition comprises a therapeutically effective amount of a polypeptide or antibody. In other embodiments, when the composition comprises an immunostimulatory molecule, the composition (a) increases inflammatory cell infiltration into the mammal tissue in need thereof, and (b) in the mammal in need thereof. Stimulate or enhance an immune response, (c) increase T-lymphocyte proliferation in a mammal in response to the antigen, (d) stimulate T-lymphocyte activity, or (e) Useful to increase vascular permeability. In a further aspect, when the composition comprises an immunosuppressive molecule, the composition (a) reduces infiltration of inflammatory cells into the mammalian tissue in need thereof, and (b) immunizes in the mammal in need thereof. Useful for inhibiting or reducing the response, (c) reducing the activity of T-lymphocytes, or (d) reducing T-lymphocyte proliferation in a mammal in need thereof in response to an antigen. . In other embodiments, the composition contains additional active ingredients that may be, for example, additional antibodies or cytotoxic or chemotherapeutic agents. Preferably the composition is sterilized.

  In another embodiment, the invention relates to a method of treating an immune related disease in a mammal in need thereof, comprising administering to the mammal an effective amount of a PRO polypeptide, an agonist or antagonist thereof. In a preferred embodiment, the immune-related disease is systemic lupus erythematosus, rheumatoid arthritis, osteoarthritis, juvenile chronic arthritis, spondyloarthropathy, systemic sclerosis, idiopathic inflammatory myopathy, Sjogren's syndrome, systemic vasculitis, Sarcoidosis, autoimmune hemolytic anemia, autoimmune thrombocytopenia, thyroiditis, diabetes mellitus, immune-mediated renal disease, central and peripheral nervous system demyelinating diseases such as multiple sclerosis, idiopathic demyelinating polyneuropathy Or Guillain-Barre syndrome, and chronic inflammatory degenerative polyneuropathy, hepatobiliary disease such as infectious, autoimmune chronic active hepatitis, primary biliary cirrhosis, granulomatous hepatitis, and sclerosing cholangitis, Inflammatory bowel disease, gluten-sensitive bowel disease, and Whipple disease, bullous skin disease, autoimmune or immune-mediated skin diseases including erythema multiforme and contact dermatitis, psoriasis, allergic Diseases such as asthma, allergic rhinitis, atopic dermatitis, food hypersensitivity and urticaria, lung immune diseases such as eosinophilic pneumonia, idiopathic pulmonary fibrosis and hypersensitivity pneumonia, rejection and graft-versus-host disease Selected from the group consisting of transplantation-related diseases.

In other embodiments, the 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 one aspect, the invention relates to an isolated antibody that binds to a PRO polypeptide. In other embodiments, the antibody mimics the activity of the PRO polypeptide (agonist antibody), or conversely, the antibody inhibits or neutralizes the activity of the PRO polypeptide (antagonist antibody). In other embodiments, the antibody is a monoclonal antibody, preferably having non-human complementarity determining region (CDR) residues and human framework region (FR) residues. The antibody may be labeled or immobilized on a solid support. In a further aspect, the antibody is an antibody fragment, a monoclonal antibody, a single chain antibody, or an anti-idiotype antibody.
In yet another embodiment, the present invention provides a composition containing an anti-PRO antibody mixed with a pharmaceutically acceptable carrier. In one aspect, the composition comprises a pharmaceutically effective amount of antibody. Preferably the composition is sterilized. The composition may be administered in the form of a liquid pharmaceutical formulation that can be stored such that prolonged stability on storage is achieved. Alternatively, the antibody is a monoclonal antibody, an antibody fragment, a humanized antibody, or a single chain antibody.

In a further embodiment, the invention provides:
(a) a composition comprising a PRO polypeptide or an agonist or antagonist thereof;
(b) a container containing the composition; and
(c) An article of manufacture comprising a label attached to the container or a package insert contained in the container, which refers to the use of the PRO polypeptide or an agonist or antagonist thereof in the treatment of immune related diseases. The composition may comprise a therapeutically effective amount of a PRO polypeptide or an agonist or antagonist thereof.

In yet another embodiment, the present invention encodes a PRO polypeptide in (a) a test sample of tissue cells obtained from a mammal, and (b) a control sample of known normal tissue cells of the same cell type. A method for diagnosing an immune-related disease in a mammal comprising detecting the expression level of a gene, wherein the mammal from which a test tissue cell is obtained when the expression level of the test sample is high or low compared to a control sample Indicates that an immune-related disease exists.
In another embodiment, the invention includes (a) contacting an anti-PRO antibody with a test sample of tissue cells obtained from a mammal, and (b) detecting complex formation between the PRO polypeptide and the antibody in the test sample. The formation of the complex indicates the presence or absence of the disease. Detection may be qualitative or quantitative and may be performed by monitoring and comparing complex formation in a control sample of known normal tissue cells of the same cell type. The large amount of complex produced in the test sample indicates the presence or absence of immune disease in the mammal from which the test tissue cells were obtained. The antibody preferably has a detectable label. Complex formation can be monitored, for example, by light microscopy, flow cytometry, fluorescence measurements, or other techniques known in the art. Usually, the test sample is taken from an individual suspected of having a defective or abnormal immune system.

In another embodiment, the invention comprises exposing a test sample of cells suspected of containing a PRO polypeptide to an anti-PRO antibody and measuring the binding of the antibody to the cell sample. Methods are provided for determining the presence or absence of a PRO polypeptide. In certain aspects, the sample comprises cells that are likely to contain a PRO polypeptide and antibodies that bind to the cells. The antibody is preferably detectably labeled and / or bound to a solid support.
In another embodiment, the invention relates to an immune-related disease diagnostic kit comprising an anti-PRO antibody and a carrier in a suitable package. The kit preferably includes instructions for using the antibody to detect the presence or absence of the PRO polypeptide. Preferably, the carrier is pharmaceutically acceptable.
In another embodiment, the invention relates to a diagnostic kit comprising an anti-PRO antibody in a suitable package. Preferably, the kit includes instructions for using the antibody to detect the PRO polypeptide.

In another embodiment, the present invention provides a method of diagnosing an immune related disease in a mammal comprising detecting the presence or absence of a PRO polypeptide in a test sample of tissue cells obtained from the mammal, wherein the test The presence or absence of the PRO polypeptide in the sample indicates the presence of an immune related disease in the mammal.
In another embodiment, the present invention provides a method for identifying an agonist of a PRO polypeptide, comprising:
(A) contacting the cell with a test compound to be screened under conditions suitable for inducing a cellular response normally elicited by the PRO polypeptide;
(B) measuring the induction of the cellular response to determine whether the test compound is an effective agonist, wherein the induction of the cellular response is an effective agonist of the test compound It shows that.

In another embodiment, the invention provides for contacting a PRO polypeptide with a candidate compound under a time and conditions sufficient to cause the two components to interact with each other, and whether the activity of the PRO polypeptide is inhibited. A method of identifying a compound capable of inhibiting the activity of a PRO polypeptide. In certain embodiments, either the candidate compound or the PRO polypeptide is immobilized on a solid support. In other embodiments, the non-immobilized component carries a detectable label. In a preferred embodiment, the method comprises:
(A) contacting the cell with a test compound to be screened under conditions suitable for inducing a cellular response in which the PRO polypeptide is present and normally elicited by the PRO polypeptide;
(B) measuring the induction of said cellular response to determine whether the test compound is an effective antagonist.
In another embodiment, the invention provides a method of identifying a compound that inhibits expression of a PRO polypeptide in a cell that normally expresses the PRO polypeptide, said method comprising contacting the cell with a test compound, Measuring whether the expression of the polypeptide is inhibited. In a preferred embodiment, the method is:
(a) contacting the cell with a test compound to be screened under conditions suitable for expressing the PRO polypeptide;
(b) comprising measuring the inhibition of expression of the polypeptide.

In a further embodiment, the invention relates to a method of treating a mammal suffering from an immune-related disease, which comprises (a) a PRO polypeptide, (b) a PRO polypeptide agonist, or (c) a PRO polypeptide. Administering to the mammal a nucleic acid molecule encoding any of the antagonists, wherein said agonist or antagonist may be an anti-PRO antibody. In a preferred embodiment, the mammal is a human. In another preferred embodiment, the nucleic acid is administered via ex vivo gene therapy. In a further preferred embodiment, the nucleic acid is contained within a vector, more preferably an adenovirus, adeno-associated virus, lentivirus or retroviral vector.
In another aspect, the present invention also provides a promoter, (a) a PRO polypeptide, (b) a PRO polypeptide agonist polypeptide, or (c) a nucleic acid encoding an PRO polypeptide antagonist polypeptide, and a polypeptide. Recombinant viral particles are provided containing a viral vector consisting essentially of a signal sequence for cell secretion, wherein the viral vector is associated with a viral structural protein. Preferably, the signal sequence is from a mammal, such as a native PRO polypeptide.
In a further embodiment, the invention also includes a nucleic acid construct that expresses a retroviral structural protein, and is a promoter, (a) a PRO polypeptide, (b) an agonist polypeptide of a PRO polypeptide, or (c) a PRO. An ex vivo producing cell further comprising a retroviral vector consisting essentially of a nucleic acid encoding an antagonist polypeptide of the polypeptide and a signal sequence for cellular secretion of the polypeptide, wherein the producing cell comprises a recombinant retroviral particle A retroviral vector related to the structural protein to produce

In a further embodiment, the invention provides a mammalian tissue comprising administering to a mammal (a) a PRO polypeptide, (b) an agonist of the PRO polypeptide, or (c) an antagonist of the PRO polypeptide. A method is provided for increasing the infiltration of inflammatory cells from the vasculature, wherein the infiltration of inflammatory cells from vascular tissue is increased in a mammal.
In yet a further embodiment, the invention provides a mammalian tissue comprising administering to a mammal (a) a PRO polypeptide, (b) a PRO polypeptide agonist, or (c) a PRO polypeptide antagonist. A method is provided for reducing inflammatory cell infiltration from the vasculature into a mammal, wherein inflammatory cell infiltration from the vasculature is reduced in a mammal.
In yet a further embodiment, the invention provides in a mammal comprising administering to the mammal (a) a PRO polypeptide, (b) an agonist of the PRO polypeptide, or (c) an antagonist of the PRO polypeptide. A method is provided for increasing the activity of T-lymphocytes, wherein the activity of T-lymphocytes in a mammal is increased.
In yet a further embodiment, the invention provides in a mammal comprising administering to the mammal (a) a PRO polypeptide, (b) an agonist of the PRO polypeptide, or (c) an antagonist of the PRO polypeptide. Methods are provided for reducing the activity of T-lymphocytes, wherein the activity of T-lymphocytes in a mammal is reduced.
In yet a further embodiment, the invention provides in a mammal comprising administering to the mammal (a) a PRO polypeptide, (b) an agonist of the PRO polypeptide, or (c) an antagonist of the PRO polypeptide. A method for increasing T-lymphocyte proliferation is provided wherein T-lymphocyte proliferation in a mammal is increased.
In yet a further embodiment, the invention provides in a mammal comprising administering (a) a PRO polypeptide, (b) a PRO polypeptide agonist, or (c) a PRO polypeptide antagonist to the mammal. A method is provided for reducing T-lymphocyte proliferation, wherein T-lymphocyte proliferation in a mammal is reduced.

In a further embodiment, the present invention provides a method of stimulating T-cell proliferation comprising contacting a T-cell with a PRO1081, PRO1274, or PRO10272 polypeptide or agonist thereof, wherein the method comprises the step of: T-cell proliferation is stimulated.
In yet a further embodiment, the present invention provides a method for inhibiting proliferation of T-lymphocytes, comprising contacting said T-lymphocytes with a PRO1199, PRO1556, PRO4401 or PRO10268 polypeptide or agonist thereof. Here, the proliferation of the T-lymphocytes is inhibited.
In yet a further embodiment, the invention relates to a method of enhancing infiltration of a mononuclear cell, eosinophil or polymorphonuclear neutrophil (PMN) into a mammalian cell comprising a PRO1754 or PRO9912 polypeptide or its The method comprises contacting an agonist and nuclear tissue, wherein the invasion is enhanced.

B. Further Embodiments In another aspect of the invention, the invention provides a vector comprising DNA encoding any of the polypeptides described herein. Also provided are host cells containing any of such vectors. As an example, the host cell may be a CHO cell, E. coli, or yeast. Further provided is a method of 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. Including.
In other embodiments, the invention provides a chimeric molecule 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 another embodiment, the invention provides an antibody that specifically binds 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 isolating genomic and cDNA nucleotide sequences or antisense probes, which probes are from any of the nucleotide sequences described above or below. Can be induced.

In another embodiment, the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence that encodes 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 with or without a signal peptide disclosed herein A DNA molecule encoding a PRO polypeptide having the extracellular domain of a protein, or any fragment specifically defined in addition to the full-length amino acid sequence disclosed herein, or (b) the complementary strand of the DNA molecule of (a) Against 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, or 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% nucleus Sequence identity, or 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, or at least about 96% nucleic acid sequence Nucleotide sequences comprising identity, or at least about 97% nucleic acid sequence identity, or at least about 98% nucleic acid sequence identity, or at least about 99% nucleic acid sequence identity.

  In other embodiments, an 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 that lacks a signal peptide disclosed herein, and disclosed herein. A DNA molecule comprising the coding sequence of the extracellular domain of a transmembrane PRO polypeptide with or without a signal peptide, or the coding sequence of any specially defined fragment other than 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 complementary strand 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, or at least about 86 Of nucleic acid sequence identity, or at least about 87% nucleic acid sequence identity, or 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, or at least about 96% nucleic acid sequence identity, or at least about 97% nucleic acid sequence identity, or at least about 98% nucleic acid sequence identity, or at least about 99% nucleic acid sequence identity Comprising a nucleotide sequence.

  In a further aspect, the invention provides (a) a DNA molecule encoding the same mature polypeptide encoded by any of the human protein cDNAs deposited with the ATTC disclosed herein, or (b) 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 complementary strand of the DNA molecule Or 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, or 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% nucleus 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 at least Comprising nucleotide sequences having about 96% nucleic acid sequence identity, or at least about 97% nucleic acid sequence identity, or at least about 98% nucleic acid sequence identity, or at least about 99% nucleic acid sequence identity An isolated nucleic acid molecule comprising

Another aspect of the present invention is a nucleotide sequence encoding a PRO polypeptide in which the transmembrane domain is deleted or the transmembrane domain is inactivated, or is complementary to such an encoded nucleotide sequence An isolated nucleic acid molecule comprising a transmembrane domain of such a polypeptide is disclosed herein. Accordingly, the soluble extracellular domains of the PRO polypeptides described herein are contemplated.
Other embodiments relate to a fragment of the PRO polypeptide coding sequence, or its complementary strand, which encodes, for example, a fragment of the PRO polypeptide that encodes a polypeptide that optionally includes a binding site for an anti-PRO antibody. Applications are found as hybridization probes or as antisense oligonucleotide probes. Such nucleic acid fragments are usually at least about 20 nucleotides in length, or at least about 30 nucleotides in length, or at least about 40 nucleotides in length, or at least about 50 nucleotides in length, or at least about 60 nucleotides in length, or at least about 70 Nucleotide length, or at least about 80 nucleotide length, or at least about 90 nucleotide length, or at least about 100 nucleotide length, or at least about 110 nucleotide length, or at least about 120 nucleotide length, or at least about 130 nucleotides. Long, or at least about 140 nucleotides long, or at least about 150 nucleotides long, or at least about 160 nucleotides long, or at least about 170 nucleotides long, or at least about 180 Nucleotide length, or at least about 190 nucleotide length, or at least about 200 nucleotide length, or at least about 250 nucleotide length, or at least about 300 nucleotide length, or at least about 350 nucleotide length, or at least about 400 nucleotide length Or at least about 450 nucleotides, or at least about 500 nucleotides, or at least about 600 nucleotides, or at least about 700 nucleotides, or at least about 800 nucleotides, or at least about 900 nucleotides, or The term “about” means a reference nucleotide sequence length that is plus or minus 10% of its referenced length. Novel fragments of a PRO polypeptide-encoding nucleotide sequence can be used to align a PRO polypeptide-encoding nucleotide sequence to other known nucleotide sequences using any of a number of well-known sequence alignment programs. It is noted that the polypeptide-encoding nucleotide sequence fragment (s) can be determined in a conventional manner by determining whether they are novel. All such PRO polypeptide-encoding nucleotide sequences are contemplated herein. Also contemplated are PRO polypeptide fragments encoded by these nucleotide molecule fragments, preferably those PRO polypeptide fragments comprising a binding site for an anti-PRO antibody.

In another embodiment, the invention provides an isolated PRO polypeptide encoded by any of the isolated nucleic acid sequences identified above.
In certain aspects, the invention provides a full-length amino acid sequence disclosed herein, an amino acid sequence that lacks a signal peptide disclosed herein, an extracellular domain of a transmembrane protein with or without a signal peptide disclosed herein, or At least about 80% amino acid sequence identity, or at least about 81% amino acid sequence identity to a PRO polypeptide having any other specifically defined fragment of the full-length amino acid sequence disclosed herein, or at least About 82% amino acid sequence identity, or at least about 83% amino acid sequence identity, or at least about 84% amino acid sequence identity, or 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, or at least about 88% Mino acid sequence identity, or at least about 89% amino acid sequence identity, or at least about 90% amino acid sequence identity, or 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, or at least about 94% amino acid sequence identity, or at least about 95% amino acid sequence identity, or at least about 96% amino acid sequence identity, or at least about 97%. It relates to an isolated PRO polypeptide comprising an amino acid sequence identity, or an amino acid sequence having at least about 98% amino acid sequence identity, or at least about 99% amino acid sequence identity.

  In a further aspect, the invention provides at least about 80% amino acid sequence identity, or at least about 81% to the amino acid sequence encoded by any of the human protein cDNAs deposited with the ATTC disclosed herein. Amino acid sequence identity, or at least about 82% amino acid sequence identity, or at least about 83% amino acid sequence identity, or at least about 84% amino acid sequence identity, or 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, or at least about 88% amino acid sequence identity, or at least about 89% amino acid sequence identity, or at least about 90%. Amino acid sequence identity, or 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, or at least about 94% amino acid sequence identity, or at least about 95% amino acid sequence identity, or at least about 96%. An isolation comprising an amino acid sequence identity, or an amino acid sequence having at least about 97% amino acid sequence identity, or at least about 98% amino acid sequence identity, or at least about 99% amino acid sequence identity Related PRO polypeptides.

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, which is encoded by a nucleotide sequence that encodes such an amino acid sequence described above. Methods for producing it are also described herein, wherein these methods are used to cultivate a host cell comprising a vector containing a suitable encoding nucleic acid molecule under conditions suitable for expression of the PRO polypeptide. Recovering the PRO polypeptide from the culture.
In another aspect, the invention provides an isolated PRO polypeptide in which the transmembrane domain has been deleted or the transmembrane domain has been inactivated. Methods for producing it are also described herein, wherein these methods are used to cultivate a host cell comprising a vector containing a suitable encoding nucleic acid molecule under conditions suitable for expression of the PRO polypeptide. Recovering the PRO polypeptide from the culture.
In yet another embodiment, the present invention relates to agonists and antagonists of the native PRO polypeptides defined herein. In certain embodiments, the agonist or antagonist is an anti-PRO antibody or small molecule.
In a further embodiment, the present invention relates to a method of identifying an agonist or antagonist of a PRO polypeptide, which comprises contacting the PRO polypeptide with a candidate molecule and monitoring the 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 of matter 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 useful for the treatment of a disease state caused by 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. The use for the preparation of a medicament.

(Detailed description of preferred embodiments)
I. Definitions The terms “PRO polypeptide” and “PRO” as used herein refer to various polypeptides when followed by a numerical designation, where the full code (ie, PRO / number) Refers to the specific polypeptide sequence described. The terms “PRO / number polypeptide” and “PRO / number”, where “number” is given as the actual numerical designation used herein, are native sequence polypeptides and polypeptide variants (as defined further herein). Included). 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 described herein. All disclosures in this specification that mean “PRO polypeptides” mean each of the polypeptides individually and together. For example, descriptions of preparation, purification, induction, formation, administration thereof, compositions containing the same, treatment of diseases using the same, and the like are associated with 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 described herein is a mature or full-length native sequence polypeptide comprising the full-length amino acid sequence shown in the accompanying drawings. Start and stop codons are shown in bold and underlined in the figure. However, although the PRO polypeptide disclosed in the accompanying drawings is shown to begin with a methionine residue designated herein as amino acid position 1 in the drawings, others are located upstream or downstream of amino acid position 1 in the drawings. It is conceivable or possible to use the methionine residue as the starting amino acid residue of the PRO polypeptide.
The PRO polypeptide “extracellular domain” or “ECD” refers to a form of the PRO polypeptide that has essentially no 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. . The exact boundaries of the transmembrane domain can vary, but it appears that it does not exceed about 5 amino acids from either end of the domain originally identified here. Thus, the PRO polypeptide extracellular domain may optionally comprise about 5 or less amino acids from either side of the transmembrane domain / extracellular domain boundary, as identified in the Examples or specification. Often, such polypeptides with and without signal peptides and nucleic acids encoding them are contemplated by the present invention.

  The approximate location of the “signal peptide” of the various PRO polypeptides disclosed herein is indicated herein and / or in the accompanying drawings. However, as noted, the C-terminal boundary of the signal peptide can vary, but it appears that it does not exceed about 5 amino acids on either side of the signal peptide C-terminal boundary as defined herein, The C-terminal boundary of the signal peptide can be identified according to criteria routinely used in the art 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 the polynucleotides encoding them, which are cleaved within the range that the signal peptide does not exceed about 5 amino acids on either side of the C-terminal boundary of the signal peptide identified herein, To be considered.

  A “PRO polypeptide variant” refers to a full-length native sequence PRO polypeptide sequence disclosed herein, a PRO polypeptide sequence that lacks the signal peptide disclosed herein, a PRO with or without the signal peptide disclosed herein. It means an active PRO polypeptide as described above or below having at least about 80% amino acid sequence identity with the extracellular domain of the polypeptide or other fragment of the full-length PRO polypeptide sequence 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 a full-length native sequence PRO polypeptide sequence disclosed herein, a PRO polypeptide sequence that lacks the signal peptide disclosed herein, a PRO polypeptide with or without the signal peptide disclosed herein. At least about 80% amino acid sequence identity, or at least about 81% amino acid sequence identity with the extracellular domain of the peptide or any other specifically defined fragment of the full-length PRO polypeptide sequence disclosed herein, or At least about 82% amino acid sequence identity, or at least about 83% amino acid sequence identity, or at least about 84% amino acid sequence identity, or 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, or low At least about 88% amino acid sequence identity, or at least about 89% amino acid sequence identity, or at least about 90% amino acid sequence identity, or 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, or at least about 94% amino acid sequence identity, or at least about 95% amino acid sequence identity, or at least about 96% amino acid sequence identity, or at least It has about 97% amino acid sequence identity, or at least about 98% amino acid sequence identity, and / or at least about 99% amino acid sequence identity. Typically, the PRO variant polypeptide is at least about 10 amino acids long, or at least about 20 amino acids long, or at least about 30 amino acids long, or at least about 40 amino acids long, or at least about 50 amino acids long, or at least about 60 amino acids long. Or at least about 70 amino acids long, or at least about 80 amino acids long, or at least about 90 amino acids long, or at least about 100 amino acids long, or at least about 150 amino acids long, or at least about 200 amino acids long, or at least about 300 amino acids long, Or more.

  “Percent (%) amino acid sequence identity” relative to the PRO polypeptide sequence identified herein introduces gaps as necessary to align the sequences and obtain maximum percent sequence identity, and any conservation Substitution is also defined as the percentage of amino acid residues in a candidate sequence that are identical to amino acid residues in a particular PRO polypeptide sequence, 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 are obtained using the sequence comparison computer program ALIGN-2, which provides the complete source code for the ALIGN-2 program in Table 1 below. It is done. 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, US Copyright Registration Number TXU510087 Registered under. The ALIGN-2 program is publicly available from Genentech, Inc., South San Francisco, California, and may be compiled from the source code given 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, the% amino acid sequence identity of a given amino acid sequence A with or against a given amino acid sequence B (with or with a given amino acid sequence B) A given amino acid sequence A (which can also be referred to as having or containing 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. If the length of amino acid sequence A is different from the length of amino acid sequence B, it will be appreciated that 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, Tables 2 and 3 show the calculation of% amino acid sequence identity to the amino acid sequence designated “PRO” of the amino acid sequence designated “Comparative Protein”. Wherein “PRO” represents the amino acid sequence of the subject temporary PRO polypeptide, “comparison protein” represents the amino acid sequence of the polypeptide to which the “PRO” polypeptide of interest is compared, “X”, “Y” and “Z” each represent a different virtual amino acid sequence.

  Unless otherwise noted, all% amino acid sequence identity values used herein are obtained using the ALIGN-2 computer program as described in the immediately preceding paragraph. However,% amino acid sequence identity values can also be obtained using the WU-BLAST-2 computer program (Altschul et al., Methods in Enzymology 266: 460-480 (1996)), as described below. 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 using WU-BLAST-2, the% amino acid sequence identity value is determined from (a) the subject PRO polypeptide having a sequence derived from a native PRO polypeptide, as determined by WU-BLAST-2. The number of identical identical amino acid residues between the amino acid sequence and the subject comparative amino acid sequence (i.e., a sequence that may be a PRO polypeptide variant against which the subject PRO polypeptide is compared) is expressed as (b ) Determined by the quotient divided by the total number of amino acid 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 with amino acid sequence B”, amino acid sequence A is the target comparative amino acid sequence, and amino acid sequence B is the target. The amino acid sequence of the PRO polypeptide.

Percent amino acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST2 (Altschul et al., Nucleic Acids Res. 25: 3389-3402 (1997)). The NCBI-BLAST2 sequence comparison program may be downloaded from http://www.ncbi.nlm.nih.gov or separately from the National Institute of Health, Bethesda, MD. NCBI-BLAST2 uses several search parameters, all of which are set to initial values, for example, unmask = possible, 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, the% amino acid sequence identity of a given amino acid sequence A with or against a given amino acid sequence B (with or against a given amino acid sequence B) (Which can also be referred to as a given amino acid sequence A) having or containing 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 NCBI-BLAST2, and Y is the total amino acid residue of B Is a number. If the length of amino acid sequence A is different from the length of amino acid sequence B, it will be recognized that the% amino acid sequence identity of A to B is different from the% amino acid sequence identity of B to A.

By “PRO variant polynucleotide” or “PRO variant nucleic acid sequence” is meant a nucleic acid molecule that encodes an active PRO polypeptide, as defined below, and the full-length native sequence PRO polypeptide disclosed herein. Any of the full-length native sequence PRO polypeptide sequence lacking the signal peptide disclosed herein, the extracellular domain of the PRO polypeptide with or without the signal peptide disclosed herein, or the full-length polypeptide sequence disclosed herein. Have at least 80% nucleic acid sequence identity with the nucleotide sequence encoding the other fragments. Typically, a PRO polypeptide variant polynucleotide comprises a full-length native sequence PRO polypeptide sequence disclosed herein, a full-length native sequence PRO polypeptide sequence that lacks a signal peptide disclosed herein, a signal sequence disclosed herein. At least about 80% nucleic acid sequence identity, or at least about 81 with a nucleic acid sequence encoding the extracellular domain of the PRO polypeptide sequence with or without, or any other fragment of the full-length PRO polypeptide sequence disclosed herein. % Nucleic acid sequence identity, or at least about 82% nucleic acid sequence identity, 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 Or at least about 86% nucleic acid sequence identity, or at least about 87% nucleic acid sequence identity, or 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, or at least about 96% nucleic acid sequence identity, or It has at least about 97% nucleic acid sequence identity, or at least about 98% nucleic acid sequence identity, or at least about 99% nucleic acid sequence identity. Variants do not contain the native nucleotide sequence.
Typically, the PRO variant polynucleotide is at least about 30 nucleotides in length, or at least about 60 nucleotides in length, or at least about 90 nucleotides in length, or at least about 120 nucleotides in length, or at least about 150 nucleotides in length, or At least about 180 nucleotides, or at least about 210 nucleotides, or at least about 240 nucleotides, or at least about 270 nucleotides, or at least about 300 nucleotides, or at least about 450 nucleotides, or at least about 600 nucleotides in length, or at least about 900 nucleotides in length, or longer.

  “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, Defined as the percentage of nucleotides in the candidate sequence that are identical to the nucleotides of the sequence. 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. However, for purposes herein,% nucleic acid sequence identity values are obtained using the sequence comparison computer program ALIGN-2, the complete source code for the ALIGN-2 program being given in Table 1 below. It is done. 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 with user documentation and under US Copyright Registration Number TXU510087 It is registered with. The ALIGN-2 program is publicly available from Genentech, South San Francisco, California, and may be compiled from the source code given 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 (with or to a given nucleic acid sequence D) A given nucleic acid sequence C (which can also be referred to as having or containing some% nucleic acid sequence identity) is calculated as follows:
100 times the fraction W / Z, where W is the number of nucleotides with a score matched by C and D alignment of the sequence alignment program ALIGN-2, and Z is the total number of nucleotides in D. If the length of nucleic acid sequence C is different from the length of nucleic acid sequence D, it will be recognized that 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, Tables 4 and 5 show how to calculate% nucleic acid sequence identity for a nucleic acid sequence called “PRO-DNA” of a nucleic acid sequence called “Comparative DNA”. Where “PRO-DNA” represents the tentative PRO-encoded nucleic acid sequence of interest, “comparison DNA” represents the nucleotide sequence of the nucleic acid molecule to which the “PRO-DNA” nucleic acid molecule of interest is compared, “N”, “L” and “V” each represent a different virtual nucleotide.

  Unless otherwise indicated, all% nucleic acid sequence identity values used herein are obtained using the ALIGN-2 computer program as described in the immediately preceding paragraph. However,% nucleic acid sequence identity values can also be obtained using the WU-BLAST-2 computer program (Altschul et al., Methods in Enzymology 266: 460-480 (1996)), as described below. 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 using WU-BLAST-2, the% nucleic acid sequence identity value is calculated as follows: (a) a PRO of a subject having a sequence derived from a native sequence PRO polypeptide-encoding nucleic acid as determined by WU-BLAST-2; A match between the nucleic acid sequence of the polypeptide-encoding nucleic acid molecule and the subject comparative nucleic acid molecule (ie, the sequence that may be a mutated PRO polynucleotide to which the subject PRO polypeptide-encoding nucleic acid molecule is compared). The number of identical nucleotides is determined by (b) the quotient divided by the total number of nucleotides of the subject PRO polypeptide-encoding nucleic acid sequence. For example, in the description “an isolated nucleic acid molecule comprising nucleic acid sequence A having or having at least 80% nucleic acid sequence identity with nucleic acid sequence B”, nucleic acid sequence A is a subject comparative nucleic acid molecule, Sequence B is the nucleic acid sequence of the subject PRO polypeptide-encoding nucleic acid molecule.

Percent nucleic acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST2 (Altschul et al., Nucleic Acids Res. 25: 3389-3402 (1997)). The NCBI-BLAST2 sequence comparison program may be downloaded from http://www.ncbi.nlm.nih.gov or separately from the National Institute of Health, Bethesda, MD. NCBI-BLAST2 uses several search parameters, all of which are set to initial values, for example, unmask = possible, 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 sequence comparison, the% nucleic acid sequence identity of, or relative to, a given nucleic acid sequence C (to or against a given nucleic acid sequence D) (Which can also be referred to as a given nucleic acid sequence C having or containing a certain percentage of nucleic acid sequence identity) is calculated as follows:
100 times the fraction W / Z, where W is the number of nucleotides in the score that are identical by the C and D alignment of the sequence alignment program NCBI-BLAST2, and Z is the total number of nucleotides in D. If the length of nucleic acid sequence C is different from the length of nucleic acid sequence D, it will be recognized that 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 polynucleotide encodes an active PRO polypeptide and is capable of hybridizing to a nucleotide sequence encoding the full-length PRO polypeptide disclosed herein, preferably under stringent hybridization and wash conditions. Nucleic acid molecule. 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 polypeptide in situ within recombinant cells, since at least one component of PRO polypeptide in its natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step.
An “isolated” PRO polypeptide-encoding nucleic acid or other polypeptide-encoding nucleic acid is identified and separated from at least one contaminating nucleic acid molecule normally associated with the natural source of the polypeptide-encoding nucleic acid. Is a molecule. An isolated polypeptide-encoding nucleic acid molecule is other than in the form or setting in which it is found in nature. Thus, an isolated polypeptide-encoding nucleic acid is distinguished from a specific polypeptide-encoding nucleic acid molecule present in natural cells. However, isolated polypeptide-encoding nucleic acid molecules include, for example, those contained in cells that normally express a polypeptide in which the nucleic acid molecule is at a chromosomal location different from that of natural cells.

The term “control sequence” refers to a DNA sequence necessary to express a coding sequence operably linked 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 contributes to 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 monoclonal antibody (including agonists, antagonists, and neutralizing antibodies), anti-PRO antibody compositions with multi-epitope specificity, single chain anti-antibody It specifically covers PRO antibodies and anti-PRO antibody fragments (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 individual antibodies in the population may be present in small amounts. Refers to an antibody obtained from a population.
The “stringency” of a hybridization reaction is usually 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 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 the stringency. 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 cleaning. 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; or (3) 50% formamide at 42 ° C. 5 × SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH .8), 0.1% sodium pyrophosphate, 5 × Denhardt's solution, sonicated salmon sperm DNA (50 μg / ml), 0.1% SDS, and 10% dextran sulfate and 0.2 × SSC at 42 ° C. ( Sodium chloride / sodium citrate) and 50% formamide at 55 ° C., followed by a high stringency wash consisting of 0.1 × SSC with EDTA at 55 ° C.
“Moderate stringency conditions” are identified as described in Sambrook et al., Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Press, 1989, and wash solutions and hybridizations below the stringency described above. Including the use of conditions (eg, temperature, ionic strength and% SDS). Examples of moderate stringency conditions are: 20% formamide, 5 × SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5 × Denhardt's solution, 10% dextran sulfate, and 20 mg / such as overnight incubation at 37 ° C. in a solution containing mL of denatured sheared salmon sperm DNA, followed by washing the filter at 37-50 ° C. in 1 × SSC. Those skilled in the art will recognize how to adjust temperature, ionic strength, etc. as needed to accommodate factors such as probe length.

The term “epitope tag” as used herein refers to a chimeric polypeptide comprising a PRO polypeptide fused to a “tag polypeptide”. A tag polypeptide has a sufficient number of residues to provide an epitope from which the antibody can be produced, but its length is short enough not to inhibit the activity of the fused PRO polypeptide. 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 amino acid residues).
The term “immunoadhesin” as used herein refers to an antibody-like molecule that combines the binding specificity of a heterologous protein (“adhesin”) with the effector function of an immunoglobulin constant domain. Structurally, immunoadhesins comprise a fusion of an amino acid sequence with the desired binding specificity other than the antigen recognition and binding site of an antibody (ie, a “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. Immunoadhesin immunoglobulin constant domain sequences 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.

For purposes herein, “active” or “activity” refers to a form of a polypeptide that retains the biological and / or immunological activity of a naturally or naturally occurring PRO, where “biological” A “logical” activity is a biological function (inhibitory or stimulatory) caused by a naturally or naturally occurring PRO that is capable of generating antibodies against the antigenic epitope of the naturally or naturally occurring PRO. "Immological" activity refers to the ability to induce the production of antibodies against the antigenic epitope of a naturally occurring or naturally occurring PRO.
The term “antagonist” is used in the broadest sense and includes any molecule that partially or fully prevents, inhibits, or neutralizes the biological activity of a native PRO polypeptide disclosed herein. Similarly, the term “agonist” is also used in the broadest sense and includes 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, antisense oligonucleotides, 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 molecule and measuring a detectable change in one or more biological activities normally associated with the PRO polypeptide. May be included.

“Treatment” refers to both curative treatment, prophylactic therapy, and preventive therapy, in which a patient is prevented or reduced (reduced) in a targeted pathological condition or disease. Those in need of treatment include those already suffering from the disease, as well as those susceptible to the disease or those in which the disease has been prevented.
“Chronic” administration refers to administration of a drug in a continuous manner, unlike the acute manner, and maintaining the initial therapeutic effect (activity) for a long time. An “intermittent” administration is a treatment that is not made continuously without interruption, but rather is essentially periodic.
“Mammals” for therapeutic purposes include humans, household and agricultural animals, and zoo, sports or pet animals such as dogs, cats, cows, horses, sheep, pigs, goats, rabbits, etc. Refers to any animal classified as a mammal. 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 dextrin; 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 ^™ , polyethylene glycol (PEG), and PLURONICS ^™ .

“Antibody fragments” comprise a portion of an intact antibody, preferably the antigen binding or variable region of the intact antibody. Examples of antibody fragments 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 variable domain interact to determine the antigen binding site on the surface of the V _H -V _L dimer. Correctly, the six CDRs confer antigen binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for 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 usually produced as pairs of Fab ′ fragments, with a hinge cysteine between them. Other chemical couplings of antibody fragments are also known.
The “light chains” of antibodies (immunoglobulins) from any vertebrate species are assigned one of two distinct types called kappa and lambda, based on the amino acid sequence of their constant domains.
Depending on the amino acid sequence of the heavy chain constant domain, immunoglobulins can be assigned to different classes. There are five main classes of immunoglobulins: IgA, IgD, IgE, IgG and IgM, some of which are further divided into subclasses (isotypes) such as IgG1, IgG2, IgG3 and IgG4, IgA and IgA2.

“Single-chain Fv” or “sFv” antibody fragments comprise the V _H and V _L domains of antibody, wherein these domains are present in a single polypeptide chain. Preferably, the Fv polypeptide further comprises a polypeptide linker between the _VH and _VL domains that allows the sFv to form the desired structure for antigen binding. For a review of sFv, see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore, 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 domain of the other chain to produce two antigen binding sites. Diabodies are well described, for example, in 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. Contaminant components of the natural environment are substances that interfere with the use of the antibody in diagnosis or therapy, and include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In a preferred embodiment, the antibody comprises (1) at least 15 residues by using a spinning cup sequenator until (1) greater than 95% by weight, most preferably greater than 99% by weight as measured by the Lori method. Sufficient to obtain the N-terminal or internal amino acid sequence of (2), 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 of a specific polypeptide does not substantially bind to any other polypeptide or polypeptide epitope, and It binds to a specific polypeptide or an epitope of a specific polypeptide.
The term “label” when used herein refers to a detectable compound or composition that binds directly or indirectly to the antibody to produce a “labeled” antibody. 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.

The term “immune related disease” refers to a disease in which a component of the mammalian immune system is responsible for, mediates or contributes to the pathological condition of the mammal. Also included are diseases in which an improved effect is imparted to the progression of the disease by stimulation or intervention of an immune response. Included within this term are immune-mediated inflammatory diseases, non-immune-mediated inflammatory diseases, infectious diseases, immune deficiencies, abnormal growth and the like.
The term “T cell mediated disease” means a disease in which T cells directly or indirectly mediate or contribute to a mammalian morbidity. T cell mediated diseases are associated with cell mediated effects, lymphokine mediated effects, etc., and even B cell related effects if, for example, B cells are stimulated by lymphokines secreted by T cells.
Examples of immune related and inflammatory diseases that can be treated according to the present invention, some of which are immune or T cell mediated include systemic lupus erythematosus, rheumatoid arthritis, juvenile chronic arthritis, spondyloarthritis, systemic Sclerosis (scleroderma), idiopathic inflammation myopathy (dermatomyositis, polymyositis), Sjogren's syndrome, systemic vasculitis, sarcoidosis, autoimmune hemolytic anemia (immune regenerative anemia, paroxysmal nocturnal hemoglobinuria) , Autoimmune thrombocytopenia (idiopathic thrombocytopenic purpura, immune-mediated thrombocytopenia), thyroiditis (Graves disease, Hashimoto thyroiditis, juvenile lymphocytic thyroiditis, atrophic thyroiditis), diabetes mellitus, immune mediation Kidney disease (glomerulonephritis, tubulointerstitial nephritis), demyelinating diseases of the central and peripheral nervous systems, such as multiple sclerosis, idiopathic discontinuous polyneuropathy, or Guillain-Barre syndrome, and chronic inflammatory prolapse Voluntary Polyneuropathy, hepatobiliary diseases such as infectious hepatitis (A, B, C, D, E, and other nonhepatotropic viruses), autoimmune chronic active hepatitis, primary bile Cirrhosis, granulomatous hepatitis, and sclerosing cholangitis, inflammatory bowel disease (ulcerative colitis; Crohn's disease), gluten-sensitive bowel disease, and Whipple's disease, bullous skin disease, erythema multiforme and contact Autoimmune or immune-mediated skin diseases including atopic dermatitis, psoriasis, allergic diseases such as asthma, allergic rhinitis, atopic dermatitis, food hypersensitivity and urticaria, pulmonary immune diseases such as eosinophilic pneumonia, idiopathic Transplantation related diseases including idiopathic pulmonary fibrosis and hypersensitivity pneumonia, rejection and graft versus host disease. Infectious diseases such as viral diseases such as AIDS (HIV infection), hepatitis A, B, C, D and E, herpes, bacterial infection, fungal infection, protozoan infection and parasitic infection are also included .

  The term “effective amount” refers to the concentration or amount of PRO polypeptide and / or agonist / antagonist that results in the achievement of a specifically stated purpose. An “effective amount” of a PRO polypeptide or agonist or antagonist thereof can be determined empirically. Further, “therapeutically effective amount” refers to the concentration or amount of PRO polypeptide and / or agonist / antagonist effective to achieve the stated therapeutic effect. This amount can also be determined empirically.

The term “cytotoxic agent” as used herein refers to a substance that inhibits or prevents the function of cells and / or causes destruction of cells. The term includes radioisotopes (eg, I ¹³¹ , I ¹²⁵ , Y ⁹⁰ and Re ¹⁸⁶ ), chemotherapeutic agents, and toxins such as enzymatically active toxins from bacteria, fungi, plants or animals, or fragments thereof. Is done.
A “chemotherapeutic agent” is a chemical compound useful in the treatment of cancer. Examples of chemotherapeutic agents include adriamycin, doxorubicin, epirubicin, 5-fluorouracil, cytosine arabinoside ("Ara-C"), cyclophosphamide, thiotepa, busulfan, cytoxin, taxoids such as paclitaxel (Taxol, Bristol -Myers Squibb Oncology, Princeton, NJ) and doxetaxel (Taxotere, Rhone-Poulenc Rorer, Antony, France), taxotere, methotrexate, cisplatin, melphalan, vinblastine, bleomycin, etoposide, ifosfamide, mitomycin C, mitoxantrone, bincristron Vinorelbine, carboplatin, teniposide, daunomycin, carminomycin, aminopterin, dactinomycin, mitomycin, esperamicin (see U.S. Pat.No. 4,675,187), melphalan And other related nitrogen mustards. Also included in this definition are hormone-like drugs that act to regulate or inhibit hormonal action on tumors such as tamoxifen and onapristone.
As used herein, a “growth inhibitor” refers to a compound or composition that inhibits the growth of cells, particularly cancer cells that overexpress any gene identified herein, in vitro or in vivo. That is, growth inhibitors significantly reduce the proportion of cells that overexpress such genes in the S phase. Examples of growth inhibitory agents include agents that block cell cycle progression (at a place other than S phase), such as agents that induce G1 arrest or M-phase arrest. Classic M-phase blockers include vincas (vincristine and vinblastine), taxol, and topo II inhibitors such as doxorubicin, epirubicin, daunorubicin, etoposide, and bleomycin. These agents that cause G1 arrest also overflow S phase arrest, for example DNA alkylating agents such as tamoxifen, prednisone, dacarbazine, mechloretamine, cisplatin, methotrexate, 5-fluorouracil, and ara-C. More information can be found in The Molecular Basis of Cancer, Mendelsohn and Israel, ed., Chapter 1, Title `` Cell cycle reguration, oncogene, and antineoplastic drugs '', Murakami et al. (WB Saunders: Philadelphia, 1995), especially p13. it can.

The term “cytokine” is a general term for proteins that are released from one cell population and act as intercellular mediators to other cells. Examples of such cytokines are lymphokines, monokines, and traditional polypeptide hormones. Cytokines include growth hormones such as human growth hormone, N-methionyl human growth hormone, and bovine growth hormone; parathyroid hormone; thyroxine; insulin; proinsulin; relaxin; prorelaxin; glycoprotein hormones such as follicle stimulating hormone ( FSH), thyroid stimulating hormone (TSH), and luteinizing hormone (LH); liver growth factor; fibroblast growth factor; prolactin; placental lactogen; tumor necrosis factor-α and -β; Mueller inhibitor; mouse gonadotropin related Activin; vascular endothelial growth factor; integrin; thrombopoietin (TPO); nerve growth factor such as NGF-β; platelet growth factor; transforming growth factor (TGF) such as TGF-α and TGF-β; insulin-like Growth factor-I and II Erythropoietin (EPO); osteoinductive factor; interferons such as interferon-α, -β, and -γ; colony stimulating factors (CSFs) such as macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF) ); And granulocyte-CSF (G-CSF); interleukins (ILs) such as IL-1, IL-1α, IL-2, IL-3, IL-4, IL-5, IL-6, IL- 7, IL-8, IL-9, IL-11, IL-12; tumor necrosis factors such as TNF-α and TNF-β; and other polypeptide factors including LIF and kit ligand (KL). As used herein, the term cytokine includes proteins from natural sources or from recombinant cell culture and is the biologically active equivalent of native sequence cytokines.
The term “immunoadhesin” as used herein refers to an antibody-like molecule that combines the binding specificity of a heterologous protein (“adhesin”) with the effector function of an immunoglobulin constant domain. Structurally, immunoadhesins comprise a fusion of an amino acid sequence with the desired binding specificity other than the antigen recognition and binding site of an antibody (ie, a “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. Immunoadhesin immunoglobulin constant domain sequences 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.
The term “inflammatory cells” as used herein refers to cells that enhance an inflammatory response, such as mononuclear cells, eosinophils, macrophages, and polymorphonuclear neutrophils (PMN).

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 disclosed in further detail in the Examples below. Note that proteins produced in separate rounds of expression are given different PRO numbers, but UNQ numbers are unique to any given DNA and encoded protein 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 herein referred to as their origin or form of preparation. Regardless, it is referred to as “PRO / number”.
As disclosed in the examples below, various cDNA clones have been deposited with the ATCC. The de facto 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 PRODNA and / or by synthesizing the desired PRO polypeptide. One skilled in the art will recognize 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 PRO.
Mutations in the native full-length sequence PRO or various domains of the PRO described herein may be made using any of the techniques and guidelines for conservative and non-conservative mutations described, for example, in US Pat. No. 5,364,934. be able to. A mutation may be a substitution, deletion or insertion of one or more codons that encode a PRO that results in a change in the amino acid sequence of the PRO as compared to the native sequence PRO. In some cases, the mutation is a substitution of at least one amino acid PRO by one or more domains of any other amino acid. Guidance on which amino acid residues are inserted, substituted or deleted without adversely affecting the desired activity is compared by comparing the sequence of PRO with that of known protein molecules of homology. Found by minimizing the number of amino acid sequence changes made within the region. 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 or deletions can optionally be in the range of 1 to 5 amino acids. Permissible mutations are determined by systematically making amino acid insertions, deletions or substitutions in the sequence and testing the resulting mutants for activity exhibited by the full-length or mature native protein.

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.

ＰＲＯポリペプチドの機能又は免疫学的同一性の実質的な修飾は、(ａ)置換領域のポリペプチド骨格の構造、例えばシート又は螺旋配置、(ｂ)標的部位における分子の電荷又は疎水性、又は(ｃ)側鎖の嵩を維持しながら、それらの効果において実質的に異なる置換基を選択することにより達成される。自然に生じる残基は共通の側鎖特性に基づいてグループに分けることができる：
(１)疎水性：ノルロイシン, met, ala, val, leu, ile;
(２)中性の親水性：cys, ser, thr;
(３)酸性：asp, glu;
(４)塩基性：asn, gln, his, lys, arg;
(５)鎖配向に影響する残基：gly, pro; 及び
(６)芳香族：trp, tyr, phe。 In a particular embodiment, subject conservative substitutions are shown in Table 6 under the preferred substitutions. If such a substitution results in a change in biological activity, a more substantial change is introduced and the product screened as shown in Table 6 as an exemplary substitution or as further described in the amino acid classification below. Is done.

Substantial modification of the function or immunological identity of the PRO polypeptide may include: (a) the structure of the polypeptide backbone of the substitution region, such as a sheet or helical arrangement, (b) the molecular charge or hydrophobicity at the target site, or (c) achieved by selecting substituents that differ substantially in their effect while maintaining the bulk of the side chains. 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) Aromatic: trp, tyr, phe.

Non-conservative substitutions are those that require one member of these classes to be exchanged for another. Residues so substituted can also be introduced at conservative substitution sites, or preferably at the remaining (non-conserved) sites.
Mutations can be made using methods known in the art such as oligonucleotide-mediated (site-specific) mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis [Carter et al., Nucl. Acids Res., 13: 4331 (1986); Zoller et al., Nucl. Acids Res., 10: 6487 (1987)], cassette mutagenesis [Wells et al., Gene, 34: 315 (1985)], restricted selective mutagenesis [Wells et al., Philos. Trans. R. Soc. London SerA, 317: 415 (1986)], or other known techniques performed on cloned DNA Thus, PRO mutant DNA can also be prepared.
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, (WH Freeman & Co., NY); 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 are included within the scope of the present invention. One type of covalent modification involves reacting an amino acid residue targeted by a PRO polypeptide with an organic derivatization reagent capable of reacting with a selected side chain or N- or C-terminal residue of PRO. . 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 and vice versa. Commonly used crosslinking agents are, for example, 1,1-bis (diazoacetyl) -2-phenylethane, glutaraldehyde, N-hydroxysuccinimide ester, such as 4-azidosalicylic acid, 3,3′-dithiobis (succinimidyl) Homobifunctional imide esters including disuccinimidyl esters such as propionate), bifunctional maleimides such as bis-N-maleimide-1,8-octane, and methyl-3-[(p-azidophenyl)- Includes drugs such as dithio] propioimidate.
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. For purposes herein, “altering the native glycosylation pattern” refers to the deletion of one or more carbohydrate moieties found in the native sequence PRO (removal of potential glycosylation sites or chemical and / or enzymatic means). Is intended to mean the addition of one or more glycosylation sites that are not present in the native sequence PRO. In addition, this phrase 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 alteration 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 generate 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). Are listed.
Removal of carbohydrate moieties present on the PRO polypeptide can be accomplished either 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 exo-glycosidases as described in Thotakura et al., Meth. Enzymol. 138: 350 (1987).

Another type of covalent modification of PRO is described in US Pat. No. 4,640,835 to one of various non-proteinaceous polymers of PRO polypeptides, such as polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylene. No. 4,496,689; No. 4,301,144; No. 4,670,417; No. 4,791,192 or No. 4,179,337.
The PRO polypeptides of the present invention may also be modified by methods that form chimeric molecules comprising PRO fused to other heterologous polypeptides or amino acid sequences.
In one embodiment, such a chimeric molecule comprises a fusion of a PRO with a tag 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 PRO. The presence of such an epitope tag form of PRO can be detected using an antibody against the tag polypeptide. The provision of the epitope tag also allows the PRO to be easily 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) tag; 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 a bivalent form of a chimeric molecule (also referred to as “immunoadhesin”), such a fusion may be the Fc region of an IgG1 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 of 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, CA (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 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. PRO-encoded genes can also be obtained by genomic libraries, oligonucleotide synthesis, or other known synthetic methods (eg, automated nucleic acid synthesis).
Libraries can be screened with probes designed to identify the gene of interest or the protein encoded thereby (eg, an antibody to PRO or an oligonucleotide of at least about 20-80 bases). Screening of cDNA or genomic libraries with selected probes is performed using standard procedures described, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989). can do. Another means of isolating the gene encoding PRO is by using PCR [Sambrook et al., Supra; Dieffenbach et al., PCR Primer: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995)].
The following examples describe screening techniques for cDNA libraries. 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. Labeling methods 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 given by Sambrook et al., Supra.

Sequences identified in such library screening methods can be compared and aligned with other well-known sequences deposited in public databases such as Genbank or other personal sequence databases and made available to the public. . Sequence identity (either at the amino acid or nucleotide level) within a defined region of the molecule or over the full length sequence can be determined using methods known in the art and described herein. it can.
Nucleic acids having protein coding sequences use the deduced amino acid sequences disclosed herein for the first time and, if necessary, Sambrook et al. 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 described herein for PRO production, promoters derived, transformants selected, or the desired sequence encoded. 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 one 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.
Methods of eukaryotic cell transfection and prokaryotic cell transformation, such as CaCl ₂ , CaPO ₄ , liposome-mediated and electroporation, are generally 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 described in Sambrook et al., Supra, is generally used for prokaryotes. Infection with Agrobacterium tumefaciens has been identified in certain species as described in Shaw et al., Gene, 23: 315 (1983) and WO 29/05859 published 29 June 1989. Used for transformation of plant cells. For mammalian cells without such cell walls, the calcium phosphate precipitation method of Graham and van der Eb, Virology, 52: 456-457 (1978) can be used. 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 for introducing DNA into cells, such as nuclear microinjection, electroporation, intact cells, or bacterial protoplast fusion using polycations such as polybrene, polyornithine, etc. are also used. For various techniques for transforming mammalian cells, see Keown et al., Methods in Enzymology, 185: 527-537 (1990) and Mansour et al., Nature, 336: 348-352 (1988).

Suitable host cells for cloning or expressing DNA in the vectors 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 suitable 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 (e.g., Bacillicenifol as described in DD 266,710 published April 12, 1989). Miss 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 affect gene mutations in genes encoding foreign proteins in the host, examples of such hosts include E. coli W3110 strain 1A2 having the complete genotype tonA. E. coli W3110 strain 9E4 with complete genotype tonA ptr3; E. coli W3110 strain 27C7 (ATCC 55,244) with complete genotype tonA prt3 phoA E15 (argF-lac) 169 degP ompT kan ^r ; complete genotype tonA ptAph3 US patents issued and August 7, 1990; W3110 strain 40B4 E. coli is a 37D6 shares with a non-kanamycin resistant degP deletion mutation; E15 (argF-lac) 169 degP ompT rbs7 ilvG kan r E. coli W3110 strain 37D6 with a An E. coli strain having disclosed mutated periplasmic protease No. 4,946,783. Alternatively, in vitro methods of cloning such as PCR or other nucleic acid polymerase polymerase reactions are preferred.

  In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for PRO-encoding vectors. Saccharomyces cerevisia is a commonly used lower eukaryotic host microorganism. Other examples include Schizosaccharomyces pombe (Beach and Nurse, Nature, 290: 140 [1981]; EP 139,383 issued May 2, 1985); Kluyveromyces hosts (US Pat. No. 4,943,529; Fleer et al., Bio / Technology, 9: 968-975 (1991)), e.g., 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), K. wickeramii (ATCC 24,178), K. waltii (ATCC 56,500), Cedro 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; Trichodel Malaysia (reesia) ( EP 244,234); red mold (Case et al., Proc. Natl. Acad. Sci. USA, 76: 5259-5263 [1979]); schwanniomyces, eg, schwaniomyces occidentalis (1990 EP 394,538, issued October 31, 1991); and filamentous fungi such as Neurospora, Penicillium, Tolypocladium (WO 91/00357 published January 10, 1991); For example, pseudonogenic Koji fungi (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 black mold (Kelly and Hynes, EMBO J., 4: 475-479 [1985]). Methylotropic yeast is suitable here, but is not limited to: Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula A yeast capable of growing on methanol selected from the genus consisting of A list of specific species, illustrative of this yeast classification, can be found in C. Anthony, The Biochemistry of Methylotrophs, 269 (1982).

  Suitable host cells for the expression of glycosylated PRO are derived from multicellular organisms. Examples of invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, and plant cells. Examples of useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples are 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 tumors Contains cells (MMT 060562, ATTC CCL51). The selection of an appropriate host cell is considered to be within the skill in the art.

3. Selection and use of replicable vectors Nucleic acids encoding PRO (eg, cDNA or genomic DNA) are inserted into replicable vectors 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 suitable vectors containing one or more of these components.
PRO is not only produced directly by recombinant techniques, but also as a fusion peptide with a heterologous polypeptide that is a signal sequence or a mature protein or other polypeptide having a specific cleavage site at the N-terminus of the polypeptide. Is also produced. 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, for example, the yeast invertase leader, alpha factor leader (Saccharomyces and Kluyveromyces alpha factor leader, the latter described in US Pat. Or acid phosphatase leader, C. albicans glucoamylase leader (EP 362,179, issued April 4, 1990), or WO 90/13646 published on November 15, 1990. May be the signal described in the issue. In mammalian cell expression, signal sequences derived from the same or related species of secreted polypeptides as well as mammalian signal sequences such as viral secretion leaders may be used for direct secretion of proteins.

Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast and viruses. The origin of replication from 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 selectable markers suitable for mammalian cells are those that allow the identification of cells that can take up the PRO-encoding nucleic acid, such as DHFR or thymidine kinase. A suitable host cell using wild type DHFR is a CHO strain defective in DHFR activity prepared and grown as described by Urlaub et al., Proc. Natl. Acad. Sci. USA, 77: 4216 (1980). Cell. 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); Kingman et al., Gene, 7: 141 (1979); Tschemper et al., Gene, 10: 157 (1980)]. The trp1 gene provides a selectable marker for a mutant strain of yeast lacking the ability to grow in the presence of tryptophan, such as ATCC No. 44076 or PEP4-1 [Jones, Genetics, 85:12 (1977)].

Expression and cloning vectors usually contain a promoter operably linked to the PRO-encoding nucleic acid sequence and directed to mRNA synthesis. Promoters that are recognized by a variety of potential 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 PRO.
Examples of suitable promoter sequences for use in yeast hosts include 3-phosphoglycerate kinase [Hitzeman et al., J. Biol. Chem., 255: 2073 (1980)] or other glycolytic enzymes [Hess et al. , J. Adv. Enzyme Reg., 7: 149 (1968); Holland, Biochemistry, 17: 4900 (1978)], eg enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphoflur Ctokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triose phosphate isomerase, phosphoglucose isomerase, and glucokinase.
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 dehydrogenases and enzymes that utilize maltose and galactose. Suitable vectors and promoters for use in expression by yeast are further described in EP 73,657.

PRO transcription from vectors in mammalian host cells is, for example, polyomavirus, infectious epithelioma virus (UK 2,211,504 published July 5, 1989), adenovirus (eg adenovirus 2), bovine papilloma virus, avian Promoters derived from genomes of viruses such as sarcoma virus, cytomegalovirus, retrovirus, hepatitis B virus and simian virus 40 (SV40), heterologous mammalian promoters such as actin promoter or immunoglobulin promoter, and heat shock promoter Are controlled as long as such promoters are compatible with the host cell system.
Transcription of PRO-encoding DNA 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 of replication origin (100-270 base pairs), the cytomegalovirus early promoter enhancer, the late polyoma enhancer of replication origin and the adenovirus enhancer. Enhancers can be spliced into the vector at positions 5 'or 3' of the PRO coding sequence, but are preferably located 5 'from the promoter.
Also, expression vectors used in eukaryotic host cells (nucleated cells from yeast, fungi, insects, plants, animals, humans, or other multicellular organisms) are required for transcription termination and mRNA stabilization. Also includes sequences. 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 that are transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding PRO.
In addition, other methods, vectors and host cells suitable for adapting to the synthesis of PRO in recombinant vertebrate cell culture are described in Gething et al., Nature, 293: 620-625 (1981); Mantei et al., Nature, 281: 40-46 (1979); EP 117,060; and EP 117,058.

4). Gene Amplification / Expression Detection Gene amplification and / or expression can be performed using a suitably labeled probe based on the sequences provided herein, for example, the conventional Northern blotting method to quantify mRNA transcription [Thomas , Proc. Natl. Acad. Sci. USA, 77: 5201-5205 (1980)], Southern blotting, 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 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 PRO expression 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 PRO from recombinant cell proteins or polypeptides. The following procedure 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; SDS-PAGE; Precipitation; gel filtration using, for example, Sephadex G-75; protein A sepharose column excluding contaminants such as IgG; and metal chelation column to bind the epitope tag form of PRO. Various 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) may be used. 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. Tissue distribution The location of a tissue that expresses PRO can be identified by measuring mRNA expression in various human tissues. The location of such genes provides information on tissues that are most likely to be affected by the PRO polypeptide stimulatory and inhibitory activity. The location of the gene in a particular tissue also provides sample tissue for the activity inhibition assay discussed below.
As described above, gene expression in various tissues is determined by conventional Southern blot, Northern blot for quantification of mRNA transcription (Thomas, Proc. Natl. Acad. Sci. USA, 77: 5201-5205 [1980]. ), Dot blot (DNA analysis), or in situ hybridization, using appropriate labeled probes based on the sequences provided herein. Alternatively, antibodies capable of recognizing specific duplexes including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes may be used.
Alternatively, gene expression in various tissues can also be measured by immunological methods such as immunohistological staining of tissue fragments and cell culture or body fluid assays to directly quantify gene products. Antibodies useful for immunohistological staining and / or assay of sample solutions may be monoclonal or polyclonal and are prepared from any animal. Conveniently, the antibody is fused to the native sequence PRO polypeptide, or to a synthetic peptide based on a DNA sequence encoding the PRO polypeptide, or to a DNA encoding the PRO polypeptide and encodes a specific antibody epitope. It can be prepared against exogenous sequences. General techniques for generating antibodies and specific protocols for Northern blots and in situ hybridization are provided below.

F. Antibody Binding Studies The activity of PRO polypeptides can be further demonstrated by antibody binding studies, in which the ability of anti-PRO antibodies to inhibit each of the effects of PRO polypeptides on tissue cells is tested. The Exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heteroconjugate antibodies, the preparation of which is described below.
Antibody binding studies may be performed with known assays, such as competitive binding assays, direct and indirect sandwich assays, and immunoprecipitation assays. Zola, Monoclonal Antibodies: A Manual of Techniques, pp. 147-158 (CRC Press, Inc., 1987).
Competitive binding assays are based on the ability of a labeled standard to compete with a test analyte for binding to a limited amount of antibody. The amount of target protein in the test sample is inversely proportional to the amount of standard that binds to the antibody. To facilitate the measurement of the amount of standard bound, the antibody is preferably insolubilized before or after competition, easily from standards and analytes in which the standard and analyte bound to the antibody remain unbound. Make it separable.
The sandwich assay involves the use of two antibodies, each capable of binding to a different immunogenic portion, or epitope, of the protein to be detected. In the sandwich assay, the test sample analyte binds to the first antibody immobilized on the solid support, and then the second antibody binds to the analyte, thus forming an insoluble ternary complex. See, for example, US Pat. No. 4,376,110. The second antibody may be labeled with a detectable moiety (direct sandwich assay) or measured using an anti-immunoglobulin antibody labeled with a detectable moiety (indirect sandwich assay). For example, one form of sandwich assay is an ELISA assay, in which case the detectable component is an enzyme.
For immunohistochemistry, tissue samples may be fresh or frozen, embedded in paraffin, and fixed with a preservative such as formalin, for example.

G. Cell-based assays Cell-based assays and animal models of immune-related diseases can be used to further understand the relationship between the genes and polypeptides identified herein and the progression and pathology of immune-related diseases. .
In a different method, cells of a cell type known to be involved in a particular immune related disease are transfected with the cDNAs described herein and the ability of these cDNAs to stimulate or inhibit immune function is analyzed. Appropriate cells are transfected with the desired gene and immune function activity is monitored. Such transfected cell lines are then used to test the ability of a poly- or monoclonal antibody or antibody composition to stimulate or inhibit immune function, for example to modulate T cell proliferation or inflammatory cell invasion. it can. Cells transfected with the coding sequences of the genes identified here can further be used to identify candidate drugs for the treatment of immune related diseases.
In addition, primary cultures derived from transgenic animals (as described below) can be used for the cell-based assays herein, but stable cell lines are preferred. Techniques for deriving continuous cell lines from transgenic animals are well known in the art (see Small et al., Mol. Cell. Biol. 5, 642-648 [1985]).
One suitable cell-based assay is the mixed lymphocyte reaction (MLR). Current Protocols in Immunology, unit 3.12; published by JE Coligan, AMKruisbeek, DHMarglies, EMShevach, W. Strober, National Institutes of Health, John Wiley & Sons, Inc. In this assay, the ability of a test compound to stimulate or inhibit the proliferation of activated T cells is assayed. The suspension of responder T cells is cultured with allogeneic stimulator cells, and the proliferation ability of the T cells is measured by incorporation of tritiated thymidine. This assay is a common measure of T cell reactivity. Because many T cells respond and activate to produce IL-2, the difference in responsiveness in this assay partially reflects the difference in IL-2 production by the responding cells. MLR results can be confirmed by standard lymphokine (IL-2) detection assays. See Current Protocols in Immunology, above, 3.15.6.3.
Proliferative T cell responses in the MLR assay are due to the direct mitogenic properties of the molecule being assayed or to activation induced by an external antigen. Further proof of the T cell stimulating activity of the PRO polypeptide can be obtained by a costimulation assay. T cell activation includes an antigen-specific signal mediated through a T cell receptor (TCR) and a costimulatory signal mediated through a second ligand binding interaction, eg, a B7 (CD80, CD86) / CD28 binding interaction. is required. CD28 cross-linking increases secretion of lymphokines by activated T cells. T cell activation has both negative and positive controls through the binding of ligands with negative or positive effects. CD28 and CTLA-4 are related glycoproteins of the Ig superfamily that bind to B7. CD28 binding to B7 has a positive costimulatory effect on T cell activation; conversely, CTLA-4 binding to B7 has a negative T cell deactivating effect. Chambers. CA and Allison. JP, Curr. Opin. Immunol. (1997) 9: 396. Schwartz, RH, Cell (1992) 71: 1065; Linsey, PS and Ledbetter. JA Annu. Rev. Immunol. (1993) 11: 191; June, CH, et al. Immunol. Today (1994) 15: 321; Immunity (1994) 1: 405. In a costimulation assay, the PRO polypeptide is assayed for T cell costimulatory or inhibitory activity.

PRO polypeptides, and other compounds of the present invention, are stimulators of T cell proliferation (costimulators) and agonists such as agonist antibodies as determined by MLR and costimulation assays, but are, for example, attenuated, optimal Useful for treating immune related diseases characterized by low or poor immune function. These diseases are treated by stimulating T cell proliferation and activation (and T cell mediated immunity) and enhancing immune responses in mammals by administration of stimulatory compounds, such as stimulatory PRO polypeptides. The stimulatory polypeptide can be, for example, a PRO polypeptide or an agonist antibody thereof.
Direct use of stimulatory compounds as in the present invention is tumor necrosis that binds to 4-1BB glycoprotein, a ligand expressed on prime T cells (4-1BBL) and signals T cell activation and growth. This was demonstrated in experiments using members of the factor receptor family. Alderson, ME et al., J. Immunol. (1994) 24: 2219.
The use of agonist stimulating compounds has also been demonstrated experimentally. Activation of 4-1BB by treatment with an agonist anti-4-1BB antibody enhances eradication of the tumor. Hellstrom. I. and Hellstrom, KE, Crit. Rev. Immunol. (1998) 18: 1. Immunoadjuvant treatment for tumor treatment, described in more detail below, is another example of the use of the stimulatory compounds of the present invention.
In addition, an immune stimulating or enhancing effect can be achieved by antagonizing or inhibiting the activity of PRO found to be inhibitory in the MLR assay. By negating the inhibitory activity of the compound, a net stimulatory effect is produced. A suitable antagonist / inhibitory compound is an antibody or fragment thereof that recognizes and binds to the inhibitory protein, thereby blocking the effective interaction between the protein and its receptor and inhibiting signaling through the receptor. Is done. This effect has been demonstrated in experiments using anti-CTLA-4 antibodies that enhance T cell proliferation, possibly by eliminating inhibitory signals caused by CTLA-4 binding. Walunas, TL et al., Immunity (1994) 1: 405.

Alternatively, the immune stimulating or enhancing effect can be achieved by administration of PRO having vascular permeability enhancing properties. Enhanced vascular permeability may be beneficial for diseases that can be alleviated by inflammation and local infiltration of immune cells (eg monocytes, eosinophils, PMN).
On the other hand, PRO polypeptides and other compounds of the present invention are direct inhibitors of T cell proliferation / activation, lymphokine secretion, and / or vascular permeability, but should be used directly to suppress immune responses. Can do. These compounds reduce the extent of the immune response and are useful in the treatment of immune related diseases characterized by overactivity, superoptimal or autoimmune responses. This use of the compounds of the present invention has been demonstrated by the above-described experiments where CTLA-4 binding to receptor B7 deactivates T cells. The direct inhibitory compounds of the invention function in a similar manner. The use of compounds that inhibit vascular permeability is expected to reduce inflammation. Such use is beneficial for the treatment of medical conditions involving excessive inflammation.
Alternatively, compounds that bind to stimulatory PRO polypeptides and block the stimulatory effects of these molecules, such as antibodies, create a net inhibitory effect and inhibit T cell proliferation / activation and / or lymphokine secretion. Can be used to suppress T cell mediated immune responses. By blocking the stimulatory effect of the polypeptide, the immune response of the mammal is suppressed. This application has been demonstrated in experiments using anti-IL2 antibodies. In these experiments, the antibody binds to IL2 and inhibits the binding of IL2 to its receptor, thereby achieving a T cell inhibitory effect.

H. Animal Model In addition, the results of in vitro cell-based assays can be demonstrated by in vivo animal models and T cell functional assays. To further understand the role of the genes identified herein in the progression and pathogenesis of immune related diseases and to test the efficacy of candidate therapeutics including antibodies and other agonists of natural polypeptides including small molecule antagonists For this purpose, various well-known animal models can be used. The in vivo nature of these models can predict response in human patients. Animal models of immune related diseases include both non-recombinant and recombinant (transgenic) animals. Non-recombinant animal models include, for example, rodents such as mouse models. Such a model is created by introducing cells into syngeneic mice by standard techniques such as subcutaneous injection, tail vein injection, spleen transplantation, intraperitoneal transplantation, subrenal transplantation, and the like.
Graft-versus-host disease occurs when immunocompetent cells are transplanted into immunosuppressed or resistant patients. Donor cells recognize and react to host antigens. Responses range from severe life-threatening inflammation to mild cases such as diarrhea and weight loss. The graft versus host disease model provides a means of assessing T cell reactivity against MHC antigens and small amounts of transplant antigen. A suitable procedure is described in detail in Current Protocols in Immunology, above, unit 4.3. An animal model for skin allograft rejection is a means of testing the ability of T cells to mediate tissue destruction in vivo and is an indicator of their role in transplant rejection. The most common and accepted model uses mouse tail skin grafts. Repeated experiments have shown that skin allograft rejection is mediated by T cells, helper T cells and killer-effector T cells, but not by antibodies. Auchincloss, H. Jr. and Sachs, DH, Fundamental Immunology, 2nd ed., WEPaul ed., Raven Press, NY, 1989, 889-992. A suitable procedure is described in detail in Current Protocols in Immunology, supra, unit 4.4. Other transplant rejection models that can be used to test compounds of the present invention are described by Tanabe, M. et al., Transplantation (1994) 58:23 and Tinubu, SA et al., J. Immunol. (1994) 4330-4338. There is an allocardial graft model.

Animal models of delayed type hypersensitivity also provide assays for cell-mediated immune function. A delayed-type hypersensitivity reaction is a T cell-mediated in vivo immune response characterized by inflammation that does not peak until the elapsed time after challenge. These reactions also occur in tissue-specific autoimmune diseases such as multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE, a model for MS). A suitable procedure is described in detail in Current Protocols in Immunology, above, unit 4.5.
EAE is a T cell mediated autoimmune disease characterized by T cell and mononuclear cell inflammation followed by axonal demyelination in the central nervous system. EAE is generally considered to be a related animal model of MS in humans. Bolton. C., Multiple Sclerosis (1995) 1: 143. Both acute and recurrent relaxation models have been developed. The compounds of the present invention can be tested for T cell stimulatory or inhibitory activity against immune-mediated demyelinating diseases using the protocols described in Current Protocols in Immunology, above, units 15.1 and 15.2. See also a model of myelin disease in which oligodendrocytes or Schwann cells are transplanted into the central nervous system as described in Duncan. ID et al., Molec. Med. Today (1997) 554-561.
Contact hypersensitivity is a simple delayed hypersensitivity in vivo assay of cell-mediated immune function. In this procedure, the skin is exposed to an exogenous hapten that produces a delayed-type hypersensitivity reaction, and the response is measured and quantified. Contact hypersensitivity is the first sensitization stage followed by the manifestation stage. The manifestation phase occurs when T lymphocytes encounter an antigen that they have contacted in the past. Swelling and inflammation occur, creating an excellent model of human allergic contact dermatitis. Suitable procedures are described in detail in Current Protocols in Immunology, JE Coligan, AM Kruisbeek, DHMarglies, EMShevach, and W. Strober, John Wiley & Sons, Inc, unit 4.2. See also Grabbe, S. and Schwarz, T. Immun. Today 19 (1): 37-44 (1998).

An animal model for arthritis is collagen-induced arthritis. This model shares the clinical, histological and immunological characteristics of human autoimmune rheumatoid arthritis and is an acceptable model for human autoimmune arthritis. The mouse and rat models are characterized by synovitis, cartilage erosion and subchondral bone. The compounds of the present invention can be tested for activity against autoimmune arthritis using the protocol described in Current Protocols in Immunology, above, unit 15.5. See also the model using monoclonal antibodies against CD18 and VLA-4 integrin described in Issekutz, AC et al., Immunology (1996) 88: 569.
Describes an asthma model in which antigen-induced hyperrespiratory hyperresponsiveness, pulmonary eosinophilia and inflammation are sensitized to animals with ovalbumin and exposed to similar proteins delivered by aerosol . Several animal models (guinea pigs, rats, non-human primates) showed signs similar to human atopic asthma upon exposure to aerosol antigen. The mouse model has many features of human asthma. Suitable procedures for testing the compounds of the present invention for activity and efficacy in the treatment of asthma are cited therein, Wolyniec, WW et al., Am. J. Respir. Cell Mol. Biol. (1998) 18: 777. It is described in the literature.
Furthermore, the compounds of the invention can be tested in animal models of psoriasis diseases. Some evidence suggests that T cells are the pathogen of psoriasis. The compounds of the invention can be tested in the scid / scid mouse model described by Schon. MP et al., Nat. Med. (1997) 3: 183, in which the mice are histopathology similar to psoriasis. Indicates a typical skin lesion. Another suitable model is the human skin / scid mouse chimera prepared as described in Nickoloff, BJ et al., Am. J. Path. (1995) 146: 580.

Recombinant (transgenic) animal models can be designed by introducing the coding portion of the genes identified herein into the animal genome of interest using standard techniques for transgenic animal production. Animals that can be provided as targets for genetic engineering manipulation include, but are not limited to, mice, rats, rabbits, guinea pigs, sheep, goats, pigs, and non-human primates such as baboons, chimpanzees and monkeys. Techniques known in the art for introducing transgenes into these animals include pronuclear microinjection (Hoppe and Wanger, US Pat. No. 4,873,191); germline retrovirus-mediated gene transfer (eg, Van der Putten et al., Proc. Natl. Acad. Sci. USA 82, 6148-615 [1985]); Gene targeting in embryonic hepatocytes (Thompson et al., Cell 56, 313-321 [1989]); (Lo, Mol. Cel. Biol. 3, 1803-1814 [1983]); sperm-mediated gene transfer (Lavitrano et al., Cell 57, 717-73 [1989]). For review, see, for example, US Pat. No. 4,736,866.
For the purposes of the present invention, transgenic animals include those having the transgene only in a portion of their cells (“mosaic animals”). The transgene is integrated as a single transgene or as a concatamer, eg, head-to-head or head-to-tail tandem. Selective introduction of transgenes into specific cell types is also possible, for example, according to the technique of Lasko et al., Proc. Natl. Acad. Sci. USA 89, 6232-636 (1992).
Transgene expression in transgenic animals can be monitored by standard techniques. For example, Southern blot analysis or PCR amplification is used to confirm transgene integration. The level of mRNA expression can then be analyzed using techniques such as in situ hybridization, Northern blot analysis, PCR, or immunohistochemistry.

The animal may further be examined for signs of pathogenicity of the immune disease, for example by histological examination, to determine the wetness of immune cells into specific tissues. Block experiments can also be performed in which transgenic animals are treated with the compounds of the present invention to measure the degree of T cell proliferation stimulation or inhibition of the compounds. In these experiments, a blocking antibody that binds to a PRO polypeptide prepared as described above is administered to an animal and the effect on immune function is measured.
Alternatively, it encodes the polypeptide identified here as a result of homologous recombination between the modified genomic DNA encoding the polypeptide introduced into the embryonic cells of the animal and the endogenous gene encoding the same polypeptide. A “knock-out” animal can be created that has a defective or altered gene. For example, cDNA encoding a particular polypeptide can be used for cloning genomic DNA encoding that polypeptide according to established techniques. A portion of the genomic DNA encoding a particular polypeptide can be deleted or replaced with another gene, such as a gene encoding a selectable marker used to monitor integration. Typically, the vector contains several kilobases of unmodified flanking DNA (both 5 'and 3' ends) [eg, Thomas and Capecchi, Cell, 51: 503 (1987)]. Vectors are introduced into embryonic stem cells (eg, by electroporation) and cells are selected in which the introduced DNA is homologously recombined 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 said to be transplanted into an appropriate pseudopregnant female nanny to create a “knockout” animal. 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 protect against certain pathological conditions and progression of pathological conditions due to the absence of the polypeptide.

I. Immunoadjuvant Therapy In one embodiment, the immunostimulatory compounds of the present invention can be used for immunoadjuvant therapy in tumor (cancer) therapy. It is well established that T cells recognize human tumor-specific antigens. A group of tumor antigens encoded by the MAGE, BAGE and GAGE families of genes are silent in normal tissues of all adults, but in tumors such as melanoma, lung tumors, head and neck tumors, bladder cancer Expressed in significant amounts. DeSmet. C. et al. (1996) Proc. Natl. Acad. Sci. 93: 7149. Co-stimulation of T cells has been shown to induce tumor regression and anti-tumor responses both in vitro and in vivo. Melero. I. et al., Nature Medicine (1997) 3: 682; Kwon. ED et al., Proc. Natl. Acad. Sci. USA (1997) 94: 8099; Finn. OJ and Lotze. MT, J. Immunol. (1998) 21: 114. The stimulatory compounds of the present invention can be administered as an adjuvant alone or with a growth regulator, cytotoxic agent or chemotherapeutic agent to stimulate T cell proliferation / activation and an anti-tumor response to tumor antigens. Growth regulators, cytotoxic agents or chemotherapeutic agents can be administered in conventional amounts used in known administration methods. Immunostimulatory activity with the compounds of the present invention can reduce the amount of growth regulator, cytotoxic agent or chemotherapeutic agent, and thus potentially reduce toxicity to the patient.

J. et al. Screening Assay for Candidate Drugs Screening assays for candidate drugs include polypeptides encoded by the genes identified herein, or compounds that bind or complex with biologically active fragments thereof, or encoded polypeptides. Designed to identify compounds that inhibit the interaction between and other cellular proteins. Such screening assays include assays that follow high-throughput screening of chemical libraries that make them particularly suitable for the identification of small molecule drug candidates. Small molecules considered include synthetic organic or inorganic compounds, which are peptides, preferably soluble peptides, (poly) peptide-immunoglobulin fusions, in particular, but not limited to poly- and monoclonal antibodies and antibody fragments. Single-chain antibodies, anti-idiotype antibodies, and chimeric or humanized forms of those antibodies or fragments, as well as antibodies, including human antibodies and antibody fragments. The assays can be performed in a variety of formats and include well-characterized protein-protein binding assays, biochemical screening assays, immunoassays and cell-based assays in the field. All assays require that the candidate drug be contacted with the polypeptide encoded by the nucleic acid identified herein under conditions and for a time sufficient for these two components to interact. Common.
In binding assays, the interaction is binding and the complex formed is isolated or detected in the reaction mixture. In a special embodiment, the polypeptide encoded by the gene identified herein, i.e. the candidate drug, is immobilized on a solid phase, e.g. a microtiter plate, by covalent or non-covalent bonding. Non-covalent binding is generally achieved by coating a solid surface with a solution of the polypeptide and drying. Alternatively, an immobilized antibody specific to the polypeptide to be immobilized, such as a monoclonal antibody, can be used to adhere to the 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 with a specific protein encoded by the gene identified here but does not bind, its interaction with the protein is assayed by well-known methods to detect protein-protein interactions can do. Such assays include traditional techniques such as cross-linking, co-immunoprecipitation, and simultaneous purification through a gradient or chromatography column. In addition, protein-protein interactions are described in Fields and co-workers [Fiels and Song, Nature, as disclosed in Chevray and Nathans Proc. Natl. Acad. Sci. USA 89, 5789-5793 (1991). (London) 340, 245-246 (1989); Chien et al., Proc. Natl. Acad. Sci. USA 88, 9578-9582 (1991)] to monitor by using a yeast-based gene system. 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 published literature (generally called “2-hybrid system”) takes advantage of this property and uses two hybrid proteins, while the target protein is the DNA binding domain of GAL4. On the other hand, the 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 a particular protein interaction as well as the identification of amino acid residues important for this interaction.
In order to find compounds that inhibit the interaction of the gene identified here with other intracellular or extracellular components, the reaction mixture usually has conditions and times that allow the interaction and binding of the two products. And is prepared to contain the product of the gene and intracellular or extracellular components. In order to test the ability of the test compound to inhibit binding, the reaction is performed with or without the test compound. In addition, a placebo may be added to the third reaction mixture as a positive control. The binding (complex formation) between the test compound present in the mixture and the intracellular or external components is monitored as described above. The formation of a complex in the control reaction and not in the reaction mixture containing the test compound indicates that the test compound interferes with the interaction between the test compound and its reaction partner.

K. Compositions and Methods for the Treatment of Immune Related Diseases Compositions useful for the treatment of immune related diseases include, but are not limited to, for example, T cell proliferation / activation, lymphokine release, or immune cell infiltration. Proteins, antibodies, small organic molecules, peptides, phosphorylated peptides, antisense and ribozyme molecules, triple helix molecules, etc.
For example, antisense RNA and RNA molecules act to directly block translation of mRNA by hybridizing to the target mRNA and preventing protein translation. When antisense DNA is used, oligodeoxyribonucleotides that are removed from the translation initiation site, eg, between approximately -10 and +10 positions of the target gene nucleotide sequence, are preferred.
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 September 18, 1997).
Nucleic acid molecules in triplex 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 require a resizable extension of purine or pyrimidine on one strand of the duplex And For further details see, for example, PCT Publication No. WO 97/33551, supra.
These molecules can be identified by any or any combination of the screening assays discussed above and / or by any other screening technique well known to those skilled in the art.

L. Anti-PRO Antibody The present invention further provides an anti-PRO antibody. Exemplary 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 produced 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 couple 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 generate lymphocytes that can be generated. Trigger. Lymphocytes can also be immunized in vitro.
The immunizing agent typically comprises a PRO polypeptide or a fusion protein thereof. Generally, peripheral blood lymphocytes ("PBL") are used when cells derived from humans 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, in particular 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 culture 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 culture medium of the hybridoma 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 or the American Type Culture Collection in Manassas, Virginia. Human myeloma and mouse-human heteromyeloma cell lines for generating human monoclonal antibodies have also been described [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 assay by Munson and Pollard, Anal. Biochem., 107: 220 (1980).
After the desired hybridoma cells have been identified, clones can be subcloned by limiting dilution and grown by standard methods [Goding, supra]. Suitable media for this purpose include, for example, Dulbecco's Modified Eagle's 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 prepared 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 incorporated into expression vectors that are transfected into host cells, such as monkey COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not produce immunoglobulin proteins. Monoclonal antibodies can be synthesized in recombinant host cells. Alternatively, the DNA may be non-immune to immunoglobulin coding sequences, eg, by replacing 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]. Modification can be made by covalently binding part or all of the coding sequence of a globulin 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. Digestion of antibodies to produce antibody fragments, particularly Fab fragments, can be accomplished using standard 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 cases, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also contain residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. Generally, a humanized antibody has at least one, typically all or almost all CDR regions corresponding to those of a non-human immunoglobulin and all or almost all FR regions of a human immunoglobulin consensus sequence, typically Contains substantially all of the two variable domains. Humanized antibodies optimally comprise at least part of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin [Jones et al., Nature, 321: 522-525 (1986); Riechmann et al., Nature, 332: 323-329 (1988); and Presta, Curr. Op Struct. Biol., 2: 593-596 (1992)].
Methods for humanizing non-human antibodies are well known in the art. Generally, 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 is basically performed by replacing the relevant sequence of a human antibody with a rodent CDR or CDR sequence [Jones et al., Nature, 321: 522-525 (1986); Riechmann et al., Nature 332: 323-327 (1988); Verhoeyen et al., Science 239: 1534-1536 (1988)]. 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. 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 (1992); Marks et al., J. Mol. Biol., 222: 581 (1991)]. It can also be created using various methods known in Techniques such as 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); Boerner et al., J. Immunol ., 147 (1): 86-95 (1991)] Similarly, human antibodies introduce human immunoglobulin loci into transgenic animals, eg, endogenous immunoglobulin genes, partially or completely inactivated in mice. 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. For example, US Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, and the following scientific literature: Marks et al., Bio / Technology 10, 779- 783 (1992); Lonberg et al., Nature 368 85 6-859 (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).
The antibody may also be affinity matured using the known selection and / or mutagenesis methods described above. Preferred affinity matured antibodies are 5 times, more preferably 10 times, more preferably 20 or 30 times more affinity than that of the starting antibody from which the mature antibody was prepared (generally mouse, humanized or human). Have

4). Bispecific antibodies Bispecific antibodies are monoclonal antibodies, preferably human or humanized antibodies, that have binding specificities for at least two different antigens. In this 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 accomplished 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 is preferably with an immunoglobulin heavy chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred that 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 approach 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 where the large amino acid side chain is replaced by 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 preparation of _two fully humanized bispecific antibodies F (ab '). 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 cells overexpressing ErbB2 receptor and normal human T cells, and induces cytolytic activity of human cytotoxic lymphocytes against human breast tumor targets. Become.

Various techniques 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 the 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 anti-PRO polypeptide arm may be a trigger molecule on a leukocyte such as a T cell receptor molecule (eg, CD2, CD3, CD28, or B7) or FcγRI so as to focus the cytoprotective mechanism on a particular PRO polypeptide expressing cell. It can bind to an arm that binds to an Fc receptor for IgG (FcγR) such as (CD64), FcγRII (CD32) and FcγRIII (CD16). Bispecific antibodies can also be used to localize cytotoxic agents to cells that express a particular PRO polypeptide. These antibodies have a PRO-binding arm and an arm that binds 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 [WO 91/00360; WO 92/200373; EP 03089]. 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 functions It is desirable to modify the antibodies of the present invention for effector functions, for example to improve the effectiveness of the antibodies in the treatment of cancer. For example, a cysteine residue may be introduced into the Fc region, thereby forming an interchain disulfide bond in this region. The homodimeric antibody thus generated can have improved internalization ability and / or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp. Med. 176: 1191-1195 (1992) and Shopes, J. Immunol. 148: 2918-2922 (1992). In addition, homodimeric antibodies with improved anti-tumor activity can also be prepared using heterobifunctional crosslinks 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). Immune conjugates It also relates to an immune complex comprising a bound antibody.
Chemotherapeutic agents useful for generating such immunoconjugates 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, modesin A chain, alpha- Sarcin, Sinabragi protein, dianthin protein, pokeweed protein (PAPI, PAPII, and PAP-S), vine reinhibitor, crusin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin , Restrictocin, phenomycin, enomycin and trichothecene. 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.
Conjugates of antibodies and cytotoxic agents can be selected from various bifunctional protein coupling agents such as N-succinimidyl-3- (2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), imidoester bifunctional 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 the antibody. See WO 94/11026.
In other embodiments, the antibody may be conjugated to a “receptor” (such as streptavidin) for use in tumor pre-targeting, the antibody-receptor conjugate is administered to the patient, and then a clarifier is applied. Used to remove unbound conjugates from the circulation, followed by administration of a “ligand” (eg, avidin) conjugated to a cytotoxic agent (eg, a radionucleotide).

8). Immunoliposomes The proteins and antibodies disclosed herein may 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 defined pore size filter to produce liposomes having the desired diameter. Fab ′ fragments of antibodies of the invention can be bound 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).

M.M. Pharmaceutical Compositions Active PRO molecules of the invention (e.g., PRO polypeptides, anti-PRO antibodies, and / or variants thereof), and other molecules identified in the screening assays described above, are for the treatment of immune related diseases. It can be administered in the form of a pharmaceutical composition.
A therapeutic formulation of an active PRO molecule, preferably a polypeptide or antibody of the present invention, which comprises the active molecule with the desired degree of purity, in the form of a lipophilic formulation or an aqueous solution, any pharmaceutically acceptable carrier, Prepared and stored by mixing with excipients or stabilizers (Remington's Pharmaceutical Science 16th edition, Osol, A. Ed. [1980]). Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations used, and buffers such as phosphate, citrate, and other organic acids; ascorbic acid and methionine Preservatives (octadecyldimethylbenzylammonium cloid; hexamethonium croid; benzalkonium croid; benzethonium croid; phenol; butyl or benzyl alcohol; alkyl paraben such as methyl or propylparaben; catechol; resorcinol; Cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptide; protein such as serum albumin, gelatin, or immunoglobulin; hydrophilic polymer such as polyvinylpyrrolidone; glycine, glutamine , Aspa Amino acids such as gin, histidine, arginine or lysine; monosaccharides, disaccharides and other carbohydrates including glucose, mannose or dextrin; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; sodium etc. Non-ionic such as TWEEN (trade name), PLURONICS (trade name), and polyethylene glycol (PEG); metal salt (eg, Zn-protein complex); and / or Contains a surfactant.

Compounds identified in the screening assays disclosed herein can be formulated in a similar manner using standard techniques known in the art.
Lipofection or liposomes can also be used to introduce PRO molecules 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 and / or produced by recombinant DNA techniques. (See, for example, Marasco et al., Proc. Natl. Acad. Sci. USA 90, 7889-7893 [1993]).
The formulations 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.
Active PRO molecules can also be produced in colloidal drug delivery systems (e.g., hydroxymethylcellulose or gelatin-microcapsules and poly (methyl methacrylate) microcapsules, respectively) prepared by coacervation techniques or by interfacial polymerization. For example, liposomes, albumin globules, microemulsions, nanoparticles and nanocapsules) or microemulsions may be included. These techniques are disclosed in Remington's Pharmaceutical Science 16th edition, Osol, A. Ed. (1980).
The formulation used for in vivo administration must be sterile. This is easily accomplished by filtration through sterile filtration membranes.

Sustained release formulations or PRO molecules 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 polyesters, hydrogels (eg poly (2-hydroxyethyl-methacrylate) or poly (vinyl alcohol)), polylactides (US Pat. No. 3,773,919), L-glutamic acid and γ-ethyl-L- Degradable lactic acid-glycolic acid copolymers such as glutamate copolymers, non-degradable ethylene-vinyl acetate, LUPRON DEPOT ^™ (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), poly- (D) -3- Contains 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.

N. Therapeutic Methods Polypeptides, antibodies and other active agents of the invention are characterized by infiltration of inflammatory cells into the tissue, stimulation of T cell proliferation, inhibition of T cell proliferation, increase or decrease in vascular permeability or inhibition thereof It is believed that it can be used to treat various immune related diseases and conditions such as T cell mediated diseases, including those attached.
Examples of conditions or diseases to be treated with the polypeptides, antibodies and other compounds of the present invention include, but are not limited to, systemic lupus erythematosus, rheumatoid arthritis, juvenile chronic arthritis, osteoarthritis, spine Arthropathy, systemic sclerosis (scleroderma), idiopathic inflammation myopathy (dermatomyositis, polymyositis), Sjogren's syndrome, systemic vasculitis, sarcoidosis, autoimmune hemolytic anemia (immune regenerative anemia, seizures) Nocturnal hemoglobinuria), autoimmune thrombocytopenia (idiopathic thrombocytopenic purpura, immune-mediated thrombocytopenia), thyroiditis (Graves disease, Hashimoto thyroiditis, juvenile lymphocytic thyroiditis, atrophic thyroiditis), Diabetes mellitus, immune-mediated nephropathy (glomerulonephritis, tubulointerstitial nephritis), demyelinating diseases of the central and peripheral nervous systems such as multiple sclerosis, idiopathic discontinuous polyneuropathy, or Guillain- Valley syndrome Chronic hepatic biliary diseases such as infectious hepatitis (types A, B, C, D, hepatitis E and other non-hepatic viruses), autoimmune chronic activity Hepatitis, primary biliary cirrhosis, granulomatous hepatitis, and sclerosing cholangitis, inflammatory bowel disease (ulcerative colitis; Crohn's disease), gluten-sensitive bowel disease, and Whipple's disease, bullous skin disease, many Autoimmune or immune-mediated skin diseases including erythema and contact dermatitis, psoriasis, allergic diseases such as asthma, allergic rhinitis, atopic dermatitis, food hypersensitivity and urticaria, lung immune diseases such as favorable Included are transplant-related diseases including pneumonitis, idiopathic pulmonary fibrosis and hypersensitivity pneumonia, rejection and graft-versus-host disease.
In systemic lupus erythematosus, the central mediator of the disease is the production of autoreactive antibodies against self-proteins / tissues, followed by the development of immune-mediated inflammation. Antibodies mediate tissue injury directly or indirectly. Although T lymphocytes have not been shown to be directly involved in tissue damage, T lymphocytes are required for the development of autoreactive antibodies. Thus, disease development is dependent on T lymphocytes. Multiple organs and systems are clinically affected, including kidney, lung, musculoskeletal, mucocutaneous, eye, central nervous system, cardiovascular system, gastrointestinal tract, bone marrow and blood.

Rheumatoid arthritis (RA) is a chronic systemic autoimmune inflammatory disease primarily involving the synovial membrane of multiple joints, resulting in damage to articular cartilage. The pathogen is T lymphocyte dependent and is associated with the production of rheumatoid factors, autoantibodies to self IgG, resulting in immune complexes reaching high levels in synovial fluid and blood. These complexes in the joints induce significant infiltration of lymphocytes and monocytes into the synovium followed by significant synovial changes; infiltration of similar cells with the addition of multiple neutrophils If done, it is also true for joint space / fluid. The affected tissues are often symmetric patterns, mainly joints. However, two main forms of extra-articular disease also occur. One form is the development of extra-articular disorders with ongoing progressive joint disease and typical lesions of pulmonary fibrosis, vasculitis, and skin ulcers. A second form of extra-articular disease is the so-called Felty syndrome, which occurs late in the RA disease process, sometimes after the joint disease has subsided, and is responsible for the presence of neutropenia, thrombocytopenia and splenic hypertrophy. This is accompanied by vasculitis in multiple organs with the formation of infarcts, skin ulcers and gangrene. In many cases, patients develop rheumatoid nodules in the subcutaneous tissue on the diseased joint; the nodules have a necrotic center surrounded by mixed inflammatory cell infiltration at the end. Other signs that can occur in RA include: epicarditis, pleurisy, coronary arteritis, interstitial pneumonia with pulmonary fibrosis, dry keratoconjunctivitis, and rheumatoid nodules.
Juvenile chronic arthritis is a chronic idiopathic inflammatory disease that often begins before the age of 16 years. Its phenotype has some similarities to RA; some patients positive for rheumatoid factor are classified as juvenile rheumatoid arthritis. The disease is subdivided into three main categories: pauarticular, polyarticular and systemic. Arthritis is severe and typically devastating, leading to arthrosis and slow growth. Other signs include chronic anterior uveitis and systemic amyloidosis.

Spondyloarthropathies are a group of diseases that have a common association between several common clinical features and expression of the HLA-B27 gene product. The diseases include: Bechterew's disease (ankylosing sponylitis), Reiter's syndrome (reactive arthritis), arthritis associated with inflammatory bowel disease, spondylitis associated with psoriasis, juvenile spondyloarthropathy and anaplastic spondyloarthropathy It is. Prominent features include sacroiliac arthritis with or without spondylitis; inflammation asymmetric arthritis; association with HLA-B27 (a serologically defined allele at the HLA-B locus of class I MHC); This includes the absence of autoantibodies associated with eye inflammation and other rheumatic diseases. The most implicated cell as a key to disease induction is CD8 + T lymphocytes, which target cells presented by class I MHC molecules. CD8 + T cells respond to the class I MHC allele HLA-B27 as if it were a foreign peptide expressed by MHC class I molecules. It has been postulated that the epitope of HLA-B27 mimics the antigenic epitope of bacterial or other microorganisms and thus elicits a CD8 + cell response.
Systemic sclerosis (scleroderma) is not well known for its etiology. A prominent feature of the disease is skin induration; this appears to be triggered by an active inflammatory process. Scleroderma is local or systemic: vascular lesions are common, and endothelial cell injury in the microvasculature is an early critical event in the development of systemic sclerosis; vascular injury can be immune-mediated . Immunological criteria are guided by the presence of mononuclear cell infiltration in skin lesions and the presence of anti-nuclear antibodies in many patients. In many cases, ICAM-1 is up-regulated on the cell surface of skin foci fibroblasts, suggesting that T cell interactions with these cells play a role in disease pathogenesis. Other organs involved: Gastrointestinal tract: resulting abnormal peristalsis / motility Smooth muscle atrophy and fibrosis: Kidney: affects arch and interlobular arteries, resulting in renal cortical blood flow Concentric subendothelial proliferation that results in decreased proteinuria, high nitrogen hematuria and hypertension: skeletal muscle: atrophy, interstitial fibrosis: inflammation: lung: interstitial pneumonia and interstitial fibrosis: and heart : Contraction band necrosis, scar / fibrosis.

Idiopathic inflammatory myopathy, including dermatomyositis, polymyositis and others, is a chronic muscular inflammatory disease of unknown etiology that leads to muscle weakness. Muscle injury / inflammation is often contrasting and progressive. Autoantibodies are associated with many forms. These myositis-specific autoantibodies are produced against components involved in protein synthesis, proteins and RNA, and inhibit their functions.
Sjogren's syndrome is due to immune-mediated inflammation and subsequent functional disruption of the lacrimal and salivary glands. The disease may be associated with or associated with inflammatory connective tissue disease. This disease is associated with autoantibody production against Ro and La antigens, both small RNA-protein complexes. The lesions are psoriatic keratoconjunctivitis, xerostomia, with biliary cirrhosis, peripheral or sensory neuropathy, and other signs or associations including overt purpura.
Systemic vascular inflammation is the inflammation of the primary lesion, which subsequently damages the blood vessels, resulting in ischemia / necrosis / degeneration in the tissues supplied by the affected vessels, and in some cases the final end It is a disease that causes organ dysfunction. Vasculitides may also occur as a secondary or secondary lesion of other immune inflammation-mediated diseases such as rheumatoid arthritis, systemic sclerosis, especially diseases related to immune complex formation . For diseases of the primary systemic vascular inflammation group: systemic necrotizing vasculitis: polyarteritis nodosa, allergic vasculitis and granulomatosis, polyvasculitis: Wegener's granulomatosis; lymphoma-like granulation Tumors: and giant cell arteritis. Other vasculitis: mucocutaneous lymph node syndrome (MLNS or Kawasaki disease), isolated CNS vasculitis, Behet's disease, obstructive thrombotic vasculitis (Berger's disease) and skin necrotizing phlebitis ( venulitis). The pathogenesis mechanism of most types of listed vasculitis is thought to be due mainly to the attachment of immunoglobulin complexes to the vessel wall followed by the induction of an inflammatory response via ADCC, complement activity or both. ing.
Sarcoidosis is a condition with little known etiology characterized by the presence of epithelioid granulomas in almost all tissues in the body; pulmonary involvement is the most common. Etiology is associated with residual active macrophages and lymphocytes at the disease site, followed by chronic sequelae as a result of the release of local or systemic active products released from these cell types.
Autoimmune hemolytic anemia, including autoimmune hemolytic anemia, immunoregenerative anemia, and paroxysmal nocturnal hemoglobinuria, are antigens expressed on the surface of red blood cells (in some cases other blood cells that also contain platelets). This is a result of the production of antibodies that react with, and is reflected in the removal of the antibody-coated cells via complement-mediated lysis and / or ADCC / Fc-receptor-mediated mechanisms.

In autoimmune thrombocytopenia, including thrombocytopenic purpura and immune-mediated thrombocytopenia in other clinical settings, platelet destruction / removal involves antibody or complement conjugation to platelets followed by complement lysis, ADCC or Fc As a result of being removed by a -receptor-mediated mechanism.
Thyroiditis, including Graves' disease, Hashimoto's thyroiditis, juvenile lymphocytic thyroiditis, and atrophic thyroiditis, is a thyroid that involves the production of antibodies that are present in the thyroid and often react with thyroid-specific proteins. This is due to the result of an autoimmune response to the antigen. There are experimental models that include immunization of animals with either natural models: rats (BUF and BB rats) and chicken (obese chicken species); inducible models: thyroglobulin, thyroid microsomal antigen (thyroid peroxidase).
Type I diabetes mellitus or insulin-dependent diabetes is the autoimmune destruction of pancreatic islets of Langerhans; this destruction is mediated by autoantibodies and autoreactive T cells. Also, antibodies against insulin or insulin-like receptors can create an insulin-non-reactive phenotype.
Immune-mediated renal disease, including glomerulonephritis and tubulointerstitial nephritis, can occur directly as a result of the production of autoreactive antibodies or T cells to the kidney antigen or to other non-renal antigens. It is due to antibody or T cell mediated injury in the kidney tissue indirectly as a result of the deposition of certain antibodies and / or immune complexes in the kidney. Thus, immune-mediated renal disease can also be induced as an indirect sequelae by other immune-mediated diseases resulting in the production of immune complexes. Both direct and indirect immune mechanisms result in an inflammatory response that causes or induces lesion development in the renal tissue, which impairs organ function and in some cases progresses to renal dysfunction. Both humoral and cellular immune mechanisms can be involved in the pathogenesis of the disorder.
Demyelinating diseases of the central and peripheral nervous system, including multiple sclerosis; idiopathic and isolated polyneuropathy or Guillain-Barre syndrome; and chronic inflammatory degenerative polyneuropathy have causes in autoimmunity and It is believed that neuronal demyelination occurs as a result of damage directly caused by dendrocytes or myelin. In MS, there is evidence to suggest that disease induction and progression is dependent on T lymphocytes. Multiple sclerosis is a demyelinating disease that is T lymphocyte dependent and has either a recurrent relaxation pathway or a chronic progression pathway. The etiology is not well known, but viral infection, genetic predisposition, environment and autoimmunity all contribute. The lesion contains the predominant T cell-mediated microglia wetting and infiltrating microphages; CD4 + T lymphocytes are the predominant cell type in the lesion. The mechanism of oligodendrocyte cell death and subsequent demyelination is not well known, but appears to be driven by T lymphocytes.
Uncontrolled immune inflammatory responses are associated with inflammation and fibrotic lung disease, including eosinophilic pneumonia; idiopathic pulmonary fibrosis and hypersensitivity pneumonia. Inhibiting the response would be therapeutically beneficial.
Autoimmune or immune-mediated skin diseases, including bullous skin disease, erythema multiforme and contact dermatitis, are mediated by autoantibodies, the pathogenesis of which is T lymphocyte dependent.
Psoriasis is a T lymphocyte mediated inflammatory disease. Lesions include infiltration of T lymphocytes, macrophages and antigen processing cells and certain neutrophils.

Allergic diseases including asthma; allergic rhinitis; atopic dermatitis; food hypersensitivity and urticaria are T lymphocyte dependent. These diseases are mainly mediated by T lymphocyte-induced inflammation, IgE-mediated inflammation, or a combination of both.
Transplant-related diseases, including rejection and graft-versus-host disease (GVHD), are T lymphocyte dependent; they are ameliorated by inhibiting T lymphocyte function.
Other diseases for which intervention in immune and / or inflammatory responses is beneficial include, but are not limited to, viral infections (including but not limited to AIDS, A, B, C, D, E) Hepatitis and herpes), bacterial infections, fungal infections, protozoan infections and parasitic infections (molecules (or derivatives / agonists) that stimulate MLR can be used in therapy to enhance immune responsiveness to infectious agents) Infectious diseases including: immune deficiency diseases (molecules) that can be used therapeutically to stimulate, utilize, generate, acquire and enhance immune responses to infection-induced (eg, HIV infection) conditions / Derivative / agonist) or iatrogenic (ie from chemotherapy) immune deficiency, and abnormal growth.
It has been demonstrated that some human cancer patients generate antibodies and / or T lymphocytes that react to antigens on abnormally proliferating cells. In animal models with abnormal growth, it has also been shown that enhancing the immune response results in rejection or regression of specific abnormal growth. Molecules that enhance the T lymphocyte response in the MLR have in vivo utility to enhance the immune response to abnormal growth. Molecules that enhance the T lymphocyte proliferative response in the MLR (or small molecule agonists or antibodies that have antagonistically affected the same receptor) can be used therapeutically in the treatment of cancer. Also, molecules that inhibit lymphocyte responses in MLR function in vivo to suppress immune responses to neoplasms during abnormal growth; such molecules can be expressed by neoplastic cells themselves or Expression can be induced by neoplasms in other cells. The antagonism of such inhibitory molecules (by antibodies, small molecule antagonists or other means) enhances immune mediated tumor rejection.
In addition, inhibiting molecules with pro-inflammatory properties include reperfusion injury; stroke; myocardial infarction; atherosclerosis; acute lung injury; hemorrhagic shock; burns; septic / septic shock; Endometriosis; useful for the treatment of degenerative joint disease and pancreatis.

The compounds of the present invention, such as polypeptides or antibodies, can be administered to mammals, preferably humans, in a well-known manner, such as intravenous administration as a bolus or by continuous infusion over time, intramuscular, intraperitoneal, intracerebral spinal cord, It is administered by subcutaneous, inter-articular, intrasynovial, intrathecal, oral, topical, or inhalation (intranasal, intrapulmonary) routes, and the like. Intravenous or inhalation administration of polypeptides and antibodies is preferred.
In immunoadjuvant treatment, other dosage regimes, such as administration of anticancer agents, may be combined with administration of the protein, antibody or compound of the invention. For example, patients treated with the immunoadjuvants of the present invention may receive anticancer agents (chemotherapeutic agents) or radiation therapy. The preparation method and dosage schedule for such chemotherapeutic agents are either used according to the manufacturer's instructions or determined empirically by skilled practitioners. Preparation methods and dose schedules for such chemotherapy are also described in Chemotherapy Service Ed. MC Perry, Ed. Williams & Wilkins, Baltimore, MD (1992). The chemotherapeutic agent may be administered prior to or subsequent to administration of the immunoadjuvant, or may be administered concurrently therewith. In addition, anti-estrogenic compounds such as tamoxifen or anti-progesterones such as onapristone (see EP 616812) may be given at doses known for those molecules.

It is also possible to administer antibodies against antigens associated with other immune diseases or associated with tumors, such as antibodies that bind to CD20, CD11a, CD18, ErbB2, EGFR, ErbB3, ErbB4, or vascular endothelial factor (VEGF). preferable. Alternatively or additionally, two or more antibodies that bind to the same antigen or two or more different antigens disclosed herein may be co-administered to the patient. Often it is also beneficial to administer one or more cytokines to the patient. In one embodiment, the PRO polypeptide is co-administered with a growth inhibitor. For example, a growth inhibitor is administered first, followed by a PRO polypeptide. However, simultaneous administration or administration first is also conceivable. A suitable dose for a growth inhibitor is the amount currently used, but can be reduced by the combined (synergistic) effect of the growth inhibitor and the PRO polypeptide.
For the treatment or reduction of serious immune-related diseases, an appropriate dose of the compound of the present invention is the type of disease to be treated, the severity and course of the disease, as defined above, for prevention or treatment purposes. It depends on whether the drug is administered, the previous treatment, the patient's clinical history and response to the compound, and the discretion of the attending physician. The compound is suitably administered to the patient at one time or over a series of treatments.
For example, depending on the type and severity of the disease, about 1 μg / kg to 15 mg / kg (eg, 0.1-20 mg / kg) polypeptide or antibody may be administered, for example, in one or more separate doses or Either continuous infusion is the first candidate dose for administration to a patient. A typical daily dose will be in the range of about 1 μg / kg to 100 mg / kg or more, depending on the above factors. For repeated administrations over several days or longer, depending on the condition, the treatment is continued until a desired suppression of disease symptoms appears. However, other dose schedules may be useful. The progress of this therapy is easily monitored by conventional techniques and assays.

O. Articles of Manufacture In another embodiment of the invention, an article of manufacture containing materials useful for the diagnosis or treatment of the above diseases (eg, those containing PRO molecules) is provided. This article of manufacture comprises a container and instructions for use. Suitable containers include, for example, bottles, vials, syringes, and test tubes. The container may be formed from a variety of materials such as glass or plastic. The container contains a composition effective for diagnosing and treating the condition and may have a sterile access port (e.g., the container may be an intravenous solution bag or vial with a stopper pierceable by a hypodermic needle). May be). The active agent in the composition is usually a polypeptide or antibody of the invention. Instructions or labels on the container or attached indicate that the composition is used for diagnosis or treatment of the selected condition. The article of manufacture may further comprise a second container containing a pharmaceutically acceptable buffer such as phosphate buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.

P. Diagnosis and prediction of immune related diseases Cell surface proteins such as proteins overexpressed in certain immune related diseases are excellent targets for candidate drugs or disease treatment. The same protein, together with secreted proteins encoded by genes amplified in immune related diseases, finds additional uses in the diagnosis and prognosis of these diseases. For example, antibodies against protein products of genes amplified in multiple sclerosis, rheumatoid arthritis, or other immune-related diseases can be used as a diagnosis or prognosis.
For example, an antibody comprising an antibody fragment can be used for qualitative or quantitative detection of the expression of a protein (“marker gene product”) encoded by an amplified or overexpressed gene. The antibody is preferably detectable, eg, equipped with a fluorescent label, and binding can be monitored by light microscopy, flow cytometry, fluorometry, or other techniques known in the art. These techniques are particularly appropriate when the overexpressed gene encodes a cell surface protein. Such binding assays are performed essentially as described above.
In situ detection of antibodies that bind to the marker gene product can be performed, for example, by immunofluorescence or immunoelectron microscopy. For this purpose, a labeled antibody is applied to the histological sample from the patient, preferably by overlaying the antibody on the biological sample. This approach also allows the distribution of the marker gene product in the tissue being tested to be determined. It will be apparent to those skilled in the art that a wide variety of histological methods are readily available for in situ detection.
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)
Commercially available reagents referred to in the examples were used according to manufacturer's instructions unless otherwise indicated. The source of cells identified by ATCC accession number throughout the following examples and specification is American Type Culture Collection, Manassas, VA.
Example 1: Extracellular domain homology screening to identify novel polypeptides and cDNAs encoding them
Extracellular domain (ECD) sequences (including secreted signal sequences, if present) from approximately 950 known secreted proteins from the Swiss-Prot public database were used to search the EST database. EST databases include public databases (eg, Dayhoff, GenBank) and corporate databases (eg, LIFESEQ ^™ , 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, a consensus DNA sequence was constructed against other identified EST sequences using phrap. Furthermore, the resulting consensus DNA sequence is often (but not always) extended using BLAST or BLAST-2 and phrap repeat cycles, and the consensus sequence is as long as possible using the sources of EST sequences discussed above. Elongated.
Probes for synthesizing oligonucleotides based on the consensus sequence obtained as described above, identifying a cDNA library containing the sequence of interest by PCR, and isolating a clone of the full-length coding sequence of the PRO polypeptide Used for use as. 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 according to 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 to isolate the cDNA clones was made by standard methods using commercially available reagents such as those from Invitrogen, San Diego, CA. The cDNA is primed with oligo dT containing a NotI site, ligated to a SalI hemikinase adapter with blunt ends, cut with NotI, appropriately sized by gel electrophoresis, and an appropriate 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 was cloned in a defined orientation at unique XhoI and NotI sites.

Example 2: Isolation of cDNA clones using specific Database Query Polypeptide-encoded nucleotide sequences can be obtained from public (eg, GenBank) and / or private (LIFESEQ ^R , Incyte Pharmaceuticals, Inc., In order to search for homology of specific genes in the Palo Alto, CA) database, they were identified using the computer programs BLAST and BLAST2 (Altshul et al., Methods in Enzymology 266: 460-480 (1996)). In this case, the researcher searched for related homologies using one gene that had been previously identified as the query sequence. The significance of homology is determined on a case-by-case basis based on each gene. If significant homology is found, this corresponds to a full-length clone to be examined and sequenced, or various tissue libraries for isolating the DNA encoding the native sequence PRO polypeptide. As a result, additional EST sequences are identified that serve as templates for the creation of cloning oligonucleotides used to screen for.

Example 3: Isolation of cDNA clones using signal algorithm analysis
Genentech inc (South San Francisco, CA ) and proprietary signal sequence finding algorithm developed by public (e. G., GenBank) and / or private ^{(LIFESEQ R, Incyte Pharmaceuticals, Inc.} , Palo Alto, CA) from the database Applied to the ESTs and to the assembled and assembled EST fragments, various polypeptide-encoding nucleic acid sequences were identified. The signal sequence algorithm calculates a secretory signal score based on the letters of the DNA nucleotide surrounding the first, possibly 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 the necessary amino acids, the second is not tested. If none of the requirements were met, the candidate sequence was not scored. In order to determine whether an EST sequence contains a genuine signal sequence, a set of seven sensors (evaluation parameters) known to be associated with the secretory signal, the DNA surrounding the ATG codon and the corresponding amino acid sequence Used to score. Using this algorithm, a number of polypeptide-encoding nucleic acid sequences are identified.

Example 4: Isolation of cDNA clones using ECD homology to genomic DNA
Extracellular domain (ECD) sequences (including secreted signal sequences, if present) from about 950 known secreted proteins from the Swiss-Prot public database were used to search the sequence database. The database includes a public database (eg, GenBank). In this case, the genomic DNA sequence from GenBank was analyzed using the gene prediction program GENSCAN licensed from Stanford University. GENSCAN analysis predicts the coding region of a gene and creates a sequence that can be the target of an ECD search. 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. If necessary, 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). Consensus DNA sequence was constructed.
Based on the consensus sequence, oligonucleotides: 1) to identify a cDNA library containing the sequence of interest by PCR, 2) for use as a probe to isolate clones of the full-length coding sequence, Synthesized. 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 according to 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.
A pool of 50 different human cDNA libraries from various tissues was used for cloning. The cDNA library used to isolate the cDNA clones was made by standard methods using commercially available reagents such as those from Invitrogen, San Diego, CA. The cDNA is primed with oligo dT containing a NotI site, ligated to a SalI hemikinase adapter with blunt ends, cut with NotI, appropriately sized by gel electrophoresis, and an appropriate 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 was cloned in a defined orientation at unique XhoI and NotI sites.
The DNA sequence of the clone isolated as described above gave the full length DNA sequence for the full length polypeptide.

Example 5: Isolation of cDNA clones using signal algorithm search against genomic DNA Potential target genes are proprietary signal sequence detection algorithms developed by Genentech, Inc. (South San Francisco, CA). Identified by applying to genomic sequences processed by GENSCAN (licensed by Stanford University) from a typical database (eg GenBank). The signal sequence algorithm calculates a secretory signal score based on the letters of the DNA nucleotide surrounding the first, possibly 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 the necessary amino acids, the second is not tested. If none of the requirements were met, the candidate sequence was not scored. In order to determine whether an EST sequence contains a genuine signal sequence, a set of seven sensors (evaluation parameters) known to be associated with the secretory signal, the DNA surrounding the ATG codon and the corresponding amino acid sequence Used to score. Using this algorithm, a number of polypeptide-encoding nucleic acid sequences are identified.
The use of the above signal sequence algorithm allows identification of the genomic sequence. The genomic sequence was then compared to various databases (eg, GenBank) to identify the presence of homology. Homology searches were performed using the computer program BLAST or BLAST-2 (Altschul et al., Methods in Enzymology 266: 460-480 (1996)). If necessary, these comparisons that do not encode a known protein and have a BLAST score of 70 (possibly 90) or higher can be found in the program “phrap” (Phil Green, University of Washington, Seattle, WA). Collected and assembled into a consensus DNA sequence.
Based on the consensus sequence, oligonucleotides: 1) to identify a cDNA library containing the sequence of interest by PCR, 2) for use as a probe to isolate clones of the full-length coding sequence, Synthesized. 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 according to 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.
A pool of 50 different human cDNA libraries from various tissues was used for cloning. The cDNA library used to isolate the cDNA clones was made by standard methods using commercially available reagents such as those from Invitrogen, San Diego, CA. The cDNA is primed with oligo dT containing a NotI site, ligated to a SalI hemikinase adapter with blunt ends, cut with NotI, appropriately sized by gel electrophoresis, and an appropriate 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 was cloned in a defined orientation at unique XhoI and NotI sites.
The DNA sequence of the clone isolated as described above gave the full length DNA sequence for the full length polypeptide.

Example 6: Isolation of cDNA clones encoding human PRO polypeptides Using the techniques described in Examples 1-5 above, a number of full-length cDNA clones encoding the PRO polypeptides disclosed herein were identified. . These cDNAs were then deposited with the American Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110-2209 USA (ATCC) according to the Budapest Treaty as shown in Table 7 below.

Table 7
Materials UNQ PRO ATCC # ATCC Deposit date DNA54229-1366 538 1081 209803 April 23, 1998 DNA64889-1541 644 1274 203250 September 9, 1998 DNA65351-1366 612 1199 209856 May 12, 1998 DNA76385-1692 827 1754 203664 1999 February 9 DNA76529-1666 764 1556 203315 October 6 1998 DNA84912-2610 1926 4401 203964 April 27, 1999 DNA108700-2802 3077 9912 PTA-1093 November 22, 1999 DNA1455583-2820 3119 10268 PTA-1179 January 11, 2000 DNA147531-2821 3120 10272 PTA-1185 January 11, 2000

Example 7: Stimulating activity assay in mixed lymphocyte reaction (MLR) (No. 24)
This example shows that the polypeptides of the present invention are active as growth stimulators of stimulated T lymphocytes. Compounds that stimulate lymphocyte proliferation are useful in treatments where an enhanced immune response is preferred. The therapeutic agent may take the form of a mouse-human chimera, humanized or human antibody to an antagonist of the PRO polypeptide of the invention, eg, a polypeptide expected to inhibit T lymphocyte proliferation.
The basic protocol for this assay is described in Current Protocols in Immunology, unit 3.12; published by JE Coligan, AMKruisbeek, DHMarglies, EMShevach, W. Strober, National Institutes of Health, John Wiley & Sons, Inc. Yes.
More specifically, in one variation of this assay, peripheral blood mononuclear cells (PBMC) are isolated from a mammalian individual, such as a human volunteer, by leucopheresis (one donor is supplied with the stimulator PBMC). Other donors will be provided with responder PBMC). If desired, after isolation, the cells are frozen in fetal calf serum and DMSO. Frozen cells are thawed overnight in assay medium (37 ° C., 5% CO ₂ ), then washed and assayed at 3 × 10 ⁶ cells / ml assay medium (RPMI; 10% fetal calf serum, 1% penicillin / streptomycin, 1 % Glutamine, 1% HEPES, 1% non-essential amino acids, 1% pyruvate).

The stimulant PBMC is prepared by irradiating cells (approximately 3000 rads). This assay is prepared by seeding a test sample diluted to 1% or 0.1% of mixture: 100: l, stimulator cells exposed to 50: l light, and 50: l responder PBMC cells in triple wells. Is done. 100 microliters of cell culture medium or 100 microliters of CD4-IgG is used as a control. The wells are then incubated for 4 days at 37 ° C., 5% CO ₂ . On day 5, each well is pulsed with tritiated thymidine (1.0 mC / well; Amersham). After 6 hours, the cells are washed three times, and then label incorporation is evaluated.
In another variation of this assay, PBMC are isolated from the spleens of Balb / c and C57B6 mice. Cells from freshly collected spleens in a microscope medium (RPMI; 10% fetal bovine serum, 1% penicillin / streptomycin, 1% glutamine, 1% HEPES, 1% non-essential amino acids, 1% pyruvate) PMBCs are isolated by chopping up for testing and overlaying these cells on Lympholyte M (Organon Teknika), centrifuged at 2000 rpm for 20 minutes, collected, and the mononuclear cell layer in the assay medium is collected. Wash and resuspend the cells in assay medium to 1 × 10 ⁷ cells / ml. The assay is then performed as described above. The results of this assay for the compounds of the invention are shown in Table 8 below. A positive increase over control is considered positive and an increase of 180% or more is preferred. However, all values above the control indicate a stimulating effect for the test protein.

Table 8
Percent increase relative to PRO PRO concentration control PRO1081 18.39 nM 275.5
PRO1274 58.32 nM 230.1
PRO10272 0.84 nM 201.5

Example 8: Cutaneous vascular permeability assay (No. 64)
This assay demonstrates that certain PRO polypeptides promote immune responses and induce inflammatory responses by inducing mononuclear cells, eosinophils and PMN infiltration at the injection site of mammals. The skin vascular permeability assay is performed as follows. Hairless guinea pigs weighing 350 grams or more are anesthetized with ketamine (75-80 mg / Kg) and 5 mg / Kg xylazine intramuscular injection (IM). A purified PRO polypeptide sample or conditioned media test sample is injected intradermally into the back of the test animal at 100 μl per injection site. Injection can be made to about 10-30, preferably about 16-24, sites per animal. 1 ml of Evans Blue dye (1% buffered with saline) is injected into the heart. The spots at the injection site are then measured (diameter mm) at 1 hour, 6 hours and 24 hours after injection. Animals are sacrificed after an appropriate time after injection. Each skin injection site is biopsied and fixed with paraformaldehyde. The skin is then prepared for histopathology examination. Each site is examined for inflammatory cell infiltration into the skin. Sites with visible inflammatory cell inflammation are scored as positive. Inflammatory cells can be neutrophils, eosinophils, monocytes, lymphocytes.
At least the infiltration around the smallest blood vessel at the injection site is recorded as positive, and when there is no infiltration at the injection site, it is recorded as negative. The results are shown in Table 9.

Table 9
PRO time (hrs) infiltration PRO1754 6.00 positive PRO9912 6.00 positive

Example 9: Inhibitory activity assay in mixed lymphocyte reaction (MLR) (No. 67)
This example demonstrates that one or more PRO polypeptides are active as growth inhibitors of stimulated T lymphocytes. Compounds that inhibit lymphocyte proliferation are useful in treatments where suppression of the immune response is preferred.
The basic protocol for this assay is described in Current Protocols in Immunology, unit 3.12; published by JE Coligan, AMKruisbeek, DHMarglies, EMShevach, W. Strober, National Institutes of Health, John Wiley & Sons, Inc. .
More specifically, in one variation of this assay, peripheral blood mononuclear cells (PBMC) are isolated from a mammalian individual, such as a human volunteer, by leucopheresis (one donor is supplied with the stimulator PBMC). Other donors will be provided with responder PBMC). If desired, after isolation, the cells are frozen in fetal calf serum and DMSO. Frozen cells are thawed overnight in assay medium (37 ° C., 5% CO ₂ ), then washed and assayed at 3 × 10 ⁶ cells / ml assay medium (RPMI; 10% fetal calf serum, 1% penicillin / streptomycin, 1 % Glutamine, 1% HEPES, 1% non-essential amino acids, 1% pyruvate). The stimulant PBMC is prepared by irradiating cells (approximately 3000 rads).
This assay is:
Test sample diluted 1% or 0.1% of 100: 1,
50: 1 irradiated stimulator cells, and
50: 1 responder PBMC cells,
Is prepared by seeding the mixture in a triple well. 100 microliters of cell culture medium or 100 microliters of CD4-IgG is used as a control. The wells are then incubated for 4 days at 37 ° C., 5% CO ₂ . On day 5, each well is pulsed with tritiated thymidine (1.0 mC / well; Amersham). After 6 hours, the cells are washed three times, and then label incorporation is evaluated.
In another modification of this assay, PBMC are isolated from the spleens of Balb / c and C57B6 mice. Cells were microscopically taken from spleens freshly recovered in assay medium (RPMI; 10% fetal bovine serum, 1% penicillin / streptomycin, 1% glutamine, 1% HEPES, 1% non-essential amino acids, 1% pyruvate) PBMCs are isolated by finely cutting for testing and overlaying these cells on lymphonite M (Organon Teknika), centrifuging at 2000 rpm for 20 minutes, collecting, washing the mononuclear cell layer in assay medium, resuspend cells to be 1x10 ⁷ cells / ml in assay media. The assay is then performed as described above.
A decrease below the control is considered positive as an inhibitory compound and a decrease of 80% or less is preferred. However, all values less than the control indicate the inhibitory effect of the test protein. The results are shown in Table 10.

Table 10
Percent decrease relative to PRO PRO concentration control PRO1199 4.97 nM 70
PRO1199 49.65 nM 66.8
PRO1199 119.99 nM 56.6
PRO1556 2.75 nM 66.2
PRO4401 1.42 nM 73.6
PRO4401 14.16 nM 66.3
PRO10268 1.77 nM 75.0
PRO10268 17.66 nM 18.0

Example 10: In situ hybridization In situ hybridization is a powerful and versatile technique for the detection and localization of nucleic acid sequences in cell or tissue preparations. It is useful, for example, in identifying gene expression sites, analyzing the tissue distribution of transcripts, identifying and locating viral infections, tracking changes in specific mRNA synthesis and assisting in chromosomal mapping.
In situ hybridization is performed using PCR-generated ³³ P-labeled riboprobe according to an optimized version of the protocol of Lu and Gillett, Cell Vision 1: 169-176 (1994). Briefly, formalin-fixed, paraffin-embedded human tissue was sectioned, deparaffinized, deproteinized with proteinase K (20 mg / ml) for 15 minutes at 37 ° C., and as described in Lu and Gillett, supra. In situ hybrid formation. [ ³³ P] UTP-labeled antisense riboprobe is generated from the PCR product and hybridized at 55 ° C. overnight. The slides are immersed in Kodak NTB2 nuclear track emulsion and exposed for 4 weeks.

³³ P-riboprobe synthesis
6.0 μl (125 mCi) of ³³ P-UTP (Amersham BF 1002, SA <2000 Ci / mmol) was speed-vacuum dried. The following components were added to each tube containing dry ³³ P-UTP: 2.0 μl of 5 × transcription buffer; 1.0 μl of DTT (100 mM); 2.0 μl of NTP mixture (2.5 mM: 10 μl of 10 mM GTP, CTP and ATP each +10 μl H ₂ O); 1.0 μl UTP (50 μM); 1.0 μl Rnasin; 1.0 μl DNA template (1 μg); 1.0 μl H ₂ O.
Tubes were incubated at 37 ° C. for 1 hour, 1.0 μl RQ1 DNase was added, and then incubated at 37 ° C. for 15 minutes. 90 μl TE (10 mM Tris pH 7.6 / 1 mM EDTA pH 8.0) was added and the mixture was pipetted onto DE81 paper. The remaining solution was loaded into a Microcon-50 ultrafiltration unit and spun using program 10 (6 minutes). The filtration unit was converted to a second tube and spun using program 2 (3 minutes). After the final recovery spin, 100 μl TE was added. 1 μl of final product was pipetted onto DE81 paper and counted with 6 ml of BIOFLUOR II.
The probe was run on a TBE / urea gel. 1-3 μl probe or 5 μl RNA MrkIII was added to 3 μl loading buffer. After heating for 3 minutes on a 95 ° C. heating block, the gel was quickly placed on ice. Gel wells were flushed, filled with sample, and run at 180-250 volts for 45 minutes. The gel was wrapped with Saran wrap and exposed to an XAR film with a reinforcing screen in a -70 ° C freezer for 1 hour to overnight.

Pretreatment of ³³ P-hybridized frozen sections Slides were removed from the freezer, placed in an aluminum tray and thawed at room temperature for 5 minutes. The tray was placed in a 55 ° C. incubator for 5 minutes to reduce condensation. Slides were fixed in 4% paraformaldehyde on ice for 10 minutes in a steam hood and washed with 0.5 × SSC for 5 minutes at room temperature (25 ml 20 × SSC + 975 ml SQ H ₂ O). After deproteinization for 10 minutes at 37 ° C. in 0.5 μg / ml proteinase (12.5 μl of 10 mg / ml stock in 250 ml preheated RNase-free RNase buffer), sections were washed with 0.5 × SSC for 10 minutes at room temperature. Sections were dehydrated in 70%, 95%, 100% ethanol for 2 minutes each.
Pretreatment of paraffin-embedded sections Slides were deparaffinized, placed in SQ H ₂ O and rinsed twice with 2 × SSC for 5 minutes each at room temperature. Sections were 20 μg / ml proteinase K (500 μl 10 mg / ml in 250 ml RNase-free RNase buffer; 37 ° C., 15 minutes) -human embryo or 8x proteinase K (100 μl in 250 ml RNase buffer, 37 ° C., 30 minutes) — Deproteinized with formalin tissue. Subsequent rinsing and dehydration with 0.5 × SSC was performed as described above.
Prehybridization Slides were arranged in plastic boxes lined with Box buffer (4 × SSC, 50% formamide) -saturated filter paper. The tissue was coated with 50 μl of hybridization buffer (3.75 g dextran sulfate + 6 ml SQ H ₂ O), vortexed, uncapped and heated in the microwave for 2 minutes. After cooling on ice, 18.75 ml formamide, 3.75 ml 20 × SSC and 9 ml SQ H ₂ O were added and the tissue was vortexed well and incubated at 42 ° C. for 1-4 hours.
Hybridization 1.0 × 10 ⁶ cp. Probe and 1.0 μl RNA (50 mg / ml stock) per slide were heated at 95 ° C. for 3 minutes. Slides were chilled on ice and 48 μl of hybridization buffer was added per slide. After vortexing, 50 μl of ³³ P mixture was added to 50 μl of prehybrid on the slide. Slides were incubated overnight at 55 ° C.
Washing Washing was performed with 2 × SSC, EDTA for 2 × 10 minutes at room temperature (400 ml 20 × SSC + 16 ml 0.25 M EDTA, V _f = 4 L) followed by RNase A treatment for 30 minutes at 37 ° C. (500 μl of 10 mg / ml in 250 ml RNase buffer). = 20 μg / ml). Slides were washed 2 × 10 minutes with 2 × SSC, EDTA at room temperature. Stringent wash conditions are as follows: 55 ° C. for 2 hours, 0.1 × SSC, EDTA (20 ml 20 × SSC + 16 ml EDTA, V _f = 4 L).

Alternatively, multi-tissue blots containing poly A ⁺ RNA (2 μg per lane) from various human tissues were purchased from Clontech (Palo alto, Calif.). The DNA probe was labeled with [α- ³² P] -dCTP by random primed DNA label beads (Pharmacia Biotech). Hybridization was performed using Expresshyb (Clontech) at 68 ° C. for 1 hour. The blot is then washed with 2 × SSC / 0.05% SDS solution for 40 minutes at room temperature, then replaced with fresh solution and washed with 0.1 × SSC / 0.1% SDS solution at 55 ° C. for 40 minutes. did. The blot was exposed to a phosphorimager.
This method quantifies gene expression, analyzes the tissue distribution of transcription, and detects changes in specific mRNA synthesis of genes / DNA and proteins of the present invention in diseased tissue isolated from a human individual suffering from a specific disease. Used to follow. These results are shown more specifically in diseased tissues in which the genes of the present invention are expressed, and more predictive of the specific localization of the therapeutic effect of the inhibitory or stimulating compounds of the present invention (and their agonists or antagonists) on the disease. is doing. Hybridization is performed according to the method described above using one or more of the following tissue and cell samples:
(a) lymphocytes and antigen-presenting cells (dendritic cells, Langerhans cells, macrophages and monocytes, NK cells);
(b) Lymphoid tissue: normal and reactive lymph nodes, thymus, bronchial associated lymphoid tissue (BALT), mucosal associated lymphoid tissue (MALT);
(c) Human disease tissue:
Synovium and joints of patients suffering from arthritis and degenerative joint disease;
The colon of patients suffering from inflammatory bowel disease including ulcerative colitis and Crohn's disease;
Skin lesions from psoriasis and other forms of dermatitis;
• Lung tissue including BALT and lymph node tissue from chronic and acute bronchitis, pneumonia, interstitial pneumonia, pleurisy;
-Lymph node tissue from asthma and lung tissue including BALT;
Nose or sinus tissue of patients suffering from rhinitis or sinusitis;
The brain and spinal cord from multiple sclerosis, Alzheimer's disease and stroke;
• Kidneys from nephritis, glomerulonephritis and systemic lupus erythematosus;
-Liver from infectious and non-infectious hepatitis and acetaminophen-induced cirrhosis;
• Neoplasm / cancer-derived tissue.
Expression is observed in one or more cells or tissue samples indicating localization of the therapeutic effect of the compounds of the invention (and agonists or antagonists thereof) in diseases associated with the cells or tissue samples.

Results DNA54229-1366
Specific pattern of mouse DNA54229-1366 expression using 5'UTR probe Normal adult large intestine: Strong segmental expression is seen in crypt cells of mucosa. This expression is present only in crypt cells and extends to approximately the upper half of the villi. Epithelial cells at the end of the villus show no signal. The pattern correlates with the density of mutable epithelial cells that can divide. Interesting is the fact that there is a region of the large intestine where this pattern is segmental, i.e. no signal.
Large intestine of inflamed adult mice (IL10 R KO (knockout) mice): The pattern and intensity of expression appears to be similar to that described above for normal colon.
Normal adult small intestine: There are a few segmental regions that develop in the crypt cells of the mucosa. Expression is very weak compared to expression in the large intestine and is found only in a small part of the small intestine; it is warranted by further evaluation of the small and large intestine.
Normal and inflamed adult mouse lungs: no signal.
Specific expression pattern results of DNA54229-1366 using 5'UTR probe in mouse tissues: The expression distribution of DNA54229-1366 was further evaluated in extensive screening of normal mouse tissues. We have already reported that expression of DNA54229-1366 is restricted to colonic epithelium by in situ hybridization.
Summary: DNA54229-1366 expression was specifically restricted to the colonic epithelium with minimal extension into the cecal epithelium. Expression was strong and scattered in these epithelial cells. No expression was seen in the ileum, jejunum, duodenal base, or stomach. No expression was seen in the following normal mouse tissues: liver, kidney, spleen, bone marrow, lung, pancreas, stomach, duodenal base, jejunum, ileum, brain, skin, testis, or mammary gland. Expression restricted to colonic epithelium is interesting because of its unusual distribution pattern.
Primer 54229 used for in situ hybridization of DNA54229-1366. p1
5 "GGA TTC TAA TAC GAC TCA CTA TAG GGC CCC TGA GCT TTC TGG AGA GTG 3" (SEQ ID NO: 19)
54229. p2
5 "CTA TGA AAT TAA CCC TCA CTA AAG GGA GTG CAG GAG ATC GTC TTA GGC3" (SEQ ID NO: 20)

DNA64889-1541
Expression of DNA64889-1541 by angiogenic tissue screening for additional novel angiogenic tissues: pulmonary vasculitis, angiomyolipoma, invasive endometrial adenocarcinoma, diabetic ophthalmopathy, rheumatoid arthritis.
Results: Moderate to weak expression is seen in fetal epidermis, lung epithelium and stroma, esophageal epithelium, and skeletal muscle at 14.5 weeks. There is no detectable expression in normal adult tissues; the endometrial carcinoma epithelium shows weak expression. One of the two human umbilical vein endothelial (HUVEC) cell pellets shows weak expression.
Primer 64889 used for in situ hybridization of DNA64889-1541. p1
5 "GGA TTC TAA TAC GAC TCA CTA TAG GGC GGC CCC CAT GAC TCC TTA CCT 3" (SEQ ID NO: 21)
64889. p2
5 "CTA TGA AAT TAA CCC TCA CTA AAG GGA CCC ATC AGC ACA CGC ATC TC3" (SEQ ID NO: 22)

DNA65351-1366
Specific patterns of mouse DNA65351-1366 expression using 5 'UTR probe in SPDI screening tissues, breast and colon adenocarcinoma Human fetal tissue:
No expression is found in fetal liver, lung, skeletal muscle, bone, spinal cord, blood vessel, heart, intestine, gonad, adrenal gland, or paravertebral ganglion.
Fetal limb: A weak signal in hematopoietic cells clustered in the bone marrow cavity of long bones.
Rhesus monkey and chimpanzee tissue brain: signal tongueless: signal stomachless: weak contradictory signal thyroid / parathyroid gland in the glandular mucosa: signal athymus: signal aneuron: signal no Lung, adrenal gland, spleen, kidney (normal and degenerated), skin, umbilical cord, liver (normal and inflammatory), breast cancer, colon adenocarcinoma, mesenteric adipose tissue, milk adipose tissue.
Eye: A weak signal in the internal ganglion eye layer.
65351. p1
5 '' GGA TTC TAA TAC GAC TCA CTA TAG GGC CGA GAG GCG CCT GCA GGA TGA 3 '' (SEQ ID NO: 23)
65351. p2
5 ″ CTA TGA AAT TAA CCC TCA CTA AAG GGA TCC AGC TCC CCC GCA ACC C3 ″ (SEQ ID NO: 24)

Example 11: Use of PRO as a hybridization probe The following method describes the use of a nucleotide sequence encoding a PRO polypeptide as a hybridization probe.
DNA containing the full-length or mature PRO coding sequence is used as a probe for screening for homologous DNAs (such as those encoding naturally occurring variants of PRO) in human tissue cDNA libraries or human tissue genomic libraries .
Hybridization and washing of the filters containing any library DNA was performed under the following high stringency conditions. Hybridization of the radiolabeled PRO-derived probe to the filter consisted of a solution of 50% formamide, 5x SSC, 0.1% SDS, 0.1% sodium pyrophosphate, 50 mM sodium phosphate, pH 6.8, 2x Denhardt's solution, and 10% dextran sulfate. In, it was performed at 42 ° C. for 20 hours. The filter was washed at 42 ° C. in an aqueous solution of 0.1 × SSC and 0.1% SDS.
The DNA having the desired sequence identity with the DNA encoding the full-length native sequence PRO can then be identified using standard methods known in the art.

Example 12: Expression of PRO in E. coli This example illustrates the preparation of an unglycosylated form of PRO by recombinant expression in E. coli.
The DNA sequence encoding PRO is first amplified using selected PCR primers. The primer must have a restriction enzyme site corresponding to the restriction enzyme site of the selected expression vector. Various 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)), which contains genes for ampicillin and tetracycline resistance. The vector is digested with restriction enzymes and dephosphorylated. The PCR amplified sequence is then ligated into a vector. The vector preferably includes an antibiotic resistance gene, trp promoter, polyhis leader (including the first 6 STII codons, polyhis sequence, and enterokinase cleavage site), PRO coding region, lambda transcription termination region, and argU gene .
The ligation mixture is then used to transform E. coli strains selected using the method described by Sambrook et al., Supra. Transformants are identified by their ability to grow on LB plates and then antibiotic resistant clones are selected. Plasmid DNA is isolated and confirmed by restriction analysis and DNA sequence analysis.
Selected clones can be grown overnight in liquid media such as LB broth supplemented with antibiotics. Overnight cultures are subsequently used for seeding large scale cultures. The cells are then grown to optimal optical density, during which the expression promoter is activated.
After further incubation for several hours, the cells can be collected by centrifugation. The cell pellet obtained by centrifugation is solubilized using various reagents known in the art, and then the solubilized PRO protein is purified under conditions that allow the protein to bind tightly using a metal chelation column. be able to.

PRO may be expressed in E. coli in poly-His tag form using the following procedure. DNA encoding PRO is first amplified using selected PCR primers. Primers provide restriction enzyme sites that correspond to the restriction enzyme sites of the selected expression vector, and efficient and reliable translation initiation, rapid purification with metal chelate columns, and proteolytic removal with enterokinase Includes other useful sequences. The PCR-amplified poly-His tag sequence is then ligated into an expression vector which is used for transformation of an E. coli host based on strain 52 (W3110 fuhA (tonA) lon galE rpoHts (htpRts) clpP (lacIq)). Transformants were initially treated with 3-5 O.D. with shaking at 30 ° C. in LB containing 50 mg / ml carbenicillin. D. Grow until reaching 600. The culture was then cultured in 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, 5.36 g Sheffield hycase SF in 500 mL water, and Dilute 50-100 times in 110 mM MPOS, pH 7.3, mixed with 0.55% (w / v) glucose and 7 mM MgSO ₄ ) and grow for about 20-30 hours with shaking at 30 ° C. A sample is removed and expression is confirmed by SDS-PAGE analysis, and the bulk culture is centrifuged to pellet the cells. The cell pellet is frozen until purification and refolding.
E. coli paste from 0.5 to 1 L fermentation (6-10 g pellet) is resuspended in 10 volumes (w / v) in 7 M guanidine, 20 mM Tris, pH 8 buffer. Solid sodium sulfate and sodium tetrathionate are added to final concentrations of 0.1 M and 0.02 M, respectively, and the solution is stirred at 4 ° C. overnight. This step results in a denatured protein with all cysteine residues blocked by sulfation. The solution is centrifuged for 30 minutes at 40,000 rpm in a Beckman Ultracentrifuge. The supernatant is diluted with 3-5 volumes of metal chelate column buffer (6 M guanidine, 20 mM Tris, pH 7.4) and clarified by filtration through a 0.22 micron filter. The clarified extract is loaded onto a 5 ml Qiagen Ni-NTA metal chelate column equilibrated with metal chelate column buffer. The column is washed with additional buffer containing 50 mM imidazole (Calbiochem, Utrol grade), pH 7.4. The protein is eluted with a buffer containing 250 mM imidazole. Fractions containing the desired protein are pooled and stored at 4 ° C. Protein concentration is estimated by its absorption at 280 nm using an extinction coefficient calculated based on its amino acid sequence.

Proteins by slowly diluting samples in freshly prepared refolding buffer consisting of 20 mM Tris, pH 8.6, 0.3 M NaCl, 2.5 M urea, 5 mM cysteine, 20 mM glycine and 1 mM EDTA Is refolded. The refolding volume is selected so that the final protein concentration is 50-100 microgram / ml. Slowly stir the refolding solution at 4 ° C. for 12-36 hours. The refolding reaction is stopped by adding TFA to a final concentration of 0.4% (pH of about 3). Prior to further purification of the protein, the solution is filtered through a 0.22 micron filter and acetonitrile is added to a final concentration of 2-10%. The refolded protein is chromatographed on a Poros R1 / H reverse phase column using elution with a 0.1% TFA transfer buffer and a 10-80% acetonitrile gradient. Aliquots of fractions with A280 absorption are analyzed on an SDS polyacrylamide gel and fractions containing homologous refolded proteins are pooled. In general, correctly refolded species of most proteins elute 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. Is done. Aggregated species are usually eluted at higher acetonitrile concentrations. In addition to removing the misfolded form of the protein from the desired form, the reverse phase process also removes endotoxin from the sample.
Fractions containing the desired folded PRO polypeptide protein are pooled and the acetonitrile is removed using a gentle stream of nitrogen directed at the solution. The protein was formulated into 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.
As noted above, many PRO polypeptides disclosed herein have been successfully expressed.

Example 13: 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 EP 307,247 published on March 15, 1989) is used as an expression vector. In some cases, PRODNA is bound to pRK5 with the selected restriction enzyme and PRODNA is inserted using a ligation method such as that described by Sambrook et al. The resulting vector is called, for example, pRK5-PRO.
In one embodiment, the selected host cell is 293 cells. Human 293 cells (ATCC CCL 1573) are grown and confluent in tissue culture plates in a medium such as DMEM supplemented with fetal bovine serum and optionally nourishing ingredients and / or antibiotics. About 10 μg of pRK5-PRODNA is mixed with about 1 μg of VARNA gene-encoding DNA [Thimmappaya et al., Cell, 31: 543 (1982)]] and dissolved in 500 μl of 1 mM Tris-HCl, 0.1 mM EDTA, 0.227 MCaCl ₂ . To this mixture is added dropwise 500 μl of 50 mM HEPES (pH 7.35), 280 mM NaCl, 1.5 mM NaPO ₄ and a precipitate is formed at 25 ° C. for 10 minutes. The precipitate is suspended and added to 293 cells and stabilized at 37 ° C. for about 4 hours. The medium is aspirated and 2 ml of 20% glycerol in PBS is added for 30 seconds. The 293 cells are then washed with serum free medium, fresh medium is added, and the cells are incubated for about 5 days.
Approximately 24 hours after transfection, the medium is 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 is collected, concentrated with a spin filter and loaded onto a 15% SDS gel. The treated gel is dried and exposed to the film for a selected time that reveals the presence of the PRO polypeptide. The medium containing the transfected cells is further incubated (in serum-free medium) and the medium is tested in the selected bioassay.

In an alternative technique, PRO is 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 is added. The cells are first concentrated from the spinner flask by centrifugation and washed with PBS. Incubate the DNA-dextran precipitate on the cell pellet for 4 hours. Cells are 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 is centrifuged and filtered to remove cells and cell debris. The sample containing the expressed PRO is 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 culture medium can be incubated and the culture medium can be replaced with culture medium (only) or a medium containing a radioactive label such as ³⁵ S-methionine. After determining 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.
The epitope tag polypeptide may also be expressed in host CHO cells. PRO may be subcloned outside the pRK5 vector. The subclone insert can be subjected to PCR and fused to a frame with a selected epitope tag, such as a poly-his tag in a baculovirus expression vector. The poly-his tag polypeptide insert can then be subcloned into an SV40 derived vector / enhancer containing a selectable marker such as DHFR for selection of stable clones. Finally, CHO cells can be transfected (as described above) with the SV40 promoter / enhancer containing the vector. In order 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 any selected method, such as Ni ²⁺ -chelate affinity chromatography.
PRO may also be expressed in CHO and / or COS cells by a transient expression method, or in CHO cells by other stable expression methods.

Stable expression in CHO cells was performed using the following method. Proteins are IgG constructs (immunoadhesins) in which the coding sequence (eg, extracellular domain) of each protein solubilized form is fused to an IgG1 constant region sequence comprising the hinge, CH2 and CH2 domains, and / or poly-his. Expressed as a tag form.
Following PCR amplification, each 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 for expression in CHO cells are as described in Lucas et al., Nucl. Acids res. 24: 9, 1774-1779 (1996), and the subject cDNA and dihydrofolate reductase (DHFR) SV40 early promoter / enhancer is used to control the expression of. DHFR expression allows selection for stable maintenance of the plasmid following transfection.
Twelve micrograms of the desired plasmid DNA, using commercially available transfection reagents Superfect ^R (Quiagen), using Dosper ^R or Fugene ^R (Boehringer Mannheim) is introduced into Yakuichi ten million CHO cells. Cells are grown as described in Lucas et al. Approximately 3 × 10 ⁻⁷ cells are frozen in ampoules for further growth and production as described below.
Ampoules containing plasmid DNA are placed in a water bath and 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 selective medium (0.2 μm filtered PS20, 5% 0.2 μm diafiltered fetal bovine 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 medium and incubated at 37 ° C. After a further 2-3 days, seed 250 mL, 500 mL and 2000 mL spinners at 3 × 10 ⁵ cells / mL. The cell medium is 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 was used. Seed 3 L production spinner at 1.2 × 10 ⁶ cells / mL. On day 0, cell number and pH are measured. On the first day, the spinner is sampled and sprayed with filtered air. On the second day, sample the spinner, change the temperature to 33 ° C, and add 500 g / L glucose and 30 mL of 0.6 mL of 10% antifoam (e.g. 35% polydimethylsiloxane emulsion, Dow Corning 365 Medical Grade Emulsion). To do. Throughout production, the pH was adjusted and maintained near 7.2. After 10 days or until viability is below 70%, the cell culture medium is collected by centrifugation and filtered through a 0.22 μm filter. The filtrate is stored at 4 ° C. or immediately loaded into a purification column.

For the poly-His tag construct, 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 medium was 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 0.25M imidazole. The highly purified protein was subsequently desalted with 25 ml G25 Superfine (Pharmacia) in storage buffer containing 10 mM Hepes, 0.14 M NaCl and 4% mannitol and stored 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 loading, wash the column thoroughly with equilibration buffer before eluting with 100 mM citric acid, pH 3.5. The eluted protein is immediately neutralized by collecting 1 ml fractions into 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. Homogeneity 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 14: 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. A plasmid in which DNA encoding PRO is selected for secretion is added to DNA encoding the ADH2 / GAPDH promoter, native sequence PRO signal peptide or other mammalian signal peptide, or, for example, yeast alpha factor or invertase secretion signal / It can be cloned with a leader sequence and (if necessary) a linker sequence for PRO expression.
Yeasts such as yeast strain AB110 can then be transformed with the above expression plasmid and cultured in the selected fermentation medium. Transformed yeast supernatants 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 15: Expression of PRO in baculovirus infected insect cells The following method describes recombinant expression of PRO in baculovirus infected insect cells.
The sequence encoding PRO is 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, the sequence encoding PRO or the desired portion of the coding sequence of PRO, such as the sequence encoding the extracellular domain of a transmembrane protein or the sequence encoding the mature protein when the protein is extracellular, is 5 ′ and Amplified by PCR with primers complementary to the 3 'region. The 5 ′ primer may include a restriction enzyme site located on the side (selected). The product is then digested with selected restriction enzymes and subcloned into an expression vector.
Recombinant baculovirus is co-transfected with the above plasmid and BaculoGold ^™ viral DNA (Pharmingen) into Spodoptera frugiperda (“Sf9”) cells (ATCC CRL 1711) using lipofectin (commercially available from GIBCO-BRL). Created by. After incubation at 28 ° C. for 4-5 days, the released virus is collected and used for further amplification. Viral infection and protein expression are 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 can then be purified by, for example, Ni ²⁺ -chelate affinity chromatography as follows. Extracts are 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; 0.4 M KCl) Resuspended in and sonicated twice on ice for 20 seconds. The sonicated product is clarified by centrifugation, and the supernatant is diluted 50-fold with packing 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) is prepared with a total volume of 5 mL, washed with 25 mL of water and equilibrated with 25 mL of packing buffer. The filtered cell extract is loaded onto the column at 0.5 mL per minute. The column is washed with packing buffer to A ₂₈₀ baseline where fraction collection begins. The column is then washed with a secondary wash buffer (50 mM phosphate; 300 mM NaCl, 10% glycerol, pH 6.0) that elutes non-specifically bound protein. After reaching A ₂₈₀ baseline again, the column is developed with a 0 to 500 mM imidazole gradient in the secondary wash buffer. 1 mL fractions are 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 -tag PRO are pooled and dialyzed against packing 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 16: 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, supra. Immunogens that can be used include purified PROs of the invention, fusion proteins comprising PRO, and cells that express 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 in an amount of 1-100 micrograms. Alternatively, the immunogen is emulsified in MPL-TDM adjuvant (Ribi Immunochemical Research, Hamilton, MT) 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 bleeds may be taken periodically from mice for testing in an ELISA assay for detection of anti-PRO antibodies.
After the appropriate antibody titer has been detected, animals that are “positive” for antibodies can be injected with the last intravenous injection of PRO. Three to four days later, the mice are sacrificed and spleen cells are removed. The spleen cells were then (using 35% polyethylene glycol), P3X63AgU. Fusion to 1st selected mouse myeloma cell line. The hybridoma cells are generated by fusion and then plated on 96-well tissue culture plates containing HAT (hypoxanthine, aminopterin, and thymidine) medium to inhibit the growth of unfused 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 binding property of the antibody to protein A or protein G can also be used.

Example 17: Purification of PRO polypeptides using specific antibodies Native or recombinant PRO polypeptides can be purified by various standard protein purification methods in the art. For example, a 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 coupled to a chromatographic resin such as CnBr-activated Sepharose ^™ (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, or a high concentration of chaotrope such as urea or thiocyanate ions), and the PRO polypeptide is recovered. The

Example 18: Drug Screening The present invention is particularly useful for screening compounds by using PRO polypeptides or binding fragments thereof in any of a variety of 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 in a competitive binding assay. Such cells can be used in standard binding assays in either viable or immobilized form. For example, the formation of a complex between the PRO polypeptide or fragment and the reagent being tested may be measured. Alternatively, the reduction in complex formation between the PRO polypeptide and its target cell or target receptor 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. Assaying for the presence of the complex between them by methods well known in the art. 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. Has been. 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 that neutralizing antibodies capable of binding to the PRO polypeptide are used in competitive drug screening assays that 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 19: Rational Drug Design The purpose of rational drug design is to construct the biologically active polypeptide of interest (eg, PRO polypeptide) or the small molecule with which they interact, such as an agonist, antagonist, or inhibitor Is to produce similar products. Any of these examples can be used to create more active and stable forms of the PRO polypeptide or drugs that enhance or inhibit the function of the 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 approach in principle produces a pharmacore on which subsequent drug design can be based. Protein crystallography can be bypassed by generating anti-idiotype antibodies (anti-ids) against functional and pharmacologically active antibodies. As a mirror image of the mirror image, the anti-ids binding site can be predicted to be an analog of the original receptor. The anti-id can then be used to identify and isolate the peptide from a bank of chemically or biologically produced peptides. The isolated peptide will function as a pharmacore.
In accordance with the present invention, sufficient amounts of PRO polypeptides are available to perform analytical experiments such as X-ray crystallography. Furthermore, the knowledge of the PRO polypeptide amino acid sequence provided herein provides guidance for use in computer modeling techniques to replace or add to X-ray crystallography.

  The above written description is considered to be sufficient to enable one skilled in the art to practice the invention. The deposited example is an illustration of one aspect of the invention, and all functionally equivalent constructs are within the scope of the invention, so the deposited constructs may It is not limited. The deposit of material herein does not admit that the written description contained herein is sufficient to enable the implementation of all aspects of the invention, including its best mode, it represents. It is not to be construed as limiting the scope of the claims to the specific illustrations. Indeed, various modifications of the invention in addition to those shown and described herein will be apparent to those skilled in the art from the foregoing description and are intended to be within the scope of the following claims.

FIG. 1 shows the nucleotide sequence of the native sequence PRO1081 cDNA (SEQ ID NO: 1), which is a clone referred to herein as “DNA54229-1366”. FIG. 2 is a view showing an amino acid sequence (SEQ ID NO: 2) derived from the coding sequence of SEQ ID NO: 1 shown in FIG. FIG. 3 shows the nucleotide sequence of the native sequence PRO1274 cDNA (SEQ ID NO: 3), which is a clone referred to herein as “DNA64889-1541”. FIG. 4 is a view showing an amino acid sequence (SEQ ID NO: 4) derived from the coding sequence of SEQ ID NO: 3 shown in FIG. FIG. 5 shows the nucleotide sequence of the native sequence PRO1199 cDNA (SEQ ID NO: 5), which is a clone referred to herein as “DNA65351-1366”. FIG. 6 is a view showing an amino acid sequence (SEQ ID NO: 6) derived from the coding sequence of SEQ ID NO: 5 shown in FIG. FIG. 7 shows the nucleotide sequence (SEQ ID NO: 7) of the native sequence PRO1754 cDNA, which is a clone referred to herein as “DNA76385-1692”. FIG. 8 is a view showing an amino acid sequence (SEQ ID NO: 8) derived from the coding sequence of SEQ ID NO: 7 shown in FIG. FIG. 9 shows the nucleotide sequence of the native sequence PRO1556 cDNA (SEQ ID NO: 9), which is a clone referred to herein as “DNA76529-1666”. FIG. 10 is a view showing an amino acid sequence (SEQ ID NO: 10) derived from the coding sequence of SEQ ID NO: 9 shown in FIG. FIG. 11A shows a part of the nucleotide sequence of the native sequence PRO4401 cDNA (SEQ ID NO: 11), which is part of a clone referred to herein as “DNA84912-2610”. FIG. 11B shows a portion of the nucleotide sequence of the native sequence PRO4401 cDNA (SEQ ID NO: 12), which is a portion of a clone referred to herein as “DNA84912-2610”. FIG. 12 is a view showing an amino acid sequence (SEQ ID NO: 12) derived from the coding sequence of SEQ ID NO: 11 shown in FIGS. 11A-11B. FIG. 13 shows the nucleotide sequence of the native sequence PRO9912 cDNA (SEQ ID NO: 13), which is a clone referred to herein as “DNA108700-2802”. FIG. 14 is a view showing an amino acid sequence (SEQ ID NO: 14) derived from the coding sequence of SEQ ID NO: 13 shown in FIG. FIG. 15 shows the nucleotide sequence of the native sequence PRO10268 cDNA (SEQ ID NO: 15), which is a clone referred to herein as “DNA145583-2820”. FIG. 16 is a view showing an amino acid sequence (SEQ ID NO: 16) derived from the coding sequence of SEQ ID NO: 16 shown in FIG. FIG. 17 shows the nucleotide sequence of the native sequence PRO10272 cDNA (SEQ ID NO: 17), which is a clone referred to herein as “DNA147531-2828”. FIG. 18 is a view showing an amino acid sequence (SEQ ID NO: 18) derived from the coding sequence of SEQ ID NO: 17 shown in FIG.

Claims (31)

(a) a nucleotide sequence encoding the polypeptide shown in FIG. 8 (SEQ ID NO: 8);
(b) a nucleotide sequence encoding the polypeptide shown in FIG. 8 (SEQ ID NO: 8) and lacking its associated signal peptide;
(c) a nucleotide sequence encoding the extracellular domain of the polypeptide shown in FIG. 8 (SEQ ID NO: 8) and associated signal peptide;
(d) a nucleotide sequence encoding the extracellular domain of the polypeptide shown in FIG. 8 (SEQ ID NO: 8) and lacking its associated signal peptide;
An isolated nucleic acid having a nucleic acid sequence identity of at least 80% relative to a nucleic acid encoding a polypeptide having activity to enhance infiltration of inflammatory cells into mammalian tissue. 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 shown in Figure 7 (SEQ ID NO: 7), to mammalian tissue of inflammatory cells A nucleic acid encoding a polypeptide having an activity of enhancing the invasion of. An isolated nucleic acid having at least 80% nucleic acid sequence identity to a nucleotide sequence selected from the group consisting of the full-length coding sequence of the nucleotide sequence shown in Figure 7 (SEQ ID NO: 7), comprising: A nucleic acid encoding a polypeptide having an activity of enhancing infiltration into mammalian tissue. An isolated nucleic acid having at least 80% nucleic acid sequence identity to the full length coding sequence of DNA76385-1692 deposited on Feb. 9, 1999 under ATCC Deposit No. 203664, comprising mammalian tissue of inflammatory cells A nucleic acid encoding a polypeptide having an activity to enhance invasion into the body. A vector comprising the nucleic acid according to claim 1. 6. The vector of claim 5 operably linked to a control sequence recognized by a host cell transformed with the vector. A host cell comprising the vector of claim 5. The host cell according to claim 7, wherein the cell is a CHO cell, an E. coli cell, or a yeast cell. A method for producing a PRO polypeptide, comprising culturing the host cell according to claim 7 under conditions suitable for expression of the PRO polypeptide, and recovering the PRO polypeptide from the cell culture. (a) the amino acid sequence of the polypeptide shown in FIG. 8 (SEQ ID NO: 8);
(b) the amino acid sequence of the polypeptide shown in FIG. 8 (SEQ ID NO: 8), lacking its associated signal peptide;
(c) the amino acid sequence of the extracellular domain of the polypeptide shown in FIG. 8 (SEQ ID NO: 8), with its associated signal peptide; or
(d) the amino acid sequence of the extracellular domain of the polypeptide shown in FIG. 8 (SEQ ID NO: 8), lacking its associated signal peptide;
An isolated polypeptide having at least 80% amino acid sequence identity to said polypeptide, and having an activity of enhancing infiltration of inflammatory cells into mammalian tissue. 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 at ATCC Deposit No. 203664, wherein the inflammatory cell is introduced into mammalian tissue. A polypeptide having an activity of enhancing infiltration. A chimeric molecule comprising the polypeptide of claim 10 fused to a heterologous amino acid sequence. The chimeric molecule according to claim 12, wherein the heterologous amino acid sequence is an epitope tag sequence or an Fc region of an immunoglobulin. An antibody that specifically binds to the polypeptide of claim 10. The antibody according to claim 14, wherein the antibody is a monoclonal antibody, a humanized antibody or a single chain antibody. In combination with a carrier, (a) a polypeptide according to claim 10, or a composition containing an antibody that binds to (b) the polypeptide. The composition of claim 16, wherein the carrier is a pharmaceutically acceptable carrier. 17. The composition of claim 16, useful for the treatment of a mammal immune-related disease. 17. The composition of claim 16, wherein (a), (b), (c) or (d) is capable of increasing inflammatory cell infiltration into mammalian tissue. 17. A composition according to claim 16, comprising a therapeutically effective amount of (a), (b), (c) or (d). container;
Label on said container; are accommodated in and the container (a) a polypeptide according to claim 10, or comprising, a composition comprising an antibody that binds to (b) the polypeptide article of manufacture An article of manufacture wherein the label on the container indicates that the composition can be used to treat an immune related disease. A composition for treating an immune-related disease in a mammal in need polypeptide according to a therapeutically effective amount of (a) according to claim 10, or an antibody that binds to (b) the polypeptide A composition comprising. A method for determining the presence of a polypeptide in a sample suspected of containing the polypeptide of claim 10, wherein the sample is exposed to an antibody against the polypeptide of claim 10, Measuring the binding of an antibody to a component of the sample. The expression level of the gene encoding the polypeptide of claim 10 in (a) a test sample of tissue cells obtained from a mammal and (b) a control sample of known normal tissue cells of the same cell type. the method comprising detecting. (a) contacting an antibody against the polypeptide of claim 10 with a test sample of tissue cells obtained from said mammal; and (b) detecting the formation of a complex between the polypeptide and the antibody in the test sample. a process that comprises. The method for identifying a compound that inhibits the activity of a polypeptide according to claim 10, wherein a cell that normally responds to the polypeptide is contacted with (a) the polypeptide and (b) a candidate compound, An identification method comprising measuring the lack of reactivity to (a) by A method for identifying a compound that inhibits expression of a gene encoding a polypeptide according to claim 10, wherein a cell that normally expresses the polypeptide is brought into contact with a candidate compound, and measurement of lack of expression of the gene is performed. An identification method comprising: 28. The method of claim 27 , wherein the candidate compound is an antisense nucleic acid. A method for identifying a compound that mimics the activity of a polypeptide according to claim 10, wherein a cell that normally reacts to the polypeptide is contacted with a candidate compound, and the reactivity of the cell to the candidate compound is measured. An identification method comprising. A composition for enhancing the infiltration of inflammatory cells mammalian tissues, an effective amount of (a) comprising the polypeptide de of claim 10 composition. 31. The composition of claim 30 , wherein the inflammatory cells are mononuclear cells, eosinophils or polymorphonuclear neutrophils (PMNs).

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