Btnl9 proteins, nucleic acids, and antibodies and uses thereof

Abstract

The invention provides novel BTNL9 proteins, including multimers, fragments, and variants of a human BTNL9 protein. In addition, antibodies that can bind to BTNL9 proteins and nucleic acids encoding BTNL9 proteins are provided. Uses for BTNL9 proteins, and agonists or antagonists thereof, are described.

What is claimed is: 
     
         1 - 67 . (canceled) 
     
     
         68 . An isolated soluble BTNL9 protein comprising
 (a) a polypeptide having an amino acid sequence at least 90% identical to amino acids 35-257 of SEQ ID NO:2, and   (b) a second polypeptide having an amino acid sequence at least 90% identical to amino acids 35-257 of SEQ ID NO:2,   wherein the alignment window of the amino acid sequences of the polypeptides of (a) and (b) with amino acids 35-257 of SEQ ID NO:2 is at least 80 amino acids long,   wherein BTNL9 protein has a molecular weight greater than about three times as large as that of a polypeptide of (a), and   wherein the BTNL9 protein can inhibit the proliferation of a T cell stimulated by an anti-CD3 antibody.   
     
     
         69 . The BTNL9 protein of  claim 68 , wherein the polypeptides of (a) and (b) are at east 95% identical to amino acids 35-257 of SEQ ID NO:2. 
     
     
         70 . The BTNL9 protein of  claim 69 , wherein the polypeptides of (a) and (h) comprise the amino acid sequence of amino acids 35-257 of SEQ ID NO:2. 
     
     
         71 . The BNTL9 protein of  claim 68 , which does not comprise amino acids 258 to 277 of SEQ ID NO:2. 
     
     
         72 . The BTNL9 protein of  claim 68 , wherein the polypeptides of (a) and (b) each comprise another polypeptide. 
     
     
         73 . The BTNL9 protein of  claim 72 , wherein the other polypeptide comprises an Fc portion of an antibody, wherein the Fc portion comprises an amino acid sequence that has not more than 15 insertions, deletions, or substitutions of a single amino acid relative to the amino acid sequence of a native, human IgG Fc region, wherein the BTNL9 protein can bind to FcRn. 
     
     
         74 . The BTNL9 protein of  claim 73 , wherein the Fc portion has not more than 10 insertions, deletions, or substitutions of a single amino acid relative to the amino acid sequence of the native human Fc region. 
     
     
         75 . The BTNL9 protein of  claim 74 , wherein the Fc portion has not more than 5 insertions, deletions, or substitutions of a single amino acid relative to the amino acid sequence of the native human Fc region. 
     
     
         76 . The BTNL9 protein of  claim 75 , which comprises the amino acid sequence of the native human IgG Fc region, wherein the native human IgG Fr region is of the IgG1, IgG2, or IgG4 isotype. 
     
     
         77 . The BTNL9 protein of  claim 68 , wherein:
 (i) the BTNL9 protein has a molecular weight at least about 8 times as large as the molecular weight of a polypeptide of (a) or (b);   (ii) the BTNL9 protein is a homotetramer or a higher order homomultimer   (iii) the BTNL9 protein is a homomultimer which is of a higher order than a homotetramer; and/or   (iv) the BTNL9 protein is a heteromultimer.   
     
     
         78 . A BTNL9 fusion protein comprising
 (a) a first polypeptide comprising an amino acid sequence at least 90% identical to amino acids 35-257 of SEQ ID NO:2, wherein the alignment window of the amino acid sequence of the BTNL9 fusion protein with amino acids 35-257 is SEC) ID NO:2 is at least 80 amino acids long, and   (b) a second polypeptide,   wherein the BTNL9 fusion protein can inhibit the proliferation of a T cell stimulated by an anti-CD3 antibody.   
     
     
         79 . The BTNL9 fusion protein of  claim 78 , wherein the second polypeptide is an Fc portion an antibody, wherein the Fc portion has an amino acid sequence that contains not more than 15 insertions, deletions, or substitutions of a single amino acid relative to the amino acid sequence of a native human IgG Fc region, and wherein the BTNL9 fusion protein can bind to FcRn. 
     
     
         80 . The BTNL9 fusion protein of  claim 79 , wherein the Fc portion has an amino acid sequence containing not more than 10 insertions, deletions, or substitutions of a single amino acid relative to the native human IgG Fc region. 
     
     
         81 . The BTNL9 fusion protein of  claim 80  comprising the amino acid sequence of the native human IgG Fc region, wherein the native human Fc region is of the IgG1, IgG2, or IgG4 isotype. 
     
     
         82 . The BTNL9 fusion protein of  claim 78 , wherein the first polypeptide at least 95% identical to amino acids 35-257 of SEQ ID NO:2. 
     
     
         83 . The BTNL9 fusion protein of  claim 82 , wherein the first polypeptide comprises amino acids 35-257 of SEQ ID NO:2. 
     
     
         84 . The BTNL9 fusion protein of  claim 78 , which comprises an amino acid sequence that is substantially similar to SEQ ID NO:19, wherein the amino acid sequence comprises not more that 20 insertions, deletions, or substitutions of a single amino acid relative to SEQ ID NO:19. 
     
     
         85 . The BTNL9 fusion protein of  claim 84 , comprising no more than 10 insertions, deletions, or substitutions of a single amino acid relative to SEQ ID NO: 19. 
     
     
         86 . The BTNL9 fusion protein of  claim 85 , comprising no more than 5 insertions, deletions, or substitutions of a single amino acid relative to SEQ ID NO:19. 
     
     
         87 . The BTNL9 fusion protein of  claim 78 , wherein the fusion protein is aggregated such that its molecular weight is at least about eight times the molecular weight of a monomer species of the BTNL9 fusion protein. 
     
     
         88 . An isolated nucleic acid encoding a BTNL9 protein, wherein the BTNL9 protein comprises one or more polypeptides selected from the group consisting of:
 (a) a polypeptide having an amino acid sequence at least 90% identical to amino acids 35-257 of SEQ ID NO:2, and a second polypeptide having an amino acid sequence at least 90% identical to amino acids 35-257 of SEQ ID NO:2, wherein the alignment window of the amino acid sequences of the polypeptide and the second polypeptide with amino acids 35-257 of SEQ ID NO:2 is at least 80 amino acids long and wherein the BTNL9 protein has a molecular weight greater than about three times as large as that of the polypeptide; and   (b) a first polypeptide comprising an amino acid sequence at least 90% identical to amino acids 35-257 of SEQ ID NO:2, wherein the alignment window of the amino acid sequence of the BTNL9 fusion protein with amino acids 35-257 is SEQ ID NO:2 is at least 80 amino acids long, and another polypeptide; and   (c) an encoded polypeptide, which is encoded by the nucleic acid, wherein the nucleic acid comprises (i) a polynucleotide which consists of the nucleotide sequence of nucleotides 334 to 1002 of SEQ ID NO:1 or which hybridizes under stringent conditions to a polynucleotide which consists of the nucleotide sequence of nucleotides 334 to 1002 of SEQ ID NO:1 and (ii) a polynucleotide that does not hybridize to a polynucleotide consisting of the sequence of SEQ ID NO:1 and encodes a polypeptide in frame with the polypeptide encoded by the polynucleotide of (I);   wherein the BTNL9 protein can inhibit the proliferation of a T cell stimulated by an anti-CD3 antibody.   
     
     
         89 . A host cell containing the nucleic acid of  claim 88 . 
     
     
         90 . A method of making a BTNL9 protein comprising
 culturing the host cell of  claim 89  in a medium under conditions suitable for expression of the nucleic acid and   recovering the expressed protein from the cells or the culture medium.   
     
     
         91 . A method for treating a patient having an autoimmune or inflammatory disease comprising:
 (a) administering to the patient a therapeutically effective dose of a BTNL9 protein comprising (i) the amino acid sequence of amino acids 35-257 of SEQ ID NO:2, (ii) an amino acid sequence at least 90% identical to amino acids 35-257 of SEQ ID NO:2, wherein the alignment window of the amino acid sequence with amino acids 35-257 of SEQ. ID NO:2 is at least 80 amino acids long, or (iii) art amino acid sequence that has no more than 20 insertions, deletions, or substitutions of a single amino acid relative to the sequence of amino acids 35-257 of SEQ ID NO:2, wherein the BTNL9 protein can inhibit the proliferation of a T cell stimulated by an anti-CD3 antibody;   (b) administering to the patient a therapeutically effective dose of an anti-BTNL9 antibody, wherein the anti-BTNL9 antibody increases the inhibition of proliferation of a T cell by a BTNL9 protein comprising the sequence of amino acid 35-257 of SEQ ID NO:2 and wherein the anti-BTNL9 antibody binds to a protein consisting of the amino acid sequence of amino acids 35 to 257 of SEQ ID NO:2; or   (c) a process comprising the following steps:
 (i) removing T cells from the patient, 
 (ii) stimulating the T cells with a combination of proteins comprising an anti-CD3 antibody and a BTNL9 protein, wherein the BTNL9 protein comprises (1) the amino acid sequence of amino acids 35-257 of SEQ ID NO:2, (2) an amino acid sequence at least 90% identical to amino acids 35-257 of SEQ ID NO:2, wherein the alignment window of the amino acid sequence with amino acids 35-257 of SEQ ID NO:2 is at least 80 amino acids long, or (3) an amino acid sequence that has no more than 20 insertions, deletions, or substitutions of a single amino acid relative to the sequence of amino acids 35-257 of SEQ ID NO:2, and wherein the BTNL9 protein can inhibit the proliferation of a T cell stimulated by an anti-CD3 antibody, 
 (iii) harvesting the stimulated T cells; and 
 (iv) returning the harvested T cells to the patient. 
   
     
     
         92 . The method of  claim 91 , wherein the autoimmune or inflammatory disease is selected from the group consisting of systemic lupus erythematosus, rheumatoid arthritis, an inflammatory bowel disease, Crohn's disease, ulcerative colitis, psoriasis, sarcoidosis, asthma, or a fibrotic disease. 
     
     
         93 . A method of treating a cancer patient comprising administering to the patient a therapeutically effective amount of an antibody that binds to a BTNL9 protein consisting of amino acids 35 to 257 of SEQ ID NO:2, wherein the antibody is an antagonistic antibody. 
     
     
         94 . The method of  claim 93 , wherein the cancer is selected from the group consisting of acute or chronic leukemias, lymphoma, non-Hodgkin's lymphoma, Hodgkin's disease, lymphocytic leukemias, lymphocytic or cutaneous lymphomas, carcinomas, sarcomas, thymomas, neoplasms of the mediastinum, breast cancer, prostate cancer, cancers of the head and neck, lung cancer, non-small cell lung cancer, small cell lung cancer, various kinds of skin cancer, cancer of the bladder, malignant gliomas, cancer of the esophagus, cancer of the stomach, cancer of the pancreas, hepatobiliary neoplasms, cancer of the small intestine, colon, or rectum, cancer of the kidney or ureter, testicular cancer, cancer of the urethra or penis, gynecologic tumors, ovarian cancer, sarcomas of the bone, cancers of the endocrine system, cutaneous melanoma, intraocular melanoma, neoplasms of the central nervous system, and plasma cell neoplasms. 
     
     
         95 . A vaccine for vaccinating a patient against a cancer comprising an antigen that is highly expressed on the cancer cells and an antagonistic anti-BTNL9 antibody that binds to a protein consisting of amino acids 35 to 257 of SEQ ID NO:2.