Compositions and methods for modulating immune responses

Abstract

The present invention provides a newly identified B7 receptor, zB7R1 that functions as lymphocyte inhibitory receptor, which is a PD-1-like molecule and is expressed on T cells. The present invention also provides the discovery of zB7R1's ability to bind to CD155. Methods and compositions for modulating zB7R1-mediated negative signaling and interfering with the interaction of its counter-receptor for therapeutic, diagnostic and research purposes are also provided.

1 . An isolated soluble zB7R1 polypeptide comprising a sequence of amino acid residues having at least 95% sequence identity with amino acid residues 16-140 of SEQ ID NO:2 or amino acid residues 27-208 of SEQ ID NO:6, and wherein the polypeptide mediates T cell activation.  
     
     
         2 . An isolated soluble zB7R1 polypeptide comprising a sequence of amino acid residues having at least 95% sequence identity with amino acid residues 16-140 of SEQ ID NO:2 or amino acid residues 27-208 of SEQ ID NO:6, and wherein the polypeptide increases or upregulates T cell activation.  
     
     
         3 . An isolated soluble zB7R1 polypeptide comprising a sequence of amino acid residues having at least 95% sequence identity with amino acid residues 16-140 of SEQ ID NO:2 or amino acid residues 27-208 of SEQ ID NO:6, and wherein the polypeptide decreases or inhibits T cell activation.  
     
     
         4 . An isolated soluble zB7R1 polypeptide comprising a sequence of amino acids selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:9, and SEQ ID NO:10.  
     
     
         5 . An isolated soluble zB7R1 polypeptide comprising an amino acid sequence selected from a group consisting of: SEQ ID NO: 25 and SEQ ID NO:68.  
     
     
         6 . An isolated polynucleotide comprising nucleotides selected from the group consisting of: SEQ ID NO:1, SEQ ID NO:5, and SEQ ID NO:8.  
     
     
         7 . An isolated polynucleotide that hybridizes to a polynucleotide of  claim 6  under stringent conditions of hybridization in buffer containing 5×SSC, 5× Denhardt's, 0.5% SDS, 1 mg salmon sperm/25 mls of hybridization solution incubated at 65° C. overnight, followed by high stringency washing with 0.2×SSC/0.1% SDS at 65° C., wherein the isolated polynucleotide encodes a soluble polypeptide that inhibits the costimulation T cells.  
     
     
         8 . An expression vector comprising the following operably linked elements: 
 a transcription promoter;    a DNA segment encoding a polypeptide of  claim 1;  and    a transcription terminator.    
     
     
         9 . A cultured cell into which has been introduced an expression vector of  claim 8 , wherein the cell expresses the polypeptide encoded by the DNA segment.  
     
     
         10 . A method of producing a polypeptide comprising: 
 culturing a cell into which has been introduced an expression vector of  claim 8 , wherein the cell expresses the polypeptide encoded by the DNA segment; and    recovering the expressed polypeptide.    
     
     
         11 . An antibody or antibody fragment that specifically binds to a polypeptide of  claim 1 .  
     
     
         12 . The antibody or antibody fragment of  claim 11 , wherein said antibody blocks or inhibits the interaction of zB7R1 with CD155.  
     
     
         13 . An antibody or antibody fragment that specifically binds to CD155, wherein said antibody blocks or inhibits the interaction of CD155 with zB7R1.  
     
     
         14 . The antibody or antibody fragment of  claim 11 , wherein said antibody replaces or augments the interaction of zB7R1 with its counter-receptor.  
     
     
         15 . The antibody of  claim 14 , wherein the counter-receptor is CD155.  
     
     
         16 . The antibody of  claim 11 , wherein the antibody is selected from the group consisting of a polyclonal antibody, a murine monoclonal antibody, a humanized antibody derived from a murine monoclonal antibody, an antibody fragment, neutralizing antibody, and a human monoclonal antibody.  
     
     
         17 . The antibody fragment of  claim 11 , wherein the antibody fragment is selected from the group consisting of F(ab′), F(ab), F(ab′) 2 , Fab′, Fab, Fv, scFv, and minimal recognition unit.  
     
     
         18 . An anti-idiotype antibody comprising an anti-idiotype antibody that specifically binds to the antibody of  claim 11 .  
     
     
         19 . The antibody of  claim 13 , wherein the antibody is selected from the group consisting of a polyclonal antibody, a murine monoclonal antibody, a humanized antibody derived from a murine monoclonal antibody, an antibody fragment, neutralizing antibody, and a human monoclonal antibody.  
     
     
         20 . The antibody fragment of  claim 13 , wherein the antibody fragment is selected from the group consisting of F(ab′), F(ab), F(ab′) 2 , Fab′, Fab, Fv, scFv, and minimal recognition unit.  
     
     
         21 . An anti-idiotype antibody comprising an anti-idiotype antibody that specifically binds to the antibody of  claim 13 .  
     
     
         22 . A fusion protein comprising a polypeptide comprising a sequence of amino acid residues having at least 95% sequence identity with amino acid residues 16-140 of SEQ ID NO:2 or 27-208 of SEQ ID NO:5; and a polyalkyl oxide moiety, wherein the fusion protein mediates T cell activation.  
     
     
         23 . The fusion protein of  claim 22  wherein the polyalkyl oxide moiety is polyethylene glycol.  
     
     
         24 . The fusion protein of  claim 23  wherein the polyethylene glycol is N-terminally or C-terminally attached to the polypeptide.  
     
     
         25 . The fusion protein of  claim 23  wherein the polyethylene glycol is mPEG propionaldehyde.  
     
     
         26 . The fusion protein of  claim 23  wherein the polyethylene glycol is branched or linear.  
     
     
         27 . The fusion protein of  claim 23  wherein the polyethylene glycol has a molecular weight of about 5 kD, 12 kD, 20 kD, 30 kD, 40 kD or 50 kD.  
     
     
         28 . A fusion protein comprising a polypeptide comprising a sequence of amino acid residues having at least 95% sequence identity with SEQ ID NO:68 or SEQ ID NO:69.  
     
     
         29 . The fusion protein of  claim 28  wherein the immunoglobulin heavy chain constant region is an Fc fragment.  
     
     
         30 . The fusion protein of  claim 28  wherein the immunoglobulin heavy chain constant region is an isotype selected from the group consisting of an IgG, IgM, IgE, IgA and IgD.  
     
     
         31 . The fusion protein of  claim 30  wherein the IgG isotype is IgG1, IgG2, IgG3, or IgG4.  
     
     
         32 . A fusion protein comprising a VASP domain and zB7R1.  
     
     
         33 . The fusion protein of  claim 32 , wherein zB7R1 comprises SEQ ID NO:3.  
     
     
         34 . A fusion protein comprising SEQ ID NO:25.  
     
     
         35 . A formulation comprising: 
 an isolated soluble polypeptide comprising a sequence of amino acid residues having at least 95% sequence identity with amino acid residues 16-140 of SEQ ID NO:2 or amino acid residues 27-208 of SEQ ID NO:6; and    a pharmaceutically acceptable vehicle.    
     
     
         36 . A kit comprising the formulation of  claim 35 .  
     
     
         37 . A formulation comprising: 
 an antibody or antibody fragment according to  claim 11;  and    a pharmaceutically acceptable vehicle.    
     
     
         38 . A formulation comprising: 
 an antibody or antibody fragment according to  claim 13;  and    a pharmaceutically acceptable vehicle.    
     
     
         39 . A kit comprising the formulation of  claim 37 .  
     
     
         40 . A kit comprising the formulation of  claim 38 .  
     
     
         41 . A method for modulating lymphocyte activity, comprising contacting a zB7R1-positive lymphocyte with a bioactive agent capable of modulating zB7R1-mediated signaling in an amount effective to modulate at least one lymphocyte activity.  
     
     
         42 . The method according to  claim 41 , wherein said agent comprises an antagonist of zB7R1-mediated signaling, and wherein said contacting inhibits the attenuation of lymphocyte activity mediated by zB7R1 signaling.  
     
     
         43 . The method according to  claim 42 , wherein said contacting increases lymphocyte activity.  
     
     
         44 . The method according to  claim 42 , wherein said antagonist comprises a blocking agent capable of interfering with the functional interaction of zB7R1 and its counter-receptor.  
     
     
         45 . The method of  claim 44 , wherein said counter-receptor is CD155.  
     
     
         46 . The method according to  claim 44 , wherein said blocking agent comprises an anti-zB7R1 antibody capable of specifically binding to the extracellular domain of zB7R1 (SEQ ID NO:3), and wherein said binding interferes with the interaction of zB7R1 and its counter-receptor.  
     
     
         47 . The method according to  claim 44 , wherein said blocking agent comprises a soluble zB7R1 protein.  
     
     
         48 . The method according to  claim 47 , wherein the soluble zB7R1 protein comprises a sequence of amino acid residues sequence selected  
     
     
         49 . The method according to  claim 44 , wherein said blocking agent comprises a soluble zB7R1 fusion protein.  
     
     
         50 . The method according to  claim 44 , wherein the blocking agent is selected from the group consisting of anti-zB7R1 antibodies, zB7R1 polypeptides, and zB7R1 fusion proteins.  
     
     
         51 . The method according to  claim 41 , wherein said agent comprises an agonist of zB7R1-mediated signaling, and said contacting decreases lymphocyte activity.  
     
     
         52 . The method according to  claim 51 , wherein said agonist comprises a mimicking agent capable of mimicking the functional interaction of zB7R1 and its counter-receptor.  
     
     
         53 . The method according to  claim 52 , wherein said agonist comprises a mimicking agent capable of augmenting the functional interaction of zB7R1 and its counter-receptor.  
     
     
         54 . The method according  claim 41 , wherein said lymphocyte is a T lymphocyte and said lymphocyte activity is selected from the group consisting of activation, differentiation, proliferation, survival, cytolytic activity and cytokine production.  
     
     
         55 . The method according  claim 41 , wherein said lymphocyte is a B lymphocyte and said lymphocyte activity is selected from the group consisting of activation, differentiation, proliferation, survival, and antibody production.  
     
     
         56 . The method according to  claim 1 , wherein said lymphocyte activity comprises a host immune response to a target antigen, said target antigen selected from the group consisting of a pathogen antigen, a vaccine antigen, and a tumor-associated antigen other than Its counter-receptor.  
     
     
         57 . A method for treating cancer in a patient having zB7R1-positive tumor cells comprising administering to the patient an antagonist of zB7R1-mediated signaling, wherein said administration is effective to increase the host immune response against said zB7R1-positive tumor cell.  
     
     
         58 . The method according to  claim 57 , wherein said antagonist comprises a blocking agent capable of interfering with the functional interaction of zB7R1 and its counter-receptor.  
     
     
         59 . The method according to  claim 51 , wherein said blocking agent comprises an anti-zB7R1 antibody capable of specifically binding to the extracellular domain of zB7R1 (SEQ ID NO:3), wherein said binding interferes with the interaction of zB7R1 and its counter-receptor.  
     
     
         60 . A method for treating a patient having an autoimmune disease characterized by the presence of autoreactive zB7R1-positive lymphocytes, comprising administering to the patient an agonist of zB7R1-mediated signaling, wherein said administration is effective to inhibit an autoreactive immune response against non-lymphoid non-tumor host cells expressing zB7R1.  
     
     
         61 . The method according to  claim 60 , wherein said agonist comprises a mimicking agent capable of mimicking the functional interaction of zB7R1 and its counter-receptor.  
     
     
         62 . The method according to  claim 40 , wherein the counter-structure is CD155.  
     
     
         63 . The method according to  claim 41 , wherein the counter structure is CD155.  
     
     
         64 . The method according to  claim 61 , wherein the counter structure is CD155.  
     
     
         65 . A method of inhibiting T cell activation, the method comprising contacting the T cell with a zB7R1 agonist.  
     
     
         66 . A method of upregulating T cell activity, the method comprising contacting the T cell with a zB7R1 antagonist.  
     
     
         67 . The method of  claim 66 , wherein B cell activity is also upregulated.  
     
     
         68 . A method of inhibiting the co-stimulation a T cell, the method comprising contacting the T cell with a soluble zB7R1 polypeptide, the sequence of which comprises a sequence having at least 95% identify with amino acid residues 16-140 of SEQ ID NO:2 or amino acid residues 27-208 of SEQ ID NO:6.  
     
     
         69 . The method of  claim 68 , wherein the contacting comprises culturing the polypeptide with the T cell in vitro.  
     
     
         70 . The method of  claim 68 , wherein the T cell is in a patient.  
     
     
         71 . The method of  claim 68  wherein the contacting comprises administering the polypeptide to the patient.  
     
     
         72 . The method of  claim 70  wherein the contacting comprises administering a nucleic acid encoding the polypeptide to the patient.  
     
     
         73 . The method of  claim 70  wherein comprising (a) providing a recombinant cell which is the progeny of a cell obtained from the patient and has been transfected or transformed ex vivo with a nucleic acid molecule encoding the polypeptide so that the cell expresses the polypeptide; and (b) administering the cell to the patient.  
     
     
         74 . The method of  claim 70  wherein the patient is suffering from an inflammatory disease selected from the group consisting of Crohn's disease, ulcerative colitis, graft versus host disease, celiac disease, and irritable bowel syndrome.  
     
     
         75 . A method of treating, preventing, inhibiting the progression of, delaying the onset of and/or reducing at least one of the symptoms or conditions associated with a disease selected from the group consisting of Crohn's disease, ulcerative colitis, celiac disease, Graft-versus-host disease, and irritable bowel syndrome comprising administering to the patient an effective amount of the formulation of  claim 35 .  
     
     
         76 . A method of treating, preventing, inhibiting the progression of, delaying the onset of and/or reducing at least one of the symptoms or conditions associated with a disease selected from the group consisting of Crohn's disease, ulcerative colitis, celiac disease, Graft-versus-host disease, and irritable bowel syndrome comprising administering to the patient an effective amount of the formulation of  claim 37 .  
     
     
         77 . A method of treating, preventing, inhibiting the progression of, delaying the onset of and/or reducing at least one of the symptoms or conditions associated with a disease selected from the group consisting of Crohn's disease, ulcerative colitis, celiac disease, Graft-versus-host disease, and irritable bowel syndrome comprising administering to the patient an effective amount of the formulation of  claim 38.