Compositions and methods for therapy and diagnosis of lung cancer

Abstract

Compositions and methods for the therapy and diagnosis of cancer, such as lung cancer, are disclosed. Compositions may comprise one or more lung tumor proteins, immunogenic portions thereof, or polynucleotides that encode such portions. Alternatively, a therapeutic composition may comprise an antigen presenting cell that expresses a lung tumor protein, or a T cell that is specific for cells expressing such a protein. Such compositions may be used, for example, for the prevention and treatment of diseases such as lung cancer. Diagnostic methods based on detecting a lung tumor protein, or mRNA encoding such a protein, in a sample are also provided.

1 . An isolated polypeptide comprising at least an immunogenic portion of a lung tumor protein, or a variant thereof, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence selected from the group consisting of: 
 (a) sequences recited in any one of SEQ ID NO: 1, 11-13, 15, 20, 23-27, 29, 30, 33, 34, 39, 41, 43-46, 51, 52, 57, 58, 60, 62, 65-67, 69-71, 74, 76, 79, 80, 84, 86, 89-92, 95, 97, 98, 101, 110, 111, 113-119, 121-128, 130-134, 136, 138, 139, 141, 143, 146-151, 153, 154, 157-160, 162-164, 167-178, 180, 181, 183, 186-190, 192, 193, 195-220, 224, 226-231, 234, 236, 237, 240, 241, 244-246, 248, 254, 255, 261, 262, 266, 270, 275, 280, 282, 283, 288, 289, 290, 292, 295, 301, 303, 304, 309, 311, 341-782, 784 and 785;    (b) sequences that hybridize to a sequence of any one of SEQ ID NO: 1, 11-13, 15, 20, 23-27, 29, 30, 33, 34, 39, 41, 43-46, 51, 52, 57, 58, 60, 62, 65-67, 69-71, 74, 76, 79, 80, 84, 86, 89-92, 95, 97, 98, 101, 110, 111, 113-119, 121-128, 130-134, 136, 138, 139, 141, 143, 146-151, 153, 154, 157-160, 162-164, 167-178, 180, 181, 183, 186-190, 192, 193, 195-220, 224, 226-231, 234, 236, 237, 240, 241, 244-246, 248, 254, 255, 261, 262, 266, 270, 275, 280, 282, 283, 288, 289, 290, 292, 295, 301, 303, 304, 309, 311, 341-782, 784 and 785, under moderately stringent conditions; and    (c) a complement of a sequence of (a) or (b).    
     
     
         2 . An isolated polypeptide according to  claim 1 , wherein the polypeptide comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NO: 1, 11-13, 15, 20, 23-27, 29, 30, 33, 34, 39, 41, 43-46, 51, 52, 57, 58, 60, 62, 65-67, 69-71, 74, 76, 79, 80, 84, 86, 89-92, 95, 97, 98, 101, 110, 111, 113-119, 121-128, 130-134, 136, 138, 139, 141, 143, 146-151, 153, 154, 157-160, 162-164, 167-178, 180, 181, 183, 186-190, 192, 193, 195-220, 224, 226-231, 234, 236, 237, 240, 241, 244-246, 248, 254, 255, 261, 262, 266, 270, 275, 280, 282, 283, 288, 289, 290, 292, 295, 301, 303, 304, 309, 311, 341-782, 784 and 785, or a complement of any of the foregoing polynucleotide sequences.  
     
     
         3 . An isolated polynucleotide encoding at least 15 amino acid residues of a lung tumor protein, or a variant thereof that differs in one or more substitutions, deletions, additions and/or insertions such that the ability of the variant to react with antigen-specific antisera is not substantially diminished, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide comprising a sequence recited in any one of SEQ ID NO: 1, 11-13, 15, 20, 23-27, 29, 30, 33, 34, 39, 41, 43-46, 51, 52, 57, 58, 60, 62, 65-67, 69-71, 74, 76, 79, 80, 84, 86, 89-92, 95, 97, 98, 101, 110, 111, 113-119, 121-128, 130-134, 136, 138, 139, 141, 143, 146-151, 153, 154, 157-160, 162-164, 167-178, 180, 181, 183, 186-190, 192, 193, 195-220, 224, 226-231, 234, 236, 237, 240, 241, 244-246, 248, 254, 255, 261, 262, 266, 270, 275, 280, 282, 283, 288, 289, 290, 292, 295, 301, 303, 304, 309, 311, 341 782, 784 and 785, or a complement of any of the foregoing sequences.  
     
     
         4 . An isolated polynucleotide encoding a lung tumor protein, or a variant thereof, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide comprising a sequence recited in any one of SEQ ID NO: 1, 11-13, 15, 20, 23-27, 29, 30, 33, 34, 39, 41, 43-46, 51, 52, 57, 58, 60, 62, 65-67, 69-71, 74, 76, 79, 80, 84, 86, 89-92, 95, 97, 98, 101, 110, 111, 113-119, 121-128, 130-134, 136, 138, 139, 141, 143, 146-151, 153, 154, 157-160, 162-164, 167-178, 180, 181, 183, 186-190, 192, 193, 195-220, 224, 226-231, 234, 236, 237, 240, 241, 244-246, 248, 254, 255, 261, 262, 266, 270, 275, 280, 282, 283, 288, 289, 290, 292, 295, 301, 303, 304, 309, 311, 341-782, 784 and 785 or a complement of any of the foregoing sequences.  
     
     
         5 . An isolated polynucleotide comprising a sequence recited in any one of SEQ ID NO: 1, 11-13, 15, 20, 23-27, 29, 30, 33, 34, 39, 41, 43-46, 51, 52, 57, 58, 60, 62, 65-67, 69-71, 74, 76, 79, 80, 84, 86, 89-92, 95, 97, 98, 101, 110, 111, 113-119, 121-128, 130-134, 136, 138, 139, 141, 143, 146-151, 153, 154, 157-160, 162-164, 167-178, 180, 181, 183, 186-190, 192, 193, 195-220, 224, 226-231, 234, 236, 237, 240, 241, 244-246, 248, 254, 255, 261, 262, 266, 270, 275, 280, 282, 283, 288, 289, 290, 292, 295, 301, 303, 304, 309, 311, 341-782, 784 and 785.  
     
     
         6 . An isolated polynucleotide comprising a sequence that hybridizes to a sequence recited in any one of SEQ ID NO: 1, 11-13, 15, 20, 23-27, 29, 30, 33, 34, 39, 41, 43-46, 51, 52, 57, 58, 60, 62, 65-67, 69-71, 74, 76, 79, 80, 84, 86, 89-92, 95, 97, 98, 101, 110, 111, 113-119, 121-128, 130-134, 136, 138, 139, 141, 143, 146-151, 153, 154, 157-160, 162-164, 167-178, 180, 181, 183, 186-190, 192, 193, 195-220, 224, 226-231, 234, 236, 237, 240, 241, 244-246, 248, 254, 255, 261, 262, 266, 270, 275, 280, 282, 283, 288, 289, 290, 292, 295, 301, 303, 304, 309, 311, 341-782, 784 and 785 under moderately stringent conditions.  
     
     
         7 . An isolated polynucleotide complementary to a polynucleotide according to any one of claims  3 - 6 .  
     
     
         8 . An expression vector comprising a polynucleotide according to any one of claims claim  3 - 6 .  
     
     
         9 . A host cell transformed or transfected with an expression vector according to  claim 8 .  
     
     
         10 . An expression vector comprising a polynucleotide according  claim 7 .  
     
     
         11 . A host cell transformed or transfected with an expression vector according to  claim 10 .  
     
     
         12 . A pharmaceutical composition comprising a polypeptide according to  claim 1 , in combination with a physiologically acceptable carrier.  
     
     
         13 . A vaccine comprising a polypeptide according to  claim 1 , in combination with an immunostimulant.  
     
     
         14 . A vaccine according to  claim 13 , wherein immunostimulant is an adjuvant.  
     
     
         15 . A vaccine according to  claim 13 , wherein immunostimulant induces a predominantly Type I response.  
     
     
         16 . A pharmaceutical composition comprising a polynucleotide according to  claim 3 , in combination with a physiologically acceptable carrier.  
     
     
         17 . A vaccine comprising a polynucleotide according to  claim 3 , in combination with a immunostimulant.  
     
     
         18 . A vaccine according to  claim 17 , wherein the immunostimulant is an adjuvant.  
     
     
         19 . A vaccine according to  claim 17 , wherein the immunostimulant induces a predominantly Type I response.  
     
     
         20 . An isolated antibody, or antigen-binding fragment thereof, that specifically binds to a lung tumor protein that comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NO: 1, 11-13, 15, 20, 23-27, 29, 30, 33, 34, 39, 41, 43-46, 51, 52, 57, 58, 60, 62, 65-67, 69-71, 74, 76, 79, 80, 84, 86, 89-92, 95, 97, 98, 101, 110, 111, 113-119, 121-128, 130-134, 136, 138, 139, 141, 143, 146-151, 153, 154, 157-160, 162-164, 167-178, 180, 181, 183, 186-190, 192, 193, 195-220, 224, 226-231, 234, 236, 237, 240, 241, 244-246, 248, 254, 255, 261, 262, 266, 270, 275, 280, 282, 283, 288, 289, 290, 292, 295, 301, 303, 304, 309, 311, 341-782, 784 and 785 or a complement of any of the foregoing polynucleotide sequences.  
     
     
         21 . A pharmaceutical composition comprising an antibody or fragment thereof according to  claim 17 , in combination with a physiologically acceptable carrier.  
     
     
         22 . A pharmaceutical composition comprising an antigen-presenting cell that expresses a polypeptide according to  claim 1 , in combination with a pharmaceutically acceptable carrier or excipient.  
     
     
         23 . A pharmaceutical composition according to  claim 22 , wherein the antigen presenting cell is a dendritic cell or a macrophage.  
     
     
         24 . A vaccine comprising an antigen-presenting cell that expresses a polypeptide according to  claim 1 , in combination with an immunostimulant.  
     
     
         25 . A vaccine according to  claim 24 , wherein the immunostimulant is an adjuvant.  
     
     
         26 . A vaccine according to  claim 24 , wherein the immunostimulant induces a predominantly Type I response.  
     
     
         27 . A vaccine according to  claim 24 , wherein the antigen-presenting cell is a dendritic cell.  
     
     
         28 . A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of a polypeptide according to  claim 1 , and thereby inhibiting the development of a cancer in the patient.  
     
     
         29 . A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of a polynucleotide according to  claim 3 , and thereby inhibiting the development of a cancer in the patient.  
     
     
         30 . A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of an antibody or antigen-binding fragment thereof according to  claim 20 , and thereby inhibiting the development of a cancer in the patient.  
     
     
         31 . A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of an antigen-presenting cell that expresses a polypeptide according to  claim 1 , and thereby inhibiting the development of a cancer in the patient.  
     
     
         32 . A method according to  claim 31 , wherein the antigen-presenting cell is a dendritic cell.  
     
     
         33 . A method according to any one of claims  28 - 31 , wherein the cancer is lung cancer.  
     
     
         34 . A fusion protein comprising at least one polypeptide according to  claim 1 .  
     
     
         35 . A fusion protein according to  claim 34 , wherein the fusion protein comprises an expression enhancer that increases expression of the fusion protein in a host cell transfected with a polynucleotide encoding the fusion protein.  
     
     
         36 . A fusion protein according to  claim 34 , wherein the fusion protein comprises a T helper epitope that is not present within the polypeptide of  claim 1 .  
     
     
         37 . A fusion protein according to  claim 34 , wherein the fusion protein comprises an affinity tag.  
     
     
         38 . An isolated polynucleotide encoding a fusion protein according to  claim 34 .  
     
     
         39 . A pharmaceutical composition comprising a fusion protein according to  claim 31 , in combination with a physiologically acceptable carrier.  
     
     
         40 . A vaccine comprising a fusion protein according to  claim 34 , in combination with an immunostimulant.  
     
     
         41 . A vaccine according to  claim 40 , wherein the immunostimulant is an adjuvant.  
     
     
         42 . A vaccine according to  claim 40 , wherein the immunostimulant induces a predominantly Type I response.  
     
     
         43 . A pharmaceutical composition comprising a polynucleotide according to  claim 3 , in combination with a physiologically acceptable carrier.  
     
     
         44 . A vaccine comprising a polynucleotide according to  claim 3 , in combination with an immunostimulant.  
     
     
         45 . A vaccine according to  claim 44 , wherein the immunostimulant is an adjuvant.  
     
     
         46 . A vaccine according to  claim 44 , wherein the immunostimulant induces a predominantly Type I response.  
     
     
         47 . A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of a pharmaceutical composition according to any one of claims  39  and  43 .  
     
     
         48 . A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of a vaccine according to any one of claims  40  and  44 .  
     
     
         49 . A method for removing tumor cells from a biological sample, comprising contacting a biological sample with T cells that specifically react with a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence selected from the group consisting of: 
 (i) polynucleotides recited in any one of SEQ ID NO: 1-782, 784 and 785; and    (ii) complements of the foregoing polynucleotides;    wherein the step of contacting is performed under conditions and for a time sufficient to permit the removal of cells expressing the antigen from the sample.    
     
     
         50 . A method according to  claim 49 , wherein the biological sample is blood or a fraction thereof.  
     
     
         51 . A method for inhibiting the development of a cancer in a patient, comprising administering to a patient a biological sample treated according to the method of  claim 49 .  
     
     
         52 . A method for stimulating and/or expanding T cells specific for a lung tumor protein, comprising contacting T cells with one or more of: 
 (i) a polypeptide encoded by a polynucleotide comprising a sequence of any one of SEQ ID NO: 1-782, 784 and 785;    (ii) a polynucleotide encoding such a polypeptide; and/or    (iii) an antigen presenting cell that expresses such a polypeptide;    under conditions and for a time sufficient to permit the stimulation and/or expansion of T cells.    
     
     
         53 . An isolated T cell population, comprising T cells prepared according to the method of  claim 52 .  
     
     
         54 . A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of a T cell population according to  claim 53 .  
     
     
         55 . A method for inhibiting the development of a cancer in a patient, comprising the steps of: 
 (a) incubating CD4 +  and/or CD8 +  T cells isolated from a patient with at least one component selected from the group consisting of: 
 (i) a polypeptide encoded by a polynucleotide comprising a sequence of any one of SEQ ID NO: 1-782, 784 and 785;  
 (ii) a polynucleotide encoding such a polypeptide; or  
 (iii) an antigen-presenting cell that expresses such a polypeptide;  
   such that T cells proliferate; and    (b) administering to the patient an effective amount of the proliferated T cells, and thereby inhibiting the development of a cancer in the patient.    
     
     
         56 . A method for inhibiting the development of a cancer in a patient, comprising the steps of: 
 (a) incubating CD4 +  and/or CD8+ T cells isolated from a patient with at least one component selected from the group consisting of: 
 (i) a polypeptide encoded by a polynucleotide comprising a sequence of any one of SEQ ID NO: 1-782, 784 and 785;  
 (ii) a polynucleotide encoding such a polypeptide; or  
 (iii) an antigen-presenting cell that expresses such a polypeptide;  
   such that T cells proliferate;    (b) cloning at least one proliferated cell; and    (c) administering to the patient an effective amount of the cloned T cells, and thereby inhibiting the development of a cancer in the patient.    
     
     
         57 . A method for determining the presence or absence of a cancer in a patient, comprising the steps of: 
 (a) contacting a biological sample obtained from a patient with a binding agent that binds to a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence selected from the group consisting of: 
 (i) polynucleotides recited in any one of SEQ ID NO: 1-782, 784 and 785; and  
 (ii) complements of the foregoing polynucleotides;  
   (b) detecting in the sample an amount of polypeptide that binds to the binding agent; and    (c) comparing the amount of polypeptide to a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient.    
     
     
         58 . A method according to  claim 57 , wherein the binding agent is an antibody.  
     
     
         59 . A method according to  claim 58 , wherein the antibody is a monoclonal antibody.  
     
     
         60 . A method according to  claim 57 , wherein the cancer is lung cancer.  
     
     
         61 . A method for monitoring the progression of a cancer in a patient, comprising the steps of: 
 (a) contacting a biological sample obtained from a patient at a first point in time with a binding agent that binds to a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NO: 1-782, 784 and 785 or a complement of any of the foregoing polynucleotides;    (b) detecting in the sample an amount of polypeptide that binds to the binding agent;    (c) repeating steps (a) and (b) using a biological sample obtained from the patient at a subsequent point in time; and    (d) comparing the amount of polypeptide detected in step (c) to the amount detected in step (b) and therefrom monitoring the progression of the cancer in the patient.    
     
     
         62 . A method according to  claim 61 , wherein the binding agent is an antibody.  
     
     
         63 . A method according to  claim 62 , wherein the antibody is a monoclonal antibody.  
     
     
         64 . A method according to  claim 61 , wherein the cancer is a lung cancer.  
     
     
         65 . A method for determining the presence or absence of a cancer in a patient, comprising the steps of: 
 (a) contacting a biological sample obtained from a patient with an oligonucleotide that hybridizes to a polynucleotide that encodes a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NO: 1-782, 784 and 785 or a complement of any of the foregoing polynucleotides;    (b) detecting in the sample an amount of a polynucleotide that hybridizes to the oligonucleotide; and    (c) comparing the amount of polynucleotide that hybridizes to the oligonucleotide to a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient.    
     
     
         66 . A method according to  claim 65 , wherein the amount of polynucleotide that hybridizes to the oligonucleotide is determined using a polymerase chain reaction.  
     
     
         67 . A method according to  claim 65 , wherein the amount of polynucleotide that hybridizes to the oligonucleotide is determined using a hybridization assay.  
     
     
         68 . A method for monitoring the progression of a cancer in a patient, comprising the steps of: 
 (a) contacting a biological sample obtained from a patient with an oligonucleotide that hybridizes to a polynucleotide that encodes a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NO: 1-782, 784 and 785 or a complement of any of the foregoing polynucleotides;    (b) detecting in the sample an amount of a polynucleotide that hybridizes to the oligonucleotide;    (c) repeating steps (a) and (b) using a biological sample obtained from the patient at a subsequent point in time; and    (d) comparing the amount of polynucleotide detected in step (c) to the amount detected in step (b) and therefrom monitoring the progression of the cancer in the patient.    
     
     
         69 . A method according to  claim 68 , wherein the amount of polynucleotide that hybridizes to the oligonucleotide is determined using a polymerase chain reaction.  
     
     
         70 . A method according to  claim 68 , wherein the amount of polynucleotide that hybridizes to the oligonucleotide is determined using a hybridization assay.  
     
     
         71 . A diagnostic kit, comprising: 
 (a) one or more antibodies according to  claim 20;  and    (b) a detection reagent comprising a reporter group.    
     
     
         72 . A kit according to  claim 71 , wherein the antibodies are immobilized on a solid support.  
     
     
         73 . A kit according to  claim 72 , wherein the solid support comprises nitrocellulose, latex or a plastic material.  
     
     
         74 . A kit according to  claim 71 , wherein the detection reagent comprises an anti-immunoglobulin, protein G, protein A or lectin.  
     
     
         75 . A kit according to  claim 71 , wherein the reporter group is selected from the group consisting of radioisotopes, fluorescent groups, luminescent groups, enzymes, biotin and dye particles.  
     
     
         76 . An oligonucleotide comprising 10 to 40 contiguous nucleotides that hybridize under moderately stringent conditions to a polynucleotide that encodes a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NO: 1, 11-13, 15, 20, 23-27, 29, 30, 33, 34, 39, 41, 43-46, 51, 52, 57, 58, 60, 62, 65-67, 69-71, 74, 76, 79, 80, 84, 86, 89-92, 95, 97, 98, 101, 110, 111, 113-119, 121-128, 130-134, 136, 138, 139, 141, 143, 146-151, 153, 154, 157-160, 162-164, 167-178, 180, 181, 183, 186-190, 192, 193, 195-220, 224, 226-231, 234, 236, 237, 240, 241, 244-246, 248, 254, 255, 261, 262, 266, 270, 275, 280, 282, 283, 288, 289, 290, 292, 295, 301, 303, 304, 309, 311, 341-782, 784 and 785 or a complement of any of the foregoing polynucleotides.  
     
     
         77 . A oligonucleotide according to  claim 76 , wherein the oligonucleotide comprises 10-40 contiguous nucleotides recited in any one of SEQ ID NO: 1, 11-13, 15, 20, 23-27, 29, 30, 33, 34, 39, 41, 43-46, 51, 52, 57, 58, 60, 62, 65-67, 69-71, 74, 76, 79, 80, 84, 86, 89-92, 95, 97, 98, 101, 110, 111, 113-119, 121-128, 130-134, 136, 138, 139, 141, 143, 146-151, 153, 154, 157-160, 162-164, 167-178, 180, 181, 183, 186-190, 192, 193, 195-220, 224, 226-231, 234, 236, 237, 240, 241, 244-246, 248, 254, 255, 261, 262, 266, 270, 275, 280, 282, 283, 288, 289, 290, 292, 295, 301, 303, 304, 309, 311, 341-782, 784 and 785.  
     
     
         78 . A diagnostic kit, comprising: 
 (a) an oligonucleotide according to  claim 76;  and    (b) a diagnostic reagent for use in a polymerase chain reaction or hybridization assay.