Identification of Tumor-Associated Markers for Diagnosis and Therapy

Abstract

The present technology relates to genetic products the expression of which is associated with cancer diseases. The present technology also relates to the therapy and diagnosis of diseases in which the genetic products are expressed or aberrantly expressed, in particular cancer diseases.

1 . A pharmaceutical composition, comprising an agent which
 (I) inhibits expression or activity of a tumor-associated antigen and/or   (II) has tumor-inhibiting activity, and is selective for cells expressing or abnormally expressing a tumor-associated antigen and/or   (III) when administered, selectively increases the amount of complexes between an MHC molecule and a tumor-associated antigen or a part thereof,   said tumor-associated antigen having a sequence encoded by a nucleic acid which is selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 541, 1-540, 545, 549, 553, 557, 560, 563, 566, 570, 574, 577, 580, 583, 587, 591, 595, 599, 602, 606, 610, 613, 617, 620, and 624, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c). 
   
     
     
         2 . The pharmaceutical composition as claimed in  claim 1 , in which the agent under (II) causes induction of cell death, reduction in cell growth, damage to the cell membrane or secretion of cytokines. 
     
     
         3 . The pharmaceutical composition as claimed in  claim 1 , in which the agent under (I) or (II) is an antisense nucleic acid which hybridizes selectively with the nucleic acid coding for the tumor-associated antigen. 
     
     
         4 . The pharmaceutical composition as claimed in  claim 1 , in which the agent under (I) or (II) is an antibody which binds selectively to the tumor-associated antigen. 
     
     
         5 . The pharmaceutical composition as claimed in  claim 1 , in which the agent comprises one or more components selected from the group consisting of:
 (i) the tumor-associated antigen or a part thereof,   (ii) a nucleic acid which codes for the tumor-associated antigen or a part thereof,   (iii) an antibody which binds to the tumor-associated antigen or a part thereof,   (iv) an antisense nucleic acid which hybridizes specifically with a nucleic acid coding for the tumor-associated antigen,   (v) an siRNA directed against a nucleic acid coding for the tumor-associated antigen,   (vi) a host cell which expresses the tumor-associated antigen or a part thereof, and   (vii) isolated complexes between the tumor-associated antigen or a part thereof and an MHC molecule.   
     
     
         6 . The pharmaceutical composition as claimed in  claim 1 , in which the agent comprises two or more agents which in each case selectively inhibit expression or activity of different tumor-associated antigens, which are in each case selective for cells expressing or abnormally expressing different tumor-associated antigens or which increase the amount of complexes between MHC molecules and different tumor-associated antigens or parts thereof,
 with at least one of said tumor-associated antigens having a sequence encoded by a nucleic acid which is selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 541, 1-540, 545, 549, 553, 557, 560, 563, 566, 570, 574, 577, 580, 583, 587, 591, 595, 599, 602, 606, 610, 613, 617, 620, and 624, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c). 
   
     
     
         7 . A pharmaceutical composition, comprising one or more components selected from the group consisting of:
 (i) a tumor-associated antigen or a part thereof,   (ii) a nucleic acid which codes for a tumor-associated antigen or a part thereof,   (iii) an antibody which binds to a tumor-associated antigen or a part thereof,   (iv) an antisense nucleic acid which hybridizes specifically with a nucleic acid coding for a tumor-associated antigen,   (v) an siRNA directed against a nucleic acid coding for a tumor-associated antigen,   (vi) a host cell which expresses a tumor-associated antigen or a part thereof, and   (vii) isolated complexes between a tumor-associated antigen or a part thereof and an MHC molecule,   said tumor-associated antigen having a sequence encoded by a nucleic acid which is selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 541, 1-540, 545, 549, 553, 557, 560, 563, 566, 570, 574, 577, 580, 583, 587, 591, 595, 599, 602, 606, 610, 613, 617, 620, and 624, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c). 
   
     
     
         8 . The pharmaceutical composition as claimed in  claim 5  or  7 , in which the nucleic acid of (ii) is present in an expression vector. 
     
     
         9 . The pharmaceutical composition as claimed in  claim 5  or  7 , in which the host cell secretes the tumor-associated antigen or the part thereof. 
     
     
         10 . The pharmaceutical composition as claimed in  claim 5  or  7 , in which the host cell additionally expresses an MHC molecule which binds to the tumor-associated antigen or the part thereof. 
     
     
         11 . The pharmaceutical composition as claimed in  claim 10 , in which the host cell expresses the MHC molecule and/or the tumor-associated antigen or the part thereof in a recombinant manner. 
     
     
         12 . The pharmaceutical composition as claimed in  claim 10 , in which the host cell expresses the MHC molecule endogenously. 
     
     
         13 . The pharmaceutical composition as claimed in  claim 5 ,  7 ,  10  or  12 , in which the host cell is an antigen-presenting cell. 
     
     
         14 . The pharmaceutical composition as claimed in  claim 4 ,  5  or  7 , in which the antibody is a monoclonal, chimeric or humanized antibody, or is a fragment of an antibody. 
     
     
         15 . The pharmaceutical composition as claimed in  claim 4 ,  5 ,  7 , or  14  in which the antibody is coupled to a therapeutic or diagnostic agent. 
     
     
         16 . The pharmaceutical composition as claimed in any of  claims 1 - 15 , which may be used for the treatment or prevention of cancer. 
     
     
         17 . The pharmaceutical composition as claimed in  claim 16 , in which the cancer is a lung tumor, a breast tumor, a prostate tumor, a melanoma, a colon tumor, a gastric tumor, a pancreatic tumor, an ENT tumor, an ovarian tumor, a colorectal tumor, a cervical carcinoma, a colon carcinoma or a mammary carcinoma. 
     
     
         18 . The pharmaceutical composition as claimed in any of  claims 1 ,  2 ,  5 - 13 ,  16  and  17 , which is in the form of a vaccine. 
     
     
         19 . The pharmaceutical composition as claimed in  claim 18  for therapeutic and/or prophylactic use. 
     
     
         20 . A method of diagnosing or monitoring a cancer disease, which method comprises detecting or determining the quantity
 (i) of a tumor-associated nucleic acid or of a part thereof, and/or   (ii) of a tumor-associated antigen or of a part thereof, and/or   (iii) of an antibody to the tumor-associated antigen or a part thereof and/or   (iv) of T lymphocytes which are specific to the tumor-associated antigen or to a part thereof   in a biological sample isolated from a patient,   said tumor-associated nucleic acid being selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 541, 1-540, 545, 549, 553, 557, 560, 563, 566, 570, 574, 577, 580, 583, 587, 591, 595, 599, 602, 606, 610, 613, 617, 620, and 624, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c), and 
   said tumor-associated antigen having a sequence encoded by a nucleic acid which is selected from said group of nucleic acids.   
     
     
         21 . The method as claimed in  claim 20 , in which the detection or determination of the quantity comprises
 (i) contacting the biological sample with an agent which binds specifically to the tumor-associated nucleic acid or to the part thereof, to the tumor-associated antigen or the part thereof, to the antibody or to the T lymphocytes, and   (ii) detecting the formation of or determining the quantity of a complex between the agent and the nucleic acid or the part thereof, the tumor-associated antigen or the part thereof, the antibody or the T lymphocytes.   
     
     
         22 . The method as claimed in  claim 21 , in which the agent which binds specifically to the tumor-associated nucleic acid or to the part thereof is an oligonucleotide or polynucleotide, which hybridizes specifically to said nucleic acid or to said part thereof. 
     
     
         23 . The method as claimed in  claim 21 , in which the agent which binds specifically to the tumor-associated antigen or the part thereof is an antibody binding specifically to said tumor-associated antigen or to said part thereof. 
     
     
         24 . The method as claimed in  claim 21 , in which the agent which binds specifically to the antibody is a protein or peptide binding specifically to said antibody. 
     
     
         25 . The method as claimed in  claim 21 , in which the agent which binds specifically to the T lymphocytes is a cell presenting the complex between the tumor-associated antigen or the part thereof and an MHC molecule. 
     
     
         26 . The method as claimed in any of  claims 20  to  25  wherein said monitoring of said disease comprises determining regression, course or onset of said disease in a sample from a patient who has said disease or is suspected of falling ill with said disease. 
     
     
         27 . The method as claimed in  claim 26 , which comprises a detection or determination of the quantity in a first sample at a first point in time and in a further sample at a second point in time and a comparison of the two samples. 
     
     
         28 . The method as claimed in any of  claims 21 - 27 , in which the agent is labeled in a detectable manner. 
     
     
         29 . The method as claimed in any of  claims 20 - 28 , in which the sample comprises body fluid and/or body tissue. 
     
     
         30 . The method as claimed in any of  claims 20 - 29 , in which said cancer disease is characterized by expression or abnormal expression of said tumor-associated nucleic acid. 
     
     
         31 . The method as claimed in  claim 30 , in which said cancer disease is further characterized by expression or abnormal expression of a tumor-associated antigen encoded by said tumor-associated nucleic acid. 
     
     
         32 . A method of treating or preventing a disease characterized by expression or abnormal expression of a tumor-associated antigen, which method comprises administration of a pharmaceutical composition as claimed in any of  claims 1 - 19 ,
 said tumor-associated antigen having a sequence encoded by a nucleic acid which is selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 541, 1-540, 545, 549, 553, 557, 560, 563, 566, 570, 574, 577, 580, 583, 587, 591, 595, 599, 602, 606, 610, 613, 617, 620, and 624, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c). 
   
     
     
         33 . A method of treating, preventing, diagnosing or monitoring a disease characterized by expression or abnormal expression of a tumor-associated antigen, which method comprises administering an antibody binding to said tumor-associated antigen or to a part thereof and coupled to a therapeutic or diagnostic agent,
 said tumor-associated antigen having a sequence encoded by a nucleic acid which is selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 541, 1-540, 545, 549, 553, 557, 560, 563, 566, 570, 574, 577, 580, 583, 587, 591, 595, 599, 602, 606, 610, 613, 617, 620, and 624, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c). 
   
     
     
         34 . The method as claimed in  claim 23  or  33 , in which the antibody is a monoclonal, chimeric or humanized antibody, or is a fragment of an antibody. 
     
     
         35 . A method of treating a patient having a disease characterized by expression or abnormal expression of a tumor-associated antigen, which method comprises:
 (i) providing a sample containing immunoreactive cells,   (ii) contacting said sample with a host cell expressing said tumor-associated antigen or a part thereof, under conditions which favor production of cytolytic or cytokine-releasing T cells against said tumor-associated antigen or said part thereof, and   (iii) introducing the cytolytic or cytokine-releasing T cells into the patient in an amount suitable for lysing cells expressing the tumor-associated antigen or a part thereof,   said tumor-associated antigen having a sequence encoded by a nucleic acid which is selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 541, 1-540, 545, 549, 553, 557, 560, 563, 566, 570, 574, 577, 580, 583, 587, 591, 595, 599, 602, 606, 610, 613, 617, 620, and 624, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c). 
   
     
     
         36 . The method as claimed in  claim 35 , in which the host cell recombinantly expresses an MHC molecule binding to the tumor-associated antigen or to a part thereof. 
     
     
         37 . The method as claimed in  claim 35 , in which the host cell endogenously expresses an MHC molecule binding to the tumor-associated antigen or to a part thereof. 
     
     
         38 . A method of inhibiting the development of cancer in a patient, which method comprises administering an effective amount of a pharmaceutical composition as claimed in any of  claims 1 - 19 . 
     
     
         39 . An agent, which binds specifically to a protein or polypeptide or to a part thereof, said protein or polypeptide being encoded by a nucleic acid selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 541, 1-540, 545, 549, 553, 557, 560, 563, 566, 570, 574, 577, 580, 583, 587, 591, 595, 599, 602, 606, 610, 613, 617, 620, and 624, a part or derivative thereof,   (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions,   (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and   (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c).   
     
     
         40 . The agent as claimed in  claim 39 , which is an antibody. 
     
     
         41 . The agent as claimed in  claim 40 , in which the antibody is a monoclonal, chimeric or humanized antibody, or is a fragment of an antibody. 
     
     
         42 . An antibody, which binds selectively to a complex of:
 (i) a protein or polypeptide or a part thereof and   (ii) an MHC molecule to which said protein or polypeptide or said part thereof binds,   with said antibody not binding to (i) or (ii) alone and said protein or polypeptide being encoded by a nucleic acid selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 541, 1-540, 545, 549, 553, 557, 560, 563, 566, 570, 574, 577, 580, 583, 587, 591, 595, 599, 602, 606, 610, 613, 617, 620, and 624, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c). 
   
     
     
         43 . The antibody as claimed in  claim 42 , which is a monoclonal, chimeric or humanized antibody, or is a fragment of an antibody. 
     
     
         44 . A conjugate between an agent as claimed in any of  claims 39 - 41  or an antibody as claimed in any of  claims 42 - 43  and a therapeutic or diagnostic agent. 
     
     
         45 . The conjugate as claimed in  claim 44 , in which the therapeutic or diagnostic agent is a toxin. 
     
     
         46 . A kit for detecting cancer, which kit comprises agents for detecting or determining the quantity
 (i) of a tumor-associated nucleic acid or of a part thereof, and/or   (ii) of a tumor-associated antigen or of a part thereof, and/or   (iii) of antibodies which bind to the tumor-associated antigen or to a part thereof, and/or   (iv) of T cells which are specific for a complex between the tumor-associated antigen or a part thereof and an MHC molecule,   said tumor-associated nucleic acid being selected from the group consisting of:
 (a) a nucleic acid which comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 541, 1-540, 545, 549, 553, 557, 560, 563, 566, 570, 574, 577, 580, 583, 587, 591, 595, 599, 602, 606, 610, 613, 617, 620, and 624, a part or derivative thereof, 
 (b) a nucleic acid which hybridizes with the nucleic acid of (a) under stringent conditions, 
 (c) a nucleic acid which is degenerate with respect to the nucleic acid of (a) or (b), and 
 (d) a nucleic acid which is complementary to the nucleic acid of (a), (b) or (c), and 
   said tumor-associated antigen having a sequence encoded by a nucleic acid which is selected from said group of nucleic acids.   
     
     
         47 . The pharmaceutical composition as claimed in any of  claims 1 - 19  or the method as claimed in any of  claims 20 - 38  in which the tumor-associated antigen comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 542, 546, 550, 554, 567, 571, 584, 588, 592, 596, 603, 607, 614, 621, and 625, a part or derivative thereof. 
     
     
         48 . The agent as claimed in any of  claims 39 - 41 , the antibody as claimed in any of  claims 42 - 43  or the conjugate as claimed in any of  claims 44 - 45  in which the protein or polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 542, 546, 550, 554, 567, 571, 584, 588, 592, 596, 603, 607, 614, 621, and 625, a part or derivative thereof.