Compositions for the treatment and diagnosis of breast cancer and methods for their use

Abstract

Compounds and methods for the treatment and diagnosis of breast cancer are provided. The inventive compounds include polypeptides containing at least a portion of a breast tumor antigen. Vaccines and pharmaceutical compositions for immunotherapy of breast cancer comprising such polypeptides, or polynucleotides encoding such polypeptides, are provided, together with polynucleotides for preparing the inventive polypeptides. The inventive polypeptides may be used to generate antibodies useful for the diagnosis and monitoring of breast cancer.

1 . An isolated polypeptide comprising an immunogenic portion of a breast antigen or a variant thereof, wherein said antigen comprises an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of: (a) nucleotide sequences recited in SEQ ID NO: 2, 4-15, 18-33, 35-47, 49-56, 58, 59, 63-73, 88-116, 141-159, 175, 178 and 180; (b) complements of said nucleotide sequences; and (c) sequences that hybridize to a sequence of (a) or (b) under moderately stringent conditions.  
     
     
         2 . The isolated polypeptide of  claim 1 , wherein the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 62, 176, 179 and 181.  
     
     
         3 . An isolated polynucleotide comprising a nucleotide sequence encoding the polypeptide of  claim 1 .  
     
     
         4 . An isolated polynucleotide of  claim 3 , wherein the polynucleotide comprises a sequence provided in SEQ ID NO: 2, 4-15, 18-33, 35-47, 49-56, 58, 59, 63-73, 88-116, 141-159, 175, 178 or 180.  
     
     
         5 . An expression vector comprising a polynucleotide according to any one of claims  3  and  4 .  
     
     
         6 . A host cell transformed with the expression vector of  claim 5 .  
     
     
         7 . The host cell of  claim 6  wherein the host cell is selected from the group consisting of  E. coli , yeast and mammalian cell lines.  
     
     
         8 . A pharmaceutical composition comprising the polypeptide of  claim 1  and a physiologically acceptable carrier.  
     
     
         9 . A vaccine comprising the polypeptide of  claim 1  and a non-specific immune response enhancer.  
     
     
         10 . The vaccine of  claim 9  wherein the non-specific immune response enhancer is an adjuvant.  
     
     
         11 . A vaccine comprising a polynucleotide of any one of claims  3  and  4  and a non-specific immune response enhancer.  
     
     
         12 . The vaccine of  claim 11  wherein the non-specific immune response enhancer is an adjuvant.  
     
     
         13 . A pharmaceutical composition for the treatment of breast cancer comprising a polypeptide and a physiologically acceptable carrier, the polypeptide comprising an immunogenic portion of a breast antigen, wherein said antigen comprises an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of: (a) nucleotide sequences recited in SEQ ID NO: 1, 3, 16, 17, 34, 48, 57, 60, 61, 74-87, 117-140 and 160-174; (b) complements of said nucleotide sequences; and (c) sequences that hybridize to a sequence of (a) or (b) under moderately stringent conditions.  
     
     
         14 . A vaccine for the treatment of breast cancer comprising a polypeptide and a non-specific immune response enhancer, said polypeptide comprising an immunogenic portion of a breast antigen, wherein said antigen comprises an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of: (a) nucleotide sequences recited in SEQ ID NO: 1, 3, 16, 17, 34, 48, 57, 60, 61, 74-87, 117-140 and 160-174; (b) complements of said nucleotide sequences; and (c) sequences that hybridize to a sequence of (a) or (b) under moderately stringent conditions.  
     
     
         15 . The vaccine of  claim 14  wherein the non-specific immune response enhancer is an adjuvant.  
     
     
         16 . A vaccine for the treatment of breast cancer comprising a polynucleotide and a non-specific immune response enhancer, the polynucleotide comprising a sequence selected from the group consisting of: (a) nucleotide sequences recited in SEQ ID NO: 1, 3, 16, 17, 34, 48, 57, 60, 61, 74-87, 117-140 and 160-174; (b) complements of said nucleotide sequences; and (c) sequences that hybridize to a sequence of (a) or (b) under moderately stringent conditions.  
     
     
         17 . The vaccine of  claim 16 , wherein the non-specific immune response enhancer is an adjuvant.  
     
     
         18 . A method for inhibiting the development of breast cancer in a patient, comprising administering to the patient an effective amount of the pharmaceutical composition of claims  8  or  13 .  
     
     
         19 . A method for inhibiting the development of breast cancer in a patient, comprising administering to the patient an effective amount of the vaccine of; any one of claims  9 ,  11 ,  14  or  16 .  
     
     
         20 . A fusion protein comprising at least one polypeptide according to  claim 1 .  
     
     
         21 . A pharmaceutical composition comprising a fusion protein according to  claim 20  and a physiologically acceptable carrier.  
     
     
         22 . A vaccine comprising a fusion protein according to  claim 20  and a non-specific immune response enhancer.  
     
     
         23 . The vaccine of  claim 22  wherein the non-specific immune response enhancer is an adjuvant.  
     
     
         24 . A method for inhibiting the development of breast cancer in a patient, comprising administering to the patient an effective amount of the pharmaceutical composition of  claim 21 .  
     
     
         25 . A method for inhibiting the development of breast cancer in a patient, comprising administering to the patient an effective amount of the vaccine of  claim 22 .  
     
     
         26 . A method for detecting breast cancer in a patient, comprising: 
 (a) contacting a biological sample obtained from the patient with a binding agent which is capable of binding to a polypeptide, the polypeptide comprising an immunogenic portion of a breast antigen, wherein said antigen comprises an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of nucleotide sequences recited in SEQ ID NO: 1-61, 63-175, 178 and 180, complements of said nucleotide sequences, and sequences that hybridize to a sequence provided in SEQ ID NO: 1-61, 63-175, 178 and 180 under moderately stringent conditions; and    (b) detecting in the sample a polypeptide that binds to the binding agent, thereby detecting breast cancer in the patient.    
     
     
         27 . The method of  claim 26  wherein the binding agent is a monoclonal antibody.  
     
     
         28 . The method of  claim 26  wherein the binding agent is a polyclonal antibody.  
     
     
         29 . A method for monitoring the progression of breast cancer in a patient, comprising: 
 (a) contacting a biological sample obtained from the patient with a binding agent that is capable of binding to a polypeptide, said polypeptide comprising an immunogenic portion of a breast antigen, wherein said antigen comprises an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of nucleotide sequences recited in SEQ ID NO: 1-61, 63-175, 178 and 180, complements of said nucleotide sequences and sequences that hybridize to a sequence provided in SEQ ID NO: 1-61, 63-175, 178 and 180 under moderately stringent conditions;    (b) determining in the sample an amount of a protein or polypeptide that binds to the binding agent;    (c) repeating steps (a) and (b); and    (d) comparing the amount of polypeptide detected in steps (b) and (c) to monitor the progression of breast cancer in the patient.    
     
     
         30 . A monoclonal antibody that binds to a polypeptide comprising an immunogenic portion of a breast antigen or a variant of said antigen, wherein said antigen comprises an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of: (a) nucleotide sequences recited in SEQ ID NO: 2, 4-15, 18-33, 35-39, 40-47, 49-56, 58, 59, 63-73, 88-116, 141-159, 175, 178 and 180; (b) complements of said nucleotide sequences; and (c) sequences that hybridize to a sequence of (a) or (b) under moderately stringent conditions.  
     
     
         31 . A method for inhibiting the development of breast cancer in a patient, comprising administering to the patient a therapeutically effective amount of a monoclonal antibody according to  claim 30 .  
     
     
         32 . The method of  claim 31  wherein the monoclonal antibody is conjugated to a therapeutic agent.  
     
     
         33 . A method for detecting breast cancer in a patient comprising: 
 (a) obtaining a biological sample from the patient;    (b) contacting the sample with at least two oligonucleotide primers in a polymerase chain reaction, wherein at least one of the oligonucleotides is specific for a polynucleotide encoding a polypeptide comprising an immunogenic portion of a breast antigen, said antigen comprising an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of nucleotide sequences recited in SEQ ID NO: 1-61, 63-175, 178 and 180, complements of said nucleotide sequences, and sequences that hybridize to a sequence of SEQ ID NO: 1-61, 63-175, 178 and 180 under moderately stringent conditions; and    (c) detecting in the sample a DNA sequence that amplifies in the presence of the oligonucleotide primers, thereby detecting breast cancer.    
     
     
         34 . The method of  claim 33 , wherein at least one of the oligonucleotide primers comprises at least about 10 contiguous nucleotides of a polynucleotide comprising a sequence selected from SEQ ID NO: 1-61, 63-175, 178 and 180.  
     
     
         35 . A diagnostic kit comprising: 
 (a) one or more monoclonal antibodies of  claim 30;  and    (b) a detection reagent.    
     
     
         36 . A diagnostic kit comprising: 
 (a) one or more monoclonal antibodies that bind to a polypeptide encoded by a polynucleotide comprising a sequence selected from the group consisting of SEQ ID NO: 1, 3, 16, 17, 34, 48, 57, 60, 61, 74-87, 117-140 and 160-174, complements of said sequences, and sequences that hybridize to a sequence of SEQ ID NO:, 1, 3, 16, 17, 34, 48, 57, 60, 61, 74-87, 117-140 and 160-174 under moderately stringent conditions; and    (b) a detection reagent.    
     
     
         37 . The kit of claims  35  or  36  wherein the monoclonal antibodies are immobilized on a solid support.  
     
     
         38 . The kit of  claim 37  wherein the solid support comprises nitrocellulose, latex or a plastic material.  
     
     
         39 . The kit of claims  35  or  36  wherein the detection reagent comprises a reporter group conjugated to a binding agent.  
     
     
         40 . The kit of  claim 39  wherein the binding agent is selected from the group consisting of anti-immunoglobulins, Protein G, Protein A and lectins.  
     
     
         41 . The kit of  claim 39  wherein the reporter group is selected from the group consisting of radioisotopes, fluorescent groups, luminescent groups, enzymes, biotin and dye particles.  
     
     
         42 . A diagnostic kit comprising at least two oligonucleotide primers, at least one of the oligonucleotide primers being specific for a polynucleotide encoding a polypeptide comprising an immunogenic portion of a breast antigen, said antigen comprising an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of nucleotide sequences recited in SEQ ID NO: 1-61, 63-175, 178 and 180, complements of said nucleotide sequences, and sequences that hybridize to a sequence of SEQ ID NO: 1-61, 63-175, 178 and 180 under moderately stringent conditions.  
     
     
         43 . A diagnostic kit of  claim 42  wherein at least one of the oligonucleotide primers comprises at least about 10 contiguous nucleotides of a polynucleotide having a sequence selected from SEQ ID NO: 1-61, 63-175, 178 and 180.  
     
     
         44 . A method for detecting breast cancer in a patient, comprising: 
 (a) obtaining a biological sample from the patient;    (b) contacting the biological sample with an oligonucleotide probe specific for a polynucleotide encoding a polypeptide comprising an immunogenic portion of a breast antigen, said antigen comprising an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of nucleotide sequences recited in SEQ ID NO: 1-61, 63-175, 178 and 180, complements of said nucleotide sequences, and sequences that hybridize to a sequence of SEQ ID NO: 1-61, 63-175, 178 and 180 under moderately stringent conditions; and    (c) detecting in the sample a DNA sequence that hybridizes to the oligonucleotide probe, thereby detecting breast cancer in the patient.    
     
     
         45 . The method of  claim 44  wherein the oligonucleotide probe comprises at least about 15 contiguous nucleotides of a polynucleotide comprising a sequence selected from the group consisting of SEQ ID NO: 1-61, 63-175, 178 and 180.  
     
     
         46 . A diagnostic kit comprising an oligonucleotide probe specific for a polynucleotide encoding a polypeptide comprising an immunogenic portion of a breast antigen, said antigen comprising an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of nucleotide sequences recited in SEQ ID NO: 1-61, 63-175, 178 and 180, complements of said nucleotide sequences, and sequences that hybridize to a sequence of SEQ ID NO: 1-61, 63-175, 178 and 180 under moderately stringent conditions.  
     
     
         47 . The diagnostic kit of  claim 46 , wherein the oligonucleotide probe comprises at least about 15 contiguous nucleotides of a polynucleotide comprising a sequence selected from the group consisting of SEQ ID NO: 1-61, 63-175, 178 and 180.  
     
     
         48 . A method for treating breast cancer in a patient, comprising the steps of: 
 (a) obtaining peripheral blood cells from the patient;    (b) incubating the cells in the presence of at least one polypeptide of  claim 1 , such that T cells proliferate; and    (c) administering the proliferated T cells to the patient.    
     
     
         49 . A method for treating breast cancer in a patient, comprising the steps of: 
 (a) obtaining peripheral blood cells from the patient;    (b) incubating the cells in the presence of at least one polynucleotide of  claim 3 , such that T cells proliferate; and    (c) administering to the patient the proliferated T cells.    
     
     
         50 . The method of any one of claims  48  and  49  wherein the step of incubating the T cells is repeated one or more times.  
     
     
         51 . The method of any one of claims  48  and  49  wherein step (a) further comprises separating T cells from the peripheral blood cells, and the cells incubated in step (b) are the T cells.  
     
     
         52 . The method of any one of claims  48  and  49  wherein step (a) further comprises separating CD4+ cells or CD8+ cells from the peripheral blood cells, and the cells proliferated in step (b) are CD4+ or CD8+ T cells.  
     
     
         53 . The method of any one of claims  48  and  49  wherein step (b) further comprises cloning one or more T cells that proliferated in the presence of the polypeptide.  
     
     
         54 . A composition for the treatment of breast cancer in a patient, comprising T cells proliferated in the presence of a polypeptide of  claim 1 , in combination with a pharmaceutically acceptable carrier.  
     
     
         55 . A composition for the treatment of breast cancer in a patient, comprising T cells proliferated in the presence of a polynucleotide of  claim 3 , in combination with a pharmaceutically acceptable carrier.  
     
     
         56 . A method for treating breast cancer in a patient, comprising the steps of: 
 (a) incubating antigen presenting cells in the presence of at least one polypeptide of  claim 1;  and    (b) administering to the patient the incubated antigen presenting cells.    
     
     
         57 . A method for treating breast cancer in a patient, comprising the steps of: 
 (a) incubating antigen presenting cells in the presence of at least one polynucleotide of  claim 3;  and    (b) administering to the patient the incubated antigen presenting cells.    
     
     
         58 . The method of claims  56  or  57  wherein the antigen presenting cells are selected from the group consisting of dendritic cells and macrophage cells.  
     
     
         59 . A composition for the treatment of breast cancer in a patient, comprising antigen presenting cells incubated in the presence of a polypeptide of  claim 1 , in combination with a pharmaceutically acceptable carrier.  
     
     
         60 . A composition for the treatment of breast cancer in a patient, comprising antigen presenting cells incubated in the presence of a polynucleotide of  claim 3 , in combination with a pharmaceutically acceptable carrier.