Compositions, kits, and methods for identification, assessment, prevention, and therapy of breast cancer

Abstract

The invention relates to newly discovered nucleic acid molecules and proteins associated with breast cancer. Compositions, kits, and methods for detecting, characterizing, preventing, and treating human breast cancers are provided.

1 . A method of assessing whether a patient is afflicted with breast cancer, the method comprising comparing:
 a) the level of expression of an M678 marker in a patient sample, and   b) the normal level of expression of the M678 marker in a control non-breast cancer sample,
 wherein a significant increase in the level of expression of the M678 marker in the patient sample and the normal level is an indication that the patient is afflicted with breast cancer. 
   
     
     
         2 . The method of  claim 1 , wherein the level of expression of the M678 marker in the sample is assessed by detecting the presence of a protein corresponding to SEQ ID NO:381 in the sample. 
     
     
         3 . The method of  claim 2 , wherein the presence of the protein is detected using a reagent which specifically binds the protein. 
     
     
         4 . The method of  claim 3 , wherein the reagent is labeled. 
     
     
         5 . The method of  claim 4 , wherein the label is selected from the group consisting of: a radio-label, a biotin-label, a chromophore-label, a fluorophore-label, and an enzyme-label. 
     
     
         6 . The method of  claim 3 , wherein the reagent is a non-antibody peptide. 
     
     
         7 . The method of  claim 3 , wherein the reagent is selected from the group consisting of an antibody, an antibody derivative, and an antibody fragment. 
     
     
         8 . The method of  claim 7 , wherein the antibody, antibody derivative, or antibody fragment is a monoclonal antibody. 
     
     
         9 . The method of  claim 7 , wherein the antibody, antibody derivative, or antibody fragment is a polyclonal antibody. 
     
     
         10 . The method of  claim 1 , wherein the level of expression of the M678 marker in the sample is assessed by detecting the presence of a transcribed polynucleotide or portion thereof, wherein the transcribed polynucleotide comprises SEQ ID NO:380 or a portion thereof. 
     
     
         11 . The method of  claim 10 , wherein the transcribed polynucleotide is an mRNA. 
     
     
         12 . The method of  claim 10 , wherein assessing the presence of a transcribed polynucleotide or a portion thereof comprises amplifying the transcribed polynucleotide. 
     
     
         13 . The method of  claim 1 , wherein the patient sample comprises a breast-associated body fluid. 
     
     
         14 . The method of  claim 13 , wherein the breast-associated body fluid is selected from the group consisting of blood, breast fluid, lymph fluid, cystic fluid, nipple aspirates, and fluid collected from a lump biopsy. 
     
     
         15 . The method of  claim 1 , wherein the patient sample comprises cells obtained from a breast tissue sample. 
     
     
         16 . The method of  claim 1 , wherein the level of expression of the M678 marker in the sample differs from the normal level of expression of the M678 marker in a patient not afflicted with breast cancer by a factor of at least about 2 or at least about 5. 
     
     
         17 . A kit for assessing whether a patient is afflicted with breast cancer, the kit comprising reagents for assessing expression of an M678 marker. 
     
     
         18 . A method for predicting the clinical outcome of a breast cancer patient, the method comprising:
 a) determining the level of expression of an M678 marker in a patient sample;   b) determining the level of expression of the M678 marker in a sample from a control subject having a good clinical outcome; and   c) comparing the level of expression of the M678 marker in the patient sample and in the sample from the control subject;   wherein a significantly higher level of expression in the patient sample as compared to the expression level in the sample from the control subject is an indication that the patient has a poor clinical outcome.   
     
     
         19 . A method for monitoring the progression of breast cancer in a patient, the method comprising:
 a) determining the level of expression of an M678 marker in a patient sample from a first point in time;   b) determining the level of expression of the M678 marker in a sample from the patient at a subsequent point in time; and   c) comparing the level of expression detected in steps a) and b), thereby monitoring the progression of breast cancer in the patient,   wherein a change in expression of the M678 marker is indicative of either progression or regression of breast cancer.   
     
     
         20 . A method of assessing the efficacy of a therapy for inhibiting breast cancer in a patient, the method comprising:
 a) determining the expression of an M678 marker in a first sample obtained from the patient prior to administering at least a portion of the therapy to the patient;   b) determining the expression of the M678 marker in a second sample obtained from the patient subsequent to administering the portion of the therapy;   c) comparing the expression of the M678 marker in the first and second samples; and   d) determining the therapy is efficacious for inhibiting breast cancer in the patient when there is a significantly lower level of expression of the M678 marker in the second sample, relative to the first sample.   
     
     
         21 . A kit for assessing whether a patient is afflicted with breast cancer, the kit comprising reagents suitable for performing the method of  claim 1  and instructions for use. 
     
     
         22 . The kit of  claim 21 , wherein the reagents comprise an antibody or fragment thereof that selectively binds to a protein encoded by the M678 marker.