Detection of genes regulated by EGF in breast cancer

Abstract

The present invention relates to a combination comprising a plurality of polynucleotide probes that are modulated in response to EGF and which are associated with breast cancer, and which may be used in their entirety or in part as to diagnose, to stage, to treat, or to monitor the treatment of a subject with a breast cancer.

What is claimed is:  
     
         1 . A combination comprising a plurality of cDNAs, selected from SEQ ID NOs:1-16 or their complements, whose expression is modulated by EGF and is associated with breast cancer.  
     
     
         2 . The combination of  claim 1 , wherein the cDNAs are immobilized on a substrate.  
     
     
         3 . A high throughput method for detecting differential expression of one or more cDNAs in a sample containing nucleic acids, the method comprising: 
 (a) hybridizing the substrate of  claim 2  with nucleic acids of the sample, thereby forming one or more hybridization complexes;    (b) detecting the hybridization complexes; and    (c) comparing the hybridization complexes with those of a standard, wherein differences between the standard and sample hybridization complexes indicate differential expression of cDNAs in the sample.    
     
     
         4 . The method of  claim 3 , where in the nucleic acids of the sample are amplified prior to hybridization.  
     
     
         5 . The method of  claim 3 , wherein the sample is from a subject with a breast carcinoma and comparison with a standard defines an early, mid, or late stage of that disease.  
     
     
         6 . A high throughput method of screening a plurality of molecules or compounds to identify a ligand which specifically binds a cDNA, the method comprising: 
 (a) combining the combination of  claim 1  with the plurality of molecules or compounds under conditions to allow specific binding; and    (b) detecting specific binding between each cDNA and at least one molecule or compound, thereby identifying a ligand that specifically binds to each cDNA.    
     
     
         7 . The method of  claim 6  wherein the plurality of molecules or compounds are selected from DNA molecules, RNA molecules, peptide nucleic acid molecules, mimetics, peptides, transcription factors, repressors, and regulatory proteins.  
     
     
         8 . An isolated cDNA, or the complement thereof, selected from SEQ ID NOs:12-16.  
     
     
         9 . A composition comprising a cDNA of  claim 8  in conjunction with a suitable pharmaceutical carrier.  
     
     
         10 . A method of using a cDNA to purify a ligand that specifically binds the cDNA, the method comprising; 
 a) combining a cDNA of  claim 8  with a sample under conditions which allow specific binding;    b) recovering the cDNA bound to the ligand; and    c) separating the cDNA from the ligand thereby obtaining purified ligand.    
     
     
         11 . A vector containing a probe selected from the cDNA of  claim 8 .  
     
     
         12 . A host cell containing the vector of  claim 11 .  
     
     
         13 . A method for producing a protein, the method comprising the steps of: 
 (a) culturing the host cell of  claim 12  under conditions for expression of protein; and    (b) recovering the protein from the host cell culture.    
     
     
         14 . A protein or a portion thereof produced by the method of  claim 13 .  
     
     
         15 . A high-throughput method for using a protein to screen a plurality of molecules or compounds to identify at least one ligand which specifically binds the protein, the method comprising: 
 (a) combining the protein of  claim 14  with the plurality of molecules or compounds under conditions to allow specific binding; and    (b) detecting specific binding between the protein and a molecule or compound, thereby identifying a ligand which specifically binds the protein.    
     
     
         16 . The method of  claim 15  wherein the plurality of molecules or compounds is selected from DNA molecules, RNA molecules, peptide nucleic acid molecules, mimetics, peptides, proteins, agonists, antagonists, antibodies or their fragments, immunoglobulins, inhibitors, drug compounds, and pharmaceutical agents.  
     
     
         17 . A method of using a protein to produce an antibody, the method comprising: 
 a) immunizing an animal with the protein of  claim 14  under conditions to elicit an antibody response;    b) isolating animal antibodies; and    c) screening the isolated antibodies with the protein, thereby identifying an antibody which specifically binds the protein.    
     
     
         18 . A method of purifying an antibody, the method comprising: 
 a) combining the protein of  claim 14  with a sample under conditions to allow specific binding;    b) recovering the bound protein; and    c) separating the protein from the antibody, thereby obtaining purified antibody.