Biomarkers for breast cancer

Abstract

Methods and compositions are provided for the detection of breast cancer based upon the identification of three biomarkers for non-normal breast cells. The biomarkers were identified based upon multiple sampling of reference breast tissue samples from independent cases of breast cancer. Two biomarkers display increased expression in non-normal cells while the third biomarker displays decreased expression in non-normal cells.

We claim:  
     
         1 . A method to determine the presence of non-normal or abnormal breast cells in a sample from a human subject comprising assaying said sample for increased expression of one or more human CRIP1 or HN1 sequences.  
     
     
         2 . The method of  claim 1  wherein said assaying is for increased expression of human CRIP1 sequences.  
     
     
         3 . The method of  claim 1  wherein said assaying is for increased expression of human HN1 sequences.  
     
     
         4 . The method of  claim 1  wherein said sample is from a subject afflicted with, or suspected of having, breast cancer.  
     
     
         5 . The method of  claim 1  wherein said sample is obtained by solid tissue biopsy or a non-invasive procedure.  
     
     
         6 . The method of  claim 5  wherein said non-invasive procedure is selected from ductal lavage, fine needle aspiration, or a needle biopsy.  
     
     
         7 . The method of  claim 5  wherein microdissection is used to isolate breast cells from said sample before assaying for nucleic acid expression.  
     
     
         8 . The method of  claim 1  wherein said assaying is by hybridization to a polynucleotide comprising sequences of at least 24 nucleotides from the 3′ untranslated region, the coding region, or the 5′ untranslated region, of human CRIP1.  
     
     
         9 . The method of  claim 1  wherein said assaying is by hybridization to a polynucleotide comprising sequences of at least 24 nucleotides from the 3′ untranslated region, the coding region, or the 5′ untranslated region, of human HN1.  
     
     
         10 . The method of  claim 1  wherein said assaying is by PCR amplification of said sequences.  
     
     
         11 . The method of  claim 10  wherein said PCR is quantitative PCR.  
     
     
         12 . The method of  claim 1  wherein said non-normal cells are ADH, DCIS, or IDC cells.  
     
     
         13 . A method to determine the presence of non-normal or abnormal breast cells in a sample from a human subject comprising assaying said sample for decreased expression of human ESE-2/ELF5 sequences.  
     
     
         14 . The method of  claim 13  wherein said sample is from a subject afflicted with, or suspected of having, breast cancer.  
     
     
         15 . The method of  claim 13  wherein said sample is obtained by solid tissue biopsy or a non-invasive procedure.  
     
     
         16 . The method of  claim 15  wherein said non-invasive procedure is selected from ductal lavage, fine needle aspiration, or a needle biopsy.  
     
     
         17 . The method of  claim 16  wherein microdissection is used to isolate breast cells from said sample before assaying for nucleic acid expression.  
     
     
         18 . The method of  claim 17  wherein said assaying is by hybridization to a polynucleotide comprising sequences of at least 24 nucleotides from the 3′ untranslated region, the coding region, or the 5′ untranslated region, of human ESE-2/ELF5.  
     
     
         19 . The method of  claim 13  wherein said assaying is by PCR amplification of said ESE-2/ELF5 sequence.  
     
     
         20 . The method of  claim 19  wherein said assaying is by quantitative PCR.  
     
     
         21 . The method of  claim 13  wherein said assaying is for inactivation or methylation of ESE-2/ELF5 sequences.  
     
     
         22 . The method of  claim 13  wherein said assaying comprises detection of increased mRNA degradation.  
     
     
         23 . The method of  claim 13  wherein said non-normal cells are ADH, DCIS, or IDC cells.  
     
     
         24 . A polynucleotide comprising 
 a segment consisting of a fragment of an HN I sequence selected from SEQ ID NOS: 29-83 of between 24 and 500 nucleotides and    one or more non-HN1 nucleic acid molecules.    
     
     
         25 . A polynucleotide consisting of a fragment of an HN1 sequence selected from SEQ ID NOS: 29-83 of between 24 and 500 nucleotides.  
     
     
         26 . A population of singled stranded nucleic acid molecules comprising one or both strands of a human CRIP1 or HN1 sequence wherein at least a portion of said population is hybridized to one or both strands of a nucleic acid molecule quantitatively amplified from RNA of a non-normal or abnormal breast cell.  
     
     
         27 . The population of  claim 26  wherein the population is immobilized on a solid support.  
     
     
         28 . The population of  claim 27  wherein said solid support is a microarray.  
     
     
         29 . The population of  claim 26  wherein said nucleic acid molecules amplified from a non-normal or abnormal breast cell are amplified by quantitative real time PCR (RT-PCR).  
     
     
         30 . The population of  claim 29  wherein said quantitative RT-PCR is of amplified RNA of said breast cancer cell.  
     
     
         31 . The population of  claim 26  wherein said population of single stranded molecules is equal to or in excess of all of one or both strands of the nucleic acid molecules amplified from a non-normal or abnormal breast cell such that the population is sufficient to hybridize to all of one or both strands.  
     
     
         32 . The population of  claim 26  wherein said population of single stranded molecules comprising sequences of at least 24 nucleotides from the 3′ untranslated region, the coding region, or the 5′ untranslated region, of human CRIP1.  
     
     
         33 . The population of  claim 26  wherein said population of single stranded molecules comprising sequences of at least 24 nucleotides from the 3′ untranslated region, the coding region, or the 5′ untranslated region, of human HN1.  
     
     
         34 . The population of  claim 26  wherein said non-normal cells are ADH, DCIS, or IDC cells.