Left-Right Gene Expression Signature for Triple Negative Breast Cancer

Abstract

Methods and materials are described for use in clinical and research applications directed to cancers. Products include binding arrays, e.g., hybridization or other specific binding arrays, such as genomic or proteomic microarrays. The binding arrays include binding agents developed based upon the recognition of heterogeneity between left-arising and right-arising breast cancer tumors. The arrays can include as binding agents materials that bind transcripts or proteins that are over-expressed in only one of or in both of left-arising or right-arising breast cancer tumors.

What is claimed is: 
     
         1 . A method for forming a binding array, comprising:
 obtaining a first tissue sample from a first subject diagnosed with a breast cancer, the breast cancer diagnosis of the first subject comprising a left breast tumor;   determining a first expression level of a first expression product in the first tissue sample;   obtaining a second tissue sample from a second subject diagnosed with the breast cancer, the breast cancer diagnosis of the second subject comprising a right breast tumor;   determining a second expression level of the first expression product in the second tissue sample;   comparing the first expression level with the second expression level;   determining that a differential expression level between the first expression level and the second expression level is 2-fold or greater; and   immobilizing a first binding agent for the first expression product or for a gene that encodes the first expression product to a surface of a binding array substrate.   
     
     
         2 . The method of  claim 1 , wherein the breast cancer diagnosis comprises a triple negative breast cancer diagnosis. 
     
     
         3 . The method of  claim 1 , wherein the first expression product comprises a first polynucleotide. 
     
     
         4 . The method of  claim 1 , wherein the first expression product comprises a polypeptide. 
     
     
         5 . The method of  claim 1 , further comprising immobilizing to the surface of the binding array substrate one or more additional binding agents for the first expression product or for a gene that encodes the first expression product. 
     
     
         6 . The method of  claim 5 , wherein the first expression product comprises a polynucleotide and wherein the first binding agent and the one or more additional binding agents comprise polynucleotides that together are complementary to 2% or more of the polynucleotide of the first expression product. 
     
     
         7 . The method of  claim 6 , wherein the first binding agent and the one or more additional binding agents are immobilized on the surface of the binding array substrate in a single discrete location. 
     
     
         8 . The method of  claim 1 , wherein the first expression level is greater than the second expression level. 
     
     
         9 . The method of  claim 1 , wherein the first expression level is less than the second expression level. 
     
     
         10 . The method of  claim 1 , wherein the first binding agent is immobilized on the surface of the binding array substrate via covalent bonding, ionic bonding, UV crosslinking, or via reaction of affinity molecules. 
     
     
         11 . The method of  claim 1 , wherein the first binding agent comprises a detectable label. 
     
     
         12 . A method for forming a binding array, comprising:
 obtaining a first tissue sample from a first subject diagnosed with a breast cancer, the breast cancer diagnosis of the first subject comprising a left breast tumor;   determining a first expression level of a first expression product in the first tissue sample and a second expression level of a second expression product in the first tissue sample;   obtaining a second tissue sample from a second subject diagnosed with the breast cancer, the breast cancer diagnosis of the second subject comprising a right breast tumor;   determining a third expression level of the first expression product in the second tissue sample and a fourth expression level of the second expression product in the second tissue sample;   comparing the first expression level with the third expression level;   determining that a first differential expression level between the first expression level and the third expression level is 2-fold or greater;   immobilizing a first binding agent for the first expression product or for a gene that encodes the first expression product to a surface of a binding array substrate;   comparing the second expression level with the fourth expression level;   determining that a second differential expression level between the second expression level and the fourth expression level is 2-fold or greater; and   immobilizing a second binding agent for the second expression product or for a gene that encodes the second expression product to the surface of the binding array substrate.   
     
     
         13 . The method of  claim 12 , wherein the first binding agent and the second binding agent are immobilized in separate, discrete locations. 
     
     
         14 . The method of  claim 12 , wherein the first binding agent and the second binding agent are immobilized in a single discrete location. 
     
     
         15 . The method of  claim 12 , wherein the first expression product and the second expression product are members of a single biochemical pathway. 
     
     
         16 . The method of  claim 12 , wherein the first expression product is a member of a first biochemical pathway and wherein the second expression product is a member of a second biochemical pathway. 
     
     
         17 . The method of  claim 12 , wherein the first expression product and the second expression product comprise first and second polynucleotides, respectively. 
     
     
         18 . The method of  claim 12 , wherein the first expression product and the second product comprise first and second polypeptides, respectively. 
     
     
         19 . The method of  claim 12 , wherein the first expression level is greater than the third expression level and wherein the second expression level is greater than the fourth expression level. 
     
     
         20 . The method of  claim 12 , wherein the first expression level is less than the third expression level and wherein the second expression level is less than the fourth expression level. 
     
     
         21 . The method of  claim 12 , wherein the first expression level is greater than the third expression level and wherein the second expression level is less than the fourth expression level. 
     
     
         22 . The method of  claim 12 , wherein the first expression level is less than the third expression level and wherein the second expression level is greater than the fourth expression level.