Phage microarray profiling of the humoral response to disease

Abstract

The present invention relates to compositions and methods for cancer diagnostics, including but not limited to, cancer markers. In particular, the present invention provides methods and compositions for phage microarray profiling of cancer (e.g., prostate, lung, or breast cancer). The present invention further provides novel markers useful for the diagnosis, characterization, and treatment of cancers.

We claim: 
     
         1 . A method, comprising: a) providing a phage library, wherein said phage library comprises a plurality of phage clones, each of said phage clones comprising a cDNA obtained from a mRNA sample of a subject with a disease; b) enriching said phage library for phage clones comprising cDNAs acid specific to said disease, where said enriching comprises binding said phage library to a control IgG to remove non-disease specific phage clones followed by binding said phage library to a disease specific IgG to enrich said phage library for disease specific phage clones, thereby generating an enriched phage library; c) exposing said enriched phage library to serum from patients having said disease to generate a immunoglobulin bound phage library; and d) identifying phage clones that react with said serum from said patients having said disease. 
     
     
         2 . The method of  claim 1 , wherein said exposing step further comprises the step of exposing said enriched phage library to serum from control subjects not having said disease. 
     
     
         3 . The method of  claim 2 , further comprising the step of identifying phage clones that react with said serum from said patients having said disease but not with said serum from said control subjects not having said disease. 
     
     
         4 . The method of  claim 1 , wherein said identifying comprises contacting said immunoglobulin bound phage library with a first immunoglobulin that binds to immunoglobulins from said serum from patients having said disease and a second immunoglobulin that binds to a phage capsid protein. 
     
     
         5 . The method of  claim 4 , wherein said identifying further comprises the step of exposing said first and second immunoglobulins to third and fourth immunoglobulins wherein said third immunoglobulin binds to said first immunoglobulin and wherein said third immunoglobulin comprises a first label, and wherein said fourth immunoglobulin binds to said second immunoglobulin and wherein said fourth immunoglobulin comprises a second label. 
     
     
         6 . The method of  claim 5 , wherein said first and second labels are fluorescent dyes and wherein said first label emits fluorescence at a different wavelength than said second label. 
     
     
         7 . The method of  claim 4 , further comprising the step of exposing said labeled phage library to an image scanner to identify phage clones that react with said serum from said patients with said disease but not with said serum from said control subjects not having said disease. 
     
     
         8 . The method of  claim 7 , further comprising the step of determining the identify of genes contained in said phage clones that react with said serum from said patients with said disease but not with said serum from said control subjects not having said disease. 
     
     
         9 . The method of  claim 1 , wherein said disease is selected from the group consisting of cancer, autoimmune disease, inflammatory disease, cardiovascular disease, and diabetes. 
     
     
         10 . The method of  claim 7 , wherein said cancer is selected from the group consisting of prostate cancer, breast cancer, and lung cancer. 
     
     
         11 . The method of  claim 1 , wherein said enriched phage library is arrayed on a solid surface. 
     
     
         12 . The method of  claim 1 , wherein said disease specific IgG is purified from the serum of a patient having said disease. 
     
     
         13 . The method of  claim 1 , wherein step b) is repeated 2 or more times. 
     
     
         14 . The method of  claim 1 , wherein step b) is repeated 5 or more times. 
     
     
         15 . The method of  claim 3 , wherein said disease is cancer and said phage clones that react with said serum from said patients with said disease but not with said serum from said control subjects not having said disease are cDNAs encoding tumor antigens. 
     
     
         16 . A method for detecting cancer, comprising: a) providing a sample from a subject suspected of having cancer; and b) detecting the presence or absence of a humoral response to a tumor antigen selected from the group consisting of BRD2, eIF4G1, RPL22, RPL13A, HES1, hypothetical protein XP-373908, ubiquilin 1, nucleolar protein 3 (NOL3), alpha-2-glycoprotein 1 and heat shock 70 kDa protein 8 (HSPA70), thereby detecting cancer. 
     
     
         17 . The method of  claim 16 , wherein said cancer is selected from the group consisting of prostate cancer, lung cancer, and breast cancer. 
     
     
         18 . The method of  claim 16 , wherein said detecting comprises detecting the presence of an autoantibody to said tumor antigen. 
     
     
         19 . The method of  claim 16 , wherein said method further comprises step c) providing a prognosis to said subject. 
     
     
         20 . A kit for detecting the presence of cancer in a subject, comprising: a) a reagent capable of specifically detecting the presence of a tumor antigen selected from the group consisting of BRD2, eIF4G1, RPL22, RPL13A, HES1, hypothetical protein XP-373908, ubiquilin 1, nucleolar protein 3 (NOL3), alpha-2-glycoprotein 1 and heat shock 70 kDa protein 8 (HSPA70); and b) instructions for using said reagent for detecting the presence of cancer in said subject.