Amplified and overexpressed gene in colorectal cancers

Abstract

This invention relates to methods to diagnose colon cancer and other proliferative diseases by detecting amplification of genes and gene products on chromosome 20q13.2, a region whose amplification is associated with a poor cancer prognosis.

1 . A method for determining the presence or absence of a colorectal cancer cell in a patient, the method comprising determining the level of a target nucleic acid that encodes SEQ ID NO: 2 in a biological sample from the patient, thereby determining the presence or absence of the colorectal cancer cell in the patient.  
     
     
         2 . The method of  claim 1 , wherein the target nucleic acid comprises a sequence at least 80% identical to SEQ ID NO: 1.  
     
     
         3 . The method of  claim 1 , wherein the biological sample comprises isolated nucleic acids.  
     
     
         4 . The method of  claim 3 , further comprising the step of amplifying nucleic acids before the step of determining the level of the nucleic acid.  
     
     
         5 . The method of  claim 3 , wherein the isolated nucleic acids are mRNA.  
     
     
         6 . The method of  claim 1 , wherein the biological sample is colorectal tissue and the step of determining the level of target nucleic acid is carried out using in situ hybridization.  
     
     
         7 . The method of  claim 1 , wherein the step of determining the level of target nucleic acid is carried out using a labeled nucleic acid probe that selectively hybridizes to SEQ ID NO: 1 under stringent hybridization conditions.  
     
     
         8 . The method of  claim 1 , wherein the step of determining the level of target nucleic acid is carried out using a nucleic acid probe immobilized to a solid support, wherein the probe selectively hybridizes to SEQ ID NO: 1 under stringent hybridization conditions.  
     
     
         9 . The method of  claim 1 , wherein the step of determining the level of target nucleic acid is carried out using Northern blot analysis.  
     
     
         10 . The method of  claim 1 , wherein the step of determining the level of the target nucleic acid is carried out by comparing the amount of the target nucleic acid in the biological sample to the amount of the target nucleic acid in a reference sample.  
     
     
         11 . The method of  claim 10 , wherein the reference sample is from normal colorectal tissue.  
     
     
         12 . The method of  claim 1 , wherein the patient is undergoing a therapeutic regimen to treat colorectal cancer.  
     
     
         13 . The method of  claim 1 , wherein the patient is suspected of having colorectal cancer.  
     
     
         14 . An isolated expression vector comprising a nucleic acid sequence that encodes SEQ ID NO: 2.  
     
     
         15 . The isolated expression vector of  claim 14 , wherein the nucleic acid sequence is at least 80% identical to SEQ ID NO: 1.  
     
     
         16 . A host cell comprising the expression vector of  claim 14 .  
     
     
         17 . A method for determining the presence or absence of a colorectal cancer cell in a patient, the method comprising determining the level of a target protein comprising a sequence as shown in SEQ ID NO: 2 in a biological sample from the patient, thereby determining the presence or absence of the colorectal cancer cell in the patient.  
     
     
         18 . The method of  claim 17 , wherein the step of determining the level of the target protein is carried out using an antibody.  
     
     
         19 . The method of  claim 18 , wherein the antibody is a monoclonal antibody.  
     
     
         20 . The method of  claim 18 , wherein the antibody is a polyclonal antibody.  
     
     
         21 . The method of  claim 18 , wherein the antibody is labeled.  
     
     
         22 . The method of  claim 21 , wherein the label is fluorescent.  
     
     
         23 . The method of  claim 17 , wherein the step of determining the level of the target protein is carried out by comparing the amount of the target protein in the biological sample to the amount of the target protein in a reference sample.  
     
     
         24 . The method of  claim 23 , wherein the reference sample is from normal colorectal tissue.  
     
     
         25 . The method of  claim 17 , wherein the patient is undergoing a therapeutic regimen to treat colorectal cancer.  
     
     
         26 . The method of  claim 17 , wherein the patient is suspected of having colorectal cancer.  
     
     
         27 . A method for treating a cancer that overexpresses a 26#77 gene product comprising administering to a subject in need of such treatment a therapeutically effective amount of an inhibitor of 26#77 gene product.  
     
     
         28 . The method of  claim 27 , wherein the inhibitor of a 26#77 gene product is selected from the group consisting of an antisense RNA molecule, and an inhibitory RNA molecule.  
     
     
         29 . A method for determining the presence or absence of a colorectal cancer cell in a patient, the method comprising determining the level of a target nucleic acid that encodes SEQ ID NO:4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, or 28 in a biological sample from the patient, thereby determining the presence or absence of the colorectal cancer cell in the patient.  
     
     
         30 . A method for determining the presence or absence of a colorectal cancer cell in a patient, the method comprising determining the level of a target protein comprising a sequence as shown in SEQ ID NO:4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, or 28 in a biological sample from the patient, thereby determining the presence or absence of the colorectal cancer cell in the patient.  
     
     
         31 . A method for treating a cancer that overexpresses a Copine 1 (CPNE 1) protein, the Integrin B4 binding protein (ITGB4BP), RNA Export homolog (RAE1), bone morphogenetic protein 7 (BMP7), G protein, alpha stimulating activity polypeptide 1 (GNAS), eukaryotic translation initiation factor 2, subunit 2 beta (EIF2S2), dynein light chain A2 (DNCL2A), proteasome subunit α-7 (PSMA7), activity dependent neuroprotective protein (ADNP), C20orf129, C20orf52, C20orf20, or C20orf188 gene product comprising administering to a subject in need of such treatment a therapeutically effective amount of an inhibitor of CPNE 1, ITGB4BP, RAE1, BMP7, GNAS, EIF2S2, DNCL2A, PSMA7, ADNP, C20orf129, C20orf52, C20orf20, or C20orf188 gene product.