Gene expression profiling of egfr positive cancer

Abstract

The present invention concerns prognostic markers associated with EGFR positive cancer. In particular, the invention concerns prognostic methods based on the molecular characterization of gene expression in paraffin-embedded, fixed tissue samples of EGFR-expressing cancer, which allow a physician to predict whether a patient is likely to respond well to treatment with an EGFR inhibitor.

1 - 55 . (canceled) 
     
     
         56 . A method for predicting the likelihood that a human colon cancer patient will exhibit a clinically beneficial patient response to treatment with an EGFR inhibitor, the method comprising:
 a) assaying a normalized level of an RNA transcript in a sample comprising EGFR-expressing colon cancer cells obtained from said patient, wherein the RNA transcript is the transcript of KRT17;   b) analyzing the normalized level of the KRT17 RNA transcript; and   c) predicting the likelihood of response of the patient to treatment with the EGFR inhibitor, wherein an increased normalized level of the KRT17 RNA transcript correlates with a decreased likelihood of response to treatment with the EGFR inhibitor.   
     
     
         57 . The method of  claim 56 , wherein said sample is a tissue sample. 
     
     
         58 . The method of  claim 57 , wherein the tissue sample is fixed, paraffin-embedded, fresh, or frozen. 
     
     
         59 . The method of  claim 57 , wherein the tissue sample is derived from fine needle, core, or other types of biopsy. 
     
     
         60 . The method of  claim 56 , wherein the EGFR inhibitor is an anti-EGFR monoclonal antibody. 
     
     
         61 . The method of  claim 60 , wherein the anti-EGFR monoclonal antibody is cetuximab. 
     
     
         62 . The method of  claim 56 , wherein the EGFR inhibitor is a small molecule tyrosine-kinase inhibitor. 
     
     
         63 . The method of  claim 62 , wherein the small molecule tyrosine kinase inhibitor is gefitinib or erlotinib. 
     
     
         64 . The method of  claim 56 , further comprising the step of preparing a report comprising a prediction of the likelihood that the patient will respond to treatment with the EGFR inhibitor. 
     
     
         65 . The method of  claim 56 , wherein the normalized level of the KRT17 RNA transcript is determined using reverse transcription polymerase chain reaction (RT-PCR). 
     
     
         66 . The method of  claim 56 , wherein the normalized level of the KRT17 RNA transcript is determined using an array comprising polynucleotides hybridizing to a KRT17 gene immobilized on a solid surface. 
     
     
         67 . The method of  claim 56 , wherein RNA is isolated from colon cancer cells present in a fixed, paraffin-embedded tissue by a procedure comprising:
 (a) incubating one or more sections of said fixed, paraffin-embedded tissue at a temperature of about 56° C. to 70° C. in a lysis buffer, in the presence of a protease, without prior dewaxing, to form a lysis solution;   (b) cooling the lysis solution to a temperature where the paraffin solidifies, thereby generating a cooled lysis solution; and   (c) isolating the RNA from said cooled lysis solution.