Method for Selecting a Treatment for Non-Small Cell Lung Cancer Using Gene Expression Profiles

Abstract

The present invention identifies and quantifies changes in gene expression associated with non-small cell lung cancer NSCLC by examining gene expression in tissue from normal lung and diseased lung. The present invention also identifies and quantifies expression profiles which serve as useful diagnostic markers as well as markers that are useful to monitor disease states, disease progression, drug toxicity, drug efficacy and drug metabolism.

What is claimed is: 
     
         1 . A method for diagnosing bronchogenic carcinoma in an individual, the method comprising the steps of:
 a) providing a lung cell and/or tissue sample from the individual;   b) determining levels of c-myc, E2F-1, and p21 gene products in the lung cell and/or tissue sample, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both,   c) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step b), calculating a gene expression ratio of c-mycxE2F-1/p21; and   d) diagnosing bronchogenic carcinoma in an individual when the calculated gene expression ratio is greater than or equal to 7.20E 3  (as molecules per 10 6  β-actin molecules).   
     
     
         2 . The method of  claim 1 , wherein the lung cell and/or tissue sample is collected by fine needle biopsy. 
     
     
         3 . The method of  claim 1 , wherein the levels of mRNA for each of c-myc, E2F-1, and p21 in the lung cell and/or tissue sample is determined by StaRT-PCR. 
     
     
         4 . The method of  claim 1 , wherein the individual is diagnosed as having bronchogenic carcinoma when the calculated gene expression ratio is greater than or equal to 1.0E 4  (as molecules per 10 6  β-actin molecules). 
     
     
         5 . The method of  claim 1 , wherein the individual is diagnosed as having bronchogenic carcinoma when the calculated gene expression ratio is 7.20E 3 -3.6E 6  (as molecules per 10 6  β-actin molecules). 
     
     
         6 . The method of  claim 1 , wherein the individual is diagnosed as having bronchogenic carcinoma when the calculated gene expression ratio is 1.0E 4 -3.6E 6  (as molecules per 10 6  β-actin molecules). 
     
     
         7 . A method for diagnosing bronchogenic carcinoma in an individual, the method comprising the steps of:
 a) providing a lung cell and/or tissue sample from the individual;   b) determining levels of c-myc, E2F-1, and p21 gene products in the lung cell and/or tissue sample, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both,   c) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step b), calculating a gene expression ratio of c-mycxE2F-1/p21;   d) comparing the calculated gene expression to a control gene expression ratio; and   e) diagnosing bronchogenic carcinoma in an individual when the calculated gene expression ratio is greater than the control gene expression ratio.   
     
     
         8 . The method of  claim 7 , wherein the control gene expression ratio is determined by:
 a) providing a lung cell and/or tissue sample from a healthy, cancer-free individual;   b) determining levels of c-myc, E2F-1, and p21 gene products in the lung cell and/or tissue sample, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both; and   c) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step b), calculating a control gene expression ratio of c-mycxE2F-1/p21.   
     
     
         9 . The method of  claim 8 , wherein the control gene expression ratio is determined by:
 a) providing a lung cell and/or tissue sample from two or more healthy, cancer-free individuals;   b) determining levels of c-myc, E2F-1, and p21 gene products in the lung cell and/or tissue sample for each cancer-free individual, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both;   c) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step b), calculating a gene expression ratio of c-mycxE2F-1/p21 for each cancer-free individual; and   d) determining a control gene expression ratio by calculating a mean for the gene expression ratios of the two or more healthy, cancer-free individuals.   
     
     
         10 . A method of detecting the progression of bronchogenic carcinoma in an individual, comprising the steps of:
 a) providing a first lung cell and/or tissue sample from the individual, wherein the first lung cell and/or tissue sample is collected a first point in time;   b) determining levels of c-myc, E2F-1, and p21 gene products in the first lung cell and/or tissue sample, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both,   c) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step b), calculating a first gene expression ratio of c-mycxE2F-1/p21;   d) providing a second lung cell and/or tissue sample from the individual, wherein the second lung cell and/or tissue sample is collected a second point in time, later than the first point in time;   e) determining levels of c-myc, E2F-1, and p21 gene products in the second lung cell and/or tissue sample, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both; and   f) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step e), calculating a second gene expression ratio of c-mycxE2F-1/p21,   wherein the second gene expression ratio being higher than the first gene expression ratio is indicative of progression of bronchogenic carcinoma in the individual.   
     
     
         11 . The method of  claim 10 , wherein both the first and second lung cell and/or tissue samples is collected by fine needle biopsy. 
     
     
         12 . The method of  claim 10 , wherein the levels of mRNA for each of c-myc, E2F-1, and p21 in both the first and second lung cell and/or tissue samples is determined by StaRT-PCR. 
     
     
         13 . A method of diagnosing bronchogenic carcinoma in an individual, comprising detecting and quantifying the level of expression of c-myc, E2F-1 and p21 genes in a lung cell and/or tissue sample from the individual, wherein differential expression of the c-myc, E2F-1 and p21 genes is diagnostic of bronchogenic carcinoma in the individual. 
     
     
         14 . The method of  claim 13 , wherein the tissue sample is collected by fine need biopsy. 
     
     
         15 . The method of  claim 13 , wherein the steps of detecting and quantifying are carried out by microarray analysis, quantitative RT-PCR, or a combination of both. 
     
     
         16 . The method of  claim 13 , wherein the type of RT-PCR employed is StarRT-PCR. 
     
     
         17 . A method of detecting the progression of bronchogenic carcinoma in an individual, comprising detecting and quantifying the level of expression of c-myc, E2F-1 and p21 genes in a lung cell and/or tissue sample from the individual, wherein differential expression of the c-myc, E2F-1 and p21 genes is indicative of bronchogenic carcinoma progression in the individual. 
     
     
         18 . The method of  claim 17 , wherein the tissue sample is collected by fine need biopsy. 
     
     
         19 . The method of  claim 17 , wherein the steps of detecting and quantifying are carried out by microarray analysis, quantitative RT-PCR, or a combination of both. 
     
     
         20 . The method of  claim 17 , wherein the type of RT-PCR employed is StarRT-PCR. 
     
     
         21 . A method of monitoring treatment of bronchogenic carcinoma in an individual, comprising the steps of:
 a) administering one or more pharmaceutical compositions to the individual;   b) providing a first lung cell and/or tissue sample from the individual, wherein the first lung cell and/or tissue sample is collected a first point in time;   c) determining levels of c-myc, E2F-1, and p21 gene products in the first lung cell and/or tissue sample, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both,   d) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step c), calculating a first gene expression ratio of c-mycxE2F-1/p21;   e) providing a second lung cell and/or tissue sample from the individual, wherein the second lung cell and/or tissue sample is collected a second point in time, later than the first point in time;   f) determining levels of c-myc, E2F-1, and p21 gene products in the second lung cell and/or tissue sample, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both; and   g) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step f), calculating a second gene expression ratio of c-mycxE2F-1/p21,   wherein the second gene expression ratio being higher than the first gene expression ratio is indicative of progression of bronchogenic carcinoma in the individual, and the second gene expression ratio being lower than the first gene expression ratio is indicative of improvement of bronchogenic carcinoma.   
     
     
         22 . A method of monitoring treatment of bronchogenic carcinoma in an individual, comprising the steps of:
 a) administering one or more pharmaceutical compositions to the individual;   b) providing a lung cell and/or tissue sample from the individual;   c) determining levels of c-myc, E2F-1, and p21 gene products in the lung cell and/or tissue sample, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both,   d) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step b), calculating a gene expression ratio of c-mycxE2F-1/p21; and   e) comparing the calculated gene expression to a control gene expression ratio,   wherein the calculated gene expression ratio being higher than the control gene expression ratio is indicative of a need to continue treatment of the individual.   
     
     
         23 . The method of  claim 22 , wherein the method is repeated one or more times during treatment of the individual. 
     
     
         24 . The method of  claim 22 , wherein the control gene expression ratio is determined by:
 a) providing a lung cell and/or tissue sample from a healthy, cancer-free individual;   b) determining levels of c-myc, E2F-1, and p21 gene products in the lung cell and/or tissue sample, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both; and   c) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step b), calculating a control gene expression ratio of c-mycxE2F-1/p21.   
     
     
         25 . The method of  claim 22 , wherein the control gene expression ratio is determined by:
 a) providing a lung cell and/or tissue sample from two or more healthy, cancer-free individuals;   b) determining levels of c-myc, E2F-1, and p21 gene products in the lung cell and/or tissue sample for each cancer-free individual, wherein the levels are determine by microarray analysis, quantitative RT-PCR, or a combination of both;   c) utilizing the levels of c-myc, E2F-1, and p21 gene products determined in step b), calculating a gene expression ratio of c-mycxE2F-1/p21 for each cancer-free individual; and   d) determining a control gene expression ratio by calculating a mean for the gene expression ratios of the two or more healthy, cancer-free individuals.