Methods for diagnosing and treating cancer by means of the expression status and mutational status of nrf2 and downstream target genes of said gene

Abstract

The invention provides methods of identifying a subject having cancer, such as lung cancer, by analyzing expression levels of one or more NRF2 splice variants or NRF2 target genes. The invention also provides methods of treating cancer in a subject with a NRF2 pathway antagonist, wherein the subject expresses one or more NRF2 splice variants or overexpresses one or more NRF2 target genes.

1 . A method of diagnosing a cancer in a subject, the method comprising:
 (a) determining the expression levels of the following 27 genes: AKR1B10, AKR1C2, SRXN1, OSGIN1, FECH, GCLM, TRIM16, ME1, KYNU, CABYR, SLC7A11, TRIM16L, AKR1C4, CYP4F11, RSPO3, ABCC2, AKR1B15, NR0B1, UGDH, TXNRD1, GSR, AKR1C3, TALDO1, PGD, TXN, NQO1, and FTL in a sample obtained from the subject; and   (b) comparing the expression level of each of the 27 genes to a reference expression level of each of the 27 genes, wherein an increase in the expression level of each of the 27 genes in the sample relative to the respective reference expression level of each of the 27 genes identifies the subject having a cancer.   
     
     
         2 . The method of  claim 1 , wherein the method further comprises:
 determining if the subject's cancer is a NRF2-dependent cancer, wherein an increase in the expression level of each of the 27 genes in the sample relative to the respective reference expression level of each of the 27 genes identifies the subject as having a NRF2-dependent cancer.   
     
     
         3 - 8 . (canceled) 
     
     
         9 . The method of  claim 1 , wherein
 (a) the expression level of each of the 27 genes in the sample is an average expression level of each of the 27 genes of the sample;   (b) the reference expression level of each of the 27 genes is an average expression level of each of the 27 genes of the reference; and   (c) the average expression level of each of the 27 genes of the sample is compared to the average of each of the 27 genes of the reference.   
     
     
         10 - 11 . (canceled) 
     
     
         12 . The method of  claim 1 , wherein the reference expression level of each of the 27 genes is the mean level of expression of each of the 27 genes in a population of subjects having the cancer. 
     
     
         13 . The method of  claim 12 , wherein the reference expression level is the mean level of expression of each of the 27 genes in a population of subjects having lung cancer, optionally a non-small cell lung cancer (NSCLC), optionally a squamous NSCLC. 
     
     
         14 - 15 . (canceled) 
     
     
         16 . The method of  claim 1 , wherein the expression level is an mRNA expression level, optionally wherein the mRNA expression level is determined by PCR, RT-PCR, RNA-seq, gene expression profiling, serial analysis of gene expression, or microarray analysis. 
     
     
         17 . (canceled) 
     
     
         18 . The method of  claim 1 , wherein the expression level is a protein expression level, optionally wherein the protein expression level is determined by western blot, immunohistochemistry, or mass spectrometry. 
     
     
         19 . (canceled) 
     
     
         20 . The method of  claim 1 , further comprising determining a DNA sequence of NRF2, optionally wherein the DNA sequence is determined by PCR, exome-seq, microarray analysis, or whole genome sequencing. 
     
     
         21 - 32 . (canceled) 
     
     
         33 . The method of  claim 1 , further comprising administering to the subject a therapeutically effective amount of a NRF2 pathway antagonist and/or a therapeutically effective amount of an anti-cancer agent. 
     
     
         34 - 40 . (canceled) 
     
     
         41 . A method of treating a subject having a cancer, the method comprising administering to the subject a therapeutically effective amount of a NRF2 pathway antagonist, wherein the expression level of each of the following 27 genes AKR1B10, AKR1C2, SRXN1, OSGIN1, FECH, GCLM, TRIM16, ME1, KYNU, CABYR, SLC7A11, TRIM16L, AKR1C4, CYP4F11, RSPO3, ABCC2, AKR1B15, NR0B1, UGDH, TXNRD1, GSR, AKR1C3, TALDO1, PGD, TXN, NQO1, and FTL in a sample obtained from the subject has been determined to be increased relative to a respective reference expression level of each of the 27 genes. 
     
     
         42 - 47 . (canceled) 
     
     
         48 . The method of  claim 41 , wherein
 (a) the expression level of each of the 27 genes in the sample is an average expression level of each of the 27 genes of the sample;   (b) the reference expression level of each of the 27 genes is an average expression level of each of the 27 genes of the reference; and   (c) the average expression level of each of the 27 genes of the sample is compared to the average of each of the 27 genes of the reference.   
     
     
         49 - 50 . (canceled) 
     
     
         51 . The method of  claim 41 , wherein the reference expression level is the mean level of expression of each of the 27 genes in a population of subjects having the cancer, optionally lung cancer, optionally NSCLC, optionally squamous NSCLC. 
     
     
         52 - 53 . (canceled) 
     
     
         54 . The method of  claim 41 , wherein the expression level is an mRNA expression level, optionally wherein the mRNA expression level is determined by PCR, RT-PCR, RNA-seq, gene expression profiling, serial analysis of gene expression, or microarray analysis. 
     
     
         55 - 56 . (canceled) 
     
     
         57 . The method of  claim 41 , wherein the expression level is a protein expression level, optionally wherein the protein expression is determined by western blot, immunohistochemistry, or mass spectrometry. 
     
     
         58 . (canceled) 
     
     
         59 . The method of  claim 41 , further comprising determining a DNA sequence of the NRF2, optionally wherein the DNA sequence is determined by PCR, exome-seq, microarray analysis, or whole genome sequencing. 
     
     
         60 - 78 . (canceled) 
     
     
         79 . The method of  claim 1 , wherein the sample obtained from the subject is from a biopsy sample. 
     
     
         80 . (canceled) 
     
     
         81 . The method of  claim 1 , wherein the subject:
 (a) is a previously untreated subject; and/or   (b) has a lung cancer or a head and neck cancer.   
     
     
         82 . The method of  claim 81 , wherein the lung cancer is a non-small cell lung cancer (NSCLC). 
     
     
         83 . The method of  claim 82 , wherein the NSCLC is a squamous NSCLC. 
     
     
         84 . The method of  claim 81 , wherein the head and neck cancer is a squamous head and neck cancer.