Markers for Determining Tumor Hypoxia

Abstract

The present application relates to the field of cancer, particular to hypoxic tumors. It was found that hypoxia is an important driver for hypermethylation of (promoters of) tumor suppressor genes. As this hypermethylation is a stable signature that is also present in circulating tumor DNA in peripheral blood, detecting this methylation pattern is a surrogate marker for tumor hypoxia. This can be used to adapt therapy as well.

1 - 7 . (canceled) 
     
     
         8 . A method of determining tumor hypoxia via detecting hypermethylation in a cancer patient, comprising:
 obtaining from a subject a tissue sample comprising circulating tumor DNA, wherein the circulating tumor DNA comprises one or more promoters of tumor suppressor genes;   detecting whether methylation status of the one or more promoters of tumor suppressor genes is at least 3% higher compared to normoxic tissue, by determining methylation status of a normoxic tissue and methylation status of the one or more promoters of tumor suppressor genes.   
     
     
         9 . The method of  claim 8 , wherein the methylation status is determined by measuring 5hmC level of the normoxic tissue and of the one or more promoters of tumor suppressor genes. 
     
     
         10 . The method of  claim 8 , comprising detecting whether the methylation status of the one or more promoters of tumor suppressor genes is at least 6% higher compared to normoxic tissue. 
     
     
         11 . The method of  claim 8 , comprising detecting whether the methylation status of the one or more promoters of tumor suppressor genes is at least 15% higher compared to normoxic tissue. 
     
     
         12 . The method of  claim 8 , wherein the cancer is bladder, breast, colorectal, head and neck, kidney, lung adeno, lung squamous and uterine carcinoma, gliobastoma multiforme, or non-small cell lung cancer. 
     
     
         13 . The method of  claim 12 , wherein the cancer is breast cancer. 
     
     
         14 . The method of  claim 8  wherein the tumor suppressor gene is HIC1, KDM6A, NF2, KDM5C, IGFBP2, ARNT2, PTEN, MGMT, ATM, MLH1, BRCA1, SEMA3B, TIMP3, THBD, or CLDN3. 
     
     
         15 . The method of  claim 8 , further comprising after the detecting step adapting the dose or nature of cancer therapy to the level of hypermethylation. 
     
     
         16 . The method of  claim 8 , wherein the tissue sample is obtained from a subject receiving cancer therapy. 
     
     
         17 . A method of determining tumor hypoxia via detecting demethylation of one or more promoters of tumor suppressor genes in a cancer patient, comprising:
 obtaining from a subject receiving cancer therapy a tissue sample comprising circulating tumor DNA, wherein the circulating tumor DNA comprises one or more promoters of tumor suppressor genes;   detecting whether methylation status of the one or more promoters of tumor suppressor genes is at least 3% lower compared to normoxic tissue, by determining methylation status of a normoxic tissue and methylation status of the one or more promoters of tumor suppressor genes.   
     
     
         18 . The method according to  claim 17 , further comprising after the detecting step adapting the dose or nature of the cancer therapy to the level of demethylation. 
     
     
         19 . A kit for detecting tumor hypoxia, comprising primers or probes to detect hypermethylation or demethylation of one or more promoters of tumor suppressor genes. 
     
     
         20 . The kit of  claim 19  wherein the tumor suppressor gene is HIC1, KDM6A, NF2, KDM5C, IGFBP2, ARNT2, PTEN, MGMT, ATM, MLH1, BRCA1, SEMA3B, TIMP3, THBD, or CLDN3.