Integrated Analysis of Somatic DNA Variants and DNA Methylation of Tumor Suppressor Genes in Colorectal Cancer

DNA methylation of tumor suppressor genes in cancer is known to be a mechanism for silencing gene expression, but much remains unknown about its extent and relationship to somatic variants at the DNA sequence level. In this study, we comprehensively analyzed DNA methylation and somatic variants of all gene regions across the genome of the major tumor suppressor genes, APC, TP53, SMAD4, and mismatch repair genes in colorectal cancer using a novel next-generation sequencing-based analysis method. The Targeted Methyl Landscape (TML) shows that DNA hypermethylation patterns of these tumor suppressor genes in colorectal cancer are more complex and widespread than previously thought. Extremely high levels of DNA methylation were observed in relatively long regions around exon 1A of APC and exon 1 and surrounding region of MLH1. DNA hypermethylation occurred whether or not somatic DNA variants were present in the tumor. Even in tumors where the loss of heterozygosity has been demonstrated by somatic variants alone, additional methylation of the same gene can occur. Our data demonstrate that somatic variants and hypermethylation of these tumor suppressor genes were considered independent, parallel events, not exclusive of each other or having one event affecting the other.