Functional Identification of DNA Methylation Patterns of Tumor Suppressor Genes in Cancer (LB127)

Abstract

Promoter hypermethylation is a well‐studied epigenetic modification that regulates gene expression. During tumorigenesis, hypermethylation of the entire CpG‐rich region (CpG island) at the promoter of tumor suppressor genes can silence gene expression and lead to cell proliferation. However, analyses of clinical genomic data rarely find hypermethylation at the entire promoter. DNA methyltransferase inhibitors (DNMTis) have been successfully used therapeutically on the basis that they reverse this hypermethylation effect but it is unclear which partial changes affect gene silencing and thus which patients can benefit from these targeted therapies. We seek to pinpoint individual CpGs that contribute to gene silencing using the promoter region of a known tumor suppressor gene, cyclin‐dependent kinase inhibitor 2A (CDKN2A). We generated a library of CDKN2A promoter sequences with random CpG methylation. The library is then used with a cell reporter system to separate methylation patterns that lead to gene silencing from those that lead to expression. Using highly parallelized bisulfite sequencing, we have pinpointed methylation events at individual CpG sites that contribute to gene silencing. Our analysis will advance our understanding DNA methylation's role in gene regulation. Furthermore, pinpointing functional promoter hypermethylation patterns could improve identification of patients that benefit from DNMTis.