Genome-wide analysis of focal DNA hypermethylation in IDH-mutant AML samples

Altered DNA methylation is a common feature of acute myeloid leukemia (AML) and is thought to play a significant role in disease pathogenesis. Gain of function mutations in IDH1 or IDH2 result in widespread but highly focal regions of hypermethylation across the genome that occurs due to the production of 2-hydroxyglutarate that inhibits TET-mediated demethylation. We used whole-genome bisulfite sequencing to identify canonical regions of DNA hypermethylation that are associated specifically with IDH1 and IDH2 mutations in primary AML samples. Consistent with previous reports, IDH mutant (IDHmut) AMLs were the most hypermethylated among all mutationally-defined AML categories analyzed. We observed notable differences in the degree of hypermethylation associated with IDH mutation type, with IDH1mut AMLs having more profound hypermethylation at specific regions than IDH2mut samples. AMLs with biallelic inactivating mutations in TET2 displayed more modest DNA methylation changes compared to normal hematopoietic stem/progenitor cells, but methylation in these samples was increased in the IDHmut-specific regions, providing further support that these mutations act on the same TET-mediated demethylation pathway. Focal hypermethylated regions in IDHmut AML samples tended to occur in regions with low steady state methylation levels in normal stem/progenitor cells, which implies that both DNA methylation and demethylation pathways are active at these loci. Indeed, analysis of AML samples containing mutations in both IDH1 or IDH2 and DNMT3AR882 were less hypermethylated, providing evidence that focal IDHmut-associated hypermethylation is mediated by DNMT3A. IDHmut-specific regions of hypermethylation were largely distinct from CpG island hypermethylation, and showed a significant enrichment for putative enhancers. Analysis of three-dimensional genome interactions from primary hematopoietic cells showed that differentially methylated enhancers formed direct interactions with highly expressed genes, including MYC and ETV6. Taken together, these results suggest that focal hypermethylation in IDH-mutant AML cells occurs by disrupting the balance of DNA methylation and demethylation, which is highly active in genomic regions involved in gene regulation.