DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia

SummaryWe hypothesized that DNA methylation distributes into specific patterns in cancer cells, which reflect critical biological differences. We therefore examined the methylation profiles of 344 patients with acute myeloid leukemia (AML). Clustering of these patients by methylation data segregated patients into 16 groups. Five of these groups defined new AML subtypes that shared no other known feature. In addition, DNA methylation profiles segregated patients with CEBPA aberrations from other subtypes of leukemia, defined four epigenetically distinct forms of AML with NPM1 mutations, and showed that established AML1-ETO, CBFb-MYH11, and PML-RARA leukemia entities are associated with specific methylation profiles. We report a 15 gene methylation classifier predictive of overall survival in an independent patient cohort (p < 0.001, adjusted for known covariates).

► Specific and distinct DNA methylation patterns characterize distinct forms of AML
► DNA methylation profiling identified 5 novel clinically relevant subtypes of AML
► A 15-gene DNA methylation classifier predicted clinical outcome of AML patients
► A set of 45 genes was consistently aberrantly methylated across all AML subtypes.