Abstract 5302: Genome-wide methylation analysis reveals multiple epigenetic subtypes of acute myeloid leukemia
Authors: Kelly Andrew D. , Kroeger Heike , Yamazaki Jumpei , Taby Rodolphe , Neumann Frank , Lee Justin T. , He Rong , Liang Shoudan , Lu Yue , Cesaroni Matteo , Pierce Sherry A. , Kornblau Steven M. , Bueso-Ramos Carlos E. , Ravandi Farhad , Kantarjian Hagop M. , Jelinek Jaroslav , Issa Jean-Pierre J. 
Published: August 2015

Abstract
Background: Acute myeloid leukemia (AML) is a highly heterogeneous malignancy for which known molecular features, while useful, are inadequate for determining the likelihood of durable remission following chemotherapy. Our study examines multiple DNA methylation patterns associated with AML curability and clinical features, and expands on preliminary work relating epigenomic phenotype to survival.
Methods: To measure genome-wide CpG methylation we used Digital Restriction Enzyme Analysis of Methylation (DREAM) on a cohort of 101 AML samples and 25 normal blood controls. We used methylation data from 194 patient samples from The Cancer Genome Atlas (TCGA) on the Illumina Infinium HumanMethylation450 platform as validation. Statistical analysis was done using R.
Results: DREAM analysis of 3,003 CpG sites (with standard deviation &gt; 20% across AML cases) revealed three distinct DNA methylation patterns by hierarchical clustering. A group of 22 AML cases demonstrated significant hypermethylation at many loci compared to normal blood, consistent with a CpG Island Methylator Phenotype (CIMP). Kaplan-Meier analysis demonstrated that CIMP-AML cases had significantly longer OS than either non-CIMP cluster (median OS, years: CIMP = 14, hypomethylator = 1.47, non-CIMP-2 = 1.04, log-rank p = 0.0021). In this dataset CIMP was prognostic independent of cytogenetic risk, and antecedent hematologic malignancy (AHD). We also found that CIMP-AML was significantly enriched in IDH1/2 mutations (32% of CIMP-AML vs. 9% of non-CIMP-AML, p = 0.02). Differential methylation analysis to characterize the specific CpG sites within the genome that define CIMP-AML demonstrated widespread hypermethylation predominantly at CGIs. Using a robust Cox regression approach, we identified candidate markers of CIMP in our DREAM dataset (sensitivity = 73%, specificity = 100%). We validated the presence of CIMP-AML in independent data from TCGA which demonstrated a consistent pattern regarding survival (median OS, years: CIMP = 2, non-CIMP = 1, log-rank p = 0.0109), and the enrichment of IDH1/2 mutations (30% of CIMP-AML vs. 14% of non-CIMP-AML, p = 0.02). Our DREAM analysis also revealed a distinct cluster of AML cases with a hypomethylator phenotype (HMP). This novel HMP-AML subtype was more common than CIMP, and was associated with intermediate OS. Differential methylation analysis revealed that HMP-AML is defined by loss of methylation predominantly at non-CGIs. HMP-AML demonstrated a relative enrichment for DNMT3A mutations (24% of HMP-AML vs. 7% of non-HMP-AML, p = 0.10).
Conclusions: We propose that CIMP-AML is associated with CGI hypermethylation, IDH1/2 mutations, and favorable prognosis. Our Cox regression strategy identified a small group candidate biomarkers of CIMP-AML. In addition, we identified a novel HMP-AML phenotype associated with non-CGI hypomethylation, DNMT3A mutations, and an intermediate prognosis.
Citation Format: Andrew D. Kelly, Heike Kroeger, Jumpei Yamazaki, Rodolphe Taby, Frank Neumann, Justin T. Lee, Rong He, Shoudan Liang, Yue Lu, Matteo Cesaroni, Sherry A. Pierce, Steven M. Kornblau, Carlos E. Bueso-Ramos, Farhad Ravandi, Hagop M. Kantarjian, Jaroslav Jelinek, Jean-Pierre J. Issa. Genome-wide methylation analysis reveals multiple epigenetic subtypes of acute myeloid leukemia. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5302. doi:10.1158/1538-7445.AM2015-5302