Abstract 2302: CpG hypermethylation marks potentially curable acute myeloid leukemia

Abstract

Abstract Purpose: Acute myeloid leukemia (AML) is a heterogeneous blood malignancy. Genetic markers identify distinct subgroups. Epigenetics can refine the classification and prognostic stratification. Our pilot data on a small subset of genes suggested that DNA hypermethylation was an indicator of prolonged survival. Experimental Design: To expand the analysis, we used Digital Restriction Enzyme Analysis of Methylation (DREAM) for high resolution quantification of CpG methylation at CCCGGG sequences across the genome. We analyzed pretreatment bone marrow samples from 100 AML patients and 19 control samples of normal blood leukocytes. Results: We quantified methylation at 22,576 CpG sites and identified 3004 variable CpG sites with the standard deviation of methylation in AML greater than 20%. Hierarchical clustering of methylation values at these variable sites divided the patients into three clusters. Cluster 1 showed extensive hypomethylation when compared to the remaining AML patients and normal controls. Mutations of DNMT3A in the R882 codon were observed in 8/32 (25%) patients while 2 patients (6%) had an IDH mutation. Cluster 2 had the methylation pattern similar to normal controls. IDH mutations were found in 5/45 (11%) patients. DNMT3A R882 mutations were detected in 3 patients (7%); in two of them they were associated with an IDH mutation. Cluster 3 had the highest proportion of IDH mutations - 7/22 (32%) patients; two of these patients also harbored the DNMT3A R882 mutation. This cluster displayed the CpG Island Methylator Phenotype (CIMP) with hypermethylation at multiple CpG sites. We identified significant hypermethylation at 785 CpG sites (P<0.001, methylation change >20% when compared to Clusters 1 and 2). One third of the hypermethylated sites mapped within 1 kb of gene transcription start sites (TSS). We used DAVID Bioinformatics Resources 6.7 to characterize ontology of the genes associated with the hypermethylated sites. We found significant enrichment for negative regulators of transcription. Hypomethylation was rare in the CIMP Cluster 3. We did not find any significantly hypomethylated CpG sites when compared to Clusters 1 and 2. Kaplan-Meier survival analysis showed significant differences in the overall survival among the clusters of AML patients, all treated with standard ara-C + anthracycline chemotherapy. Median survival in Cluster 1 and 2 was similar, 1.5 and 1.0 years, respectively. The CIMP cluster of 29 patients showed a remarkably long median survival of 14 years (P=0.003). Conclusion: We propose that CIMP characterizes a subset of AML patients with a good response to chemotherapy and long survival. This work was supported by the NIH Leukemia SPORE grant CA100632 and by a Stand Up To Cancer-American Association for Cancer Research Dream Team Translational Cancer Research Grant, Grant Number SU2C-AACR-DT0109. Citation Format: Jaroslav Jelinek, 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-Kashani, Hagop M. Kantarjian, Jean-Pierre J. Issa. CpG hypermethylation marks potentially curable acute myeloid leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2302. doi:10.1158/1538-7445.AM2014-2302