Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes

Item Type:	Article
Title:	Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes
Creators Name:	Qu, Y. and Lennartsson, A. and Gaidzik, V.I. and Deneberg, S. and Karimi, M. and Bengtzén, S. and Höglund, M. and Bullinger, L. and Döhner, K. and Lehmann, S.
Abstract:	The extent and role of aberrant DNA methylation in promoter CpG islands (CGIs) have been extensively studied in leukemia and other malignancies. Still, CGIs represent only a small fraction of the methylome. We aimed to characterize genome-wide differential methylation of cytogenetically normal AML (CN-AML) cells compared with normal CD34(+) bone marrow cells using the Illumina 450K methylation array. Differential methylation in CN-AML was most prominent in genomic areas far from CGIs, in so called open sea regions. Furthermore, differential methylation was specifically found in genes encoding transcription factors (TFs), with WT1 being the most differentially methylated TF. Among genetic mutations in AML, DNMT3A mutations showed the most prominent association with the DNA methylation pattern, characterized by hypomethylation of CGIs (as compared with DNMT3A wild type cases). The differential methylation in DNMT3A mutant cells vs. wild type cells was predominantly found in HOX genes, which were hypomethylated. These results were confirmed and validated in an independent CN-AML cohort. In conclusion, we show that, in CN-AML, the most pronounced changes in DNA methylation occur in non-CGI regions and that DNMT3A mutations confer a pattern of global hypomethylation that specifically targets HOX genes.
Keywords:	Acute Myeloid Leukemia, DNA Methylation, Non-CGI Region, DNMT3A, Homeobox Gene Family
Source:	Epigenetics
ISSN:	1559-2294
Publisher:	Landes Bioscience
Volume:	9
Number:	8
Page Range:	1108-1119
Date:	August 2014
Official Publication:	https://doi.org/10.4161/epi.29315
PubMed:	View item in PubMed

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