CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia.

Hana Hájková,Markus Hsi-Yang Fritz,Martin Vostrý,Michaela Dostálová Merkerová,Arnošt Kostečka,Cyril Šálek,Kyra Michalová,Jiří Schwarz,Ota Fuchs,Vladimír Beneš,Zdeněk Krejčík,Petr Cetkovský,Cedrik Haškovec,Jana Marková

doi:10.1186/s13045-014-0066-4

Abstract

BackgroundStudying DNA methylation changes in the context of structural rearrangements and point mutations as well as gene expression changes enables the identification of genes that are important for disease onset and progression in different subtypes of acute myeloid leukemia (AML) patients. The aim of this study was to identify differentially methylated genes with potential impact on AML pathogenesis based on the correlation of methylation and expression data.MethodsThe primary method of studying DNA methylation changes was targeted bisulfite sequencing capturing approximately 84 megabases (Mb) of the genome in 14 diagnostic AML patients and a healthy donors’ CD34+ pool. Subsequently, selected DNA methylation changes were confirmed by 454 bisulfite pyrosequencing in a larger cohort of samples. Furthermore, we addressed gene expression by microarray profiling and correlated methylation of regions adjacent to transcription start sites with expression of corresponding genes.ResultsHere, we report a novel hypomethylation pattern, specific to CBFB-MYH11 fusion resulting from inv(16) rearrangement that is associated with genes previously described as upregulated in inv(16) AML. We assume that this hypomethylation and corresponding overexpresion occurs in the genes whose function is important in inv(16) leukemogenesis. Further, by comparing all targeted methylation and microarray expression data, PBX3 differential methylation was found to correlate with its gene expression. PBX3 has been recently shown to be a key interaction partner of HOX genes during leukemogenesis and we revealed higher incidence of relapses in PBX3-overexpressing patients.ConclusionsWe discovered new genomic regions with aberrant DNA methylation that are associated with expression of genes involved in leukemogenesis. Our results demonstrate the potential of the targeted approach for DNA methylation studies to reveal new regulatory regions.Electronic supplementary materialThe online version of this article (doi:10.1186/s13045-014-0066-4) contains supplementary material, which is available to authorized users.

Highlights

Studying DNA methylation changes in the context of structural rearrangements and point mutations as well as gene expression changes enables the identification of genes that are important for disease onset and progression in different subtypes of acute myeloid leukemia (AML) patients
Targeted methylation data were correlated with previously obtained wholegenome bisulfite (WGBS) data for 3 cross-experiment (WGBS/target enrichment) samples
As we used either peripheral blood (PB) or bone marrow (BM) as a starting material, we investigated whether there is a concordance between DNA methylation results from PB and BM in 10 AML patients with both materials at diagnosis available

Summary

Introduction

Studying DNA methylation changes in the context of structural rearrangements and point mutations as well as gene expression changes enables the identification of genes that are important for disease onset and progression in different subtypes of acute myeloid leukemia (AML) patients. DNA methylation in patients with AML has been studied extensively and may reflect either specific molecular abnormalities or characterize a group of patients without an apparent molecular aberration Specific translocations such as PML-RARA, AML1-ETO (RUNX1RUNX1T1), MLL translocations or CBFB-MYH11 fusion, as well as CEBPA, NPM1, IDH1/IDH2, DNMT3A, TET2 and RUNX1 mutations have been described to display distinct methylation signatures [2,3,4]. These epigenetic profiles are usually accompanied by specific gene expression features. The link between gene expression and DNA methylation data is needed to find pathologically relevant DNA methylation changes, especially because many (or even the majority of) DMRs reflect the tissue of origin and not leukemia (cancer) specific changes [7]

Objectives

Methods

Results

Conclusion