Extensive Promoter DNA Hypermethylation and Hypomethylation Is Associated with Aberrant MicroRNA Expression in Chronic Lymphocytic Leukemia

Constance Baer,Manuela Zucknick,Christian Philipp Pallasch,Yoon Jung Park,Christoph Plass,John C Byrd,Dieter Weichenhan,Michael Rehli,Martina Fischer,Lei Gu,Clemens-Martin Wendtner,Esther Herpel,Rainer Claus,Lukas P Frenzel

doi:10.1158/0008-5472.can-12-0803

Abstract

Dysregulated microRNA (miRNA) expression contributes to the pathogenesis of hematopoietic malignancies, including chronic lymphocytic leukemia (CLL). However, an understanding of the mechanisms that cause aberrant miRNA transcriptional control is lacking. In this study, we comprehensively investigated the role and extent of miRNA epigenetic regulation in CLL. Genome-wide profiling conducted on 24 CLL and 10 healthy B cell samples revealed global DNA methylation patterns upstream of miRNA sequences that distinguished malignant from healthy cells and identified putative miRNA promoters. Integration of DNA methylation and miRNA promoter data led to the identification of 128 recurrent miRNA targets for aberrant promoter DNA methylation. DNA hypomethylation accounted for more than 60% of all aberrant promoter-associated DNA methylation in CLL, and promoter DNA hypomethylation was restricted to well-defined regions. Individual hyper- and hypomethylated promoters allowed discrimination of CLL samples from healthy controls. Promoter DNA methylation patterns were confirmed in an independent patient cohort, with 11 miRNAs consistently showing an inverse correlation between DNA methylation status and expression level. Together, our findings characterize the role of epigenetic changes in the regulation of miRNA transcription and create a repository of disease-specific promoter regions that may provide additional insights into the pathogenesis of CLL.

Highlights

We present a systematic genome-wide profiling for epigenetic regulation of miRNAs in Chronic lymphocytic leukemia (CLL) compared with healthy B cells by simultaneous detection of aberrant DNA methylation and miRNA promoters
CLL cells exhibit specific distinct DNA methylation profiles upstream of miRNA loci To identify disease-specific differentially methylated miRNA promoters in CLL, we applied a strategy of combined DNA methylation profiling and miRNA promoter detection (Fig. 1A)
To identify regions that harbor a high potential of pathologic relevance for CLL, the most recurrent DNA methylation differences were detected by weighted averages across the posterior probabilities of all CLL samples

Summary

Introduction

Chronic lymphocytic leukemia (CLL) is the most frequent leukemia of adults in the Western world and is characterized by clonal accumulation of malignant B cells with a low proliferation rate and disrupted apoptotic mechanisms. Authors' Affiliations: 1Department of Epigenomics and Cancer Risk Factors, 2Division of Biostatistics, German Cancer Research Center (DKFZ); 3Institute of Pathology, University of Heidelberg, Heidelberg; 4Department I of Internal Medicine, 5Center of Integrated Oncology (CIO), 6Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital of Cologne, Cologne, Germany; 7Department of Nutritional Science and Food Management, Ewha Woman's University, Seoul, Republic of Korea; 8Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts; 9Department of Hematology and Institute of Pathology, University Hospital Regensburg, Regensburg, Germany; and 10Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio.

Methods

Results

Conclusion