Abstract B10: Genome-wide profiling reveals hyper- and hypomethylation at microRNA promoters in chronic lymphocytic leukemia
Authors: Baer Constance , Rehli Michael , Byrd John C. , Wendtner Clemens-Martin , Plass Christoph , Claus Rainer , Frenzel Lukas , Zucknick Manuela , Park Yoon Jung , Gu Lei , Weichenhan Dieter , Fischer Martina , Pallasch Christian 
Published: April 2013

Chronic lymphocytic leukemia (CLL) is the most common leukemia in the Western world. Dysregulation of microRNA (miRNA) expression contributes to CLL pathogenesis. Abnormal promoter methylation is involved in aberrant gene expression in leukemic cells. Here, we investigate the role of epigenetic mechanisms in the global regulation of miRNA expression in CLL.

In order to characterize disease-specific aberrant methylation upstream of miRNAs, methylated DNA from 24 CLL patients and 10 healthy age-matched controls was enriched by Methyl-CpG immunoprecipitation. Differentially methylated genomic loci were identified using a custom tiling array covering the genomic sequences 35 kb upstream and 5 kb downstream of 939 annotated miRNAs. We identified putative promoter sequences for 781 miRNAs by determining regions of enriched trimethylated histone 3 lysine 4 (H3K4me3) in CLL samples, healthy B cells or cancer cell lines.

The methylation patterns upstream of miRNAs clearly distinguished CLL cells from healthy B cells. Differentially methylated sequences are enriched in H3K4me3, suggesting that miRNA promoters are non-randomly targeted for epigenetic dysregulation. 458 miRNAs display differential methylation in at least 5 out of the 24 CLL samples. Noteworthy, hypomethylation accounted for two thirds of all differentially methylated regions at putative miRNA promoters. Hypomethylated regions are limited to strictly defined sequence stretches, predominantly found outside of CpG islands (89%).

Correlating promoter methylation with miRNA expression, we observed loss of methylation and strong transcriptional upregulation of mir-155 in CLL. Similarly, the promoter of mir-1204 showed significantly reduced methylation in CLL associated with increased expression. Mir-129-2, a well known tumor suppressor in solid tumors, could be detected among the epigenetically silenced miRNAs. Furthermore mir-551b, which has not yet been described in the context of CLL, was found to be downregulated and a target of promoter hypermethylation in CLL cells.

In conclusion, a combination of DNA methylation profiling and comprehensive miRNA promoter identification has allowed us to identified novel aberrantly regulated miRNAs in CLL. Hypomethylation, which has previously been underestimated, is determined to be a major mechanism for miRNA activation in CLL.

Citation Format: Constance Baer, Michael Rehli, John C. Byrd, Clemens-Martin Wendtner, Christoph Plass, Rainer Claus, Lukas Frenzel, Manuela Zucknick, Yoon Jung Park, Lei Gu, Dieter Weichenhan, Martina Fischer, Christian Pallasch. Genome-wide profiling reveals hyper- and hypomethylation at microRNA promoters in chronic lymphocytic leukemia [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr B10.