Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia

Kushwaha et al. Human Genomics 2016, 10(Suppl 2):18 DOI 10.1186/s40246-016-0071-5 RESEARCH Open Access Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia Garima Kushwaha1,2, Mikhail Dozmorov3, Jonathan D. Wren4, Jing Qiu5, Huidong Shi6,7* and Dong Xu1,2,8* Abstract Background: Methylation changes are frequent in cancers, but understanding how hyper- and hypomethylated region changes coordinate, associate with genomic features, and affect gene expression is needed to better understand their biological significance. The functional significance of hypermethylation is well studied, but that of hypomethylation remains limited. Here, with paired expression and methylation samples gathered from a patient/ control cohort, we attempt to better characterize the gene expression and methylation changes that take place in cancer from B cell chronic lymphocyte leukemia (B-CLL) samples. Results: Across the dataset, we found that consistent differentially hypomethylated regions (C-DMRs) across samples were relatively few compared to the many poorly consistent hypo- and highly conserved hyper-DMRs. However, genes in the hypo-C-DMRs tended to be associated with functions antagonistic to those in the hyperC-DMRs, like differentiation, cell-cycle regulation and proliferation, suggesting coordinated regulation of methylation changes. Hypo-C-DMRs in B-CLL were found enriched in key signaling pathways like B cell receptor and p53 pathways and genes/motifs essential for B lymphopoiesis. Hypo-C-DMRs tended to be proximal to genes with elevated expression in contrast to the transcription silencing-mechanism imposed by hypermethylation. HypoC-DMRs tended to be enriched in the regions of activating H4K4me1/2/3, H3K79me2, and H3K27ac histone modifications. In comparison, the polycomb repressive complex 2 (PRC2) signature, marked by EZH2, SUZ12, CTCF binding-sites, repressive H3K27me3 marks, and “repressed/poised promoter” states were associated with hyperC-DMRs. Most hypo-C-DMRs were found in introns (36 %), 3′ untranslated regions (29 %), and intergenic regions (24 %). Many of these genic regions also overlapped with enhancers. The methylation of CpGs from 3′UTR exons was found to have weak but positive correlation with gene expression. In contrast, methylation in the 5′UTR was negatively correlated with expression. To better characterize the overlap between methylation and expression changes, we identified correlation modules that associate with “apoptosis” and “leukocyte activation”. Conclusions: Despite clinical heterogeneity in disease presentation, a number of methylation changes, both hypo and hyper, appear to be common in B-CLL. Hypomethylation appears to play an active, targeted, and complementary role in cancer progression, and it interplays with hypermethylation in a coordinated fashion in the cancer process. Keywords: Epigenetic regulation, DNA methylation, Hypomethylation, CLL, Cancer, Signaling pathway, 3′UTR, Enhancer * Correspondence: ; 6 GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA 1 Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA Full list of author information is available at the end of the article © 2016 Kushwaha et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Kushwaha et al. Human Genomics 2016, 10(Suppl 2):18 Background Loss of DNA methylation, also known as hypomethylation, in cancer cells relative to normal cells was one of the first-described epigenetic changes in human cancers. Hypomethylation has been detected at both a global level and on a local scale [1] in cancer genomes. Many cancer types have been reported to have global loss of methylation like glioblastoma [2], ovarian epithelial carcinoma [3], prostate metastatic tumors [4], B cell chronic lymphocytic leukemia [5, 6], hepatocellular carcinoma [7], cervical cancer [8], colon adenocarcinoma [9], and Wilms’ tumor [10]. However, the biological significance of DNA hypomethylation remains understudied owning to its unclear role in carcinogenesis, in contrast to hypermethylation, which is commonly viewed as a transcription silencing mechanism [11, 12]. Yet, hypomethylation of DNA, despite its unclear role, has been linked to tumor progression [8, 13] in different tumor types and in individual specimens [3, 14]. Also, some experiments have indicated the importance of induced DNA hypomethylation in oncogenesis by using DNA methylation inhibitors in vivo and in vitro [15, 16]. However, the role of hypomethylation is not clearly understood. Hence, it is critical to analyze hypomethylation data in depth to achieve a better understanding of its biological roles in carcinogenesis. DNA hypomethylation in cancer is often seen in satellite DNAs, Arthrobacter luteus (ALU) repeats, and long interspersed nuclear elements (LINEs) [17, 18], etc. These DNA repeats comprise approximately half of the genome. Hence, DNA hypomethylation is generally considered a global phenomenon not suitable for use as a biomarker. One advantage of the global hypomethylation phenomenon (as it pertains to its genome composition) is that it is often considered a technique to balance focal and conserved hypermethylation in the promoter regions of key genes. Also, it is believed that these hypomethylated genomic regions are randomly spread over the genome, mostly in repetitive regions whose functions, if any, are unclear. Again, this reported disadvantage might actually be an advantage due to recent findings indicating that ALU elements can act as enhancers [19], which further emphasizes the need for defining the role of hypomethylation in cancers. As part of our study of hypomethylation patterns, we used B cell chronic lymphocytic leukemia (B-CLL) as an example case. This B-CLL cancer type has a predominant global hypomethylation as its characteristic feature [5, 6], and it is the most common form of blood cancer. It is a clinically heterogeneous disease, with some patients experiencing rapid disease progression and others living for decades without requiring treatment [20]. Although a number of cellular and molecular prognostic markers, i.e., surface markers ZAP70 and CD38, Page 84 of 109 cytogenetic abnormalities, and IGHV mutational status [21–23], have been identified to help classify CLL into molecular and clinical subgroups and to predict their course of progression, they do (...truncated)