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

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Author(s)Kushwaha,Garima
Author(s)Dozmorov,Mikhail
Author(s)Wren,Jonathan D.
Author(s)Qiu,Jing
Author(s)Shi,Huidong
Author(s)Xu,Dong
Ordered AuthorGarima Kushwaha, Mikhail Dozmorov, Jonathan D. Wren, Jing Qiu, Huidong Shi and Dong Xu
UD AuthorQiu, Jing
Date Accessioned2017-07-19T18:48:37Z
Date Available2017-07-19T18:48:37Z
Copyright Date2016 Kushwaha et al
Publication Date7/25/16
DescriptionPublisher's PDF
AbstractBackground: 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 hyper-C-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. Hypo-C-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 hyper-C-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.
DepartmentUniversity of Delaware, Department of Applied Economics and Statistics
CitationKoylu-Alkan, O., Barandiaran, J. M., Salazar, D., & Hadjipanayis, G. C. (2016). Submicron R2Fe14B particles. Aip Advances, 6(5), 056027. doi:10.1063/1.4944771
DOI10.1186/s40246-016-0071-5
ISSN1473-9542
URLhttp://udspace.udel.edu/handle/19716/21564
LanguageEnglish
PublisherBiomed Central Ltd
dc.rightsCC BY 4.0
dc.sourceHuman Genomics
dc.source.urihttps://humgenomics.biomedcentral.com/articles/10.1186/s40246-016-0071-5
TitleHypomethylation coordinates antagonistically with hypermethylation in cancer Development: a case study of leukemia
TypeArticle
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