Roles of distal and genic methylation in the development of prostate tumorigenesis revealed by genome-wide DNA methylation analysis

Yao Wang, Rohit Ramakant Jadhav, Joseph Liu, Desiree Wilson, Yidong Chen, Ian M. Thompson, Dean A. Troyer, Javier Hernandez, Huidong Shi, Robin J. Leach, Tim H.M. Huang, Victor X. Jin

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Abstract

Aberrant DNA methylation at promoters is often linked to tumorigenesis. But many aspects of DNA methylation remain unexplored, including the individual roles of distal and gene body methylation, as well as their collaborative roles with promoter methylation. Here we performed a MBD-seq analysis on prostate specimens classified into low, high, and very high risk group based on Gleason score and TNM stages. We identified gene sets with differential methylation regions (DMRs) in Distal, TSS, gene body and TES. To understand the collaborative roles, TSS was compared with the other three DMRs, resulted in 12 groups of genes with collaborative differential methylation patterns (CDMPs). We found several groups of genes that show opposite methylation patterns in Distal and Genic regions compared to TSS region, and in general they are differentially expressed genes (DEGs) in tumors in TCGA RNAseq data. IPA (Ingenuity Pathway Analysis) reveals AR/TP53 signaling network to be a major signaling pathway, and survival analysis indicates genes subsets significantly associated with prostate cancer recurrence. Our results suggest that DNA methylation in Distal and Genic regions also plays critical roles in contributing to prostate tumorigenesis, and may act either positively or negatively with TSSs to alter gene regulation in tumors.

Original languageEnglish (US)
Article number22051
JournalScientific Reports
Volume6
DOIs
StatePublished - Jan 1 2016

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DNA Methylation
Methylation
Prostate
Carcinogenesis
Genome
Genes
Neoplasm Grading
Survival Analysis
Neoplasms
Prostatic Neoplasms
Recurrence

ASJC Scopus subject areas

  • General

Cite this

Roles of distal and genic methylation in the development of prostate tumorigenesis revealed by genome-wide DNA methylation analysis. / Wang, Yao; Jadhav, Rohit Ramakant; Liu, Joseph; Wilson, Desiree; Chen, Yidong; Thompson, Ian M.; Troyer, Dean A.; Hernandez, Javier; Shi, Huidong; Leach, Robin J.; Huang, Tim H.M.; Jin, Victor X.

In: Scientific Reports, Vol. 6, 22051, 01.01.2016.

Research output: Contribution to journalArticle

Wang, Y, Jadhav, RR, Liu, J, Wilson, D, Chen, Y, Thompson, IM, Troyer, DA, Hernandez, J, Shi, H, Leach, RJ, Huang, THM & Jin, VX 2016, 'Roles of distal and genic methylation in the development of prostate tumorigenesis revealed by genome-wide DNA methylation analysis', Scientific Reports, vol. 6, 22051. https://doi.org/10.1038/srep22051
Wang, Yao ; Jadhav, Rohit Ramakant ; Liu, Joseph ; Wilson, Desiree ; Chen, Yidong ; Thompson, Ian M. ; Troyer, Dean A. ; Hernandez, Javier ; Shi, Huidong ; Leach, Robin J. ; Huang, Tim H.M. ; Jin, Victor X. / Roles of distal and genic methylation in the development of prostate tumorigenesis revealed by genome-wide DNA methylation analysis. In: Scientific Reports. 2016 ; Vol. 6.
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