Published online Jan 27, 2018. doi: 10.4254/wjh.v10.i1.155
Peer-review started: November 5, 2017
First decision: November 15, 2017
Revised: November 17, 2017
Accepted: December 5, 2017
Article in press: December 7, 2017
Published online: January 27, 2018
To identify the key epigenetically modulated genes and pathways in HCC by performing an integrative meta-analysis of all major, well-annotated and publicly available methylation datasets using tools of network analysis.
PubMed and Gene Expression Omnibus were searched for genome-wide DNA methylation datasets. Patient clinical and demographic characteristics were obtained. DNA methylation data were integrated using the Ingenuity Pathway Analysis, a software package for visualizing and analyzing biological networks. Pathway enrichment analysis was performed using IPA, which also provides literature-driven and computationally-predicted annotations for significant association of genes to curated molecular pathways.
From an initial 928 potential abstracts, we identified and analyzed 11 eligible high-throughput methylation datasets representing 354 patients. A significant proportion of studies did not provide concomitant clinical data. In the promoter region, HIST1H2AJ and SPDYA were the most commonly methylated, whereas HRNBP3 gene was the most commonly hypomethylated. ESR1 and ERK were central genes in the principal networks. The pathways most associated with the frequently methylated genes were G-protein coupled receptor and cAMP-mediated signalling.
Using an integrative network-based analysis approach of genome-wide DNA methylation data of both the promoter and body of genes, we identified G-protein coupled receptor signalling as the most highly associated with HCC. This encompasses a diverse range of cancer pathways, such as the PI3K/Akt/mTOR and Ras/Raf/MAPK pathways, and is therefore supportive of previous literature on gene expression in HCC. However, there are novel targetable genes such as HIST1H2AJ that are epigenetically modified, suggesting their potential as biomarkers and for therapeutic targeting of the HCC epigenome.
Core tip: Hepatocellular carcinoma (HCC) is a high-fatality cancer with limited screening biomarkers and therapeutic options. It arises in the context of chronic liver disease, having accumulated epigenetic changes over time. The goal of this study was to perform an integrative network-based meta-analysis of all genome-wide DNA methylation data in HCC. Using bioinformatics tools, we identified the most important aberrantly methylated genes and associated pathways. G-protein receptor signaling was the most significantly associated with HCC based on differential methylation of involved genes, which is consistent with the implication of the Ras/Raf/MAPK and mTOR pathways. The identification of novel epigenetically modified genes such as HIST1H2AJ within known pathways suggests targeting of the epigenome as a potential therapeutic avenue for HCC.