Oncotarget

Research Papers:

Investigating the mechanism of hepatocellular carcinoma progression by constructing genetic and epigenetic networks using NGS data identification and big database mining method

Cheng-Wei Li, Ping-Yao Chang and Bor-Sen Chen _

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Oncotarget. 2016; 7:79453-79473. https://doi.org/10.18632/oncotarget.13100

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Abstract

Cheng-Wei Li1, Ping-Yao Chang1, Bor-Sen Chen1

1Laboratory of Control and Systems Biology, National Tsing Hua University, Hsinchu, Taiwan

Correspondence to:

Bor-Sen Chen, email: bschen@ee.nthu.edu.tw

Keywords: DNA methylation, multiple potential drugs, hepatocarcinogenesis, miRNAs, principal network projection

Received: February 19, 2016     Accepted: October 26, 2016     Published: November 04, 2016

ABSTRACT

The mechanisms leading to the development and progression of hepatocellular carcinoma (HCC) are complicated and regulated genetically and epigenetically. The recent advancement in high-throughput sequencing has facilitated investigations into the role of genetic and epigenetic regulations in hepatocarcinogenesis. Therefore, we used systems biology and big database mining to construct genetic and epigenetic networks (GENs) using the information about mRNA, miRNA, and methylation profiles of HCC patients. Our approach involves analyzing gene regulatory networks (GRNs), protein-protein networks (PPINs), and epigenetic networks at different stages of hepatocarcinogenesis. The core GENs, influencing each stage of HCC, were extracted via principal network projection (PNP). The pathways during different stages of HCC were compared. We observed that extracellular signals were further transduced to transcription factors (TFs), resulting in the aberrant regulation of their target genes, in turn inducing mechanisms that are responsible for HCC progression, including cell proliferation, anti-apoptosis, aberrant cell cycle, cell survival, and metastasis. We also selected potential multiple drugs specific to prominent epigenetic network markers of each stage of HCC: lestaurtinib, dinaciclib, and perifosine against the NTRK2, MYC, and AKT1 markers influencing HCC progression from stage I to stage II; celecoxib, axitinib, and vinblastine against the DDIT3, PDGFB, and JUN markers influencing HCC progression from stage II to stage III; and atiprimod, celastrol, and bortezomib against STAT3, IL1B, and NFKB1 markers influencing HCC progression from stage III to stage IV.


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