Applying NGS data to find evolutionary network biomarkers from the early and late stages of hepatocellular carcinoma

Yung Hao Wong, Chia Chou Wu, Chih Lung Lin, Ting Shou Chen, Tzu Hao Chang, Bor Sen Chen

Research output: Contribution to journalArticlepeer-review

11 Citations (Scopus)


Hepatocellular carcinoma (HCC) is a major liver tumor (80%), besides hepatoblastomas, angiosarcomas, and cholangiocarcinomas. In this study, we used a systems biology approach to construct protein-protein interaction networks (PPINs) for early-stage and late-stage liver cancer. By comparing the networks of these two stages, we found that the two networks showed some common mechanisms and some significantly different mechanisms. To obtain differential network structures between cancer and noncancer PPINs, we constructed cancer PPIN and noncancer PPIN network structures for the two stages of liver cancer by systems biology method using NGS data from cancer cells and adjacent noncancer cells. Using carcinogenesis relevance values (CRVs), we identified 43 and 80 significant proteins and their PPINs (network markers) for early-stage and late-stage liver cancer. To investigate the evolution of network biomarkers in the carcinogenesis process, a primary pathway analysis showed that common pathways of the early and late stages were those related to ordinary cancer mechanisms. A pathway specific to the early stage was the mismatch repair pathway, while pathways specific to the late stage were the spliceosome pathway, lysine degradation pathway, and progesterone-mediated oocyte maturation pathway. This study provides a new direction for cancer-targeted therapies at different stages.

Original languageEnglish
Article number391475
JournalBioMed Research International
Publication statusPublished - 2015

ASJC Scopus subject areas

  • General Immunology and Microbiology
  • General Biochemistry,Genetics and Molecular Biology


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