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 journalArticle

4 Citations (Scopus)

Abstract

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
Volume2015
DOIs
Publication statusPublished - 2015

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Protein Interaction Maps
Biomarkers
Hepatocellular Carcinoma
Liver Neoplasms
Neoplasms
Proteins
Systems Biology
Liver
Carcinogenesis
Spliceosomes
Hepatoblastoma
Hemangiosarcoma
DNA Mismatch Repair
Cholangiocarcinoma
Lysine
Oocytes
Progesterone
Tumors
Repair
Cells

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Applying NGS data to find evolutionary network biomarkers from the early and late stages of hepatocellular carcinoma. / Wong, Yung Hao; Wu, Chia Chou; Lin, Chih Lung; Chen, Ting Shou; Chang, Tzu Hao; Chen, Bor Sen.

In: BioMed Research International, Vol. 2015, 391475, 2015.

Research output: Contribution to journalArticle

Wong, Yung Hao ; Wu, Chia Chou ; Lin, Chih Lung ; Chen, Ting Shou ; Chang, Tzu Hao ; Chen, Bor Sen. / Applying NGS data to find evolutionary network biomarkers from the early and late stages of hepatocellular carcinoma. In: BioMed Research International. 2015 ; Vol. 2015.
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