Research Papers:

Identification of hub genes involved in the development of hepatocellular carcinoma by transcriptome sequencing

Yongchang Zheng, Junyu Long, Liangcai Wu, Haohai Zhang, Lin Li, Ying Zheng, Anqiang Wang, Jianzhen Lin, Xiaobo Yang, Xinting Sang, Ke Hu _, Jie Pan and Haitao Zhao

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Oncotarget. 2017; 8:60358-60367. https://doi.org/10.18632/oncotarget.19483

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Yongchang Zheng1,*, Junyu Long1,*, Liangcai Wu1,*, Haohai Zhang1,*, Lin Li2, Ying Zheng3, Anqiang Wang1, Jianzhen Lin1, Xiaobo Yang1, Xinting Sang1, Ke Hu4, Jie Pan5 and Haitao Zhao1

1Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

2School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China

3State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Science, University of Macau, Macau SAR, China

4Department of Radiation Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

5Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

*These authors have contributed equally to this work

Correspondence to:

Ke Hu, email: [email protected]

Jie Pan, email: [email protected]

Haitao Zhao, email: [email protected]

Keywords: hub gene, differentially expressed protein-coding genes, development, hepatocellular carcinoma, transcriptome sequencing

Received: April 25, 2017    Accepted: June 19, 2017    Published: July 22, 2017


Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death. The aim of this study was to identify underlying hub genes and dysregulated pathways associated with the development of HCC using bioinformatics analysis. Differentially expressed protein-coding genes were subjected to transcriptome sequencing in 11 pairs of liver cancer tissue and matched adjacent non-cancerous tissue. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed, followed by protein-protein interaction (PPI) network construction. Hub genes were identified via centralities analysis and verified using published datasets. In total, 720 significantly differentially expressed protein-coding genes were identified in the samples, including 335 upregulated genes and 385 downregulated genes. The upregulated genes were significantly enriched in cell adhesion, biological adhesion and cell-cell adhesion GO terms under biological process (BP). Conversely, the downregulated genes were significantly enriched in embryonic organ morphogenesis, embryonic organ development and embryonic morphogenesis. The KEGG pathway analysis showed that the upregulated genes were enriched in ECM-receptor interaction and focal adhesion pathways. Furthermore, the downregulated genes were enriched in the ErbB, VEGF and MAPK signaling pathways. The PPI network and centralities analysis suggested that ITGA2 and 12 alternate genes were significant hub genes. These findings improve current understanding of the molecular mechanisms underlying HCC development and may be helpful in identifying candidate molecular biomarkers for use in diagnosing, treating and monitoring the prognosis of HCC.

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