Aberrant expression of cell cycle and material metabolism related genes contributes to hepatocellular carcinoma occurrence.

Abstract

This study aims to deepen our understanding of the molecular mechanism underlying the occurrence of hepatocellular carcinoma (HCC). We first downloaded a gene expression profile dataset GSE29721 (10 HCC and 10 control samples) from Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/). Differentially expressed genes (DEGs) were identified by the paired t-test using limma package. Pathway and functional enrichment analyses were performed with DAVID tools. Transcription factors were annotated with TRANSFAC database and tumor associated genes (TAGs) were annotated with TAG and TSGene databases. Protein-protein interaction (PPI) network was conducted using STRING online tool and function module was further identified with BioNet package. Totally, 527 up-regulated DEGs and 587 down-regulated DEGs were identified. GO functional and KEGG pathway enrichment analyses showed that the up-regulated DEGs were mainly related to cell division and cell cycle, while the down-regulated DEGs were largely related to material metabolism, especially secondary metabolism. Proteins encoded by DEGs CDK1, BUB1, CDC20, NCAPG, NDC80, CDCA8, MAD2L1, CCNB1, CCNA2 and BIRC5 were hub genes with high degrees in the PPI network; further module analysis detected a subnetwork consisting of 55 proteins, such as CYP2B6, ACAA1, BHMT and ALDH2. Taken together, aberrant expression of cell cycle related genes (e.g., CDK1, CCNA2, CCNB1, BUB1, MAD2L1 and CDC20) and material metabolism related genes (e.g., CYP2B6, ACAA1, BHMT and ALDH2) may contribute to HCC occurrence.

• Authors: Hongxian Yan, Zhaohui Li, Quan Shen, Qian Wang, Jianguo Tian, Qingfeng Jiang, Linbo Gao
• Journal: Pathology, research and practice (Pathol Res Pract) Vol. 213 Issue 4 Pg. 316-321 (Apr 2017) ISSN: 1618-0631 [Electronic] Germany
• PMID: 28238542 (Publication Type: Journal Article)
• Copyright: Copyright © 2017 Elsevier GmbH. All rights reserved.

Topics

• Carcinoma, Hepatocellular (genetics, metabolism, pathology)
• Cell Cycle
• Gene Expression Profiling
• Gene Regulatory Networks (genetics)
• Humans
• Liver Neoplasms (genetics, metabolism, pathology)
• Transcriptome