J Cancer 2019; 10(2):355-366. doi:10.7150/jca.27832

Research Paper

Aberrantly DNA Methylated-Differentially Expressed Genes and Pathways in Hepatocellular Carcinoma

Changzhou Cai1, Weilin Wang1,2, Zhenhua Tu1,2,3✉

1. Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310003, China.
2. Ward of Liver transplant, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery. First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310003, China.
3. Shenzhen Key Laboratory of Hepatobiliary Disease, Shenzhen Third People`s Hospital, Shenzhen 518112, China.

Abstract

Background: Methylation plays a significant role in the etiology and pathogenesis of hepatocellular carcinoma (HCC). The aim of the present study is to identify aberrantly methylated-diferentially expressed genes (DEGs) and dysregulated pathways associated with the development of HCC through integrated analysis of gene expression and methylation microarray.

Method: Aberrantly methylated-DEGs were identified from gene expression microarrays (GSE62232, GSE74656) and gene methylation microarrays (GSE44909, GSE57958). Functional enrichment and pathway enrichment analyses were performed through the database of DAVID. Protein-protein interaction (PPI) network was established by STRING and visualized in Cytoscape. Subsequently, overall survival (OS) analysis of hub genes was performed by OncoLnc. Finally, we validated the expression level of CDCA5 by quantitative real-time PCR (qRT-PCR) and western blotting, and performed Immunohistochemical experiments utilizing a tissue microarray. Cell growth assay and flow cytometry were behaved to explore the function of CDCA5.

Results: Aberrantly methylated-DEGs were enriched in biological process, molecular function, cellular component and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Among them, cell cycle was enriched most frequently, and some terms associated with cancer were enriched, such as p53 signaling pathway, pathways in cancers, PI3K-Akt signaling pathway and AMPK signaling pathway. After survival analysis and validation in TCGA database including methylation and gene expression status, 12 hub genes were identified. Furthermore, the expression level of new gene CDCA5 was validated in HCC cell lines and hepatic normal cell lines through qRT-PCR and western blotting. In additional, immunohistochemistry experiments revealed higher CDCA5 protein expression from HCC tumor tissues compared with paracancer tissues by tissue microarray. Finally, through loss of function, we demonstrated that CDCA5 promoted proliferation by regulating the cell cycle.

Conclusions: In summary, the present study implied possible aberrantly methylated-differentially expressed genes and dysregulated pathways in HCC by bioinformatics analysis and experiments, which could be helpful in understanding the molecular mechanisms underlying the development and progression of HCC. Hub genes including CDC20, AURKB, BIRC5, RRM2, MCM2, PTTG1, CDKN2A, NEK2, CENPF, RACGAP1, GNA14 and especially the new gene CDCA5 may serve as biomarkers for diagnosis, treatment and prognosis of HCC.

Keywords: methylation, expression, bioinformatics, hepatocellular carcinoma, CDCA5

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How to cite this article:
Cai C, Wang W, Tu Z. Aberrantly DNA Methylated-Differentially Expressed Genes and Pathways in Hepatocellular Carcinoma. J Cancer 2019; 10(2):355-366. doi:10.7150/jca.27832. Available from http://www.jcancer.org/v10p0355.htm