Integrated analysis of competing endogenous RNA network revealing potential prognostic biomarkers of hepatocellular carcinoma

Authors

• Xiwen Liao, The First Affiliated Hospital of Guangxi Medical University
• Xiangkun Wang, The First Affiliated Hospital of Guangxi Medical University
• Ketuan Huang, The First Affiliated Hospital of Guangxi Medical University
• Chuangye Han, The First Affiliated Hospital of Guangxi Medical University
• Jianlong Deng, The First Affiliated Hospital of Guangxi Medical University
• Tingdong Yu, The First Affiliated Hospital of Guangxi Medical University
• Chengkun Yang, The First Affiliated Hospital of Guangxi Medical University
• Rui Huang, The First Affiliated Hospital of Guangxi Medical University
• Xiaoguang Liu, The First Affiliated Hospital of Guangxi Medical University
• Long Yu, The First Affiliated Hospital of Guangxi Medical University
• Guangzhi Zhu, The First Affiliated Hospital of Guangxi Medical University
• Hao Su, The First Affiliated Hospital of Guangxi Medical University
• Wei Qin, The First Affiliated Hospital of Guangxi Medical University
• Xianmin Zeng, The First Affiliated Hospital of Guangxi Medical University
• Bowen Han, The First Affiliated Hospital of Guangxi Medical University
• Quanfa Han, The First Affiliated Hospital of Guangxi Medical University
• Zhengqian Liu, The First Affiliated Hospital of Guangxi Medical University
• Xin Zhou, The First Affiliated Hospital of Guangxi Medical University
• Yizhen Gong, The First Affiliated Hospital of Guangxi Medical University
• Zhengtao Liu, The First Affiliated Hospital of Guangxi Medical University
• Jianlv Huang, The First Affiliated Hospital of Guangxi Medical University
• Cheryl A. Winkler, Leidos Inc.
• Stephen J. O'Brien, Saint Petersburg State UniversityFollow
• Xinping Ye, The First Affiliated Hospital of Guangxi Medical University
• Tao Peng, The First Affiliated Hospital of Guangxi Medical University

Document Type

Article

Publication Title

Journal of Cancer

ISSN

18379664

Publication Date

1-1-2019

Keywords

Bioinformatics, Competing endogenous RNA, Hepatocellular carcinoma, Prognosis, TCGA

Abstract

Objective: The goal of our study is to identify a competing endogenous RNA (ceRNA) network using dysregulated RNAs between HCC tumors and the adjacent normal liver tissues from The Cancer Genome Atlas (TCGA) datasets, and to investigate underlying prognostic indicators in hepatocellular carcinoma (HCC) patients. Methods: All of the RNA- and miRNA-sequencing datasets of HCC were obtained from TCGA, and dysregulated RNAs between HCC tumors and the adjacent normal liver tissues were investigated by DESeq and edgeR algorithm. Survival analysis was used to confirm underlying prognostic indicators. Results: In the present study, we constructed a ceRNA network based on 16 differentially expressed genes (DEGs), 7 differentially expressed microRNAs and 34 differentially expressed long non-coding RNAs (DELs). Among these dysregulated RNAs, three DELs (AP002478.1, HTR2A-AS1, and ERVMER61-1) and six DEGs (enhancer of zeste homolog 2 [EZH2], kinesin family member 23 [KIF23], chromobox 2 [CBX2], centrosomal protein 55 [CEP55], cell division cycle 25A [CDC25A], and claspin [CLSPN]) were used for construct a prognostic signature for HCC overall survival (OS), and performed well in HCC OS (adjusted P<0.0001, adjusted hazard ratio = 2.761, 95% confidence interval = 1.838-4.147). Comprehensive survival analysis demonstrated that this prognostic signature may be act as an independent prognostic indicator of HCC OS. Functional assessment of these dysregulated DEGs in the ceRNA network and gene set enrichment of this prognostic signature suggest that both were enriched in the biological processes and pathways of the cell cycle, cell division and cell proliferation. Conclusions: Our current study constructed a ceRNA network for HCC, and developed a prognostic signature that may act as an independent indicator for HCC OS.

DOI

10.7150/jca.29986

Volume

10

Issue

14

First Page

3267

Last Page

3283

NSUWorks Citation

Liao, Xiwen; Xiangkun Wang; Ketuan Huang; Chuangye Han; Jianlong Deng; Tingdong Yu; Chengkun Yang; Rui Huang; Xiaoguang Liu; Long Yu; Guangzhi Zhu; Hao Su; Wei Qin; Xianmin Zeng; Bowen Han; Quanfa Han; Zhengqian Liu; Xin Zhou; Yizhen Gong; Zhengtao Liu; Jianlv Huang; Cheryl A. Winkler; Stephen J. O'Brien; Xinping Ye; and Tao Peng. 2019. "Integrated analysis of competing endogenous RNA network revealing potential prognostic biomarkers of hepatocellular carcinoma." Journal of Cancer 10, (14): 3267-3283. doi:10.7150/jca.29986.