High-throughput sequencing approach for the identification of lncRNA biomarkers in hepatocellular carcinoma and revealing the effect of ZFAS1/miR-150-5p on hepatocellular carcinoma progression

Peng Zhu; Yongyan Pei; Jian Yu; Wenbin Ding; Yun Yang; Fuchen Liu; Lei Liu; Jian Huang; Shengxian Yuan; Zongyan Wang; Fangming Gu; Zeya Pan; Jinzhong Chen; Jinrong Qiu; Huiying Liu

doi:10.7717/peerj.14891

PeerJ (Feb 2023)

High-throughput sequencing approach for the identification of lncRNA biomarkers in hepatocellular carcinoma and revealing the effect of ZFAS1/miR-150-5p on hepatocellular carcinoma progression

Peng Zhu,
Yongyan Pei,
Jian Yu,
Wenbin Ding,
Yun Yang,
Fuchen Liu,
Lei Liu,
Jian Huang,
Shengxian Yuan,
Zongyan Wang,
Fangming Gu,
Zeya Pan,
Jinzhong Chen,
Jinrong Qiu,
Huiying Liu

Affiliations

Peng Zhu: Department of Hepatic Surgery (III), The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Yongyan Pei: School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan, Guangdong, China
Jian Yu: Department of General Surgery, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Wenbin Ding: Department of Hepatic Surgery (III), The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Yun Yang: Department of Hepatic Surgery (III), The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Fuchen Liu: Department of Hepatic Surgery (III), The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Lei Liu: Department of Hepatic Surgery (III), The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Jian Huang: Department of Hepatic Surgery (III), The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Shengxian Yuan: Department of Hepatic Surgery (III), The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Zongyan Wang: Department of Hepatic Surgery (III), The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Fangming Gu: Department of Hepatic Surgery (III), The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Zeya Pan: Department of Hepatic Surgery (III), The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Jinzhong Chen: State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
Jinrong Qiu: Department of Biotherapy, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
Huiying Liu: Department of Biotherapy, The Third Affiliated Hospital of Naval Medical University, Shanghai, China

DOI: https://doi.org/10.7717/peerj.14891
Journal volume & issue: Vol. 11
p. e14891

Abstract

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Aims To screen abnormal lncRNAs and diagnostic biomarkers in the progression of hepatocellular carcinoma through high-throughput sequencing and explore the underlying mechanisms of abnormal lncRNAs in the progression of hepatocellular carcinoma. Methods The transcriptome sequencing was used to analyze the RNA expression profile and identify differentially expressed RNAs. Hub lncRNAs were screened by combining (WGCNA, ceRNA regulatory network, PPI, GO and KEGG analyses, Kaplan-Meier curve analysis, Cox analysis, risk model construction and qPCR). Thereafter, the correlation between the expression of hub lncRNAs and tumor clinicopathological parameters was analyzed, and the hub lncRNAs were analyzed by GSEA. Finally, the effects of hub RNAs on the proliferation, migration and invasion of HepG2 cells were investigated in vitro. Results Compared with the control group, a total of 610 lncRNAs, 2,593 mRNAs and 26 miRNAs were screened in patients with hepatocellular carcinoma. Through miRNA target prediction and WGCNA, a ceRNA was constructed, comprising 324 nodes and 621 edges. Enrichment analysis showed that mRNAs in ceRNA were involved mainly in cancer development progression. Then, the ZFAS1/miR-150-5p interaction pair was screened out by Kaplan Meier curve analysis, Cox analysis and qPCR analysis. Its expression was related to tumor stage, TNM stage and patient age. ROC curve analysis showed that it has a good predictive value for the risk of hepatocellular carcinoma. GSEA showed that ZFAS1 was also enriched in the regulation of immune response, cell differentiation and proliferation. Loss-of-function experiments revealed that ZFAS1 inhibition could remarkably suppress HepG2 cell proliferation, migration and invasion in vitro. Bioinformatic analysis and luciferase reporter assays revealed that ZFAS1 directly interacted with miR-150-5p. Rescue experiments showed that a miR-150-5p inhibitor reversed the cell proliferation, migration and invasion functions of ZFAS1 knockdown in vitro. Conclusion ZFAS1 is associated with the malignant status and prognosis of patients with hepatocellular carcinoma, and the ZFAS1/miR-150-5p axis is involved in hepatocellular carcinoma progression.

Published in PeerJ

ISSN: 2167-8359 (Online)
Publisher: PeerJ Inc.
Country of publisher: United States
LCC subjects: Medicine; Science: Biology (General)
Website: https://peerj.com/

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