Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma

Ren-Chao Zou; Zhi-Tian Shi; Shu-Feng Xiao; Yang Ke; Hao-Ran Tang; Tian-Gen Wu; Zhi-Tang Guo; Fan Ni; Sanqi An; Lin Wang

doi:10.7717/peerj.8101

Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma

PeerJ. 2019 Dec 2:7:e8101. doi: 10.7717/peerj.8101. eCollection 2019.

Authors

Ren-Chao Zou^#¹, Zhi-Tian Shi^#¹, Shu-Feng Xiao^{1

2}, Yang Ke¹, Hao-Ran Tang¹, Tian-Gen Wu¹, Zhi-Tang Guo¹, Fan Ni¹, Sanqi An³, Lin Wang¹

Affiliations

¹ Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Kunming Medical University, kunming, China.
² Department of General Surgery, Puer People's Hospital, Puer, China.
³ Center for Stem Cell Biology and Tissue Engineering, Key Laboratory of Ministry of Education, Sun Yat-Sen University, Guangzhou, China.

^# Contributed equally.

Abstract

Background: Hepatocellular carcinoma (HCC) is the most common primary liver cancer in the world, with a high degree of malignancy and recurrence. The influence of the ceRNA network in tumor on the biological function of liver cancer is very important, It has been reported that many lncRNA play a key role in liver cancer development. In our study, integrated data analysis revealed potential eight novel lncRNA biomarkers in hepatocellular carcinoma.

Methods: Transcriptome data and clinical data were downloaded from the The Cancer Genome Atlas (TCGA) data portal. Weighted gene co-expression network analysis was performed to identify the expression pattern of genes in liver cancer. Then, the ceRNA network was constructed using transcriptome data.

Results: The integrated analysis of miRNA and RNAseq in the database show eight novel lncRNAs that may be involved in important biological pathways, including TNM and disease development in liver cancer. We performed function enrichment analysis of mRNAs affected by these lncRNAs.

Conclusions: By identifying the ceRNA network and the lncRNAs that affect liver cancer, we showed that eight novel lncRNAs play an important role in the development and progress of liver cancer.

Keywords: Diagnostic biomarkers; HCC; Micrornas; lncRNA.

Grants and funding

This work was supported by National Natural Science Foundation of China (No. 81660399 and 81860423), Yunnan Provincial Clinical Center of Hepato-biliary-pancreatic Diseases [no specific number], the Doctor Newcomer Award of Yunnan Province in 2017 [no specific number], and Ph.D. Student Innovation Fund of Kunming Medical University (No. 2019D004). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.