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Research Paper|Volume 13, Issue 12|pp 16124—16143

Identification of RNA binding protein interacting with circular RNA and hub candidate network for hepatocellular carcinoma

Binglin Cheng1, Jingdong Tian2, Yuhan Chen3
  • 1The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province 510515, China
  • 2School of Biomedical Engineering, Xinhua College of Sun Yat-Sen University, Guangzhou, Guangdong Province 510520, China
  • 3Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province 510515, China
Received: February 25, 2021Accepted: May 18, 2021Published: June 16, 2021
https://doi.org/10.18632/aging.203139

Copyright: © 2021 Cheng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

The interaction between RNA binding protein (RBP) and circular RNA (circRNA) is important for the regulation of tumor progression. This study aimed to identify the RBP-circRNA network in hepatocellular carcinoma (HCC). 22 differentially expressed (DE) circRNAs in HCC were screened out from Gene Expression Omnibus (GEO) database and their binding RBPs were predicted by Circular RNA Interactome. Among them, 17 DERBPs, which were commonly dysregulated in HCC from The Clinical Proteomic Tumor Analysis Consortium (CPTAC), The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) projects, were utilized to construct the RBP-circRNA network. Through survival analysis, we found TARDBP was the only prognostic RBP for HCC in CPTAC, TCGA and ICGC projects. High expression of TARDBP was correlated with high grade, advanced stage and low macrophage infiltration of HCC. Additionally, gene set enrichment analysis showed that dysregulated TARDBP might be involved in some pathways related to the HCC pathogenesis. Therefore, a hub RBP-circRNA network was generated based on TARDBP. RNA immunoprecipitation and RNA pull-down confirmed that hsa_circ_0004913 binds to TARDBP. These findings indicated certain RBP-circRNA regulatory network potentially involved in the pathogenesis of HCC, which provides novel insights into the mechanism study and biomarker identification for HCC.