Deng Rong, Cui Xiaohan, Dong Yuxiang, Tang Yanqiu, Tao Xuewen, Wang Shuyu, Wang Jincheng, Chen Lin
Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.
Department of General Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.
Front Genet. 2021 Feb 26;12:626764. doi: 10.3389/fgene.2021.626764. eCollection 2021.
Circular RNAs (circRNAs) are now under hot discussion as novel promising biomarkers for patients with hepatocellular carcinoma (HCC). The purpose of our study is to identify several competing endogenous RNA (ceRNA) networks related to the prognosis and progression of HCC and to further investigate the mechanism of their influence on tumor progression.
First, we obtained gene expression data related to liver cancer from The Cancer Genome Atlas (TCGA) database (http://www.portal.gdc.cancer.gov/), including microRNA (miRNA) sequence, RNA sequence, and clinical information. A co-expression network was constructed through the Weighted Correlation Network Analysis (WGCNA) software package in R software. The differentially expressed messenger RNAs (DEmRNAs) in the key module were analyzed with the Database for Annotation Visualization and Integrated Discovery (DAVID) (https://david.ncifcrf.gov/summary.jsp) to perform functional enrichment analysis including Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). The data of miRNA expression and clinical information downloaded from TCGA were utilized for survival analysis to detach the prognostic value of the DEmiRNAs of the key module.
The 201 differentially expressed miRNAs (DEmiRNAs) and 3,783 DEmRNAs were preliminarily identified through differential expression analysis. The co-expression networks of DEmiRNAs and DEmRNAs were constructed with WGCNA. Further analysis confirmed four miRNAs in the most significant module (blue module) were associated with the overall survival (OS) of patients with liver cancer, including hsa-miR-92b-3p, hsa-miR-122-3p, hsa-miR-139-5p, and hsa-miR-7850-5p. DAVID was used for functional enrichment analysis of 286 co-expressed mRNAs. The GO analysis results showed that the top enriched GO terms were oxidation-reduction process, extracellular exosome, and iron ion binding. In KEGG pathway analysis, the top three enriched terms included metabolic pathways, fatty acid degradation, and valine, leucine, and isoleucine degradation. In addition, we intersected the miRNA-mRNA interaction prediction results with the differentially expressed and prognostic mRNAs. We found that hsa-miR-92b-3p can be related to CPEB3 and ACADL. By overlapping the data of predicted circRNAs by circBank and differentially expressed circRNAs of GSE94508, we screened has_circ_0077210 as the upstream regulatory molecule of hsa-miR-92b-3p. Hsa_circ_0077210/hsa-miR-92b-3p/cytoplasmic polyadenylation element binding protein-3 (CPEB3) and acyl-Coenzyme A dehydrogenase, long chain (ACADL) were validated in HCC tissue.
Our research provides a mechanistic elucidation of the unknown ceRNA regulatory network in HCC. Hsa_circ_0077210 might serve a momentous therapeutic role to restrain the occurrence and development of HCC.
环状RNA（circRNAs）作为肝细胞癌（HCC）患者新型且有前景的生物标志物，目前正受到热烈讨论。本研究的目的是识别几个与HCC的预后和进展相关的竞争性内源RNA（ceRNA）网络，并进一步研究它们影响肿瘤进展的机制。
通过差异表达分析初步鉴定出201个差异表达的miRNA（DEmiRNAs）和3783个DEmRNAs。用WGCNA构建了DEmiRNAs和DEmRNAs的共表达网络。进一步分析证实，最显著模块（蓝色模块）中的4个miRNA与肝癌患者的总生存期（OS）相关，包括hsa-miR-92b-3p、hsa-miR-122-3p、hsa-miR-139-5p和hsa-miR-7850-5p。使用DAVID对286个共表达的mRNA进行功能富集分析。GO分析结果显示，富集程度最高的GO术语是氧化还原过程、细胞外囊泡和铁离子结合。在KEGG通路分析中，富集程度最高的前三个术语包括代谢途径、脂肪酸降解以及缬氨酸、亮氨酸和异亮氨酸降解。此外，我们将miRNA-mRNA相互作用预测结果与差异表达和预后的mRNA进行交叉分析。我们发现hsa-miR-92b-3p可能与CPEB3和ACADL相关。通过将circBank预测的circRNAs数据与GSE94508的差异表达circRNAs进行重叠，我们筛选出has_circ_0077210作为hsa-miR-92b-3p的上游调控分子。在HCC组织中验证了hsa_circ_0077210/hsa-miR-92b-3p/细胞质聚腺苷酸化元件结合蛋白3（CPEB3）和长链酰基辅酶A脱氢酶（ACADL）。
我们的研究对HCC中未知的ceRNA调控网络进行了机制阐释。Hsa_circ_0077210可能在抑制HCC的发生和发展中发挥重要的治疗作用。
