Dataset Information

Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan-cancer.

ABSTRACT: BACKGROUND:The pan-cancer analysis has recently brought us into a novel level of cancer research. Nowadays, the Circular RNAs (circRNAs) is becoming increasingly important in the occurrence and progression of tumors. Nevertheless, the specific expression patterns and functions of circRNAs in the pan-cancer remains unclear. Here we aimed to explore the expression patterns and functions of circRNAs in pan-cancer. METHODS:We combined our microarray with seven circRNA arrays from the Gene Expression Omnibus (GEO) database and transcriptome profiles were acquired from The Cancer Genome Atlas (TCGA) database. A circRNA-miRNA-mRNA network was created and analyzed using multiple bioinformatic approaches including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, Search Tool for the Retrieval of Interacting Genes (STRING) database, cytoHubba and MCODE app. Cell function assays including CCK-8 analysis, colony formation, and transwell assay were used to explore pan-circRNAs' functions. RESULTS:A panel of 6 circRNAs, 11 miRNAs, and 318 mRNAs was found to be differentially expressed (DE) in pan-cancer. A circRNA-miRNA-mRNA network was also constructed. Then, a circRNA-miRNA-hub gene network was created according to 5 pan-circRNAs, 8 pan-miRNAs, and 16 pan-mRNAs. Enrichment analysis pointed out the possible association of DEmRNAs with pan-cancer is transcriptional misregulation in cancer. Overexpression of hsa_circ_0004639 and silence of hsa_circ_0008310 can inhibit the malignant biological properties of cancer cells. CONCLUSIONS:Six pan-circRNAs were discovered and their regulating mechanisms were predicted. Those findings together will give a new insight into pan-cancer research and present potential therapy targeting as well as promising biomarkers.

SUBMITTER: Chen Z

PROVIDER: S-EPMC7541145 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan-cancer.

Chen Zhanghan Z Huang Jie J Feng Yanling Y Li Zehuan Z Jiang Ying Y

Cancer medicine 20200815 19

<h4>Background</h4>The pan-cancer analysis has recently brought us into a novel level of cancer research. Nowadays, the Circular RNAs (circRNAs) is becoming increasingly important in the occurrence and progression of tumors. Nevertheless, the specific expression patterns and functions of circRNAs in the pan-cancer remains unclear. Here we aimed to explore the expression patterns and functions of circRNAs in pan-cancer.<h4>Methods</h4>We combined our microarray with seven circRNA arrays from the ...[more]

PMID: 33094914

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Project description:IntroductionPolycystic ovary syndrome (PCOS) is caused by the hormonal environment in utero, abnormal metabolism, and genetics, and it is common in women of childbearing age. A large number of studies have reported that lncRNA is important to the biological process of cancer and can be used as a potential prognostic biomarker. Thus, we studied lncRNAs' roles in PCOS in this article.MethodsWe obtained mRNAs', miRNAs', and lncRNAs' expression profiles in PCOS specimens and normal specimens from the National Biotechnology Information Gene Expression Comprehensive Center database. The EdgeR software package is used to distinguish the differentially expressed lncRNAs, miRNAs, and mRNAs. Functional enrichment analysis was carried out by the clusterProfiler R Package, and the lncRNA-miRNA-mRNA interaction ceRNA network was built in Cytoscape plug-in BiNGO and Database for Annotation, Visualization, and Integration Discovery (DAVID), respectively.ResultsWe distinguished differentially expressed RNAs, including 1087 lncRNAs, 14 miRNAs, and 566 mRNAs in PCOS. Among them, 410 lncRNAs, 11 miRNAs, and 185 mRNAs were contained in the ceRNA regulatory network. The outcomes from Gene Ontology (GO) analysis showed that the differentially expressed mRNAs (DEMs) were mainly enriched in response to the maternal process involved in female pregnancy, morphogenesis of embryonic epithelium, and the intracellular steroid hormone receptor signaling pathway. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis data showed that DEMs were primarily enriched in pathways related to the TGF-β signaling pathway, Type I diabetes mellitus, and glycolysis/gluconeogenesis. In addition, we chose NONHSAT123397, ENST00000564619, and NONHSAT077997 as key lncRNAs due to their high bearing on PCOS.ConclusionceRNA networks play an important role in PCOS. The research indicated that specific lncRNAs were related to PCOS development. NONHSAT123397, ENST00000564619, and NONHSAT077997 could be regarded as potential diagnostic mechanisms and biomarkers for PCOS. This discovery might provide more effective and more novel insights into the mechanisms of PCOS worthy of further exploration.

Dataset Information

Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan-cancer.

Publications

Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan-cancer.

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