Bioinformatic analysis of long non-coding RNA-associated competing endogenous RNA network in adrenocortical carcinoma
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ABSTRACT: Background
Adrenocortical carcinoma (ACC) is a malignant tumor with poor prognosis and unclear pathogenesis. This study aimed to explore the role of long non-coding RNAs (lncRNAs) in ACC. Methods
We obtained the lncRNA expression profiles of 10 ACC samples and 6 normal control samples from the GEO database and identified differentially expressed RNAs using the limma package in R. Results
We obtained a total of 391 differentially expressed lncRNAs (DElncRNAs) and 1,313 differentially expressed mRNAs (DEmRNAs) between ACC samples and normal control samples. Using Cytoscape v3.7.0, we then constructed a lncRNA-miRNA-mRNA (competing endogenous RNA, or ceRNA) network consisting of 87 lncRNAs, 31 miRNAs, and 78 mRNAs. Applying GO and KEGG enrichment analysis for 78 mRNAs in the ceRNA network, we identified 9 GO terms and 21 significantly enriched pathways. A PPI network was constructed using STRING online tools and Cytoscape v3.7.0, identifying 10 key genes. Finally, through Kaplan-Meier survival analysis, we identified five lncRNAs (LINC00887, MEIS1-AS2, MIR29B2CHG, MIR503HG, and SREBF2-AS1) associated with prognosis in patients with ACC. Conclusions
In summary, we constructed a ceRNA network and propose a new method for lncRNA research in ACC. Our results provide new clues for further exploration of lncRNAs in the pathogenesis of ACC.
SUBMITTER: Zhou Y
PROVIDER: S-EPMC8798464 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND Numerous studies have demonstrated that noncoding RNAs are involved in choriocarcinoma (CC). The competing endogenous RNA (ceRNA) network plays an important role in the occurrence and development of carcinoma. However, the involvement of the ceRNA network in CC remains unclear. The current study aimed to investigate the regulatory mechanism of ceRNA in CC. MATERIAL AND METHODS We downloaded the messenger RNAs (mRNAs) expression profiles (GSE20510 and GSE65654) and microRNAs (miRNAs) expression profiles (GSE32346 and GSE130489) from GEO datasets. The limma package of R software was used to identify differentially expressed RNAs (DERNAs). Then, we performed functional annotation of the differentially expressed mRNAs (DEmRNAs). TargetScan, miRDB, miRWalk, and Starbase were used to construct a CC-specific ceRNA network and select key molecules. RESULTS The results identified a total of 177 DEmRNAs and 189 differentially expressed miRNAs (DEmiRNAs) between the trophoblast and CC cell line samples. Ten differentially expressed lncRNAs (DElncRNAs) were obtained based on experimental studies. The DEmRNAs were mainly enriched in cell proliferation, positive regulation of the apoptotic process, and cell death. A total of 10 genes were ascertained as hub genes. Based on DEmRNAs, DEmiRNAs, and DElncRNAs, a CC-specific ceRNA network was established. Five DElncRNAs, 15 DEmiRNAs, and 45 DEmRNAs were identified. In addition, LINC00261, MEG3, MALAT1, H19, and OGFRP1 were identified as 5 key lncRNAs in choriocarcinoma. CONCLUSIONS This study provides novel insights into CC mechanisms and identified potential therapeutic targets for CC.
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