基于环状 RNA 介导的竞争性内源 RNA 调控网络预测转移性前列腺癌的潜在预后生物标志物。
Prediction of potential prognostic biomarkers in metastatic prostate cancer based on a circular RNA-mediated competing endogenous RNA regulatory network.
机构信息
Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
Department of Urology, Foshan First Municipal People's Hospital, Foshan, China.
出版信息
PLoS One. 2021 Dec 3;16(12):e0260983. doi: 10.1371/journal.pone.0260983. eCollection 2021.
Recently, studies on competing endogenous RNA (ceRNA) networks have become prevalent, and circular RNAs (circRNAs) have crucial implications for the development and progression of carcinoma. However, studies relevant to metastatic prostate cancer (mPCa) are scant. This study aims to discover potential ceRNAs that may be related to the prognosis of mPCa. RNA-Seq data were obtained from the MiOncoCirc database and Gene Expression Omnibus (GEO). Differential expression patterns of RNAs were examined using R packages. Circular RNA Interactome, miRTarBase, miRDB and TargetScan were applied to predict the corresponding relation between circRNAs, miRNAs and mRNAs. The Gene Ontology (GO) annotations were performed to present related GO terms, and Gene Set Enrichment Analysis (GSEA) tools were applied for pathway annotations. Moreover, survival analysis was conducted for the hub genes. We found 820 circRNAs, 81 miRNAs and 179 mRNAs that were distinguishingly expressed between primary prostate cancer (PCa) and mPCa samples. A ceRNA network including 45 circRNAs, 24 miRNAs and 56 mRNAs was constructed. In addition, the protein-protein interaction (PPI) network was built, and 10 hub genes were selected by using the CytoHubba application. Among the 10 hub genes, survival analysis showed that ITGA1, LMOD1, MYH11, MYLK, SORBS1 and TGFBR3 were significantly connected with disease-free survival (DFS). The circRNA-mediated ceRNA network provides potential prognostic biomarkers for metastatic prostate cancer.
最近，竞争内源性 RNA（ceRNA）网络的研究变得流行起来，环状 RNA（circRNA）对癌的发生和发展有重要意义。然而，与转移性前列腺癌（mPCa）相关的研究却很少。本研究旨在发现可能与 mPCa 预后相关的潜在 ceRNA。从 MiOncoCirc 数据库和基因表达综合（GEO）中获取 RNA-Seq 数据。使用 R 包检查 RNA 的差异表达模式。应用 Circular RNA Interactome、miRTarBase、miRDB 和 TargetScan 来预测 circRNAs、miRNAs 和 mRNAs 之间的相应关系。进行基因本体论（GO）注释以呈现相关的 GO 术语，并应用基因集富集分析（GSEA）工具进行途径注释。此外，还对枢纽基因进行了生存分析。我们在原发性前列腺癌（PCa）和 mPCa 样本之间发现了 820 个区分表达的 circRNAs、81 个 miRNAs 和 179 个 mRNAs。构建了一个包含 45 个 circRNAs、24 个 miRNAs 和 56 个 mRNAs 的 ceRNA 网络。此外，构建了蛋白质-蛋白质相互作用（PPI）网络，并使用 CytoHubba 应用程序选择了 10 个枢纽基因。在这 10 个枢纽基因中，生存分析表明 ITGA1、LMOD1、MYH11、MYLK、SORBS1 和 TGFBR3 与无病生存率（DFS）显著相关。circRNA 介导的 ceRNA 网络为转移性前列腺癌提供了潜在的预后生物标志物。
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