生物信息学分析构建椎间盘退变中潜在功能性 circRNA-miRNA-mRNA 网络。
Construction of a Potentially Functional circRNA-miRNA-mRNA Network in Intervertebral Disc Degeneration by Bioinformatics Analysis.
机构信息
Department of Minimally Invasive Spine Surgery, Tianjin Hospital, 406. No, Jiefangnan Road, Hexi District, Tianjin, China 300211.
Graduate School, Tianjin Medical University, 22 Qixiangtai Road, Tianjin, China.
出版信息
Biomed Res Int. 2021 Aug 4;2021:8352683. doi: 10.1155/2021/8352683. eCollection 2021.
BACKGROUND
The competing endogenous RNA- (ceRNA-) mediated regulatory mechanisms are known to play a pivotal role in intervertebral disc degeneration (IDD). Our research intended to establish a ceRNA regulatory network related to IDD through bioinformatics analyses.
METHODS
The expression profiles of circRNA, miRNA, and mRNA were obtained from the public Gene Expression Omnibus (GEO) datasets. Then, we use sequence-based bioinformatics methods to select differentially expressed mRNAs (DEmRNAs), microRNAs (DEmiRNAs), or circRNAs (DEcircRNAs) related to IDD. We used ChEA3 to verify the targets of transcription factors (TFs). Then, we used DAVID to annotate the DEmRNAs. Finally, we constructed a potentially circRNA-miRNA-mRNA network related to IDD by predicting in the database (ENCORI, TargetScan, miRecords, miRmap, and circBank).
RESULTS
We identified 31 common DEmRNAs by Venn analysis, of which MMP2 was regarded as the key hub genes. Simultaneously, miR-423-5p and miR-185-5p were predicted as the upstream molecules of MMP2. Furthermore, a total of six DEcircRNAs were predicted as the upstream circRNAs of miR-423-5p and miR-185-5p. Then, a potential circRNA-miRNA-mRNA network related to IDD was constructed by bioinformatics analysis.
CONCLUSION
A comprehensive ceRNA regulatory network was constructed, which was found to be significant in IDD progression.
背景
竞争内源性 RNA（ceRNA）介导的调控机制在椎间盘退变（IDD）中起着关键作用。我们的研究旨在通过生物信息学分析建立与 IDD 相关的 ceRNA 调控网络。
方法
从公共基因表达综合数据库（GEO）中获取 circRNA、miRNA 和 mRNA 的表达谱。然后，我们使用基于序列的生物信息学方法来选择与 IDD 相关的差异表达的 mRNAs（DEmRNAs）、microRNAs（DEmiRNAs）或 circRNAs（DEcircRNAs）。我们使用 ChEA3 来验证转录因子（TFs）的靶标。然后，我们使用 DAVID 来注释 DEmRNAs。最后，我们通过在数据库（ENCORI、TargetScan、miRecords、miRmap 和 circBank）中进行预测，构建了一个与 IDD 相关的潜在 circRNA-miRNA-mRNA 网络。
结果
通过 Venn 分析，我们确定了 31 个共同的 DEmRNAs，其中 MMP2 被认为是关键的枢纽基因。同时，预测 miR-423-5p 和 miR-185-5p 作为 MMP2 的上游分子。此外，共预测了 6 个 DEcircRNAs 作为 miR-423-5p 和 miR-185-5p 的上游 circRNAs。然后，通过生物信息学分析构建了一个与 IDD 相关的潜在 circRNA-miRNA-mRNA 网络。
结论
构建了一个全面的 ceRNA 调控网络，该网络在 IDD 进展中具有重要意义。
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