基于生物信息学分析鉴定翼状胬肉中的功能基因。
Identification of Functional Genes in Pterygium Based on Bioinformatics Analysis.
机构信息
Department of Ophthamology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China.
Department of Corneal, Hankou Aier Eye Hospital, Wuhan, Hubei 430024, China.
出版信息
Biomed Res Int. 2020 Nov 20;2020:2383516. doi: 10.1155/2020/2383516. eCollection 2020.
PURPOSE
The competing endogenous RNA (ceRNA) network regulatory has been investigated in the occurrence and development of many diseases. This research aimed at identifying the key RNAs of ceRNA network in pterygium and exploring the underlying molecular mechanism.
METHODS
Differentially expressed long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs were obtained from the Gene Expression Omnibus (GEO) database and analyzed with the R programming language. LncRNA and miRNA expressions were extracted and pooled by the GEO database and compared with those in published literature. The lncRNA-miRNA-mRNA network was constructed of selected lncRNAs, miRNAs, and mRNAs. Metascape was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on mRNAs of the ceRNA network and to perform Protein-Protein Interaction (PPI) Network analysis on the String website to find candidate hub genes. The Comparative Toxicogenomic Database (CTD) was used to find hub genes closely related to pterygium. The differential expressions of hub genes were verified using the reverse transcription-real-time fluorescent quantitative PCR (RT-qPCR).
RESULT
There were 8 lncRNAs, 12 miRNAs, and 94 mRNAs filtered to construct the primary ceRNA network. A key lncRNA LIN00472 ranking the top 1 node degree was selected to reconstruct the LIN00472 network. The GO and KEGG pathway enrichment showed the mRNAs in ceRNA networks mainly involved in homophilic cell adhesion via plasma membrane adhesion molecules, developmental growth, regulation of neuron projection development, cell maturation, synapse assembly, central nervous system neuron differentiation, and PID FOXM1 PATHWAY. According to the Protein-Protein Interaction Network (PPI) analysis on mRNAs in LINC00472 network, 10 candidate hub genes were identified according to node degree ranking. Using the CTD database, we identified 8 hub genes closely related to pterygium; RT-qPCR verified 6 of them were highly expressed in pterygium.
CONCLUSION
Our research found LINC00472 might regulate 8 hub miRNAs (miR-29b-3p, miR-183-5p, miR-138-5p, miR-211-5p, miR-221-3p, miR-218-5p, miR-642a-5p, miR-5000-3p) and 6 hub genes (CDH2, MYC, CCNB1, RELN, ERBB4, RB1) in the ceRNA network through mainly PID FOXM1 PATHWAY and play an important role in the development of pterygium.
目的
竞争内源性 RNA（ceRNA）网络调控已在许多疾病的发生和发展中得到研究。本研究旨在鉴定翼状胬肉 ceRNA 网络中的关键 RNA，并探讨其潜在的分子机制。
方法
从基因表达综合数据库（GEO）中获取差异表达的长非编码 RNA（lncRNA）、microRNA（miRNA）和 mRNA，并使用 R 编程语言进行分析。通过 GEO 数据库提取和汇总 lncRNA 和 miRNA 的表达，并与已发表文献中的表达进行比较。选择 lncRNA、miRNA 和 mRNA 构建 ceRNA 网络的 lncRNA-miRNA-mRNA 网络。使用 Metascape 对 ceRNA 网络的 mRNAs 进行基因本体论（GO）和京都基因与基因组百科全书（KEGG）分析，并在 String 网站上进行蛋白质-蛋白质相互作用（PPI）网络分析，以找到候选枢纽基因。使用比较毒理学基因组数据库（CTD）找到与翼状胬肉密切相关的枢纽基因。使用逆转录实时荧光定量 PCR（RT-qPCR）验证枢纽基因的差异表达。
结果
筛选出 8 个 lncRNA、12 个 miRNA 和 94 个 mRNA 构建初级 ceRNA 网络。选择排名第一的节点度最高的关键 lncRNA LIN00472 来重建 LIN00472 网络。GO 和 KEGG 通路富集显示，ceRNA 网络中的 mRNAs 主要参与通过质膜黏附分子的同质细胞黏附、发育生长、调节神经元投射发育、细胞成熟、突触装配、中枢神经系统神经元分化和 PID FOXM1 通路。根据 LINC00472 网络中 mRNAs 的蛋白质-蛋白质相互作用网络（PPI）分析，根据节点度排名确定了 10 个候选枢纽基因。使用 CTD 数据库，我们鉴定出 8 个与翼状胬肉密切相关的枢纽基因；RT-qPCR 验证了其中 6 个在翼状胬肉中高表达。
结论
本研究发现 LINC00472 可能通过主要 PID FOXM1 通路调节 ceRNA 网络中的 8 个枢纽 miRNA（miR-29b-3p、miR-183-5p、miR-138-5p、miR-211-5p、miR-221-3p、miR-218-5p、miR-642a-5p、miR-5000-3p）和 6 个枢纽基因（CDH2、MYC、CCNB1、RELN、ERBB4、RB1），在翼状胬肉的发生发展中发挥重要作用。
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