Data_Sheet_1_Construction of Circular RNA–MicroRNA–Messenger RNA Regulatory Network of Recurrent Implantation Failure to Explore Its Potential Pathogenesis.CSV

Background: Many studies on circular RNAs (circRNAs) have recently been published. However, the function of circRNAs in recurrent implantation failure (RIF) is unknown and remains to be explored. This study aims to determine the regulatory mechanisms of circRNAs in RIF.Methods: Microarray data of RIF circRNA (GSE147442), microRNA (miRNA; GSE71332), and messenger RNA (mRNA; GSE103465) were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed circRNA, miRNA, and mRNA. The circRNA–miRNA–mRNA network was constructed by Cytoscape 3.8.0 software, then the protein–protein interaction (PPI) network was constructed by STRING database, and the hub genes were identified by cytoHubba plug-in. The circRNA–miRNA–hub gene regulatory subnetwork was formed to understand the regulatory axis of hub genes in RIF. Finally, the Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the hub genes were performed by clusterProfiler package of Rstudio software, and Reactome Functional Interaction (FI) plug-in was used for reactome analysis to comprehensively analyze the mechanism of hub genes in RIF.Results: A total of eight upregulated differentially expressed circRNAs (DECs), five downregulated DECs, 56 downregulated differentially expressed miRNAs (DEmiRs), 104 upregulated DEmiRs, 429 upregulated differentially expressed genes (DEGs), and 1,067 downregulated DEGs were identified regarding RIF. The miRNA response elements of 13 DECs were then predicted. Seven overlapping miRNAs were obtained by intersecting the predicted miRNA and DEmiRs. Then, 56 overlapping mRNAs were obtained by intersecting the predicted target mRNAs of seven miRNAs with 1,496 DEGs. The circRNA–miRNA–mRNA network and PPI network were constructed through six circRNAs, seven miRNAs, and 56 mRNAs; and four hub genes (YWHAZ, JAK2, MYH9, and RAP2C) were identified. The circRNA–miRNA–hub gene regulatory subnetwork with nine regulatory axes was formed in RIF. Functional enrichment analysis and reactome analysis showed that these four hub genes were closely related to the biological functions and pathways of RIF.Conclusion: The results of this study provide further understanding of the potential pathogenesis from the perspective of circRNA-related competitive endogenous RNA network in RIF.

背景：近年来，关于环状RNA（circRNAs）的研究层出不穷。然而，circRNAs在复发性植入失败（RIF）中的功能尚不明确，有待进一步探究。本研究旨在确定circRNAs在RIF中的调控机制。方法：从基因表达综合数据库（GEO）下载了RIF circRNA（GSE147442）、微RNA（miRNA；GSE71332）和信使RNA（mRNA；GSE103465）的微阵列数据，以识别差异表达的circRNA、miRNA和mRNA。利用Cytoscape 3.8.0软件构建了circRNA-miRNA-mRNA网络，随后通过STRING数据库构建了蛋白质-蛋白质相互作用（PPI）网络，并通过cytoHubba插件识别了枢纽基因。形成了circRNA-miRNA-枢纽基因调控子网络，以理解枢纽基因在RIF中的调控轴。最终，通过Rstudio软件的clusterProfiler包对枢纽基因进行了基因本体（GO）分析和京都基因与基因组百科全书（KEGG）通路富集分析，并使用Reactome功能相互作用（FI）插件进行Reactome分析，以全面分析枢纽基因在RIF中的机制。结果：在RIF中，共鉴定出八个上调的差异表达环状RNA（DECs）、五个下调的DECs、五十六个下调的差异表达miRNA（DEmiRs）、一百零四个上调的DEmiRs、四百二十九个上调的差异表达基因（DEGs）和一千零六十七个下调的DEGs。随后，预测了13个DECs的miRNA响应元件。通过预测的miRNA与DEmiRs的交集，获得了七个重叠的miRNA。然后，通过将七个miRNA的预测靶标mRNA与1,496个DEGs的交集，获得了五十六个重叠的mRNA。通过六个circRNA、七个miRNA和五十六个mRNA构建了circRNA-miRNA-mRNA网络和PPI网络；并鉴定出四个枢纽基因（YWHAZ、JAK2、MYH9和RAP2C）。在RIF中形成了包含九个调控轴的circRNA-miRNA-枢纽基因调控子网络。功能富集分析和Reactome分析表明，这四个枢纽基因与RIF的生物功能和通路密切相关。结论：本研究的结果从circRNA相关的竞争性内源RNA网络的角度，对RIF的潜在发病机制提供了更深入的理解。