基于加权基因共表达网络分析探索射血分数保留的心力衰竭中微RNA功能模块和分子调控网络

Weighted gene co-expression network analysis to identify microRNAs functional modules and gene networks of heart failure with preserved ejection fraction

目的通过生物信息学方法探索射血分数保留的心力衰竭(HFpEF)潜在的生物标志物和治疗靶点。方法使用NCBI-GEO数据库检索获得GSE53437高通量测序数据进行分析。通过加权基因共表达网络分析(WGCNA)获取与HFpEF密切相关的基因模块和核心微RNA(miRNA),利用miRNet数据库预测核心miRNA的靶向mRNA。应用R语言“clusterProfiler”程序包对靶基因进行KEGG通路和基因本体论(GO)富集分析。最后采用STRING数据库和Cytoscape软件构建蛋白质-蛋白质相互作用(PPI)网络和miRNA-mRNA基因网络。结果在基因模块与疾病相关性分析中,棕色模块与HFpEF的相关系数(r)绝对值为0.37,P值为3e-4,具有最高的正相关性。各基因模块的基因显著性(GS)分布显示,棕色模块具有最高的GS值。模块内分析显示,棕色模块的模块相关性(MM)与GS之间密切相关(r=0.61,P值为7e-52)。以MM>0.85且GS>0.40为条件,共筛选出17个与HFpEF高度相关的核心miRNA。应用miRNet数据库预测到1578个靶向mRNA。GO注释分析结果显示,该组基因参与的生物学过程包括造血调控、T细胞激活和细胞组分大小调控等,涉及的细胞成分包括转录调控复合物、运输囊泡、早期内体等的构成,分子功能主要富集在DNA结合转录抑制因子活性/RNA聚合酶Ⅱ特异性、泛素蛋白连接酶结合和生长因子活性等方面。KEGG通路分析结果显示,该组基因主要富集于Hippo信号通路、ErbB信号通路、TNF-α信号通路、Ras信号通路等。miRNA-mRNA基因网络分析显示,miRNA-3188与UBA52、HDAC2、PSMF1和SUFU相互作用,miRNA-3909与HDAC2、PSMF1、SUFU和RELA相互作用,miRNA-762与PSMF1、SUFU和RELA相互作用,miRNA548b-3p与UBA52、HDAC2和PSMF1相互作用,miRNA-3198与UBA52、PSMF1、SUFU和RELA相互作用。结论本研究可能有助于阐释HFpEF的分子机制,为识别HFpEF的生物标志物及潜在治疗靶点奠定新的理论依据。

Objective To screen for potential biomarkers and therapeutic targets for heart failure with preserved ejection fraction(HFpEF)through bioinformatics analysis.Methods The microarray dataset GSE53437 was downloaded from the NCBI Gene Expression Omnibus.Weighted gene co-expression network analysis(WGCNA)was performed to identify gene modules and hub microRNAs(miRNAs)associated with HFpEF.Potential downstream target genes of miRNAs were predicted by miRNet.Gene Ontology(GO)annotation and KEGG pathway enrichment analysis for target genes were conducted via R package“ClusterProfiler”.Protein-protein interaction(PPI)and miRNA-mRNA networks were constructed using the STRING database and Cytoscape software.Results The brown module showed the top positive correlation with HFpEF(r=0.37,P=3e-4).The brown module possessed the highest gene significance(GS)values.The intramodular analysis demonstrated a close relationship between module membership(MM)and GS of the brown module(r=0.61,P=7e-52).A total of 17 hub genes with MM>0.85 and GS>0.40 were identified as highly associated with HFpEF.A total of 1578 target mRNAs were predicted by the miRNet database.GO annotation analysis revealed that these genes were involved in the following biological processes:the regulation of hematopoiesis,activation of T cells,and the modulation of cellular component size.Cellular components implicated in these processes included the transcription regulator complex,transport vesicles,and early endosomes.In terms of molecular functions,there was a significant enrichment in activities such as DNA-binding transcription repress or activity/RNA polymeraseⅡspecificity,ubiquitin-protein ligase binding,and growth factor activity.KEGG pathway analysis indicated a substantial enrichment of these genes in signaling pathways,notably the Hippo,ErbB,TNF-α,and Ras signaling pathways.The regulatory network of miRNA-mRNA showed that miRNA-3188 interacted with UBA52,HDAC2,PSMF1 and SUFU;miRNA-3909 interacted with HDAC2,PSMF1,SUFU and RELA;miRNA-762 interacted with PSMF1,SUFU and RELA;miRNA548b-3p interacted with UBA52,HDAC2 and PSMF1;and miRNA-3198 interacted with UBA52,PSMF1,SUFU and RELA.Conclusion These findings may contribute to the interpretation of the underlying molecular mechanisms,as well as the identification of biomarkers and potential therapeutic targets for HFpEF.