支气管肺发育不良中新型miRNA-TF-mRNA共调控网络的鉴定

Identification on a novel miRNA-TF-mRNA co-regulatory network in bronchopulmonary dysplasia

目的筛选与新生儿支气管肺发育不良(BPD)发病相关的关键转录因子(TF)、微小核糖核酸(miRNA)和信使核糖核酸(mRNA), 并构建了调控网络。方法从高通量基因表达数据库GEO获取mRNA芯片数据集GSE108756, 筛选出的差异表达基因(DEGs)进行京都基因和基因百科全书(KEGG)、基因本体注释(GO)功能富集分析;参照HumanTFDB数据库获取与DEGs对应的TF后利用cytoHubba插件筛选出degree值前10的Hub TF;通过hTFtarget数据库找出Hub TF中7个TF所对应的靶基因;在GSE108756中获取7个TF及其靶基因所对应的探针表达量后做相关性分析, 筛选出最终纳入研究的6个Hub TF及所对应的正相关TF-mRNA关系队;利用Targetscan Human数据库获取靶向调控6个Hub TF的miRNAs, 并与miRNA芯片数据集GSE166762差异miRNAs取交集后匹配出负向调节的miRNA-TF关系队, 最后构建BPD患儿潜在miRNA-TF-mRNA调控网络, 进一步筛选出关键miRNA、mRNA。结果共筛选出201个差异表达基因, KEGG富集结果主要涉及B细胞受体信号通路、造血系统、原发免疫缺陷等作用, GO功能富集分析主要富集在B细胞增殖活化及免疫应答调节细胞表面受体等生物学过程中。与Hub TF(EBF1、TCF4、JUN、BCL11A、SPIB、E2F1)表达谱强关联的正相关下游靶基因有159个, 负相关的上游miRNA有120个。BPD患儿发病潜在的关键miRNA-TF-mRNA网络包括has-miR-217-TCF4-Pou2AF1、has-miR-150-5p-E2F1-ADM。结论本研究构建了新生儿BPD的miRNA-TF-mRNA共调控网络, 从转录调控的崭新视角为揭示BPD发病机制奠定理论基础。

Objective To screen key transcription factors(TFs),microRNA(miRNA)and messenger RNA(mRNA)related to the pathogenesis of neonatal bronchopulmonary dysplasia(BPD)and to set up a regulatory network.Methods The mRNA microarray dataset GSE108756 was downloaded from high throughput gene expression omnibus(GEO)database,gene-ontology(GO)enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis were applied to select differentially expressed genes(DEGs).Transcription factors(TFs)corresponding to DEGs were acquired by referring to humanTFDB database,and the Hub TFs with top 10 degrees were screened by applying the cytoHubba plug-in.Target genes corresponding to 7 TFs in Hub TF were found by hTFtarget database.The correlation analysis was performed after acquiring the corresponding probe expression levels of 7 TFs and corresponding target genes in GSE108756 to screen out the 6 Hub TFs finally included in the study and positive correlation TF-mRNA relationship team.TargetScan Human database was applied to acquire the miRNAs targeting the regulation of 6 Hub TFs,and miRNA-TF relationship team with negative regulation was matched after intersecting miRNAs with the miRNA microarray dataset GSE166762.Finally,the regulatorynetwork of potential miRNA-TF-mRNA in children withBPD was constructed to further screen out key miRNAs and mRNAs.ResultsA total of 201 differentially expressed genes were screened out,KEGG enrichment results were mainly involved in B-cell receptor signaling pathway,hematopoietic system,primary immune deficiency,etc.B cell proliferation and activation,immune response regulation cell surface receptors and other biological processes were mainly enriched in GO enrichment analysis.A total of 159 positively correlated downstream target genes and 120 negatively correlated upstream miRNAs were strongly correlated with expression profiles of Hub TF(EBF1,TCF4,JUN,BCL11A,SPIB,E2F1).Potential key miRNA-TF-mRNA networks in the pathogenesis of BPD children included has-miR-217-TCF4 Pou2AF1and has-miR-150-5p-E2F1-ADM.Conclusions The miRNA-TF-mRNA co-regulatory network of neonatal BPD is set up,laying a theoretical foundation for revealing the pathogenesis of BPDfrom the new perspective of transcriptional regulation.