基于生物信息学对心肌缺血再灌注损伤关键基因的筛选及实验验证

Screening and experimental validation of hub genes for myocardial isch emia-reperfusion injury based on bioinformatics

目的:运用生物信息学分析方法挖掘参与心肌缺血再灌注损伤(MIRI)的关键基因。方法:首先,从数据库中下载大鼠MIRI相关数据集GSE122020、E-MEXP-2098和E-GEOD-4105。其次,一方面利用微阵列数据线性模型(limma)包筛选各数据集中的差异表达基因(DEGs),再用稳健排序整合(RRA)方法筛选稳健DEGs;另一方面,利用替代变量分析(SVA)包将各数据集合并为1个数据集,再利用limma包筛选合并DEGs;将2种渠道的DEGs取交集获取共同DEGs。接着,构建共同DEGs的蛋白相互作用(PPI)网络,利用最大邻域组件密度(DMNC)算法筛选关键基因,并绘制关键基因的受试者工作特征(ROC)曲线,以评价其诊断效能。然后,构建MIRI大鼠模型,检测关键基因的mRNA和蛋白表达情况;并对关键基因参与MIRI的研究开展文献回顾分析。最后,对关键基因开展基因集富集分析(GSEA),进一步揭示其介导MIRI可能的机制。结果:共鉴定出143个稳健DEGs,48个合并DEGs,两者取交集后,获得48个共同DEGs。在共同DEGs的PPI网络中,共筛选出了5个关键基因,即MYC原癌基因bHLH转录因子(MYC)、前列腺素内过氧化物合酶2(PTGS2)、血红素加氧酶1(HMOX1)、胱天蛋白酶3(CASP3)和尿激酶型纤溶酶原激活物受体(PLAUR)。这些关键基因的ROC曲线下面积均大于0.8。在MIRI大鼠心肌组织中MYC、PTGS2、CASP3和PLAUR的mRNA和蛋白高表达,而HMOX1的mRNA和蛋白表达无显著差异。回顾文献,5个关键基因中仅PLAUR未被报道参与MIRI。PLAUR的GSEA结果显示,PLAUR的功能富集主要集中在NOD样受体信号通路、P53信号通路、Toll样受体信号通路、细胞凋亡和脂肪酸代谢等途径。结论:MYC、PTGS2、CASP3、HMOX1和PLAUR参与了MIRI的病理过程。PLAUR为潜在的关键基因,其可能通过调控NOD样受体信号通路、P53信号通路、Toll样受体信号通路、细胞凋亡和脂肪酸代谢等途径介导MIRI,结果可为进一步探讨MIRI的分子机制和治疗靶点提供参考。

AIM:Using bioinformatics analysis methods to identify the hub genes involved in myocardial isch emia-reperfusion injury(MIRI).METHODS:Firstly,the rat MIRI related dataset GSE122020,E-MEXP-2098,and E�GEOD-4105 were downloaded from the database.Secondly,differentially expressed genes(DEGs)were screened from each dataset using the linear models for microarray data(limma)package,and robust DEGs were filtered using the robust rank aggregation(RRA)method.In addition,the surrogate variable analysis(SVA)package was used to merge all datas ets into one,and merged DEGs were screened using the limma package.The common DEGs were obtained by taking the intersection of the two channels of DEGs.Next,the protein-protein interaction(PPI)network of common DEGs was con structed,and the hub genes were identified using the density-maximizing neighborhood component(DMNC)algorithm.The receiver operating characteristic curve(ROC)was plotted to evaluate the diagnostic performance of the hub gene.Then,the mRNA and protein expression levels of hub genes were detected in the rat MIRI model,and the literature re view analysis was carried out on the involvement of hub genes in MIRI.Finally,the gene set enrichment analysis(GSEA)was performed on hub gene to further reveal the possible mechanism in mediating MIRI.RESULTS:A total of 143 robust DEGs and 48 merged DEGs were identified.After taking the intersection of the two,48 common DEGs were obtained.In the PPI network of common DEGs,5 hub genes were screened out,namely MYC proto-oncogene bHLH transcription fac tor(MYC),prostaglandin-endoperoxide synthase 2(PTGS2),heme oxygenase 1(HMOX1),caspase-3(CASP3),and plasminogen activator urokinase receptor(PLAUR).The ROC results showed that the area under the curve values for all hub genes were greater than 0.8.MYC,PTGS2,CASP3,and PLAUR showed high mRNA and protein expression in rat MIRI,while there was no difference in mRNA and protein expression for HMOX1.The literature review revealed that among the 5 hub genes,only PLAUR has not been reported to be involved in MIRI.The GSEA results for PLAUR indicat ed that its functional enrichment mainly focused on pathways such as NOD-like receptor signaling pathway,P53 signaling pathway,Toll-like receptor signaling pathway,apoptosis,and fatty acid metabolism.CONCLUSION:MYC,PTGS2,CASP3,HMOX1,and PLAUR are involved in the pathological process of MIRI.PLAUR is a potential hub gene that can mediate MIRI by regulating pathways such as NOD like receptor signaling,P53 signaling,Toll like receptor signaling,cell apoptosis,and fatty acid metabolism.The results can provide reference for further investigation into the molecular mechanisms and therapeutic targets of MIRI.