参与肾纤维化和肾透明细胞癌的关键基因

Key genes involved in renal fibrosis and renal clear cell carcinoma

目的采用生物信息学方法探究影响肾纤维化(renal fibrosis,RF)和肾透明细胞癌发病机制的关键基因。方法从基因表达整合数据库(gene expression omnibus data base,GEO)下载了RF和肾透明细胞癌的基因芯片数据集,并利用GEO2R在线工具获得差异表达基因(differentially expressed gene,DEG)。然后,使用注释、可视化和集成发现数据库(the database for annotation,visualization and integrated discovery,DAVID)进行基因本体论分析(gene ontology,GO)以及京都基因与基因组百科全书(kyoto encyclopedia of genes and genomes,KEGG)富集分析。随后,我们使用检索相互作用基因/蛋白质的搜索工具(search tool for the retrieval of interaction gene/proteins,STRING)数据库并构建了蛋白质互作网络(protein-protein interaction networks,PPI),使用Cytoscape的cytoHubba插件来选择中心基因。然后,我们使用癌症基因组图谱计划数据库(the cancer genome atlas program,TCGA)、基因表达谱交互分析数据库(gene expression profiling interactive analysis,GEPIA)、肿瘤免疫评估资源数据库(tumor immune estimation resource,TIMER)数据库来验证中心基因并进一步筛选出核心基因,同时运用TargetScanHuman、miRTarbase和miRWalk数据库对核心基因调控的靶向miRNA进行逆向预测,并筛选出核心miRNA,建立了mRNA和miRNA互助网络。然后,通过基因集富集分析(gene set enrichment analysis,GSEA)工具分析LYZ基因,最后使用人类蛋白质图谱(the human protein atlas,HPA)数据库验证已鉴定核心基因的表达水平。结果我们筛选出了347个差异基因,我们对下调和上调的差异基因分别进行了功能富集分析,通过TCGA数据集、GTEx数据集、TIMER数据库和HPA数据库,在三轮验证中逐步筛选,最终选择LYZ基因,鉴定出调节该基因的上游转枢miRNA:has-miR-4649-3p和has-miR-873-3p。结论基于这些发现,提出LYZ、has-miR-4649-3p和has-miR-873-3p可能成为肾透明细胞癌的潜在预后生物标志物,并有助于预防和治疗肾纤维化,这也向我们展示了一种新的治疗理念,提供了从免疫角度治疗肾纤维化的可能性。

Objective To employ bioinformatics for exploring the key genes affecting the pathogenesis of renal fibrosis(RF)and renal clear cell carcinoma.Methods The gene chip datasets of RF and KIRC were downloaded from GEO database and differentially expressed genes(DEGs)retrieved through a GEO2R online tool.Then DAVID database was employed for GO and KEGG enrichment analyses.Then the STRING database was utilized for constructing a PPI network,Cytoscape's cytoHubba plug-in was used for selecting the central genes.Then TCGA,GEPIA and TIMER databases were utilized for verifying the central genes and further screening out the core genes.Meanwhile,TargetScanHuman,miRTarbase and miRWalk databases were utilized for reverse predict the targeted miRNA regulated by the hub genes.Core miRNA was screened out and a mutual network of mRNA/miRNA established.LYZ gene was analyzed by GSEA tool and the expression level of identified hub genes verified by HPA database.Results A total of 347 differential genes were screened out.Functional enrichment analysis was performed on down/up-regulated differential genes.Through TCGA dataset,GTEx dataset,TIMER database and HPA database,LYZ gene was gradually screened in three rounds of verification.The upstream hub regulatory miRNA was identified as has-miR-4649-3p and has-miR-873-3p.Conclusion Based upon these findings,LYZ,hasmiR-4649-3p and has-miR-873-3p may be potential prognostic biomarkers of KIRC and contribute to the prevention and treatment of RF.As a novel therapeutic concept,it offers a promising immunotherapy for RF.