摘要
目的:通过生物信息学方法构建胰腺癌(pancreatic adenocarcinoma, PAAD)患者血液外泌体中的竞争性内源RNA(competing endogenous RNA, ceRNA)调控网络,探讨其发病机制。方法:从exoRBase数据库下载PAAD患者和正常对照的血液外泌体测序数据,使用R语言分别对外泌体mRNA、长链非编码RNA(long non-coding RNA, lncRNA)及环状RNA(circular RNA, circRNA)的表达谱进行差异分析。使用TargetScan和miRanda数据库共同预测与差异表达mRNA结合的微小RNA(microRNA, miRNA)。使用miRcode数据库预测与差异表达lncRNA结合的miRNA,使用starBase数据库预测与差异表达circRNA结合的miRNA。将相关的mRNA、circRNA、lncRNA和其相对应的miRNA预测数据导入Cytoscape软件中对ceRNA网络进行可视化。并使用R语言进行基因本体论(gene ontology, GO)和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)富集。采用CytoHubba插件确定Hub基因,表达谱交互分析数据库GEPIA分析PAAD和正常样本的基因测序表达数据。比较PAAD患者和正常对照者中前10个Hub基因的表达,并绘制对应Hub基因的生存曲线。结果:筛选出120个差异表达的mRNA,48个差异表达lncRNA,23个差异表达circRNA。采用Cytoscape软件构建了ceRNA网络,共19个mRNA节点、12个lncRNA节点、3个circRNA节点、31个miRNA节点。GO富集分析显示,mRNA主要富集在富含ficolin-1颗粒腔和组蛋白脱乙酰酶结合。KEGG富集分析显示调控网络中差异表达的mRNA主要富集在黏附连接通路、结直肠癌通路和神经营养信号通路。找到关键的Hub基因小GTP酶Ras相关C3肉毒杆菌毒素底物1(the small GTPase Ras-related C3 botulinum toxin substrate 1, RAC1),GEPIA显示PAAD患者RAC1基因表达水平明显升高。生存分析结果显示RAC1低表达组PAAD患者的生存率显著高于高表达组。结论:本研究成功构建PAAD患者血液外泌体中的ceRNA调控网络,为PAAD的诊断和治疗提供确切靶点。
Objective: To construct a competitive endogenous RNA(ceRNA) regulatory network in blood exosomes of patients with pancreatic adenocarcinoma(PAAD) by using bioinformatics methods, to explore its pathogenesis. Methods: The exosome sequencing data of patients with PAAD and normal control were downloaded from the exoRBase database, and the difference analysis was performed on the expression profiles of exosome mRNA, long non-coding RNA(lncRNA), and circular RNA(circRNA) using R language. The TargetScan and miRanda databases were used together to predict and differentially express mRNA-bound microRNA(miRNA). The miRcode database was used to predict miRNA binding to differentially expressed lncRNA and the starBase database was used to predict miRNA binding to the circRNA of the difference table. Relevant mRNA, circRNA, lncRNA, and their corresponding miRNA prediction data were imported into Cytoscape software to visualize the ceRNA network. Enrichment of gene ontology(GO) and Kyoto encyclopedia of genes and genomes(KEGG) was performed using the R language. The Hub gene was identified using the CytoHubba plug-in, and the expression profile interaction analysis database, GEPIA, was used to analyze the gene sequencing expression data of PAAD and normal samples. The expression levels of the first 10 Hub genes in patients with PAAD and normal controls were compared, and the survival curve of the corresponding Hub genes was drawn. Results: 120 differentially expressed m RNA, 48 differentially expressed lncRNA, and 23differentially expressed circRNA were screened out. A ceRNA network consisting of 19 mRNA nodes, 12 lncRNA nodes, 3circRNA nodes, and 31 miRNA nodes was constructed using Cytoscape software. GO enrichment analysis showed that mRNA was mainly enriched in the ficollin-1-rich-granule and histone deacetylase binding. KEGG enrichment analysis showed that differentially expressed mRNA in the regulatory network were mainly enriched in the adherens junction pathway, colorectal cancer pathway, and neurotrophin signaling p
作者
朱康乐
许李俊
王崇宇
王庆庆
ZHU Kangle;XU Lijun;WANG Chongyu;WANG Qingqing(Department of Medicine,Xinglin College,Nantong University,Nantong 226007;Department of General Surgery,the Affiliated Hospital of Nantong University)
出处
《南通大学学报（医学版）》
2022年第3期239-243,共5页
Journal of Nantong University(Medical sciences)
基金
江苏省大学生创新创业训练计划项目(202013993009Y)
江苏省研究生科研与实践创新计划项目(SJCX22-1631)
南通大学附属医院首届医学教育家培养工程。
关键词
胰腺癌
外泌体
竞争性内源核糖核酸
调控网络
富集分析
pancreatic adenocarcinoma
exosomes
competing endogenous ribonucleic acid
regulatory networks
enrichment analysis
