胃腺癌的关键基因及通路的生物信息学分析

Bioinformatics analysis of key genes and pathways in gastric adenocarcinoma

目的通过生物信息学方法探索胃腺癌的关键基因及相关通路并进行初步验证,为确定胃腺癌相关的新型生物标志物提供候选基因。方法分析GSE103236、GSE79973和GSE54129数据集以获得差异表达基因,进行基因本体论(GO)分析和京都基因与基因组百科全书(KEGG)分析,通过STRING数据库构建蛋白质-蛋白质相互作用(PPI)网络,通过基因集富集分析(GSEA)GSE118916数据集以验证生物学过程。使用癌症基因组图谱(TCGA)胃腺癌数据库分析这些关键基因与预后的关联。通过在MKN45胃腺癌细胞系中加入5-氟脲嘧啶(5-Fu)以探索上述关键基因在化疗后的变化。结果从GSE103236、GSE79973和GSE54129分别鉴定出289、576和763个差异表达基因,其共有的差异表达基因有205个。这些差异基因主要富集在消化过程和细胞外基质形成等生物学过程和细胞色素P450对异生物质的代谢和药物代谢-细胞色素P450等通路上。通过Cytoscape的CytoHubba插件获得了9个关键基因,分别是Ⅰ型胶原α1亚基(COL1A1)、Ⅱ型胶原α1亚基(COL1A2)、Ⅳ型胶原α1亚基(COL4A1)、Ⅵ型胶原α3亚基(COL6A3)、血小板反应蛋白1(THBS1)、血小板反应蛋白2(THBS2)、双糖链蛋白多糖(BGN)、纤维连接蛋白1(FN1)和半胱氨酸的分泌性酸性蛋白(SPARC)。GSEA分析GSE118916数据集,发现与胃腺癌相关的主要富集通路是细胞外基质-受体相互作用通路和药物代谢-细胞色素P450通路等通路,与KEGG分析的结果基本一致。且COL1A1、COL4A1、THBS1、FN1和SPARC与预后显著相关。在MKN45细胞系中加入5-FU后,COL1A1、COL4A1、THBS1、FN1和SPARC mRNA表达水平均降低,与前述结果一致。结论本研究筛选出COL1A1、COL4A1、THBS1、FN1和SPARC等关键基因,这些关键基因有望成为胃腺癌发生与发展的新型预后生物标志物。

Objective To explore the key genes and related pathways of gastric adenocarcinoma by bioinformatics analysis.Methods GSE103236,GSE79973 and GSE54129 datasets were analyzed to obtain differentially expressed genes(DEGs),gene ontology(GO)analysis and Kyoto encyclopedia of genes and genomes(KEGG)analysis were performed,and protein-protein interaction(PPI)network was constructed through STRING database.GSE118916 was analyzed by GSEA enrichment to verify biological processes.The Cancer Genome Atlas(TCGA)gastric adenocarcinoma database was used to analyze the prognostic association of these key genes.Human gastric adenocarcinoma MKN45 cells were treated with 5-FU to verify changes of these key genes.Results A total of 289,576 and 763 differentially expressed genes were identified from GSE103236,GSE79973 and GSE54129 datasets respectively,and 205 DEGs were commonly identified in three datases.The DEGs were mainly enriched in biological processes such as digestion and extracellular matrix formation,as well as in the metabolism of cytochrome P450 and drug metabolism-cytochrome P450 pathways.Nine key genes(COL1A1,COL1A2,THBS2,COL6A3,COL4A1,BGN,THBS1,FN1 and SPARC)were identified by CytoHubba of Cytoscape.GSEA enrichment analysis of GSE118916 data set showed that the main enrichment pathways associated with gastric adenocarcinoma were ECM-receptor interaction pathway and drug metabolism-cytochrome P450 pathway,which were basically consistent with the results of KEGG analysis.COL1A1,COL4A1,THBS1,FN1 and SPARC were significantly associated with prognosis.The transcription of COL1A1,COL4A1,THBS1,FN1 and SPARC was significantly decreased after the adding 5-FU to MKN45 cells,which was consistent with the above results.Conclusion In this study,key genes and pathways such as COL1A1,COL4A1,THBS1,FN1 and SPARC have been screened out,and these key genes are expected to be novel prognostic biomarkers related to the occurrence and progression of gastric adenocarcinoma.