南方医科大学学报

南方医科大学学报 ›› 2024, Vol. 44 ›› Issue (3): 605-616.doi: 10.12122/j.issn.1673-4254.2024.03.23

• • 上一篇    

基于GEO数据库筛选胃癌差异表达基因及其功能和通路富集分析

梁一豪，赖颖君，袁燕文，袁 炜，张锡波，张拔山，卢志锋   

  1. 南方医科大学第十附属医院（东莞市人民医院）检验科，消化内科，病理科，广东 东莞 523059
  • 出版日期:2024-03-20 发布日期:2024-04-03

Screening of differentially expressed genes in gastric cancer based on GEO database and function and pathway enrichment analysis

LIANG Yihao, LAI Yingjun, YUAN Yanwen, YUAN Wei, ZHANG Xibo, ZHANG Bashan, LU Zhifeng   

  1. Department of Clinical Laboratory, Department of Gastroenterology, Department of Pathology, Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan 523059, China
  • Online:2024-03-20 Published:2024-04-03

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摘要： 目的 基于基因表达数据库（GEO）运用生物信息学方法挖掘胃癌诊断和预后相关的核心基因，筛选参与胃癌发生发展的分子靶标。方法 从GEO数据库中下载胃癌基因芯片数据GSE118916、GSE54129和GSE79973，筛选差异表达基因（DEGs）并进行分子功能和信号通路的富集分析，构建蛋白质互作网络（PPI），根据网络节点和位置筛选出核心基因，利用癌症基因图谱（TCGA）中胃腺癌（STAD）的全基因组测序数据对核心基因进行表达水平和诊断预后的验证分析，最后通过qRT-PCR检测核心基因在不同胃癌细胞株中的表达水平。结果 共筛选出77个DEGs，主要位于细胞外基质（ECM）与基底膜，具有氧化还原酶和ECM受体配体活性，参与机体消化和激素代谢等生物学过程，与胃酸分泌、视黄醇和激素代谢等信号通路相关。共获得9个核心基因，其中SPARC、TIMP1、THBS2、COL6A3和THY1在胃癌中表达上调（P<0.05）；而TFF1、GKN1、TFF2、PGC在胃癌中下调（P<0.05）。生存预后分析显示，SPARC、TIMP1、THBS2、COL6A3、TFF2、THY1的异常表达与胃癌患者的生存时间显著相关；ROC曲线显示，TIMP1、SPARC、THY1、THBS2对胃癌有较高的诊断价值；在胃癌患者的病理组织中SPARC、TIMP1、THBS2、COL6A3的高表达得到验证；qRT-PCR检测发现，核心基因在不同的胃癌细胞株中不尽相同，但表达趋势基本符合。结论 SPARC、TIMP1、THBS2等DEGs可能与胃癌的发生发展有关，可能作为潜在的候选分子标志物，用于胃癌的早期诊断和预后判断。

关键词: 胃癌；基因芯片；生物信息学分析；差异表达基因；分子标志物

Abstract: Objective To explore the core genes related to the diagnosis and prognosis of gastric cancer (GC) based on Gene Expression Omnibus (GEO) database and screen the molecular targets involved in the occurrence and development of GC. Methods GC microarray data GSE118916, GSE54129 and GSE79973 were downloaded from GEO database, and the differentially expressed genes (DEGs) were screened. Enrichment analysis of the signaling pathways and molecular functions were preformed and protein-protein interaction networks (PPI) were constructed to identify the hub genes, whose expression levels and diagnostic and prognostic values were verifies based on gastric adenocarcinoma data from TCGA. The expression levels of these core genes were also detected in different GC cell lines using qRT- PCR. Results Seventy-seven DEGs were identified, which encodes proteins located mainly in the extracellular matrix and basement membrane with activities of oxidoreductase and extracellular matrix receptor and ligand, involving the biological processes of digestion and hormone metabolism and the signaling pathways in retinol metabolism and gastric acid secretion. Nine hub genes were obtained, among which SPARC, TIMP1, THBS2, COL6A3 and THY1 were significantly up- regulated and TFF1, GKN1, TFF2 and PGC were significantly down-regulated in GC. The abnormal expressions of SPARC, TIMP1, THBS2, COL6A3, TFF2 and THY1 were significantly correlated with the survival time of GC patients. ROC curve analysis showed that aberrant expression of TIMP1, SPARC, THY1 and THBS2 had high diagnostic value for GC. High expressions of SPARC, TIMP1, THBS2 and COL6A3 were detected in GC tissues. In the GC cell lines, qRT- PCR revealed different expression patterns of these hub genes, but their expressions were largely consistent with those found in bioinformatics analyses. Conclusion SPARC, TIMP1, THBS2 and other DEGs are probably involved in GC occurrence and progression and may serve as potential candidate molecular markers for early diagnosis and prognostic evaluation of GC.

Key words: gastric cancer; microarray; bioinformatics analysis; differentially expressed genes; molecular markers