基于GEO数据库芯片筛选胃肠间质瘤和胃平滑肌瘤差异基因及生物信息学分析  

Differential analysis of gene expression profiles and bioinformatics between gastrointestinal stromal tumor and gastric leiomyoma based on GEO database

作　　者：邓薇[1] 翟育豪 郑智[1] 尹杰[1] 刘小野[1] 白志刚[1] 张军[1] Deng Wei;Zhai Yuhao;Zheng Zhi;Yin Jie;Liu Xiaoye;Bai Zhigang;Zhang Jun(Department of General Surgery,Beijing Friendship Hospital,Capital Medical University,Beijing 100035,China)

机构地区：[1]首都医科大学附属北京友谊医院普外科,北京100035

出　　处：《肿瘤综合治疗电子杂志》2022年第2期74-81,共8页Journal of Multidisciplinary Cancer Management(Electronic Version)

基　　金：北京市科委重大项目资金资助(D171100006517003);北京市医院管理局培育计划项目(PX2020001);北京友谊医院院启动课题(Y2018-3);首都医科大学2021年教育教学改革研究课题(2021JYY106)。

摘　　要：目的本研究旨在探索胃肠间质瘤和胃平滑肌瘤基因层面的差异,为今后诊断和治疗提供帮助。方法通过基因表达综合(Gene Expression Omnibus,GEO)数据库,调用GSE63453的相关数据,比较胃肠间质瘤和胃平滑肌瘤标本的miRNA表达差异,选择差异miRNA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 Genom,KEGG)分析。通过差异表达的miRNA进行靶基因预测,明确靶基因表型差异,并对通路表达进行GO和KEGG分析。建立蛋白质相互作用(protein-protein interaction,PPI)网络图,运用Cytoscape进行Hub基因筛选。并通过筛选临床样本,进行定量聚合酶链反应验证。对已筛选出的靶基因与免疫相关基因取交集,筛选出明确的免疫相关基因表达,明确二者在免疫方面的差异。结果本研究共筛选出包括hsa-miR-133a-3p在内的12种差异miRNA,通过GO和KEGG两种生物信息学分析方法发现了胃肠间质瘤和胃平滑肌瘤在生物功能学方面的差异,并通过数据库发现了在这两类肿瘤中可能存在差异的靶基因,建立PPI网络图,筛选出了包括PIK3CA和BDNF在内的10个Hub基因,并通过临床样本的检测对关键基因进行了外部验证,最终发现了胃肠间质瘤和胃平滑肌瘤间的差异基因。结论胃肠间质瘤和胃平滑肌瘤存在基因层面差异,可以对两类肿瘤进行鉴别和治疗。Objective Gastrointestinal stromal tumor(GIST)is a kind of potential malignant tumor.Compared with gastric leiomyoma,GIST have worse prognosis.The identification of tumor is still depending on the pathological detection.The purpose of this study is to explore the genetic differences between the two types of tumors and provide help for future diagnosis and treatment.Method Through Gene Expression Omnibus(GEO)database,GSE63453 were invoked to compare miRNA expression differences between GIST and gastric leiomyoma specimens,and the differential miRNA was selected for GO and KEGG analysis.Target genes were predicted by differentially expressed miRNAs,phenotypic differences of target genes were identified,and pathway expression was analyzed by GO and KEGG.protein-protein interaction(PPI)network were built and we used the Cytoscape to select the Hub genes,and the clinical samples were screened for quantitative polymerase chain reaction(qPCR)validation.The intersection of the target genes and immune-related genes was selected to screen out specific immune-related gene expression,and the differences between the two in immunity were identified.Result In this study,a total of 12 different miRNAs including hsa-miR-133a-3p were screened out,and the difference in biological function between GIST and gastric leiomyoma was found by two bioinformatics analysis methods including GO and KEGG.Through the databases,the target genes were obtained.PPI network was established,and 10 Hub genes including PIK3CA and BDNF were screened out.The Hub genes were verified by qPCR,and finally the differences between the two types of tumors were found.Conclusion There are genetic differences between GIST and gastric leiomyoma,and we can differentiate and treat them by that.

关 键 词：胃肠间质瘤 胃平滑肌瘤 生物信息学 差异表达基因 

分 类 号：R735[医药卫生—肿瘤]