转录组测序分析GATAD2A在食管鳞状细胞癌中的作用机制  

Mechanism of GATAD2A in esophageal squamous cell carcinoma by transcriptome sequencing analysis

作　　者：李强明 白玉[2] 张静[3] 姚文健 王建军 魏立 LI Qiangming;BAI Yu;ZHANG Jing;YAO Wenjian;WANG Jianjun;WEI Li(Department of Thoracic Surgery,Henan Provincial People's Hospital,Zhengzhou University People's Hospital,Zhengzhou,Henan 450003,China;Pathology Teaching and Research Of fice,School of Basic Medical Sciences of Xinciang Medical University,Xinziang,Henan 453000,China;Operation Center,the First Affiliated Hospital of Zhengzhou University,Zhengzhou,Henan 450003,China)

机构地区：[1]河南省人民医院胸外科郑州大学人民医院,河南郑州450003 [2]新乡医学院基础医学院病理学教研室,河南新乡453000 [3]郑州大学第一附属医院中心手术部,河南郑州450003

出　　处：《中华实用诊断与治疗杂志》2025年第1期1-8,共8页Journal of Chinese Practical Diagnosis and Therapy

基　　金：河南省科技攻关计划项目(242102310139);河南省医学科技攻关计划省部共建项目(SBGJ202302009)。

摘　　要：目的 采用生物信息学方法筛选GATAD2A调控食管鳞状细胞癌(ESCC)的关键基因和通路,探讨GATAD2A在ESCC中作用的分子机制。方法 取对数生长期ESCC细胞株KYSE-150,分为敲低组(转染GATAD2A-siRNA)和对照组(转染NC-siRNA)。转染60 h取2组细胞,采用Trizol法提取总RNA,采用转录组测序(RNA-Seq)技术检测mRNA表达,应用R软件DEGseq包筛选差异表达基因,应用R软件的clusterProfiler包对差异表达基因进行基因本体(GO)功能注释分析、京都基因与基因组百科全书(KEGG)通路富集分析、基因集富集分析(GSEA)。应用STRING 12.0在线软件构建差异表达基因的蛋白互作网络(PPI),使用Cytoscape软件的MCODE插件对PPI网络进行聚类分析,筛选出得分最高的关键子网络,使用CytoHubba插件对关键子网络中的基因进行节点度计算,筛选PPI网络核心位置的节点基因,并对节点基因进行GO/KEGG分析。自TCGA数据库收集82例ESCC患者癌组织PPI分析中节点度≥10的基因表达以及预后数据,以基因表达的中位数为阈值将ESCC患者分为高、低表达组,比较高表达组与低表达组的总生存期,筛选出影响预后的基因作为关键基因。自TCGA数据库选取ESCC患者癌组织GATAD2A及关键基因的表达数据,采用Spearman法分析GATAD2A与关键基因表达的相关性。自GTEx数据库收集正常食管组织关键基因的表达数据,与ESCC组织进行比较。结果 (1)敲低组与对照组差异表达基因有888个。与对照组比较,敲低组表达上调基因275个,表达下调基因613个。(2)GO功能注释分析结果显示,前10个差异表达的基因主要参与细胞外刺激反应、细胞因子生成的正向调控、上皮细胞增殖等生物学过程。KEGG富集分析结果显示,前10个差异表达的基因主要在人乳头瘤病毒感染、PI3K/Akt信号通路、癌症相关miRNA等通路中富集。GSEA分析结果显示,差异表达基因主要在DNA合成与复制、细胞周期相关通路中富集Objective To screen the key genes and pathways of esophageal squamous cell carcinoma(ESCC) regulated by GATAD2A with bioinformatics methods,and to explore the molecular mechanism of GATAD2A in ESCC.Methods The ESCC cell line KYSE-150cells in logarithmic growth phase were divided into knockdown group(transfected with GATAD2A-siRNA)and the control group(transfected with NC-siRNA).After 60hof transfection,cells were collected from both groups,and the total RNA was extracted with Trizol method.The mRNA expression was detected with RNA sequencing(RNA-Seq)technique.The differentially expressed genes were screened with R software's DEGseq package.The Gene Ontology(GO)functional annotation analysis,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis,and Gene Set Enrichment Analysis(GSEA)of differentially expressed genes were conducted with R software's clusterProfiler package.The protein-protein interaction(PPI)network of differentially expressed genes was constructed with STRING 12.0online software.The cluster analysis of the PPI network was conducted with Cytoscape software's MCODE plugin and the highest scoring key subnetwork was screened.The node degree of genes in the key subnetwork was calculated with CytoHubba plugin.The hub genes in the core positions of PPI network were screened and the GO/KEGG analysis was performed on the hub genes.The gene expression and prognostic data with a node degree≥10of PPI analysis were collected from 82ESCC patients in TCGA database.The ESCC patients were divided into the high-and low-expression groups based on the median of gene expression as threshold.The overall survival was compared between the high-and low-expression groups,and the genes affecting prognosis were screened as key genes.The expression data of GATAD2Aand key genes of cancer tissue were selected from ESCC patients in TCGA database,and the correlation between GATAD2Aand key genes expressions was analyzed with Spearman method.The expression data of key genes of normal esophageal tissues were coll

关 键 词：食管鳞状细胞癌 KYSE-150细胞 GATAD2A 转录组测序 信号通路 

分 类 号：R735.1[医药卫生—肿瘤]