肾透明细胞癌基因拷贝数变异与mRNA差异表达的整合分析  

Integrative Bioinformatics Analysis of DNA Copy Number Variation and Differentially Expressed Genes Involved in Kidney Clear Cell Carcinoma

作　　者：朱进 丁晓飞[2] 周军[2] 陈光 Zhu Jin;Ding Xiaofei;Zhou Jun(Department of Surgical Oncology,Municipal Hospital Affiliated to Medical School of Taizhou University,Zhejiang 318000,China)

机构地区：[1]台州学院医学院附属市立医院,318000 [2]台州学院医学院,318000

出　　处：《医学研究杂志》2020年第2期81-86,共6页Journal of Medical Research

基　　金：浙江省自然科学基金资助项目(面上项目)(LY16H310006)。

摘　　要：目的在整个基因组范围内整合分析染色体变异与基因差异表达来探讨肾透明细胞癌的发病机制。方法从肿瘤基因组图谱(The Cancer Genome Atlas,TCGA)数据库下载肾透明细胞癌DNA拷贝数和mRNA表达数据,使用GISTIC进行拷贝数变异分析;使用R软件包edgeR进行基因差异表达分析;并对差异表达基因进行KEGG和GO通路富集分析。结果GISTIC发现381个拷贝数扩增,1287个缺失;R语言包发现1171个基因mRNA表达上调,567个基因mRNA表达下调;相关性检测发现13个拷贝数增加的基因表达上调,17个拷贝数降低的基因表达下调。GO和KEGG分析发现这些差异基因主要富集在多个致癌基因,且参与肿瘤的发生、发展及免疫逃逸的信号转导。结论整合分析相关拷贝数变异和基因表达差异,能为肾透明细胞癌的诊断和治疗提供分子标记和靶点。Objective To investigate the pathogenesis of kidney clear cell carcinoma(KIRC)via the analysis of DNAcopy number variation(CNV)and mRNA expression profiles.Methods Data of DNA copy number and mRNA expression profiles of KIRC were downloaded from The Cancer Genome Atlas(TCGA).The CNV regions were identified using the bioinformatics tool GISTIC.The differentially expressed genes in these regions were identified using the edgeR of R package,then subjected to Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis.Results GISTIC analysis identified 381 significant copy number amplification regions and 1287 deletion in KIRC.R package and BH exacted test found that 1171 genes mRNA highly expressed in KIRC,while 567 genes mRNA levels were decreased in KIRC compared to normal samples.Furthermore,correlation test showed that 13 genes mRNA levelswere unregulated with DNA copy number amplification,while 17 genes mRNA levelswere downregulated with the decrease of DNA copy number.KEGG and Go enrichment analysis revealed that most of these genes were involved in tumorigenesis.Conclusion Integrative bioinformatics analysis of CNV and mRNA expression profiles can identify genes involved in tumor pathogenesis and give a novel therapeutic target of kidney cancer.

关 键 词：肾透明细胞癌 癌症和肿瘤基因图谱 拷贝数变异 MRNA 

分 类 号：R737.1[医药卫生—肿瘤]