TCGA数据库4种消化系统癌症分子特征的比较  

Comparison of molecular characteristics of four digestive cancers in TCGA database

作　　者：刘菲 袁锐 陈世龙[1] 王永翠(指导) LIU Fei;YUAN Rui;CHEN Shilong;WANG Yongcui(Key Laboratory of Crop Molecular Breeding of Qinghai Province,Northwest Institute of Plateau Biology,Chinese Academy of Sciences,Xining 810008,China)

机构地区：[1]中国科学院西北高原生物研究所青海省作物分子育种重点实验室,西宁810008 [2]中国科学院大学,北京100049

出　　处：《中国免疫学杂志》2022年第18期2252-2258,共7页Chinese Journal of Immunology

基　　金：青海省科技计划项目(2020-ZJ-719)资助。

摘　　要：目的:探索4种消化系统癌症(DSCs)分子特征的异同及分子特征同临床基本特征的关系。方法:基于生物信息学方法从TCGA数据库中获取食管癌(ESCA)、胃癌(STAD)、直肠癌(READ)、结肠癌(COAD)4种DSCs的分子特征,包括基因突变、拷贝数变异、基因表达以及甲基化,结合MIF算法、差异分析筛选出癌症驱动基因、差异甲基化基因(DMGs)以及差异表达基因(DEGs),并利用富集分析、生存分析、相关性分析比较4种癌症类型中分子特征的异同,进一步探索分子特征同临床基本特征的关系。结果:4种癌症类型具有相似的分子特征,包括:突变频率与基因表达、甲基化水平相关性很低,线性关系均不明显;MaxMIF软件获得的30个癌症驱动基因中均仅有少数几个基因具有预后效果,包括ESCA 2个、STAD 2个、READ 1个、COAD 1个;拷贝数变化数据在癌症组织样本和正常组织样本中的分布并不均匀;DEGs中仅有少部分基因具有预后效果,包括食管癌(29/829)、胃癌(0/394)、直肠癌(71/606)、结肠癌(50/591),并且KEGG通路均富集于“神经活性的配体-受体相互作用”。另外,4种癌症类型之间具有不同的癌症驱动基因、具有预后效果的DEGs,以及DMGs。结论:经分析得到4种DSCs分子特征的异同点有助于了解整个DSCs,并有望为深入理解DSCs的分子特征及相应的分子靶向治疗方案的设计提供有效的依据。Objective:To explore the similarities and differences of the molecular characteristics of the four types of digestive cancers(DSCs),and the relationship between the molecular characteristics and the basic clinical characteristics.Methods:Based on the bioinformatics methods,we obtained the molecular characteristics of four types of DSCs from The Cancer Genome Atlas(TCGA)program. The four types of digestive system cancers contained esophageal cancer(ESCA),stomach cancer(STAD),rectal cancer(READ)and colon cancer(COAD),and the molecular characteristics included gene mutation,copy number variation,gene expression,and methylation. Cancer driven genes,differential methylation genes(DMGs),and differential expression genes(DEGs)were extracted by using MIF algorithms and differential analysis. For the purpose of further explore the relationship between molecular characteristics and basic clinical characteristics,we employed enrichment analysis,survival analysis,and correlation analysis to compare the molecular characteristics of four types of cancers.Results:The four cancer types had similar molecular characteristics. The correlation between mutation rate and the level of gene expression,the level of methylation were very low,respectively,so the linear relationship was not obvious;only a few of the cancer driver genes obtained by the MaxMIF software had good prognostic characteristics,including two genes of COAD,two genes of STAD,one gene of READ,and one gene of COAD;the data of copy number variations were distributed unevenly in cancer tissue samples and normal tissue samples;only a few genes in DEGs had good prognostic characteristics,including 29/829 in esophageal cancer,70/394 in stomach cancer,71/606 in rectal cancer,and 50/591 in colon cancer,further,the KEGG pathway of four cancer types were all enriched in "neuroactive ligand-receptor interaction". In addition,the four cancer types had different types of cancer driver genes,DMGs,and DEGs which had good prognostic characteristics.Conclusion:The similarities and diff

关 键 词：消化系统癌症 TCGA数据库 癌症驱动基因 差异表达基因 差异甲基化基因 

分 类 号：R966[医药卫生—药理学]