利用加权基因共表网络识别肝细胞癌干细胞相关基因的研究  

Identification of genes related to the characteristics of cancer stem cells in hepatocellular carcinoma by weighted gene co-expression network analysis

作　　者：徐贺龙 李燕 任程晖 宋晓静 张磊[2,3,4,5,6] 李汛 XU Helong;LI yan;REN Chenghui;SONG Xiaojing;ZHANG Lei;LI Xun(The First Clinical Medical College,Lanzhou University,Lanzhou 730000,P.R.China;Gansu Province Institute of Hepatopancreatobiliary,Lanzhou 730000,P.R.China;Gansu Province Key Laboratory of Biotherapy and Regenerative Medicine,Lanzhou 730000,P.R.China;Fifth Department of General Surgery,The First Hospital of Lanzhou University,Lanzhou 730000,P.R.China;Gansu Province International Science and Technology Cooperation Base of Prevention and Control of Tumors with High Incidence and Major Chronic Diseases,Lanzhou 730000,P.R.China;Gansu Province Liver Center of Integrated Traditional Chinese and West Medicine,Lanzhou 730000,P.R.China)

机构地区：[1]兰州大学第一临床医学院,兰州730000 [2]甘肃省肝胆胰外科研究所,兰州730000 [3]甘肃省生物治疗与再生医学重点实验室,兰州730000 [4]兰州大学第一医院普外五科,兰州730000 [5]高发肿瘤及重大慢病防控甘肃省国际科技合作基地,兰州730000 [6]甘肃省中西医结合肝病治疗中心,兰州730000

出　　处：《中国普外基础与临床杂志》2020年第5期560-568,共9页Chinese Journal of Bases and Clinics In General Surgery

基　　金：国家自然科学基金面上项目(项目编号:31570509);甘肃省科技重大专项项目(项目编号:1602FKDA001);甘肃省卫生行业计划项目(项目编号:GSWSKY2016-27)。

摘　　要：目的通过加权基因共表达网络(WGCNA)方法研究肝细胞癌(HCC)中肝癌干细胞(LSCS)相关基因表达及其与预后的相关性。方法首先从公共数据库癌症基因组图谱(TCGA)中下载HCC转录组测序(RNA-seq)及临床数据,下载并整理基于mRNA表达的肿瘤干细胞干性指数(mRNAsi)表,分析mRNAsi与肝癌病理学分级及预后的关系。然后利用WGCNA方法筛选与LSCS相关的关键模块,对关键模块基因(hub基因)进行功能注释(GO分析)及信号通路富集分析(KEGG分析),通过在线数据库STRING构建hub基因编码蛋白质相互作用(PPI)网络并筛选关键基因。最后对关键基因进行表达差异分析及表达相关性分析,利用在线数据库Kaplan-Meier plotter进行生存分析并验证。结果HCC组织中的mRNAsi值显著高于正常肝组织(P<0.001),mRNAsi与高病理学等级之间存在正相关(P=0.001),高mRNAsi组的HCC患者死亡率高于低mRNAsi组(P=0.006)。GO分析结果显示,hub基因主要参与有丝分裂、DNA复制等生物过程;KEGG分析结果显示,hub基因富集在细胞周期、DNA错配修复、卵母细胞减数分裂等信号通路,其编码蛋白质之间有很强的相互作用(P<0.001)。本研究筛选了10个与LSCS相关的关键基因(包括CCNB1、CDC20、CDCA8、NDC80、KIF20A、CDC45、KIF15、MCM2、TTK及NCAPG),与正常肝组织样本相比,10个关键基因在HCC组织中均呈现高表达,在转录水平上也有很强的共表达关系且与肝癌患者的预后相关(P<0.05)。结论mRNAsi在HCC的发生发展中起着重要作用,基于WGCNA筛选的与LSCS相关的10个关键基因在LSCS的干性维持中发挥重要作用,有望作为抑制HCC干细胞特性的治疗靶标。Objective To explore the expression of genes related to hepatocellular carcinoma(HCC)stem cells and their prognostic correlation by using weighted gene co-expression network analysis(WGCNA).Methods Firstly,the transcriptome sequencing(RNA-seq)and clinical data of HCC were downloaded from the public database the Cancer Genome Atlas(TCGA),and the mRNA expression-based stiffness index(mRNAsi)table of cancer stem cells was downloaded and sorted out to analyze the relationship between mRNAsi and pathological grade and prognosis of HCC.The mRNAsi of HCC was downloaded and the prognostic value of mRNAsi was discussed.Then we used WGCNA to screen the key modules related to liver cancer stem cells(LSCS).Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for the functional and pathway enrichment analysis.The online database STRING was used to construct hub genes coding proteins interaction(PPI)network and screen key genes.Finally,the key genes were analyzed for expression differences and expression correlations.The online database Kaplan-Meier plotter was used for survival analysis and verified.Results mRNAsi was significantly upregulated in cancer tissues(P<0.001),and increased with the increase of pathological grade of HCC(P=0.001).The mortality rate of the higher mRNAsi group was higher than that of the lower mRNAsi group(P=0.006).GO analysis found that hub genes were mainly involved in biological processes,such as mitosis and DNA replication,and KEGG showed that hub genes were enriched in cell cycle,DNA mismatch repair,oocyte meiosis,and other signaling pathways.We screened 10 key genes(included CCNB1,CDC20,CDCA8,NDC80,KIF20 A,TTK,CDC45,KIF15,MCM2,and NCAPG)related to mRNAsi of HCC based on WGCNA.The key genes were highly expressed in the tumor samples compared to the normal samples.In addition,there was a strong interaction between proteins of these key genes(P<0.05),a strong co-expression relationship at the transcriptional level,and all related to prognosis of HCC.Conclusions mRNAsi plays an imp

关 键 词：肝细胞癌 肿瘤干细胞 加权基因共表达网络分析 干性指数 癌症基因组图谱 

分 类 号：R735.7[医药卫生—肿瘤]