肝细胞癌不良预后潜在基因的生物信息学分析

Identification of Potential Core Genes with Poor Prognosis in Hepatocellular Carcinoma by Bioinformatical Analysis

肝细胞癌(hepatocellular carcinoma,HCC)是我国致死率第二的癌症,其发病机制复杂。为了寻找影响肝细胞癌不良预后的核心基因,从GEO数据库中找到了3个基因芯片(GSE13471、GSE29721和GSE6222),这3个基因芯片数据集中包括了24例肝细胞癌组织样本和17例正常癌旁组织样本。利用GEO2R工具找到癌症组织与正常癌旁组织间的差异表达基因(differentially expressed genes,DEGs),发现共有65个差异基因在这3个基因芯片中共同表达,其中4个基因为下调基因,61个基因为上调基因。通过R语言编程实现差异表达基因的京都基因与基因组百科全书(KEGG)通路分析和基因本体(GO)功能注释。然后通过互作基因检索数据库检索工具分析这些差异表达基因的蛋白质-蛋白质相互关系(protein-protein interaction,PPI),并通过Cytoscape软件进行可视化。利用Cytoscape软件中的Cytohubba包筛选65个差异表达基因中连通度最高的8个基因并定义为枢纽基因(hub基因),接着通过Kaplan-Meier生存分析工具对筛选出的8个枢纽基因进行生存分析。最后,找出3个与肝细胞癌不良预后高度相关的关键基因(CCNB1、CDK1和TOP2A)。在基因表达谱交互分析数据库中验证发现,与正常样本相比,3个关键基因在肝细胞癌患者中均为高表达。对KEGG通路的重分析发现,其中两个关键核心基因(CCNB1、CDK1)显著富集在p53信号通路、孕酮介导的卵母细胞成熟、细胞周期、卵母细胞减数分裂、细胞衰老和人类免疫缺陷病毒这些与癌症相关的通路上。这个发现有助于更深入地了解肝细胞癌的病理生理机制,为后续研究肝细胞癌药物治疗的基因靶点提供依据。

Hepatocellular carcinoma(HCC)is the second deadliest cancer in China and its pathogenesis is complex.In order to seek out the core genes for poor prognosis of HCC,three gene expression profiles(GSE13471,GSE29721 and GSE6222)were found in GEO database.There were 24 HCC tissues and 17 Normal paracancer tissue in the three gene expression profiles.The differentially expressed genes(DEGs)between HCC tissues and normal tissues were identified by the GEO2 R online tool.There were total of 65 genes were consistently expressed in the three profiles,including 4 down-regulated genes and 61 up-regulated genes.The Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis and Gene Ontology(GO)functional annotation of DEGs was achieved by R software.Then protein-protein interaction(PPI)of these DEGs was analyzed through the Search Tool for the Retrieval of Interacting Genes(STRING)database and visualized by Cytoscape software.Then,eight hub genes had been identified on Cytohubba package in Cytoscape software and the pool prognostic value of eight DEGs expression in HCC patients were evaluated through the Kaplan-Meier plotter survival analysis tool.Furthermore,we identified three DEGs(CCNB1,CDK1 and TOP2 A)that were highly correlated with poor prognosis of HCC.For validation in Gene Expression Profiling Interactive Analysis(GEPIA),all 3 hub genes were proved to be over-expressed in HCC samples compared to normal samples.Re-analysis of KEGG pathway revealed that two core genes(CCNB1,CDK1)were mainly enriched in p53 signaling pathway,progesterone-mediated oocyte maturation,cell cycle,oocyte meiosis,cellular senescence and human immunodeficiency virus,which were cancer-related pathways.This paper is helpful for us to have a deeper understanding of the pathophysiological mechanism of HCC and provide basis for the gene targets of subsequent drug therapy for HCC.