基于生物信息学筛选并综合分析肝细胞癌关键基因

Screening and comprehensive analysis of key genes in liver hepatocellular carcinoma based on bioinformatics

目的:通过生物信息技术,检索肝细胞癌(LIHC)相关基因及对相关基因进行深入分析。方法:利用基因数据表达库(GEO)检索“LIHC“词条,下载GSE109903芯片数据,通过生信分析筛选对照组及组差异表达基因,对所获得差异表达基因进行GO功能分析、KEGG通路分析、差异基因特征表达分析并作可视化处理;蛋白互作网络分析并作可视化处理,筛选与LIHC相关性较强的核心基因EEF1A1与HK2。通过GEPIA、Kaplan-Meier plotter、GeneMANIA、Timer2.0数据库进行分析,明确LIHC关键基因的差异表达、预后价值和免疫细胞浸润情况。结果:共筛选到1 059个差异表达基因,包括637个上调基因、872个下调基因;功能分析显示差异基因主要参与以DNA为模版的正向转录调控、核体功能、核染色质功能、RNA结合等过程;通路分析显示差异基因参与系统性红斑狼疮、酒精中毒等疾病通路与RNA聚合酶Ⅰ启动子开放通路等;差异基因特征表达分析显示与差异基因特征相似的药物主要有CDC抑制剂、前列腺素、血清素受体拮抗剂、BAF转录阻遏抑制剂、酪氨酸磷酸酶抑制剂等;蛋白互作网络分析显示与LIHC相关的基因主要有EEF1A1、HK2、FAM38A、LAMB3等;选取EEF1A1与HK2两个基因进一步进行GEPIA分析,分析结果显示EEF1A1与HK2 mRNA在LIHC癌组织中表达较正常组织中高,并且与LIHC患者的病理分期和总生存率、无病生存率呈显著相关;EEF1A1与HK2可能是LIHC患者生存的潜在预后生物标志物;此外,差异表达的EEF1A1与HK2功能主要分别与翻译因子活性、分子伴侣介导的自噬和碳水化合物分解代谢过程、嘌呤核苷二磷酸代谢过程有关;免疫细胞浸润情况显示EEF1A1与HK2的表达与多种免疫细胞的浸润显著相关,包括6种类型的免疫细胞:CD4^(+)T细胞、巨噬细胞、中性粒细胞、B细胞、CD8^(+)T细胞和树突状细胞。结论:通过筛选差异表达基因,明确在LIHC发展过程中关键基因,为LIHC患者生存筛选潜在的预后生物标志物,同时本研究为LIHC临床治疗提供新思路和方案。

Objective:To search and analyze the related genes of liver hepatocellular carcinoma(LIHC)by using bioinformatics technology. Methods:Gene expression omnibus(GEO)was used to retrieve the entry of "Liver hepatocellular carcinoma",and GSE109903 chip data was downloaded. The differentially expressed genes in the control group and liver hepatocellular carcinoma group were screened by bioinformatics analysis. GO enrichment analysis,KEGG pathway analysis,differential gene expression analysis and visualization processing were performed for the differentially expressed genes;Protein interaction network analysis and visualization processing were used to screen core genes EEF1A1 and HK2 with strong correlation with liver hepatocellular carcinoma. GEPIA,Kaplan-Meier plotter,GeneMANIA and Timer 2.0 databases were used to analyze the differential expression,prognostic value and immune cell infiltration of key genes in LIHC. Results:A total of 1 059 differentially expressed genes were screened,including 637 up-regulated genes and 872 downregulated genes. Functional analysis showed that differentially expressed genes were mainly involved in the process of positive transcription regulation,nucleosome function,chromatin function and RNA binding. Pathway analysis showed that differentially expressed genes were involved in systemic lupus erythematosus,alcoholism and RNA polymerase I promoter opening pathway. The analysis of differential gene expression showed that the drugs with similar gene characteristics were mainly CDC inhibitors,prostaglandins,serotonin receptor antagonists,BAF transcriptional repression inhibitors,tyrosine phosphatase inhibitors,etc;Protein interaction network analysis showed that the main genes associated with LIHC were EEF1A1,HK2,FAM38A and LAMB3;EEF1A1 and HK2 genes were further analyzed by GEPIA. The results showed that the expression of EEF1A1 and HK2 mRNA in LIHC tissues was higher than that in normal tissues,and was significantly correlated with the pathological stage,overall survival rate and disease-free survival rate of LIHC patients. EEF1A1and HK2 may be potential prognostic biomarkers for LIHC patients. In addition,the functions of EEF1A1 and HK2 were mainly related to translation factor activity,molecular chaperone mediated autophagy and carbohydrate catabolism,and purine nucleoside diphosphate metabolism,respectively. Immunocyte infiltration showed that the expression of EEF1A1 and HK2 was significantly correlated with the infiltration of a variety of immune cells,including six types of immune cells:CD4^(+)T cells,macrophages,neutrophils,B cells,CD8^(+)T cells and dendritic cells. Conclusion:By screening differentially expressed genes,we can identify the key genes in the development of liver hepatocellular carcinoma,and screen potential prognostic biomarkers for the survival of patients with liver hepatocellular carcinoma. At the same time,this study provides new ideas and programs for clinical treatment of liver hepatocellular carcinoma.