非酒精性脂肪性肝炎相关肝癌关键基因的筛选及免疫浸润分析

Screening of Key Genes and Immune Infiltration Analysis of Nonalcoholic Steatohepatitis-related Hepatocellular Carcinoma

目的通过生物信息学方法探究非酒精性脂肪性肝炎(nonalcoholic steatohepatitis,NASH)进展为肝细胞癌(nonalcoholic steatohepatitis-related hepatocellular carcinoma,NASH-HCC)的关键基因,并分析其与免疫细胞浸润的关系。方法从基因表达综合(gene expression omnibus,GEO)数据库下载GSE164760数据集,利用差异表达分析获得差异基因,通过WGCNA鉴定出NASH进展为NASH-HCC的关键模块。对差异基因及关键模块取交集后获得的基因进行GO及KEGG通路富集分析,并利用STRING在线数据库及Cytoscape软件构建交集基因蛋白互作网络,进一步采用Degree算法筛选关键基因。最后通过CIBERSORT算法分析样本免疫细胞浸润情况,并对关键基因与免疫细胞的相关性进行分析。结果共筛选出93个差异表达基因和1个显著相关性WGCNA模块。对81个交集基因进行GO及KEGG通路富集分析,结果表明这些基因主要富集于代谢相关途径,如激素代谢、异生代谢、烯烃化合物代谢、药物代谢等。进一步对交集基因相互作用的蛋白进行分析,筛选出3个关键基因,即CAT、CYP2E1、GSTA1。NASH和NASH-HCC中免疫细胞浸润的比例不同,特别是CD8+T细胞、活化的NK细胞、M0巨噬细胞、静息的树突状细胞、中性粒细胞和M2巨噬细胞。免疫细胞相关性分析表明,3个关键基因均与中性粒细胞呈负相关(P<0.05)。结论CAT、CYP2E1、GSTA1是NASH进展为NASH-HCC的关键基因,可能通过调节中性粒细胞参与NASH-HCC的发生发展。

Objective To explore the key genes for the progression of nonalcoholic steatohepatitis(NASH)to nonalcoholic steatohepatitis-related hepatocellular carcinoma(NASH-HCC)by bioinformatics methods and to analyze its relationship with immune cell infiltration.Methods The dataset of GSE164760 was downloaded from GEO database.Differentially expressed genes were conducted by the difference analysis.The key module in the development of NASH into NASH-HCC was identified through WGCNA.GO and KEGG pathway enrichment analysis were conducted on the genes obtained after the intersection of differentially expressed genes and key modules.Protein-protein interaction network of the intersection genes was constructed by STRING online database and Cytoscape,and the key genes were screened by degree algorithm.Finally,the infiltration of immune cell types in each sample was calculated by the CIBERSORT algorithm,and the correlation between key genes and immune cells was analyzed.Results A total of 93 differentially expressed genes and one module with clinical significance were obtained.GO and KEGG enrichment analysis showed that the 81 intersection genes were significantly enriched in metabolism-related pathways,including hormone metabolic process,xenobiotic metabolic process,olefinic compound metabolic process,drug metabolism.We analyzed the proteins interacting with the intersection genes,and selected 3 key genes,namely CAT,CYP2E1 and GSTA1.We found that the proportions of infiltrating immune cells in NASH and NASH-HCC were different,especially in terms of CD8+T cells,activated NK cells,M0 macrophages,resting dendritic cells,neutrophils and M2 macrophages.Immune cell correlation analysis showed that 3 key genes were negatively correlated with neutrophils(P<0.05).Conclusion CAT,CYP2E1 and GSTA1 are the key genes for the progression of NASH to NASH-HCC,which may be involved in the occurrence and development of NASH-HCC by regulating neutrophils.