利用生物信息学筛查APAP诱发ALF患者外周血中的关键基因

Screening of Key Genes in Peripheral Blood of Patients with APAP-Induced ALF by Bioinformatics

从GEO数据库(https://www.ncbi.nlm.nih.gov/)下载数据集GSE80751,该数据集包含22例人体血液样本(对照组5例,ALI组5例,ALF组12例),以|Log FC|>1.5,P<0.05分别筛选出急性肝损伤(acute liver injury,ALI)组与对照组、急性肝衰竭(acute liver failure,ALF)组与对照组的差异表达基因,并分别对其进行功能富集分析和信号通路富集分析,筛选对乙酰氨基酚(acetaminophen,APAP)诱发ALF过程中的关键基因及重要通路.其次构建差异表达基因在蛋白层面的生物网络,并将网络数据导入Cytoscape实现可视化,利用Cytoscape中的插件寻找与疾病发生密切相关的功能模块及核心基因.以ALI组数据为对照,重点分析了ALF组数据,结果筛选出ALF组满足阈值要求的差异表达基因共266个,包括上调基因239个,下调基因27个,其中ALF组中特异性上调基因120个,特异性下调基因15个,且基因NAMPT在ALI组表达上调,在ALF组表达下调.ALF组差异表达基因的GO分析结果显示,上调基因主要参与细胞分化和细胞周期调控等过程,下调基因主要参与免疫反应和细胞因子介导的炎症反应等过程.KEGG通路分析结果显示,上调基因主要富集于细胞周期调控、系统性红斑狼疮、补体和凝血级联等通路,下调基因没有富集到明显通路.对比分析ALI组和ALF组所获取的疾病相关功能模块,发现p53信号通路与ALF的发生具有相关性.利用cytoHubba插件中的网络拓扑算法MCC在ALF组差异表达基因中共筛选出25个显著差异表达基因,且都表达上调,进一步验证其在发生ALF的肝组织细胞中的差异表达情况,发现NCAPG、DLGAP5、TOP2A、ASPM、NUSAP1和MKI67在ALF组血液细胞和肝细胞中都显著差异表达.本文分析结果表明,细胞周期调控,免疫、炎症反应,细胞增殖与衰老等生物过程和p53信号通路可能与ALF的发展过程相关,基因NCAPG、DLGAP5、TOP2A、ASPM、NUSAP1、MKI67和NAMPT可能是研究APAP诱发ALF发生的新靶点和潜在血液标志物.

We downloaded the data set GSE80751 from the GEO database(https://www.ncbi.nlm.nih.gov/),which contains 22 human blood samples(Control:5 cases;ALI:5 cases;ALF:12 cases).The differentially expressed genes in ALI group and control group,ALF group and control group were screened by|Log FC|>1.5,P<0.05,and the functional enrichment analysis and signal pathway enrichment analysis were performed to screen the key gen-es and important pathways in the process of acetaminophen(APAP)-induced ALF.Secondly,the biological network of differentially expressed genes at the protein level was constructed,and the network data were imported into Cytoscape to achieve visualization,and its plug-ins were used to find the functional modules and core genes closely related to the disease.Compared with the data of ALI group,the data of ALF group were analyzed.It is found that there are 266 differentially expressed genes in ALF group,including 239 up-regulated genes and 27 down-regulated genes.Among them,120 genes are specifically up-regulated and 15 genes are specifically down-regulated in ALF group,and the gene NAMPT is up-regulated in ALI group and down-regulated in ALF group.GO analysis of differentially expressed genes in ALF group shows that up-regulated genes are mainly involved in cell differentiation and cell cycle regulation,while down-regulated genes are mainly involved in immune response and cytokine-mediated inflammation.KEGG pathway analysis shows that up-regulated genes are mainly enriched in cell cycle regulation,systemic lupus erythematosus,complement and coagulation cascade,while down-regulated genes are not enriched in obvious pathways.The disease-related functional modules obtained in ALI group and ALF group were compared and analyzed,and it is found that p53 signal pathway is related to the occurrence of ALF.Using the network topology algorithm MCC in cytoHubba plug-in,25 differentially expressed genes were screened in ALF group,and all of them were up-regulated.The differential expression of NCAPG,DLGAP5,TOP2A,ASPM,NUSAP1 and MKI67 in the liver cells with ALF was further verified,and it was found that there are significant differences in the expression of several key genes in blood cells and hepatocytes in ALF group.The analysis results of this paper show that biological processes such as cell cycle regulation,immune,inflammatory response,cell proliferation and senescence,and p53 signal pathway may be related to the development of ALF.Genes NCAPG,DLGAP5,TOP2A,ASPM,NUSAP1,MKI67 and NAMPT may be new targets and potential blood markers for the study of ALF induced by APAP.