基于GEO数据库的三叉神经痛关键基因筛选及相关免疫细胞浸润分析

Screening of key genes and analysis of related immune cell infiltration for trigeminal neuralgia based on the Gene Expres⁃sion Omnibus database

目的利用生物信息学分析方法挖掘三叉神经痛(trigeminal neuralgia,TN)的关键基因并探索其重要免疫相关生物标志物。方法从基因表达综合数据库(Gene Expression Omnibus,GEO)获取与TN相关的基因表达谱数据集GSE186505,数据集中包含20个样本的芯片数据,其中10个是TN样本,10个是健康对照(healthy controls,HC)样本。用生物信息学方法对高通量测序数据进行标准化、归一化和显著性检验筛选与TN相关的差异表达基因(differentially expressed genes,DEG),并进行基因本体(gene ontology,GO)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)富集分析探索DEG的潜在生物学功能,通过蛋白质⁃蛋白质相互作用(protein⁃protein interaction,PPI)网络进一步筛选TN相关的关键基因,利用CIBERSORT分析不同样品中免疫细胞的浸润程度。结果共筛选出56个DEG,其中包括23个上调基因和33个下调基因。在PPI分析中鉴定了两个必要的PPI模块,基于STRING数据库筛选出ANXA5、ENO1、CA2、FBP1、CD9、SMPD3、VSTM1、SPNS3、PRSS33、FAS、LENG8这11个关键基因可能参与TN的发生机制。富集分析表明,TN与细胞对肿瘤坏死因子的反应、半胱氨酸型内肽酶活性的调节、膜的外在成分、磷脂结合的外部成分和嘧啶代谢等密切相关(P<0.05)。免疫细胞浸润分析显示,幼稚B细胞、M2巨噬细胞在TN样本中表达明显增加,而记忆B细胞、幼稚CD4+T细胞在HC样本中表达增加。结论TN的发病机制可能是通过调节ANXA5、ENO1、CA2、FBP1、CD9、SMPD3、VSTM1、SPNS3、PRSS33、FAS、LENG8等基因,参与细胞对肿瘤坏死因子的反应、半胱氨酸型内肽酶活性的调节等生物过程,调控嘧啶代谢、糖酵解/糖异生、碳代谢等信号通路来完成的。TN发病与幼稚B细胞、M2巨噬细胞增多密切相关。

Objective To screen the key genes of trigeminal neuralgia(TN)and explore its important immune⁃related biomarkers through bioinformatics analysis.Methods The TN⁃related GSE186505 expression profiling dataset was obtained from the Gene Expression Omnibus(GEO)database.The dataset contained microarray data from 20 samples,including 10 TN samples and 10 healthy control(HC)samples.The high⁃throughput sequencing data were analyzed by bioinformatics for standardization,normalization,and significance testing to screen TN⁃related differentially expressed genes(DEG).Furthermore,the potential biological functions of these DEGs were explored by the gene ontology(GO)term and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis.Key genes related to TN were further screened by protein⁃protein interaction(PPI)network.The degree of infiltration of immune cells in different samples was analyzed by CIBERSORT analysis package.Results A total of 56 DEGs were screened,including 23 up⁃regulated genes and 33 down⁃regulated genes.Two necessary PPI modules were identified through PPI analysis.Based on the STRING database,11 key genes,namely ANXA5,ENO1,CA2,FBP1,CD9,SMPD3,VSTM1,SPNS3,PRSS33,FAS,and LENG8,were screened,which might involve in the development of TN.Enrichment analysis demonstrated that cellular response to tumor necrosis factor,regulation of cysteine⁃type endopeptidase activity,extrinsic component of membrane,phospholipid binding and pyrimidine metabolism were strongly associated with TN(P<0.05).Immuno⁃infiltration analysis showed that naive B cells and M2 macrophages significantly increased in the TN samples,while memory B cells and naive CD4+T cells increased in the HC samples.Conclusions The pathogenesis of TN is probably mediated by regulating ANXA5,ENO1,CA2,FBP1,CD9,SMPD3,VSTM1,SPNS3,PRSS33,FAS,and LENG8 genes,in order to participate in biological processes such as cellular responses to tumor necrosis factors,regulate cysteine⁃type endopeptidase activity,and regulate signaling pathways such as pyrimidine metabolism,glycolysis/gluconeogenesis,and carbon metabolism.The pathogenesis of TN is closely associated with increased naive B cells and M2 macrophages.