基于CIBERSORT反卷积算法研究狼疮肾炎的免疫浸润机制及潜在靶向中药预测

Immune infiltration mechanism of lupus nephritis and prediction of potential traditional Chinese medicine targeting based on CIBERSORT deconvolution algorithm

目的:利用生物信息学方法探讨狼疮肾炎(LN)的免疫浸润机制,并挖掘潜在的靶向中药,为LN的临床治疗提供新方向。方法:从GEO数据库下载LN基因表达谱芯片数据集,使用R软件进行差异表达基因(DEGs)的筛选,并对这些DEGs进行GO及KEGG富集分析,应用STRING数据库对DEGs进行蛋白质互作网络分析,利用Cytoscape筛选关键基因,Nephroseq数据库验证DEGs表达,通过CIBERSORT反卷积法计算22种免疫细胞在LN中的浸润情况及相关性,最后通过Coremine Medical数据库对显著富集的免疫相关生物学过程及关键核心基因靶向中药进行预测。结果:共筛选出LN相关DEGs367个,其中253个上调,114个下调。GO主要富集于对病毒的反应、对病毒的防御反应、病毒生命周期的调控、病毒过程的调节等;KEGG主要富集于金黄色葡萄球菌感染、COVID-19、甲型流感、补体和凝血级联、百日咳等。筛选出IFIT3、OAS2、MX1、OAS1、RSAD2、XAF1、ISG15、IFIT1、ITGAM和PTPRC 10个关键基因。CIBERSORT反卷积法对应LN免疫浸润显示:单核细胞和初始B细胞高表达,而记忆B细胞、初始CD4^(+)T细胞、滤泡辅助性T细胞和未活化自然杀伤细胞低表达。免疫细胞相关性分析显示:初始B细胞和浆细胞呈正相关,未活化的自然杀伤细胞和未活化的树突状细胞呈正相关,单核细胞和调节性T细胞呈负相关,未活化的CD4^(+)记忆T细胞和单核细胞呈负相关。Coremine Medical预测发现丹参、三七、黄芩、人参、蜂蜜、猴菇、牡丹等与LN免疫关系最为密切。结论:LN的发生与发展是多基因多通路共同参与的结果,单核细胞、记忆B细胞、初始CD4^(+)T细胞和初始B细胞与LN的关系最密切,预测到丹参、三七、黄芩、人参、蜂蜜、猴菇、牡丹等可能为潜在治疗LN的靶向中药。

Objective:Using bioinformatics methods to study the immune infiltration mechanism of lupus nephritis(LN)and to explore potential target Chinese medicines,which can provide new directions for clinical treatment of LN.Methods:Gene expres⁃sion profile microarray dataset of LN was downloaded from GEO database,differential expressed genes(DEGs)were screened using R software,and GO and KEGG enrichment analysis were performed on these DEGs.Protein interaction network analysis of DEGs was performed by applying STRING database,key genes were screened by using Cytoscape,core gene expression was validated by Nephro⁃seq database,and the infiltration and correlation of 22 kinds of immune cells in LN were calculated by CIBERSORT deconvolution algorithm.Finally,herbal prediction of significantly enriched immune-related biological processes and key target genes were performed by Coremine Medical database.Results:A total of 367 LN-related DEGs were obtained,of which 253 were up-regulated and 114 were down-regulated.GO was mainly enriched in response to viruses,defense response to viruses,regulation of viral life cycle,regulation of viral processes,etc;KEGG was mainly enriched in S.aureus infection,COVID-19,influenza A,complement and coagulation cascade,pertussis,etc.Ten key genes were screened:IFIT 3,OAS 2,MX 1,OAS 1,RSAD 2,XAF 1,ISG 15,IFIT 1,ITGAM and PTPRC.Immune infiltration by CIBERSORT deconvolution algorithm showed that monocytes and initial B cells were highly expressed in LN,while memory B cells,naive CD 4^(+)T cells,follicular helper T cells and resting natural killer cells were lowly expressed in LN.Immune cell correlation analysis showed a positive correlation between initial B cells and plasma cells,a positive correlation between resting natural killer cells and resting dendritic cells,a negative correlation between monocytes and regulatory T cells,and a negative correlation between resting CD 4^(+)memory T cells and monocytes.Coremine Medical predicted that Salvia miltiorrhiza,Panax notogin⁃seng,Scutellaria baicalensis,ginseng,honey,monkey mushroom and peony were found to be most closely related to immunity in LN.Conclusion:The development and progression of LN are results of the combined involvement of multiple genes and pathways.Mono⁃cytes,memory B cells,initial CD 4^(+)T cells and initial B cells are most closely associated with LN.The predicted Salvia miltiorrhiza,Panax notoginseng,Scutellaria baicalensis,ginseng,honey,monkey mushroom and peony may be used as target herbs for the poten⁃tial treatment of LN.