背景:越来越多的证据强调了组蛋白修饰在系统性红斑狼疮(SLE)发病机制中的重要作用。然而,很少有研究全面分析SLE患者特定免疫基因位点组蛋白H3赖氨酸4(H3K4me3)的三甲基化特征。
方法:我们对SLE患者和健康对照(HC)的CD4+T细胞进行了H3K4me3染色质免疫沉淀测序(ChIP-seq)。鉴定了H3K4me3的微分峰,其次是富集分析。我们整合了在线RNA-seq和DNA甲基化数据集,以探索H3K4me3修饰之间的关系,DNA甲基化和基因表达。我们通过ChIP-qPCR验证了几个上调的峰区域,并使用RT-qPCR确认了它们对基因表达的影响。最后,我们研究了H3K4甲基转移酶KMT2A对免疫应答基因表达的影响.
结果:我们在SLE的CD4+T细胞中鉴定出147个下调和2701个上调的H3K4me3峰。上调的峰主要归类为获得的峰,并富含免疫应答基因,如FCGR2A,C5AR1、SERPING1和OASL。在SLE患者中,启动子中H3K4me3上调和DNA甲基化下调的基因高表达。这些基因,包括OAS1、IFI27和IFI44L,富含免疫应答途径。IFI44L基因座还显示出增加的H3K27ac修饰,SLE中的染色质可及性和染色质相互作用。此外,KMT2A敲低可以下调T细胞免疫应答基因的表达。
结论:我们的研究揭示了免疫应答基因位点H3K4me3修饰模式失调,在SLE患者的CD4+T细胞中也表现出下调的DNA甲基化和更高的mRNA表达。
BACKGROUND: Increasing evidence has highlighted the significant role of histone modifications in pathogenesis of systemic lupus erythematosus (SLE). However, few studies have comprehensively analyzed trimethylation of histone H3 lysine 4 (H3K4me3) features at specific immune gene loci in SLE patients.
METHODS: We conducted H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) on CD4+ T cells from SLE patients and healthy controls (HC). Differential H3K4me3 peaks were identified, followed by enrichment analysis. We integrated online RNA-seq and DNA methylation datasets to explore the relationship between H3K4me3 modification, DNA methylation and gene expression. We validated several upregulated peak regions by ChIP-qPCR and confirmed their impact on gene expression using RT-qPCR. Finally, we investigated the impact of H3K4 methyltransferases KMT2A on the expression of immune response genes.
RESULTS: we identified 147 downregulated and 2701 upregulated H3K4me3 peaks in CD4+ T cells of SLE. The upregulated peaks primarily classified as gained peaks and enriched in immune response genes such as FCGR2A, C5AR1, SERPING1 and OASL. Genes with upregulated H3K4me3 and downregulated DNA methylations in the promoter were highly expressed in SLE patients. These genes, including OAS1, IFI27 and IFI44L, were enriched in immune response pathways. The IFI44L locus also showed increased H3K27ac modification, chromatin accessibility and chromatin interactions in SLE. Moreover, knockdown of KMT2A can downregulate the expression of immune response genes in T cells.
CONCLUSIONS: Our study uncovers dysregulated H3K4me3 modification patterns in immune response genes loci, which also exhibit downregulated DNA methylation and higher mRNA expression in CD4+ T cells of SLE patients.