OBJECTIVE To determine the stage of B cell development at which a systemic lupus erythematosus (SLE)-associated DNA methylation signature originates in African American (AA) and European American (EA) subjects, and to assess whether epigenetic defects in B cell development patterns could be predictive of SLE status in individual and mixed immune cell populations. METHODS B cells from AA patients (n = 31) and EA patients (n = 49) with or without SLE were sorted using fluorescence-activated cell sorting into 5 B cell subsets. DNA methylation, measured at ~460,000 CpG sites, was interrogated in each subset. Enrichment analysis of transcription factor interaction at SLE-associated methylation sites was performed. A random forests algorithm was used to identify an epigenetic signature of SLE in the B cell subsets, which was then validated in an independent cohort of AA and EA patients and healthy controls. RESULTS Regression analysis across all B cell stages resulted in identification of 60 CpGs that reached genome-wide significance for SLE-associated methylation differences (P ≤ 1.07 × 10-7 ). Interrogation of ethnicity-specific CpGs associated with SLE revealed a hypomethylated pattern that was enriched for interferon (IFN)-regulated genes and binding of EBF1 in AA patients (each P < 0.001). AA patients with SLE could be distinguished from healthy controls when the predictive model developed with the transitional B cell subset was applied to other B cell subsets (mean receiver operating characteristic [ROC] area under the curve [AUC] 0.98), and when applied to CD19+ pan-B cells (mean ROC AUC 0.95) and CD4+ pan-T cells (mean ROC AUC 0.97) from the independent validation cohort. CONCLUSION These results indicate that SLE-specific methylation patterns are ethnicity dependent. A pattern of epigenetic changes near IFN-regulated genes early in B cell development is a hallmark of SLE in AA female subjects. EBF1 binding sites are highly enriched for significant methylation changes, implying that this may be a potential regulator of SLE-associated epigenetic changes.

中文翻译：

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系统性红斑狼疮患者B细胞谱系中表观遗传缺陷的特定群体模式。

目的确定系统性红斑狼疮（SLE）相关的DNA甲基化特征起源于非洲裔美国人（AA）和欧美人（EA）的B细胞发育阶段，并评估B细胞发育模式中的表观遗传缺陷是否可以可以预测单个和混合免疫细胞群中SLE的状态。方法使用荧光激活细胞分选法，将来自AA患者（n = 31）和EA患者（n = 49）的S细胞或不合并SLE的B细胞进行分选。在每个子集中询问在〜460,000 CpG位点测得的DNA甲基化。进行了与SLE相关的甲基化位点的转录因子相互作用的富集分析。使用随机森林算法来识别B细胞亚群中SLE的表观遗传学特征，然后在AA和EA患者以及健康对照组的独立队列中进行了验证。结果在所有B细胞阶段的回归分析中，鉴定出60个CpG，这些CpG在全基因组范围内对于SLE相关的甲基化差异具有重要意义（P≤1.07×10-7）。对与SLE相关的特定种族CpG的询问显示，AA病人中富含干扰素（IFN）调控基因和EBF1结合的低甲基化模式（每个P <0.001）。将由过渡性B细胞亚群建立的预测模型应用于其他B细胞亚群（曲线[AUC] 0.98下的平均接收者操作特征[ROC]面积），并将其应用于CD19 + pan-B细胞（平均ROC AUC 0.95）和CD4 + pan-T细胞（平均ROC AUC 0。97）来自独立验证队列。结论这些结果表明，SLE特异性甲基化模式是种族依赖性的。在B细胞发育早期，IFN调控基因附近的表观遗传变化模式是AA女性受试者SLE的标志。EBF1结合位点高度富集，可发生显着的甲基化变化，这表明它可能是SLE相关表观遗传学变化的潜在调节剂。