Table_4_Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.pdf

Objectives: To perform a cross-comparative analysis of DNA methylation in patients with systemic lupus erythematosus (SLE), patients with primary Sjögren's syndrome (pSS), and healthy controls addressing the question of epigenetic sharing and aiming to detect disease-specific alterations.
Methods: DNA extracted from peripheral blood from 347 cases with SLE, 100 cases with pSS, and 400 healthy controls were analyzed on the Human Methylation 450k array, targeting 485,000 CpG sites across the genome. A linear regression model including age, sex, and blood cell type distribution as covariates was fitted, and association p-values were Bonferroni corrected. A random forest machine learning classifier was designed for prediction of disease status based on DNA methylation data.
Results: We established a combined set of 4,945 shared differentially methylated CpG sites (DMCs) in SLE and pSS compared to controls. In pSS, hypomethylation at type I interferon induced genes was mainly driven by patients who were positive for Ro/SSA and/or La/SSB autoantibodies. Analysis of differential methylation between SLE and pSS identified 2,244 DMCs with a majority of sites showing decreased methylation in SLE compared to pSS. The random forest classifier demonstrated good performance in discerning between disease status with an area under the curve (AUC) between 0.83 and 0.96.
Conclusions: The majority of differential DNA methylation is shared between SLE and pSS, however, important quantitative differences exist. Our data highlight neutrophil dysregulation as a shared mechanism, emphasizing the role of neutrophils in the pathogenesis of systemic autoimmune diseases. The current study provides evidence for genes and molecular pathways driving common and disease-specific pathogenic mechanisms.

研究目的：本研究针对系统性红斑狼疮（systemic lupus erythematosus, SLE）患者、原发性干燥综合征（primary Sjögren's syndrome, pSS）患者及健康对照人群的DNA甲基化水平开展交叉比较分析，旨在探讨表观遗传共享现象，并识别疾病特异性的甲基化改变。
研究方法：本研究从347例SLE患者、100例pSS患者及400例健康对照的外周血中提取DNA，采用人类甲基化450K芯片（Human Methylation 450k array）进行检测，该芯片可覆盖全基因组范围内的485000个CpG位点。本研究构建了以年龄、性别及血细胞类型分布作为协变量的线性回归模型，并对关联P值进行邦费罗尼校正。此外，本研究设计了基于DNA甲基化数据预测疾病状态的随机森林机器学习分类器。
研究结果：本研究确定了与健康对照相比，SLE与pSS患者中共有的4945个差异甲基化CpG位点（differentially methylated CpG sites, DMCs）。在pSS患者中，I型干扰素诱导基因的低甲基化现象主要见于Ro/SSA和/或La/SSB自身抗体阳性的患者。通过对SLE与pSS患者之间的甲基化差异进行分析，本研究鉴定出2244个DMCs，其中大多数位点在SLE患者中的甲基化水平低于pSS患者。本研究设计的随机森林分类器在区分疾病状态方面表现良好，其曲线下面积（area under the curve, AUC）介于0.83至0.96之间。
研究结论：SLE与pSS患者之间的大部分DNA甲基化差异具有共性，但同时也存在显著的定量差异。本研究数据表明，中性粒细胞失调是两类患者共有的发病机制，强调了中性粒细胞在系统性自身免疫疾病发病过程中的重要作用。本研究为驱动两类疾病共有的及疾病特异性致病机制的基因与分子通路提供了实验证据。