Table_2_High-resolution DNA methylation screening of the major histocompatibility complex in multiple sclerosis.XLSX

BackgroundThe HLA-DRB1 gene in the major histocompatibility complex (MHC) region in chromosome 6p21 is the strongest genetic factor identified as influencing multiple sclerosis (MS) susceptibility. DNA methylation changes associated with MS have been consistently detected at the MHC region. However, understanding the full scope of epigenetic regulations of the MHC remains incomplete, due in part to the limited coverage of this region by standard whole genome bisulfite sequencing or array-based methods.MethodsWe developed and validated an MHC capture protocol coupled with bisulfite sequencing and conducted a comprehensive analysis of the MHC methylation landscape in blood samples from 147 treatment naïve MS study participants and 129 healthy controls.ResultsWe identified 132 differentially methylated region (DMRs) within MHC region associated with disease status. The DMRs overlapped with established MS risk loci. Integration of the MHC methylome with human leukocyte antigen (HLA) genetic data indicate that the methylation changes are significantly associated with HLA genotypes. Using DNA methylation quantitative trait loci (mQTL) mapping and the causal inference test (CIT), we identified 643 cis-mQTL-DMRs paired associations, including 71 DMRs possibly mediating causal relationships between 55 single nucleotide polymorphisms (SNPs) and MS risk.ResultsThe results describe MS-associated methylation changes in MHC region and highlight the association between HLA genotypes and methylation changes. Results from the mQTL and CIT analyses provide evidence linking MHC region variations, methylation changes, and disease risk for MS.

背景：位于第6号染色体6p21区域的HLA-DRB1基因是影响多发性硬化症（MS）易感性的最强遗传因素。与MS相关的DNA甲基化改变在MHC区域已得到一致检测。然而，由于标准全基因组亚硫酸氢盐测序或基于阵列的方法对该区域的覆盖范围有限，对MHC区域表观遗传调控的全貌理解尚不完整。方法：我们开发并验证了一种结合亚硫酸氢盐测序的MHC捕获协议，并对147名未接受治疗的MS研究参与者和129名健康对照者的血液样本中的MHC甲基化景观进行了全面分析。结果：我们在与疾病状态相关的MHC区域内识别了132个差异甲基化区域（DMR）。这些DMR与已确立的MS风险位点重叠。将MHC甲基组与人类白细胞抗原（HLA）遗传数据相结合表明，甲基化改变与HLA基因型显著相关。通过DNA甲基化数量性状位点（mQTL）映射和因果推断测试（CIT），我们确定了643对cis-mQTL-DMR关联，包括71个可能介导55个单核苷酸多态性（SNPs）与MS风险之间因果关系的DMR。结果：这些结果描述了MHC区域与MS相关的甲基化改变，并突出了HLA基因型与甲基化改变之间的关联。mQTL和CIT分析的结果为MHC区域变异、甲基化改变与MS疾病风险之间的联系提供了证据。