DNA methylation changes at major histocompatibility complex in multiple sclerosis

The major histocompatibility complex (MHC) region represents by far the strongest multiple sclerosis (MS) susceptibility loci. DNA methylation changes have been consistently detected at the MHC region in MS. However, understanding the full picture of epigenetic regulations of MHC in MS remains challenging, due in part to the limited coverage in the region by standard whole genome bisulfite sequencing or array-based methods. To fill this gap, we utilized a novel but validated MHC capture protocol with bisulfite sequencing and conducted a comprehensive analysis of MHC methylation landscapes in blood samples from 147 treatment naïve MS participants and 129 healthy controls. We identified 132 differentially methylated region (DMRs) within MHC regions and found they are significantly overlapped with MS risk variants. Integration of the MHC methylome to human leukocyte antigen (HLA) genetic data further 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 SNPs and MS risk. Peripheral blood was sampled by venipuncture from 147 multiple sclerosis (MS) patients and 129 healthy controls. Bloods cells were then used for DNA extraction and major histocompatibility complex (MHC) targeted bisulfite sequencing.

主要组织相容性复合体（major histocompatibility complex, MHC）区域是目前已发现的最强效的多发性硬化（multiple sclerosis, MS）易感基因座。多发性硬化患者的MHC区域中始终可检测到DNA甲基化改变。然而，由于标准全基因组亚硫酸氢盐测序或基于芯片的检测方法对该区域的覆盖度有限，我们对多发性硬化中MHC表观调控的完整图景仍缺乏充分认知。为填补这一研究空白，我们采用了一种经验证的新型MHC捕获联合亚硫酸氢盐测序方案，对147名未接受过治疗的多发性硬化患者及129名健康对照的血液样本开展了MHC区域甲基化谱的全面分析。我们在MHC区域内鉴定出132个差异甲基化区域（differentially methylated regions, DMRs），并发现这些区域与多发性硬化风险变异存在显著重叠。将MHC甲基化组与人类白细胞抗原（human leukocyte antigen, HLA）遗传数据进行整合后，进一步揭示甲基化改变与HLA基因型显著相关。通过DNA甲基化数量性状位点（methylation quantitative trait loci, mQTL）定位及因果推断测试（causal inference test, CIT），我们鉴定出643个顺式mQTL-DMR配对关联，其中71个差异甲基化区域可能介导55个单核苷酸多态性（single nucleotide polymorphism, SNP）与多发性硬化风险之间的因果关系。本研究通过静脉采血采集了147名多发性硬化患者及129名健康对照的外周血样本，随后利用血细胞完成DNA提取及MHC靶向亚硫酸氢盐测序。