Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a lifelong debilitating disease with a complex pathology not yet clearly defined. Susceptibility to ME/CFS involves genetic predisposition and exposure to environmental factors, suggesting an epigenetic association. Epigenetic studies with other ME/CFS cohorts have used array-based technology to identify differentially methylated individual sites. Changes in RNA quantities and protein abundance have been documented in our previous investigations with the same ME/CFS cohort used for this study. DNA from a well-characterised New Zealand cohort of 10 ME/CFS patients and 10 age-/sex-matched healthy controls was isolated from peripheral blood mononuclear (PBMC) cells, and used to generate reduced genome-scale DNA methylation maps using reduced representation bisulphite sequencing (RRBS). The sequencing data were analysed utilising the DMAP analysis pipeline to identify differentially methylated fragments, and the MethylKit pipeline was used to quantify methylation differences at individual CpG sites. DMAP identified 76 differentially methylated fragments and Methylkit identified 394 differentially methylated cytosines that included both hyper- and hypo-methylation. Four clusters were identified where differentially methylated DNA fragments overlapped with or were within close proximity to multiple differentially methylated individual cytosines. These clusters identified regulatory regions for 17 protein encoding genes related to metabolic and immune activity. Analysis of differentially methylated gene bodies (exons/introns) identified 122 unique genes. Comparison with other studies on PBMCs from ME/CFS patients and controls with array technology showed 59% of the genes identified in this study were also found in one or more of these studies. Functional pathway enrichment analysis identified 30 associated pathways. These included immune, metabolic and neurological-related functions differentially regulated in ME/CFS patients compared to the matched healthy controls. Major differences were identified in the DNA methylation patterns of ME/CFS patients that clearly distinguished them from the healthy controls. Over half found in gene bodies with RRBS in this study had been identified in other ME/CFS studies using the same cells but with array technology. Within the enriched functional immune, metabolic and neurological pathways, a number of enriched neurotransmitter and neuropeptide reactome pathways highlighted a disturbed neurological pathophysiology within the patient group.

中文翻译：

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肌痛性脑脊髓炎/慢性疲劳综合征患者DNA甲基化谱的变化反映全身功能障碍

肌痛性脑脊髓炎/慢性疲劳综合征 (ME/CFS) 是一种终生衰弱的疾病，其复杂的病理尚未明确定义。对 ME/CFS 的易感性涉及遗传易感性和环境因素暴露，表明存在表观遗传关联。与其他 ME/CFS 队列的表观遗传研究使用基于阵列的技术来识别差异甲基化的单个位点。RNA 数量和蛋白质丰度的变化在我们之前的调查中已经记录在案，使用与本研究相同的 ME/CFS 队列。从外周血单核 (PBMC) 细胞中分离出来自 10 名 ME/CFS 患者和 10 名年龄/性别匹配的健康对照的新西兰队列的 DNA，并用于使用减少的代表性生成减少的基因组规模的 DNA 甲基化图亚硫酸氢盐测序（RRBS）。使用 DMAP 分析流程分析测序数据以识别差异甲基化片段，并使用 MethylKit 流程量化各个 CpG 位点的甲基化差异。DMAP 鉴定了 76 个差异甲基化片段，Methylkit 鉴定了 394 个差异甲基化的胞嘧啶，包括高甲基化和低甲基化。鉴定了四个簇，其中差异甲基化的 DNA 片段与多个差异甲基化的单个胞嘧啶重叠或非常接近。这些簇确定了与代谢和免疫活动相关的 17 个蛋白质编码基因的调控区域。差异甲基化基因体（外显子/内含子）的分析确定了 122 个独特的基因。与使用阵列技术对 ME/CFS 患者和对照的 PBMC 进行的其他研究进行比较，表明在这些研究中的一项或多项研究中也发现了本研究中鉴定的 59% 的基因。功能通路富集分析确定了 30 个相关通路。这些包括与匹配的健康对照相比，ME/CFS 患者的免疫、代谢和神经相关功能差异调节。在 ME/CFS 患者的 DNA 甲基化模式中发现了主要差异，这些差异清楚地将他们与健康对照区分开来。在本研究中发现的 RRBS 基因体中发现的一半以上已在其他 ME/CFS 研究中使用相同的细胞但使用阵列技术进行了鉴定。在丰富的功能免疫、代谢和神经通路中，