Genome-Wide Profiling of DNA Methylation and Gene Expression Identifies Candidate Genes for Human Diabetic Neuropathy (RNA-Seq)

We perfomed transcriptomic and methylomic analysis of sural nerve biopsies from type 2 diabetic patients with neuropathy. Sural nerve transcriptomic and methylomic profiles were integrated and subsequent biological meaning investigated using KEGG pathway analysis of overlapping differentially expressed genes (DEGs) and differentially methylated genes (DMGs). A gene interation network was also generated including DEGs and DMGs, and common biological pathways were identified. Overall design: RNA/DNA were extracted from human sural nerves of type 2 diabetic patients with neuropathy and sequenced. Samples were initially grouped based on changes in myelinated fiber density (dMFD) over 52 weeks, representing nerve regeneration and degeneration and divided into three groups (regenerators with high nerve regeneration, degenerator with high nerve degeneration, and intermediate for all others) as described in a previous publication by our group (PMID: 24101696). However, unbiased clustering of the expression data in this study identifed three distinct groups, which were significantly different in terms of HbA1c levels (Group1: 8.66 +/- 1.59; Group2: 7.77 +/- 1.43; Group3: 8.67 +/- 1.44). Reduced representation bisulfate sequencing (RRBS) were also performed on the same sural nerve biopsies, belonging to Group1 and Group2.

本研究对合并周围神经病变的2型糖尿病患者的腓肠神经活检样本开展了转录组学与甲基化组学分析。我们整合了腓肠神经的转录组与甲基化组谱，并针对重叠的差异表达基因（DEGs）与差异甲基化基因（DMGs）开展KEGG通路分析，以探究其潜在生物学意义。此外，本研究还构建了包含DEGs与DMGs的基因互作网络，并筛选出了共通的生物学通路。
总体实验设计：从合并周围神经病变的2型糖尿病患者的人腓肠神经中提取RNA与DNA并进行测序。样本最初依据52周内的有髓神经纤维密度变化量（dMFD）进行分组，该指标可反映神经再生与变性状态，最终分为三组：高神经再生组、高神经变性组，其余样本归为中间组，分组方法参照本团队此前发表的研究（PMID: 24101696）。然而本研究中对表达谱数据的无偏聚类分析得到了三个独立组别，三组的糖化血红蛋白（HbA1c）水平存在显著差异（组1：8.66 ± 1.59；组2：7.77 ± 1.43；组3：8.67 ± 1.44）。本研究还对属于组1与组2的同一批腓肠神经活检样本开展了简化代表性亚硫酸氢盐测序（RRBS）。