Large-Scale DNA Methylation Profiling of Human Diabetic Peripheral Neuropathy in Subjects with Type 2 Diabetes Mellitus

Abstract

Diabetic peripheral neuropathy (DPN) is the most common complication of diabetes. Emerging evidence suggests that aberrant DNA methylation may play a critical role in the pathogenesis of diabetic complications. Yet, its involvement in DPN is not fully characterized. In this study, we performed a large-scale genome-wide methylation profiling of sural nerve samples obtained from subjects with type 2 diabetes mellitus (T2DM) using Reduced Representation Bisulfite Sequencing (RRBS). A total of 78 samples were sequenced and mapped to the human reference genome. Differential analysis was performed on two groups, identified by our previous transcriptomic analysis of the same samples, which showed significantly different HbA1c levels: Group 1 (=8.5%±1.6%) and Group 2 (<7.0%±1.4%). Using MethylKit R package, with an adjusted p-value < 0.01 and 15% methylation change as significance cutoffs, we identified 2,066 differentially methylated CpG sites and 440 regions, corresponding to 1,519 and 429 unique differentially methylated genes (DMGs). These genes were highly enriched in biological processes related to nervous system development, neuron fate specification and neuron differentiation. KEGG pathway enrichment analysis demonstrated that genes involved in cancer, ECM-receptor interaction and axon guidance pathways were significantly differentially methylated between the two groups, highlighting the importance of DNA methylation in DPN pathogenesis. In summary, we demonstrate that type 2 diabetic patients with peripheral neuropathy and high HbA1c show distinct variations in sural nerve methylome, suggesting that DNA methylation and DPN are associated and that these associations are at least in part HbA1c-dependent. Our results provide new insights into the role of HbA1c in epigenetic variation, and identify candidate genes relevant to the pathogenesis of DPN in human sural nerves of subjects with T2DM. Disclosure K. Guo: None. S. Elzinga: None. S. Eid: None. C. Figueroa-Romero: None. B.A. McGregor: None. G. de Anda-Jáuregui: None. C. Pacut: None. E.L. Feldman: None. J. Hur: None.