Genome-wide DNA methylation profiling of human diabetic peripheral neuropathy in subjects with type 2 diabetes mellitus

ABSTRACT

DNA methylation is an epigenetic mechanism important for the regulation of gene expression, which plays a vital role in the interaction between genetic and environmental factors. Aberrant epigenetic changes are implicated in the pathogenesis of diabetes and diabetic complications, but the role of DNA methylation in diabetic peripheral neuropathy (DPN) is not well understood. Therefore, our aim in this study was to explore the role of DNA methylation in the progression of DPN in type 2 diabetes. We compared genome-wide DNA methylation profiles of human sural nerve biopsies from subjects with stable or improving nerve fibre counts to biopsies from subjects with progressive loss of nerve fibres. Nerve fibre counts were determined by comparing myelinated nerve fibre densities between an initial and repeat biopsy separated by 52 weeks. Subjects with significant nerve regeneration (regenerators) and subjects with significant nerve degeneration (degenerators) represent the two extreme DPN phenotypes. Using reduced representation bisulfite sequencing, we identified 3,460 differentially methylated CpG dinucleotides between the two groups. The genes associated with differentially methylated CpGs were highly enriched in biological processes that have previously been implicated in DPN such as nervous system development, neuron development, and axon guidance, as well as glycerophospholipid metabolism and mitogen-activated protein kinase (MAPK) signalling. These findings are the first to provide a comprehensive analysis of DNA methylation profiling in human sural nerves of subjects with DPN and suggest that epigenetic regulation has an important role in the progression of this prevalent diabetic complication.

KEYWORDS:

• Type 2 diabetes
• diabetic peripheral neuropathy
• DNA methylation
• reduced representation bisulfite sequencing
• RRBS

Acknowledgments

The authors thank Dr. Benjamin Murdock and Dr. Stacey Sakowski-Jacoby at the University of Michigan for their expert editorial advice. Some of the data were presented as an abstract at the Keystone Bioenergetics and Metabolic Disease Symposia in Keystone, CO in January 2018.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

This work was supported by the National Institutes of Health [NIH R24 DK082841 to E.L.F. and J.H.]; the American Diabetes Association (to E.L.F.); the Novo Nordisk Foundation (to E.L.F.); the Program for Neurology Research and Discovery at University of Michigan, the A. Alfred Taubman Medical Research Institute, the Applied Systems Biology Core of the George M. O’Brien Michigan Kidney Translational Core Center [NIH P30 DK081943]; the NIDDK Diabetic Complications Consortium Pilot Grant [DiaComp, www.diacomp.org; DK076169; Sub-award #25034-75 to J.H.]; the University of North Dakota (UND) Epigenetics Center of Biological Research Excellence [CoBRE; NIH P20 GM104360]; Pilot Grant (to J.H.), UND Post-Doc Pilot Grant (to K.G.), the multidisciplinary postdoctoral training program in basic diabetes research [T32DK101357; to S.E]; and the Nathan and Rose Milstein Research Fund.