Epigenetic profiles of pre-diabetes transitioning to type 2 diabetes and nephropathy

Abstract

Aim: To examine DNA methylation profiles in a longitudinal comparison of pre-diabetes mellitus (Pre-DM) subjects who transitioned to type 2 diabetes mellitus (T2DM).

Methods: We performed DNA methylation study in bisulphite converted DNA from Pre-DM (n = 11) at baseline and at their transition to T2DM using Illumina Infinium HumanMethylation27 BeadChip, that enables the query of 27578 individual cytosines at CpG loci throughout the genome, which are focused on the promoter regions of 14495 genes.

Results: There were 694 CpG sites hypomethylated and 174 CpG sites hypermethylated in progression from Pre-DM to T2DM, representing putative genes involved in glucose and fructose metabolism, inflammation, oxidative and mitochondrial stress, and fatty acid metabolism. These results suggest that this high throughput platform is able to identify hundreds of prospective CpG sites associated with diverse genes that may reflect differences in Pre-DM compared with T2DM. In addition, there were CpG hypomethylation changes associated with a number of genes that may be associated with development of complications of diabetes, such as nephropathy. These hypomethylation changes were observed in all of the subjects.

Conclusion: These data suggest that some epigenomic changes that may be involved in the progression of diabetes and/or the development of complications may be apparent at the Pre-DM state or during the transition to diabetes. Hypomethylation of a number of genes related to kidney function may be an early marker for developing diabetic nephropathy.

Keywords: Diabetes; Epigenetic changes; Nephropathy; Pre-diabetes.

Figure 1

Global methylation profile depicting a total of 868 genes. Total of 694 were hypomethylated, 174 were hypermethylated.

Figure 2

A total of 92 genes were hypomethylated and 54 were hypermethylated in all subjects using Illumina bead studio. Significantly hypomethylated genes were compared to putative genes identified in literature review forming of a sub-group of sixteen genes related to kidney disease. These sixteen genes are represented here as cumulative average DiffScore deviations from control comparisons. Scores of ± 13 P-value of 0.05, ± 22 P-value of 0.01.

Figure 3

Hypo-methylated kidney disease associated gene loci. Six putative genes related to kidney disease were hypomethylated across patients (numbered 1-11) compared to controls (n = 2). Red bars indicate diabetic time point and blue bars representing prediabetic time point. Data represented as DiffScore with ± 13 equating to P-value 0.05, ± 22 equating to P-value of 0.01, and ± 33 equating to P-value of 0.001. SLC22A12 (a urate transporter on the proximal tubule); TRPM6 (a cation channel in the kidney); AQP9 (an aquaporin); HP (haptoglobin, which binds plasma hemoglobin); AGXT (alanine-glyoxylate aminotransferase which is involved in oxalic acid secretion); HYAL2 (a hyaluronidase).