A LECAMWASAM1,2,3, B NOVKOVIC1,5, B MEYER1,5, E I EKINCI2,4, K M DWYER3, R SAFFERY1,5
1Murdoch Children’s Research Institute, Epigenetics Research, Melbourne, Australia, 2Austin Health, Department of Endocrinology, Heidelberg, Australia, 3Deakin University, Department of Medicine, Waurn Ponds, Australia, 4University of Melbourne, Department of Medicine, Melbourne, Australia, 5University of Melbourne, Department of Paediatrics, Melbourne, Australia
Aim: We investigated a cross-sectional Epigenome-wide Association Study of patients with early and late diabetes associated chronic kidney disease (CKD), to identify epigenetic differences between the two groups as well as changes in methylation across all stages of CKD. We also evaluated the potential of using a panel of CpG sites to predict the progression of diabetic CKD.
Background: DNA methylation is the most widely studied epigenetic mark and variations in its profile have been implicated in diabetes.
Methods: DNA was extracted from 119 blood samples, using the Qiagen QIAamp® DNA Mini spin kit. Methylation analysis was performed using Illumina InfiniumMethylationEPIC BeadChips(HM850K). IDAT files were analysed using the MissMethyl package for R. We examined the degree of methylation of CpG sites in early versus late diabetic CKD patients, for CpG sites with an unadjusted p-value < 0.01 and an absolute change in methylation of 5% (n = 239 CpG sites).
Results: Hierarchical clustering of the 239 CpG sites largely separated the two groups. A heat map for all 239 CpG sites demonstrated distinct methylation patterns in the early versus late groups, with CpG sites showing evidence of progressive change. Best predictability for the two groups, involved a Receiver Operating Characteristic curve of 8 CpG sites alone and achieved an area under the curve of 0.976.
Conclusions: We have identified distinct DNA methylation patterns between early and late diabetic CKD patients as well as novel findings of progressive methylation changes across all stages of diabetic CKD at specific CpG sites. We have also shown that the use of a panel of 8 CpG sites alone helps to increase the predictability for the two groups.
Ashani Lecamwasam is a specialist physician in Nephrology. She undertook her undergraduate medical degree at the University of Adelaide and did her internship at the Royal Adelaide Hospital. She moved to Melbourne for her basic and advanced physician training. Ashani was awarded her fellowship in 2015 and currently does public work at Northern Health and private practice. She has an interest in research, specifically in Diabetic Chronic Kidney Disease and is undertaking her PhD, through Deakin University in collaboration with the Murdoch Childrens Research Institute and Austin Health. She has multiple international and national publications.