Abstract
A subset of individuals with type 1 diabetes mellitus (T1DM) are predisposed to developing diabetic kidney disease (DKD), which is the most common cause globally of end-stage kidney disease (ESKD). Emerging evidence suggests epigenetic changes in DNA methylation may have a causal role in both T1DM and DKD. The aim of this investigation was to assess differences in blood-derived DNA methylation patterns between individuals with T1DM-ESKD and individuals with long-duration T1DM but no evidence of kidney disease upon repeated testing. Blood-derived DNA from individuals (107 cases, 253 controls and 14 experimental controls) were bisulphite treated before DNA methylation patterns from both groups were generated and analysed using Illumina’s Infinium MethylationEPIC BeadChip arrays (n=862,927 sites). Differentially methylated CpG sites (dmCpGs) were identified (false discovery rate adjusted p≤×10−8 and fold change ±2) by comparing methylation levels between ESKD cases and T1DM controls at single site resolution. Gene annotation and functionality was investigated to enrich and rank methylated regions associated with ESKD in T1DM.
Top-ranked genes within which several dmCpGs were located and supported by in silico functional data, and replication where possible, include; AFF3, ARID5B, CUX1, ELMO1, FKBP5, HDAC4, ITGAL, LY9, PIM1, RUNX3, SEPTIN9, and UPF3A. Top-ranked enrichment pathways included pathways in cancer, TGF-β signalling and Th17 cell differentiation.
Epigenetic alterations provide a dynamic link between an individual’s genetic background and their environmental exposures. This robust evaluation of DNA methylation in carefully phenotyped individuals, has identified biomarkers associated with ESKD, revealing several genes and implicated key pathways associated with ESKD in individuals with T1DM.
Competing Interest Statement
The authors have declared no competing interest.
List of abbreviations
- BACR
- Bead Array Controls Reporter
- CKD
- chronic kidney disease
- DKD
- diabetic kidney disease
- dmCpGs
- differentially methylated
- eGFR
- estimated glomerular filtration rate
- eQTL
- expression quantitative trait loci
- ESKD
- end-stage kidney disease
- EWAS
- epigenome-wide association study
- FC
- fold change
- FDR
- false discovery rate
- GBM
- glomerular basement membrane width
- GENIE
- GEnetics of Nephropathy an International Effort
- GO
- gene ontology
- GoKinD
- Genetics of Kidneys in Diabetes
- GWAS
- genome wide association studies
- HbA1c
- haemoglobin A1c
- HDACs
- histone deacetylases
- KEGG
- Kyoto Encyclopedia of Genes and Genomes
- NICOLA
- Northern Ireland Cohort for the Longitudinal Study of Ageing
- P_FEN
- percent of endothelial fenestration falling on the peripheral glomerular basement membrane
- PGS
- Partek Genomics Suite
- QC
- quality control
- SF
- supplementary figure
- ST
- supplementary table
- SV
- surface volume of peripheral glomerular basement membrane per glomerulus
- T1DM
- type 1 diabetes mellitus
- T2DM
- type 2 diabetes mellitus
- VVINT
- cortical interstitial fractional volume
- VVMES
- mesangial fractional volume
- VVPC
- volume fraction of podocyte cell per glomerulus
- WCCs
- white cell counts