Abstract
Objective: We previously identified DNA methylation differences at multiple CpG (cytosine-guanine dinucleotide) loci in individuals with or without diabetic kidney disease (DKD). We aimed to study DNA methylation levels as a risk factor for the development of kidney failure in individuals with type 1 diabetes and DKD.
Design: A total of 393 individuals with macroalbuminuria at baseline were followed up until either kidney failure developed or December 31, 2017. The risk derived from each of the 763,064 studied CpG sites were analysed separately using the Cox proportional-hazards model with sex, baseline age, and six white blood cell counts as covariates.
Setting: Prospective study of Finnish individuals with type 1 diabetes and DKD.
Patients: All 393 participants were from the Finnish Diabetic Nephropathy (FinnDiane) Study; 38% were women, and mean (sd) age at baseline was 43.1 (±10.8) years. Macroalbuminuria (>200 µg/min or >300 mg/24h) was determined from two of three overnight or 24 hr urine collections. Data on kidney failure requiring dialysis and/or a transplant was collected from study visits, medical files, or hospital discharge register. Study participants were followed up for a median of 7.3 (interquartile range: 2.9–14.1) years, during which 193 kidney failure events were recorded.
Main Outcome Measurements: We analysed genome-wide white blood cell DNA methylation with Infinium HD Methylation EPIC BeadChips (Illumina) within the Northern Ireland Regional Genetics Centre in Belfast. After standard quality control steps, we extracted M-values (M = log2(β/(1–β)) for 763,064 CpG sites using the R v.4.0 and RnBeads.
Results: 49% of the cohort developed kidney failure during follow-up. Ten CpGs were associated with developing kidney failure with p < 6.6 × 10–8 – a p-value threshold corrected for the number of studied CpG sites. The top CpG cg17944885 is located on chromosome 19 between genes ZNF788P and ZNF625-ZNF20. Hypermethylation at this locus was a risk factor for kidney failure (HR = 2.3[95%CI] = 2.31[1.94, 2.75], p = 4.7 ×10–21). The same CpG was also associated with DKD in our earlier cross-sectional study, and it has been associated with kidney function both in individuals with and without diabetes. Six significant CpGs were located in or near genes; cg12272104 in DAZAP1, cg21871803 in AHCYL2, cg12065228 in PQLC2 and cg26236214 in ARHGEF7, in addition to cg19942083 in the promotor of PTPN6 and cg03262246 <1500 bps from the transcription start site of CDKN2AIPNL, while other significant CpGs were more distal to the genes. In independent replication, five out of ten significant CpGs were also associated (3.7 × 10–8 ≤ p ≤ 0.05) with eGFR in the whole blood DNA methylation analysis of the Chronic Renal Insufficiency cohort of 473 individuals with diabetes.
Conclusions: DNA methylation at CpG sites near several genes increase the risk of developing kidney failure.
Design: A total of 393 individuals with macroalbuminuria at baseline were followed up until either kidney failure developed or December 31, 2017. The risk derived from each of the 763,064 studied CpG sites were analysed separately using the Cox proportional-hazards model with sex, baseline age, and six white blood cell counts as covariates.
Setting: Prospective study of Finnish individuals with type 1 diabetes and DKD.
Patients: All 393 participants were from the Finnish Diabetic Nephropathy (FinnDiane) Study; 38% were women, and mean (sd) age at baseline was 43.1 (±10.8) years. Macroalbuminuria (>200 µg/min or >300 mg/24h) was determined from two of three overnight or 24 hr urine collections. Data on kidney failure requiring dialysis and/or a transplant was collected from study visits, medical files, or hospital discharge register. Study participants were followed up for a median of 7.3 (interquartile range: 2.9–14.1) years, during which 193 kidney failure events were recorded.
Main Outcome Measurements: We analysed genome-wide white blood cell DNA methylation with Infinium HD Methylation EPIC BeadChips (Illumina) within the Northern Ireland Regional Genetics Centre in Belfast. After standard quality control steps, we extracted M-values (M = log2(β/(1–β)) for 763,064 CpG sites using the R v.4.0 and RnBeads.
Results: 49% of the cohort developed kidney failure during follow-up. Ten CpGs were associated with developing kidney failure with p < 6.6 × 10–8 – a p-value threshold corrected for the number of studied CpG sites. The top CpG cg17944885 is located on chromosome 19 between genes ZNF788P and ZNF625-ZNF20. Hypermethylation at this locus was a risk factor for kidney failure (HR = 2.3[95%CI] = 2.31[1.94, 2.75], p = 4.7 ×10–21). The same CpG was also associated with DKD in our earlier cross-sectional study, and it has been associated with kidney function both in individuals with and without diabetes. Six significant CpGs were located in or near genes; cg12272104 in DAZAP1, cg21871803 in AHCYL2, cg12065228 in PQLC2 and cg26236214 in ARHGEF7, in addition to cg19942083 in the promotor of PTPN6 and cg03262246 <1500 bps from the transcription start site of CDKN2AIPNL, while other significant CpGs were more distal to the genes. In independent replication, five out of ten significant CpGs were also associated (3.7 × 10–8 ≤ p ≤ 0.05) with eGFR in the whole blood DNA methylation analysis of the Chronic Renal Insufficiency cohort of 473 individuals with diabetes.
Conclusions: DNA methylation at CpG sites near several genes increase the risk of developing kidney failure.
| Original language | English |
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| Publication status | Published - 27 May 2022 |
| Event | 34th Annual Meeting of the European Diabetic Nephropathy Study Group - Salzburg, Austria Duration: 27 May 2022 → 28 May 2022 https://www.signifigs.com/ednsg-34th-annual-meeting/ |
Conference
| Conference | 34th Annual Meeting of the European Diabetic Nephropathy Study Group |
|---|---|
| Abbreviated title | EDNSG |
| Country/Territory | Austria |
| City | Salzburg |
| Period | 27/05/2022 → 28/05/2022 |
| Internet address |
