Genome-Wide DNA Methylation Association Study Identifies DNA Methylation Associated with ESKD

Background: End stage renal disease (ESRD) is a leading cause of morbidity and mortality worldwide. It has been increasingly appreciated that epigenetic changes, such as DNA methylation, play an important role in kidney disease. Methods: Here, using Illumina Infinium EPIC arrays, we performed an epigenome-wide association study (EWAS) of DNA methylation in two ESRD cohorts from China (460 ESRD cases and 196 controls with CKD) and Singapore (229 ESRD cases and 508 controls with T2D). Results: Through a meta-analysis of the association evidences from the two cohorts, we discovered 2400 differentially methylated probes or CpG sites (DMP) whose DNA methylation levels were associated with ESRD at genome wide significance (P < 1.29e-8), with 39% ~ 72% of which were found to be associated with estimated glomerular filtration rate (eGFR) by several EWAS analyses of eGFR. The 2400 DMPs were mostly located in transcriptionally active enhancers, and 42.7% of them were found to be associated with transcriptomic changes according to published eQTM datasets. By interrogating these 2400 DMPs with the genomic functional information for blood, kidney and muscle tissue, we identified 3788 target genes whose transcriptions may be influenced by these DMPs. The enrichment analysis of these target genes revealed the pathways and GO terms related to immunity and inflammation, endocrinology and metabolism, particularly autophagy process, B cell receptor signaling and insulin resistance. Conclusion: Our findings have not only discovered ESRD associated DNA methylation variations that can be used as biomarkers for ESRD, but also highlighted certain biological processes that are involved in kidney disease progression to ESRD. Funding: Government Support – Non-U.S. Clinical characteristics of the subjects in the GDPH and the KTPH cohort. - GDPH cohort AHPL cohort ESRD CKD P value ESRD CKD P value Characteristics Subjects number 457 196 - 229 508 - Age 48.33(±14.29) 42.77(±15.57) < 0.0001 61.23 ± 9.94 57.68 ± 10.36 <0.0001 Male cases 246 (53.83%) 82(41.83%) 0.11 154 (67.2%) 286 (56.3%) 0.005 Complications Diabetes 36(11.25%) 16(8.98%) 0.5743 - - Hypertension 226(70.63%) 45(24.86%) <0.0001 158 (71.2%) 330 (65.7%) 0.15 Cardiovascular disease 108(33.43%) 5(2.82%) <0.0001 3 (18.8%) 31 (13.0%) 0.515 Blood biochemistry CRP(mg/L) 6.72(2.75,22.64) 3.20(2.07,6.20) <0.0001 - - - Hb A1c% 5.45(4.90,6.13) 5.60(5.20,5.90) 0.475 7.05 (6.23,8.20) 7.80 (6.90,9.00) <0.0001 Uric acid (umol/L) 432(361,520) 367(305,445) <0.0001 445 (377,523) 454 (386,534) 0.304 LDL-C (mmol/L) 2.18(1.50,2.83) 2.92(1.95,4.00) <0.0001 2.63 (1.97,3.32) 2.52 (2.11,2.97) 0.223