Epigenome-wide association study of plasma homocysteine in a Korean cohort highlights imprinted genomic domains as top regional methylation signals

Abstract

Elevated plasma homocysteine impairs DNA methylation capacity by raising the intracellular S-adenosylhomocysteine (SAH)/S-adenosylmethionine (SAM) ratio, thereby inhibiting DNA methyltransferases. Prior epigenome-wide association studies (EWAS) of homocysteine have been conducted almost exclusively in European populations, and data from East Asian populations remain limited. We performed an EWAS of fasting plasma homocysteine in 1,510 Korean adults from the Korea Genome and Epidemiology Study (KoGES/KARE) cohort using the Illumina MethylationEPIC 850 K array. Blood cell type proportions were estimated by reference-based deconvolution (EpiDISH, 12 cell types) and included as covariates alongside age, sex, BMI, smoking status, array position, and global mean methylation. We tested 845,023 CpG sites for association with log-transformed homocysteine using ordinary least squares regression. Differentially methylated regions (DMRs) were identified by positional clustering and Stouffer combined Z-scores with Benjamini-Hochberg FDR correction. We additionally performed sensitivity analyses adjusting for alcohol consumption, serum creatinine, folate, vitamin B12, and MTHFR C677T genotype. The study population had a mean homocysteine of 14.19 ± 5.51 µmol/L and a hyperhomocysteinemia prevalence of 22.7% (> 16 µmol/L). The genomic inflation factor was λ = 1.227. Three probes on chromosome 1 reached FDR < 0.05. Regional analysis identified three known imprinted loci among the top-ranked DMRs: the L3MBTL1 locus (chr20q12, 31 CpGs, Stouffer p  = 2.0 × 10 −20 ), the PEG3 / ZIM2 / MIMT1 domain (chr19q13.43, 40 CpGs, p  = 5.2 × 10 −20 ), and the BLCAP / NNAT locus (chr20q11.21, 55 CpGs, p  = 1.4 × 10 −15 ). The L3MBTL1 and PEG3 domains remained significant after adjustment for folate, vitamin B12, MTHFR C677T, alcohol, and creatinine (e.g., PEG3 FDR = 5.1 × 10 −15 after MTHFR adjustment); the BLCAP / NNAT signal was attenuated by folate/B12 adjustment. The three chromosome-1 probes lost epigenome-wide significance after MTHFR C677T adjustment (FDR ≈ 0.4), consistent with cis -meQTL confounding. This EWAS of plasma homocysteine in a Korean cohort—one of the largest population-based homocysteine EWAS reported in an East Asian population to date—highlights three imprinted genomic domains ( L3MBTL1 , PEG3 / ZIM2 / MIMT1 , BLCAP / NNAT ) as the top-ranked regional methylation signals, of which L3MBTL1 and PEG3 are robust to one-carbon-biomarker and genotype adjustment. The findings generate a biologically plausible hypothesis linking one-carbon metabolism dysregulation to altered methylation at imprinting-associated domains. Replication in independent East Asian cohorts is warranted.