Epigenome-wide association study in Asian cohort identifies novel DNA methylation markers for carotid intima-media thickness

Carotid-intima media-thickness (cIMT) predicts cardiovascular events and informs mechanistic research on cardiovascular diseases. However, cardiovascular disease research remains Eurocentric despite etiological differences across ancestries. Incorporating Asian populations, who face substantial cardiovascular disease burden with distinct etiological profiles, can enhance our understanding of cIMT biology and subclinical processes linked to CVD. This study aims to elucidate methylation-based mechanisms of cIMT by integrating DNA methylation profiling integrated with multi-omics data and Asian-tailored cIMT thresholds. We conducted an epigenome-wide association study (EWAS) of cIMT using peripheral blood DNA methylation at ~ 850,000 CpG sites in the Asian Health for Life in Singapore (HELIOS) cohort (n = 1357), followed by targeted trans-ancestry meta-analysis with European cohorts (overall n = 2765). Causal inference analyses (Summary data-based Mendelian Randomisation [SMR] and colocalisation) were used to assess evidence for shared genetic signals linking methylation, cIMT, cardiovascular disease and proximal gene expression. We derived an exploratory methylation risk score (MRS) and evaluated its association with cIMT levels indicative of elevated cardiovascular risk (≥ 75th percentile for age, sex and ethnicity). Three novel CpG-cIMT associations were identified ( P < 9.35E−07). Causal inference analyses provided evidence compatible with shared genetic signals linking cg08227773 separately to coronary artery disease risk ( P SMR = 2.91E−05, coloc PP.H4 = 0.91) and to NBEAL2 (Neurobeachin-like 2) expression ( P SMR = 9.13E−08, coloc PP.H4 = 0.69), a gene implicated in immune dysregulation. The exploratory MRS aggregating the three sentinel CpGs was associated with elevated cIMT in internal HELIOS evaluation (Odds Ratio = 2.75 for Q4 vs. Q1, 95% CI 1.47–5.13). Through Asian-led discovery, this study identifies three novel DNA methylation markers for cIMT that collectively track elevated cIMT burden in an exploratory MRS analysis. Causal inference analyses linked cg08227773- NBEAL2 to coronary artery disease risk and NBEAL2 expression through a shared genetic signal, nominating this locus for further mechanistic investigation.