Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA

Abstract

Despite the prognostic value of arterial stiffness (AS) and pulsatile hemodynamics (PH) for cardiovascular morbidity and mortality, epigenetic modifications that contribute to AS/PH remain unknown. To gain a better understanding of the link between epigenetics (DNA methylation) and AS/PH, we examined the relationship of eight measures of AS/PH with CpG sites and co-methylated regions using multi-ancestry participants from Trans-Omics for Precision Medicine (TOPMed) Multi-Ethnic Study of Atherosclerosis (MESA) with sample sizes ranging from 438 to 874. Epigenome-wide association analysis identified one genome-wide significant CpG (cg20711926-CYP1B1) associated with aortic augmentation index (AIx). Follow-up analyses, including gene set enrichment analysis, expression quantitative trait methylation analysis, and functional enrichment analysis on differentially methylated positions and regions, further prioritized three CpGs and their annotated genes (cg23800023-ETS1, cg08426368-TGFB3, and cg17350632-HLA-DPB1) for AIx. Among these, ETS1 and TGFB3 have been previously prioritized as candidate genes. Furthermore, both ETS1 and HLA-DPB1 have significant tissue correlations between Whole Blood and Aorta in GTEx, which suggests ETS1 and HLA-DPB1 could be potential biomarkers in understanding pathophysiology of AS/PH. Overall, our findings support the possible role of epigenetic regulation via DNA methylation of specific genes associated with AIx as well as identifying potential targets for regulation of AS/PH.

Figure 1

Study design. The suggestive DMP was defined as CpG with association p-value less than 1 × 10⁻⁴ and 0.05 respectively for epigenome-wide and candidate-gene approaches; the suggestive DMR was defined as co-methylated region with association p-value less than 5 × 10⁻⁴ and 0.05 respectively for epigenome-wide and candidate-gene approaches; eQTM, expression quantitative trait methylation; AIx, aortic augmentation index; CMR-PWV, aortic arch pulse-wave velocity measured by cardia magnetic resonance imaging; AAD, ascending aortic distensibility; DAD, descending aortic distensibility; YM, Young’s Elastic Modulus; DC, distensibility coefficient; PTC1 and PTC2, radial artery pressure waveform index 1 and 2.

Figure 2

FDR-significant (FDR < 0.05) differentially methylated positions associated with aortic augmentation index. (a) Multi-ancestry epigenome-wide association studies (EWAS) summary statistics of two FDR-significant CpGs. (b) Forest plots of race-stratified EWAS of two FDR-significant CpGs. Position, based on GRCh38/hg38; Estimate (se) and P-value, effect size (standard error) and P-value of CpG respectively from EWAS; FDR, false discovery rate based on multiple testing correction on 491,174 CpGs; NHW, Non-Hispanic White; AA, African American; HIS, Hispanic/Latino.

Figure 3

Three prioritized genes (ETS1, HLA-DPB1, TGFB3) for aortic augmentation index. (a) Workflow of prioritization; (b) FDR-significant KEGG pathways that three prioritized genes were involved; (c) Summary table of follow-up analyses results of three prioritized CpGs associated with aortic augmentation index; (d) Pearson’s correlation (R) of inverse-normalized gene expressions between GTEx v8 Whole-Blood and Aorta tissues for three prioritized genes. Position, based on (GRCh38/hg38); FDR, false discovery rate; functional enrichment, eFORGE 15 chromatin state enrichment analysis; GSEA, gene set enrichment analysis; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; eQTM, expression quantitative trait methylation; AS/PH, arterial stiffness and pulsatile hemodynamics.