Table 3.

Summary of EWAS-derived differentially methylated regions and enrichment in relation to transportation noise and air pollution exposure in the SAPALDIA study.

Exposure	DMRs [Genes (n)]	Average effect on DMRs	Top DMR (Gene)	CpGs in top DMR (n)	FDR $p$-value (top DMR)	Top enriched canonical pathway (TECP)	Genes in TECP	Top enriched disease networks
Aircraft Lden	14 (10)	$\downarrow$ methylation (64%)	Chr5:135415129–135416613 (VTRNA2-1)	19	$8.04\times {10}^{-14}$	NA	NA	Cell cycle, embryonic development, organismal development
Railway Lden	48 (39)	$\downarrow$ methylation (69%)	Chr5:135415129–135416613 (VTRNA2-1)	19	$3.61\times {10}^{-5}$	Type II diabetes mellitus signaling; diphthamide biosynthesis	PRKAA1, SLC27A3, TNFRSF11B, DPH6	cardiovascular system development and function, gene expression, organ development
Road traffic Lden	183 (189)	$\downarrow$ methylation (93%)	Chr20:3051954–3053196 (OXT)	13	$3.93\times {10}^{-6}$	Wnt/$\mathrm{\beta }\text{-catenin}$ signaling; cholecystokinin/gastrin-mediated signaling	CDH1, CSNK1E, SOX2, SOX8, WNT16, MEF2D, PXN, SHC1, TNF	Cell-mediated immune response, cell-to-cell signaling and interaction, cellular movement
${\mathrm{NO}}_2$	8 (8)	$\uparrow$ methylation (63%)	Chr6:28303923–28304451 (ZSCAN31)	11	$2.57\times {10}^{-6}$	NA	NA	Cell cycle, cell-to-cell signaling and interaction, post-translational modification
${\mathrm{PM}}_{2.5}$	71 (60)	$\uparrow$ methylation (93%)	Chr6:30296689–30297941 (TRIM39, HCG18, TRIM39-RPP21)	14	$4.28\times {10}^{-8}$	$\mathrm{\beta }\text{-alanine}$ and 4-aminobutyrate degradation I; systemic lupus erythematosus signaling	ABAT1, PRPF31, PRPF8, PTPN6	Cell cycle, nervous system development and function, organismal injury, and abnormalities

Note: Each DMR analysis had the corresponding multiexposure EWAS-derived parameters as input. Multiexposure EWAS derived from linear mixed-effects models, with random intercept at the level of participant, and adjusted for age; sex; educational level; area; neighborhood socioeconomic status; greenness index; smoking status; smoking pack-years; exposure to passive smoke; consumption of fruits, vegetables, and alcohol; nested study; asthma status; survey; noise truncation indicators; and leukocyte composition. In a preliminary step, DNA methylation $\mathrm{\beta }$-values were regressed on the Illumina control probe-derived first 30 principal components to correct for correlation structures and technical bias, and residuals of these regressions covering 430,477 CpGs were used as the technical bias-corrected methylation level at the CpG sites. Extreme values of the residuals (lying beyond three times the interquartile range below the first quartile and above the third quartile at each CpG site) were replaced with their corresponding detection threshold value (“modified winsorization”). The “winsorized” data were then used as the dependent variables in the EWAS. Significant ($\text{FDR}<0.05$) and annotated DMRs were used for canonical pathway and network enrichment in the Ingenuity Pathway Analysis software (Ingenuity Systems). ↓, decrease in methylation; ↑, increase in methylation; CpG, Cytosine-phosphate-Guanine; DMRs, limiting statistical power to detect enriched canonical pathways; EWAS, epigenome-wide association study; FDR, false discovery rate; Lden, day-evening-night noise level; NA, not applicable due to few significant and annotated; ${\mathrm{NO}}_2$, nitrogen dioxide; ${\mathrm{PM}}_{2.5}$, particulate matter with aerodynamic diameter $<2.5\mathrm{\mu }\mathrm{m}$; SAPALDIA, Swiss Cohort Study on Air Pollution and Lung and Heart Diseases in Adults.