Controlled human exposures to diesel exhaust: a human epigenome-wide experiment of target bronchial epithelial cells

Abstract

Diesel exhaust (DE) is a major contributor to ambient air pollution around the world. It is a known human carcinogen that targets the respiratory system and increases risk for many diseases, but there is limited research on the effects of DE exposure on the epigenome of human bronchial epithelial cells. Understanding the epigenetic impact of this environmental pollutant can elucidate biological mechanisms involved in the pathogenesis of harmful DE-related health effects. To estimate the causal effect of short-term DE exposure on the bronchial epithelial epigenome, we conducted a controlled single-blinded randomized crossover human experiment of exposure to DE and used bronchoscopy and Illumina 450K arrays for data collection and analysis, respectively. Of the 13 participants, 11 (85%) were male and 2 (15%) were female, and 12 (92%) were White and one (8%) was Hispanic; the mean age was 26 years (SD = 3.8 years). Eighty CpGs were differentially methylated, achieving the minimum possible exact P-value of P = 2.44 × 10^-4 (i.e. 2/2¹³). In regional analyses, we found two differentially methylated regions (DMRs) annotated to the chromosome 5 open reading frame 63 genes (C5orf63; 7-CpGs) and unc-45 myosin chaperone A gene (UNC45A; 5-CpGs). Both DMRs showed increased DNA methylation after DE exposure. The average causal effects for the DMRs ranged from 1.5% to 6.0% increases in DNA methylation at individual CpGs. In conclusion, we found that short-term DE alters DNA methylation of genes in target bronchial epithelial cells, demonstrating epigenetic level effects of exposure that could be implicated in pulmonary pathologies.

Keywords: DNA methylation; EWAS; diesel exhaust; epigenetics; respiratory health.

Figure 1:

Manhattan plot of exact P values and chromosome position. The dashed orange line is the minimum possible P-value. CpGs annotated to the DMRs of chr5; C5orf63 and chr15: UNC45A are colored in red.

Figure 2:

Volcano plot showing change in DNA methylation in bronchial cells against −log10 of exact P-values. The dashed orange line is the minimum possible P-value from an exact test.

Figure 3:

Circular map of genomic distribution among differentially methylated CpGs. From the outmost ring inward, the map shows gene names, chromosome number, position within the chromosome, and effect sizes among Average Causal Effects (below the gray line is a negative effect size and above the line is a positive effect size).