Exposure to air pollution is associated with DNA methylation changes in sperm

Abstract

Exposure to air pollutants has been associated with adverse health outcomes in adults and children who were prenatally exposed. In addition to reducing exposure to air pollutants, it is important to identify their biologic targets in order to mitigate the health consequences of exposure. One molecular change associated with prenatal exposure to air pollutants is DNA methylation (DNAm), which has been associated with changes in placenta and cord blood tissues at birth. However, little is known about how air pollution exposure impacts the sperm epigenome, which could provide important insights into the mechanism of transmission to offspring. In the present study, we explored whether exposure to particulate matter less than 2.5 microns in diameter, particulate matter less than 10 microns in diameter, nitrogen dioxide (NO₂), or ozone (O₃) was associated with DNAm in sperm contributed by participants in the Early Autism Risk Longitudinal Investigation prospective pregnancy cohort. Air pollution exposure measurements were calculated as the average exposure for each pollutant measured within 4 weeks prior to the date of sample collection. Using array-based genome-scale methylation analyses, we identified 80, 96, 35, and 67 differentially methylated regions (DMRs) significantly associated with particulate matter less than 2.5 microns in diameter, particulate matter less than 10 microns in diameter, NO₂, and O_3, respectively. While no DMRs were associated with exposure to all four pollutants, we found that genes overlapping exposure-related DMRs had a shared enrichment for gene ontology biological processes related to neurodevelopment. Together, these data provide compelling support for the hypothesis that paternal exposure to air pollution impacts DNAm in sperm, particularly in regions implicated in neurodevelopment.

Keywords: DNA methylation; air pollution; epigenetics; genome-scale; sperm.

Figure 1:

(Left) Volcano plots for 3996 PM2.5 DMRs Y-axis shows the −log10(FWER P) for each DMR returned by the bump hunter algorithm after 10 000 bootstrap permutations. X-axis is the CHARM DMR value, which corresponds to the smoothed effect estimate per DMR returned by bump hunter. Filled-in blue circles have FWER P < 0.05, open blue circles have FWER P < 0.1, and black circles have no nominal significance. There is no stratification by quartile. (Right) Methylation plots for the top three statistical DMRs (P < 1.0 × 10⁻⁴) identified using CHARM and PM2.5 exposure levels. The name of the gene to which the DMR is annotated is at the top of each panel. (top) MGMT, (middle) SMYD3, and (bottom) POU6F2. Panels show individual methylation levels at each probe by genomic position. Dotted vertical black lines represent the boundaries of the DMR, and colored lines represent the average methylation curve for samples grouped by quartiles of PM2.5 exposure—the exposure quartiles within each quartile are shown in the legend. The vertical colored dots represent the individual methylation levels for each individual at each genomic position. The direction of the colored lines demonstrates the direction of methylation change across the genomic positions captured by the DMR

Figure 2:

(Left) Volcano plots for 2439 PM10 DMRs Y-axis show the −log10(FWER P) for each DMR returned by the bump hunter algorithm after 10 000 bootstrap permutations. X-axis is the CHARM DMR value which corresponds to the smoothed effect estimate per DMR returned by bump hunter. Filled-in blue circles have FWER P < 0.05, open blue circles have FWER P < 0.1, and black circles have no nominal significance. There is no stratification by quartile. (Right) Methylation plots for the top three statistical DMRs (P < 1.0×10⁻⁴) identified using CHARM and PM10 exposure levels. The name of the gene to which the DMR is annotated is at the top of each panel. (Top) MAGEE2, (middle) CMA1, and (bottom) A2BP1. Panels show individual methylation levels at each probe by genomic position. Dotted vertical black lines represent the boundaries of the DMR, and colored lines represent the average methylation curve for samples grouped by quartiles of PM10 exposure—the exposure quartiles within each quartile are shown in the legend. The vertical colored dots represent the individual methylation levels for each individual at each genomic position. The direction of the colored lines demonstrates the direction of methylation change across the genomic positions captured by the DMR

Figure 3:

(Left) Volcano plots for 1649 NO₂ DMRs Y-axis shows the −log10(FWER P) for each DMR returned by the bump hunter algorithm after 10 000 bootstrap permutations. X-axis is the CHARM DMR value which corresponds to the smoothed effect estimate per DMR returned by bump hunter. Filled-in blue circles have FWER P < 0.05, open blue circles have FWER P < 0.1, and black circles have no nominal significance. There is no stratification by quartile. (Right) Methylation plots for the top three statistical DMRs (P < 1.0 × 10⁻⁴) identified using CHARM and NO₂ exposure levels. The name of the gene to which the DMR is annotated is at the top of each panel. (Top) C7orf4, (middle) FAM13A, and (bottom) C1D. Panels show individual methylation levels at each probe by genomic position. Dotted vertical black lines represent the boundaries of the DMR, and colored lines represent the average methylation curve for samples grouped by quartiles of NO₂ exposure—the exposure quartiles within each quartile are shown in the legend. The vertical colored dots represent the individual methylation levels for each individual at each genomic position. The direction of the colored lines demonstrates the direction of methylation change across the genomic positions captured by the DMR

Figure 4:

(Left) Volcano plots for 1922 O₃ DMRs Y-axis shows the −log10(FWER P) for each DMR returned by the bump hunter algorithm after 10 000 bootstrap permutations. X-axis is the CHARM DMR value, which corresponds to the smoothed effect estimate per DMR returned by bump hunter. Filled-in blue circles have FWER P < 0.05, open blue circles have FWER P < 0.1, and black circles have no nominal significance. There is no stratification by quartile. (Right) Methylation plots for the top three statistical DMRs (P < 1.0 × 10⁻⁴) identified using CHARM and O₃ exposure levels. The name of the gene to which the DMR is annotated is at the top of each panel. (Top) CTNND1, (middle) LOC646982, and (bottom) MLLT3. Panels show individual methylation levels at each probe by the genomic position. Dotted vertical black lines represent the boundaries of the DMR, and colored lines represent the average methylation curve for samples grouped by quartiles of O₃ exposure—the exposure quartiles within each quartile are shown in the legend. The vertical colored dots represent the individual methylation levels for each individual at each genomic position. The direction of the colored lines across the X-axis demonstrates the direction of methylation change across the genomic positions captured by the DMR

Figure 5:

Venn diagram of DMRs associated with one or more pollutant. No DMRs are associated with all four pollutants. PM_2.5 = blue; PM10 = pink; NO₂ = green; O₃ = gray