Research February 2018 | Volume 126 | Issue 2
Long-term Air Pollution Exposure, Genome-wide DNA Methylation and Lung Function in the LifeLines Cohort Study
1Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
2Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, Netherlands
3Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
4Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
5Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands
6Institute of Epidemiology II, Helmholtz Zentrum MünchenInstitute of Epidemiology II, Neuherberg, Germany
7Environmental Public Health Division, U.S. Environmental Protection AgencyEnvironmental Public Health Division, Chapel Hill, North Carolina, USA
8Molecular Epidemiology Unit, Helmholtz Zentrum München, Neuherberg, Germany
9Institute for Risk Assessment Sciences, Utrecht UniversityInstitute for Risk Assessment Sciences, Utrecht, Netherlands
10Julius Center for Health Sciences and Primary Care, University Medical Center UtrechtJulius Center for Health Sciences and Primary Care, Netherlands
PDF Version (264 KB)
- Long-term air pollution exposure is negatively associated with lung function, yet the mechanisms underlying this association are not fully clear. Differential DNA methylation may explain this association.
- Our main aim was to study the association between long-term air pollution exposure and DNA methylation.
- We performed a genome-wide methylation study using robust linear regression models in 1,017 subjects from the LifeLines cohort study to analyze the association between exposure to nitrogen dioxide (NO2) and particulate matter (PM2.5, fine particulate matter with aerodynamic diameter ≤2.5 μm; PM10, particulate matter with aerodynamic diameter ≤10 μm) and PM2.5absorbance, indicator of elemental carbon content (estimated with land-use-regression models) with DNA methylation in whole blood (Illumina® HumanMethylation450K BeadChip). Replication of the top hits was attempted in two independent samples from the population-based Cooperative Health Research in the Region of Augsburg studies (KORA).
- Depending on the p-value threshold used, we found significant associations between NO2 exposure and DNA methylation for seven CpG sites (Bonferroni corrected threshold p<1.19×10−7) or for 4,980 CpG sites (False Discovery Rate<0.05). The top associated CpG site was annotated to the PSMB9 gene (i.e., cg04908668). None of the seven Bonferroni significant CpG-sites were significantly replicated in the two KORA-cohorts. No associations were found for PM exposure.
- Long-term NO2 exposure was genome-wide significantly associated with DNA methylation in the identification cohort but not in the replication cohort. Future studies are needed to further elucidate the potential mechanisms underlying NO2–exposure–related respiratory disease. https://doi.org/10.1289/EHP2045
Received: 12 April 2017
Revised: 13 December 2017
Accepted: 13 December 2017
Published: 6 February 2018
Address correspondence to J.M. Vonk, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB Groningen, Netherlands. Telephone: +31 50 3610934. Email: email@example.com
Supplemental Material is available online (https://doi.org/10.1289/EHP2045).
The views in this manuscript do not necessarily represent U.S. Environmental Protection Agency policy.
The authors declare they have no actual or potential competing financial interest.
Note to readers with disabilities: EHP strives to ensure that all journal content is accessible to all readers. However, some figures and Supplemental Material published in EHP articles may not conform to 508 standards due to the complexity of the information being presented. If you need assistance accessing journal content, please contact firstname.lastname@example.org. Our staff will work with you to assess and meet your accessibility needs within 3 working days.
Supplemental Material PDF (698 KB)
Supplemental Code and Data Zip File (539 KB)
Note to readers with disabilities: EHP has provided a 508-conformant table of contents summarizing the Supplemental Material for this article (see below) so readers with disabilities may determine whether they wish to access the full, nonconformant Supplemental Material. If you need assistance accessing journal content, please contact email@example.com. Our staff will work with you to assess and meet your accessibility needs within 3 working days.
Supplemental Table of Contents PDF (81 KB)
Air pollution is a major concern in public health. Long-term air pollution exposure has been consistently associated with lower function in adults (Ackermann-Liebrich et al. 1997; Adam et al. 2015; Forbes et al. 2009), children (Barone-Adesi et al. 2015; Gehring et al. 2013; Urman et al. 2014) and in those with preexisting lung disease (Nitschke et al. 2016). In the LifeLines cohort study, a large representative sample of the north of Netherlands, a higher level of nitrogen dioxide (NO2) and particulate matter (PM) exposure was associated with lower forced expiratory volume in 1 s (FEV1) and even lower forced vital capacity (FVC), and as a consequence, a higher FEV1/FVC ratio (De Jong et al. 2016).
Activation of oxidant and pro-inflammatory pathways is suggested to be a potential mechanism underlying the acute toxicity of NO2 and PM (Lodovici and Bigagli 2011), yet the knowledge on exact mechanisms underlying the effect of long-term air pollution exposure on health is inconclusive. Although clear evidence exists for the association between genetics and lung function (Hobbs et al. 2017), the genetic background cannot entirely explain the phenotypic variability. Emerging evidence suggests that apart from specific genetic variants, epigenetic alterations in response to environmental exposure is an important determinant of respiratory health (Boezen 2009). DNA methylation, currently the most frequently studied epigenetic mechanism, occurs by the binding of a methyl group to a cytosine-guanine dinucleotide (CpG site) (Griffiths et al. 2011). Changes in DNA methylation may be induced by exposure to air pollution and may alter the gene expression profile. This change in DNA methylation is one plausible mechanism potentially mediating the adverse health effects of air pollution (Holloway et al. 2012). Differential blood DNA methylation in response to air pollution exposure has been reported in environmental (Bind et al. 2014; De Prins et al. 2013), occupational (Sanchez-Guerra et al. 2015; Tarantini et al. 2009), and experimental settings (Ding et al. 2016). The strongest epigenetic signals identified in response to air pollution exposure were found in candidate genes for inflammatory pathways (F3, ICAM-1, TLR-2, IFN–γ, IL-6) (Bind et al. 2014), detoxification metabolism system (GST) (Madrigano et al. 2011), lung function (TLR2, GCR) (Lepeule et al. 2014), lung cancer (SATα, NBL2) (Hou et al. 2014), and biological aging (Ward-Caviness et al. 2016).
Despite these findings, no study to date has examined whether the association between long-term air pollution exposure and lung function is mediated by DNA methylation (Tarantini et al. 2009). In this study, we performed a genome-wide methylation study of the long-term air pollution exposure, i.e., NO2 and PM in adults from the LifeLines cohort study. We further investigated to what extent the significant air pollution-associated DNA methylation sites mediated the association between air pollution and lung function.
Study Population and Design
This study included subjects enrolled in the LifeLines cohort study. LifeLines is a large Dutch population-based cohort study designed to investigate chronic diseases and healthy aging (Scholtens et al. 2015). Detailed information about LifeLines can be obtained at the official website (http://www.lifelines.net). The LifeLines cohort study was approved by the Medical Ethical Committee of the University Medical Center Groningen, Groningen, Netherlands. All participants provided written informed consent.
A subgroup of 1,656 subjects of the LifeLines cohort was selected based on having complete data on lung function and specific environmental exposures as well as on covariates used in the analysis: sex, age, height, and smoking history.
Air Pollution Exposure Assessment
At the baseline visit (2007–2013), the home addresses of all LifeLines individuals were geocoded and GIS (geographic information system)-derived information on distance to the nearest road, traffic intensity, built-up land, population density, and altitude was acquired. The annual average exposure to NO2, PM10 (PM with aerodynamic diameter less than 10 μm), PM2.5 (particles with aerodynamic diameter less than 2.5 μm) and PM2.5absorbance (indicator of elemental carbon content) (Cyrys et al. 2003) was then estimated using land-use regression models, developed in the ESCAPE study. In these models, the GIS-derived information was combined with annual air pollution concentrations from an intensive monitoring campaign in the ESCAPE study (Beelen et al. 2013; Eeftens et al. 2012; Zijlema et al. 2016).
Lung Function Assessment
Lung function was measured with spirometry according to standard operating procedures using the Wellch Allyn SpiroPerfect device (Wellch Allyn version 184.108.40.2069, personal computer-based SpiroPerfect™ with CardioPerfect® Workstation software). FEV1, FVC, FEV1/FVC, and forced expiratory flow between 25–75% of the FVC (FEF25–75) were used as lung-function outcomes.
Age was calculated based on the date of birth as registered in the municipal registries and the date of the baseline visit. Body mass index (BMI) is calculated as weight divided by height squared, as measured during the baseline visit using standardized procedures. Smoking status and cumulative smoking exposure (pack-years of cigarettes smoked) were assessed using the standardized European Community Respiratory Health Survey (ECRHS) questionnaire (Burney et al. 1994). Current smoking was defined as smoking in the last month, and only current smokers with a smoking history greater than five pack-years were included. Never-smokers were defined as having a smoking history of zero pack-years. To optimize the smoking exposure contrast, ex-smokers were not included in this study.
Genome-wide DNA Methylation Assessment
Genome-wide DNA methylation levels were assessed from whole blood of 1,656 subjects using standard methods. Briefly, blood samples were bisulfite-treated (EZ-96 DNA Methylation™ Kit; Zymo Research Corp.) and subsequently subjected to whole-genome amplification. DNA methylation level for each CpG site was measured using the Illumina Infinium® Human Methylation 450K array (Illumina, Inc.) and expressed quantitatively as β–value. β–Values represent the ratio of the fluorescent signal intensity measured by methylated and unmethylated probes and range from 0 (all copies of the CpG site in the sample are unmethylated) to 1 (all copies of the CpG site in the sample are methylated). Quality control (QC) included removal of samples with probes with a detection p–value>0.01 in <99% of probes, samples with incorrect sex or SNP prediction, as well as probes with a detection p–value>0.01, sex chromosome probes, probes measuring SNPs, probes where the CpG itself or the single base extension (SBE) site is an SNP, and cross-reactive probes. A total of 420,938 CpG sites passed the QC filtering criteria. The data were normalized using DASEN implemented in the wateRmelon package in R (R Core Team) (Pidsley et al. 2013).
Replication of the top CpG sites associated with air pollution exposure was attempted in two independent samples from the population-based Cooperative Health Research in the Region of Augsburg studies [Kooperative Gesundheitsforschung in der Region Augsburg, Germany (KORA F3 and KORA F4)]. The KORA F3 examinations took place from 2004 to 2005 (Aulchenko et al. 2009; Wichmann et al. 2005), and KORA F4 examinations took place from 2006 to 2008 (Rückert et al. 2011). For both examinations, health surveys were administered, and biospecimens were collected by trained personnel per published methodologies. Informed consent was provided by all participating individuals. All KORA studies were approved by the ethics committee of the Bavarian Medical Association in Munich, Germany. The KORA F3 and KORA F4 samples used for this replication study were nonoverlapping. Air pollution at the residential address was estimated using land-use regression models as developed in the ESCAPE study (Pitchika et al. 2017). DNA methylation was assessed identically for the KORA F3 and KORA F4 samples. Genome-wide DNA methylation measurement at 485,577 genomic sites was performed using the Infinium® HumanMethylation450K BeadChip (Illumina, Inc.) and expressed quantitatively as β–value. The laboratory process has been described previously (Zeilinger et al. 2013). To preprocess the DNA methylation data, first, 65 probes that represent SNPs were excluded. Next, background correction using minfi, version 1.6.0 (Aryee et al. 2014) was performed, and signals represented by fewer than three functional beads were removed. Data were normalized using quantile normalization (QN) on the raw signal intensities (Lehne et al. 2015). QN was performed on six stratified probe categories based on probe type and color channel (Bibikova et al. 2011) using the R package limma (version 3.16.5; R Core Team). Differences in the signal intensities from Infinium I vs. Infinium II probes designs were corrected using beta-mixture quantile normalization (BMIQ) (Teschendorff et al. 2012) via the R package wateRmelon, version 1.0.3 (R Core Team) (Pidsley et al. 2013). White blood cell (i.e., granulocytes, monocytes, B cells, CD4+ T cells, CD8+ T cells, and natural killer cells) proportions were estimated using the Houseman method (Houseman et al. 2012). To keep in concert with the discovery analyses, individuals with a detection p–value>0.05 for >1% of the probes were removed. After quality control, 451 samples were retained in KORA F3 and 1,424 in KORA F4.
Statistical analyses were performed using the SPSS statistics software version 23.0 (IBM) and R software version 3.2.4 revised (R Foundation). Robust linear regression models were used to test the cross-sectional association between air pollution (NO2, PM10, PM2.5, and PM2.5absorbance) exposure as a predictor and genome-wide DNA methylation levels as a response. The models were adjusted for sex, age, BMI, current smoking, pack-years, and covariates expected to influence the DNA methylation levels (technical covariates and blood cell composition). The potential technical bias was minimized using principal component analysis applied to the control probes included on the 450K chip (Lehne et al. 2015). We included all PCs that explained >1% of the variance. This resulted in the inclusion of the first 7 PCs that together explained 95.5% of total variance. Additionally, the model was adjusted for the measured white blood cell counts (eosinophils, neutrophils, basophils, lymphocytes, and monocytes) to correct for the cellular heterogeneity of blood samples (Jaffe and Irizarry 2014). We used the Bonferroni corrected threshold p–value<1.19×10−7 (0.05/420,938) to correct for the number of CpG sites tested. Sites that passed this threshold were considered genome-wide significant and were investigated further in subsequent analyses. To investigate the sensitivity of the results of the analyses between air pollution exposure and methylation to the model specifications we conducted several sensitivity analyses to the top hits of our analyses (see Supplemental Material for details): a) exclusion of outliers in the DNA-methylation levels, b) additional adjustment for possible confounders (i.e., highest educational level, chronic obstructive pulmonary disease (COPD), asthma, use of respiratory medication), and c) stratification of the models by sex, BMI, and smoking. Replication of the top hits was attempted in two independent samples from the KORA study. In this replication analysis, associations were estimated using robust linear regression models and included the following covariates: sex, age, body mass index, current smoking, pack-years, estimated cell counts, and the first 20 PCs from the control probes to adjust for technical variation (Lehne et al. 2015). As in the discovery analysis, only, never, and current smokers were included in the analysis (ex-smokers were excluded). Significant replication is defined as a p–value<0.05 in at least one of the replication cohorts, and the direction of the effect should be the same in the discovery and both replication cohorts. In addition, using the software tool provided at https://220.127.116.11:8080/GeneNetwork/pathway.html, we conducted a pathway analysis in which we included all genes annotated to CpG sites with an FDR p–value<0.01, and we investigated the association between our top methylation-sites and gene expression by searching the tables provided at https://www.genenetwork.nl/biosqtlbrowser/.
Robust linear regression models adjusted for sex, age, height, BMI, sex*age interaction, sex*height interaction, current smoking, and pack-years were used to analyze the cross-sectional association between air pollution exposure and lung function levels, as measured by: FEV1, FVC, FEV1/FVC, and FEF25–75. Two-sided p–values<0.05 were considered statistically significant.
The potential mediation by significant air pollution-associated methylation sites was assessed using mediation analysis. By applying the bootstrapping method in the “mediation” package in R (version 4.4.6; R Core Team) (Hayes 2009), we verified whether the total effect of a specific air pollutant on a lung function outcome was mediated by DNA methylation at the significant CpG sites. To test this mediation effect, two models were applied, and their estimates were used as input for the mediate function (Figure 1). The first model, the mediator model, assessed the effect of air pollution exposure on DNA methylation (association A) and, the second model, the outcome model, assessed the combined effect of air pollution exposure and the mediator (DNA methylation) on a lung function outcome (associations B and C). A total of 1,000 bootstraps were run to estimate the confidence intervals (CIs) (Mayer et al. 2014). Significant mediation by DNA methylation was considered present when the p-value of the average mediation effect (AME) was <0.05. A p-value between 0.05 and 0.10 was considered as borderline significant.
In total, 1,622 subjects passed the quality control of the DNA methylation assessment, and 1,017 subjects had complete data on air pollution exposure, DNA methylation levels, and all included covariates. Table 1 summarizes the baseline characteristics of the 1,017 subjects with complete data and 605 subjects with incomplete data. The mean age of the complete subjects was 47.3 y, 58% were male, and 56% were never smokers. In current smokers, the mean cumulative smoking exposure was 20.5 pack-years. Mean levels of lung function measured at the baseline visit were: FEV1 3.5L (98% of predicted normal values), FVC 3.5L (111% of predicted), FEV1/FVC 73.4%, and FEF25–75 2.8 L/s (70% of predicted) (Quanjer et al. 1993). No significant differences were found between the incomplete and complete subjects. The annual average estimated concentration (range) of exposure was 16.3 (9.4−32.8) μg/m3 for NO2; 24.1 (23.7−27.6) μg/m3 for PM10; 15.5 (15.1−18.2) μg/m3 for PM2.5, and 0.9 (0.8−1.6)×10−5m−1 for PM2.5absorbance. The correlation (Pearson correlation coefficient) among the annual average concentration of pollutants is presented in Supplemental Material (Table S1).
|Characteristic||Incomplete data||Complete data||Difference|
|N (%)||605 (37.3)||1,017 (62.7)|
|Male||341 (56.4)||587 (57.7)||0.59|
|Never smoking||343 (56.7)||574 (56.4)||0.92|
|Current smokinga||262 (43.3)||443 (43.6)|
Note: Data are presented as mean±standard deviation (SD) for continuous variables or N (%) for categorical variables; BMI, body mass index; FEV1, forced expiratory volume in 1 second; FCV, forced vital capacity; FEV1/FVC, forced expiratory volume in 1 sec to forced vital capacity ratio; FEF25–75, forced expiratory flow between 25–75% of the FVC; NO2, nitrogen dioxide; PM10, particles with aerodynamic diameter <10 μm; PM2.5, particles with aerodynamic diameter ≤2.5 μm; PM2.5absorbance, indicator of elemental carbon content.
aCurrent smoking is defined as smoking in the last month and only current smokers with a smoking history greater than five pack-years were included.
bCumulative smoking defined by pack-years of cigarettes smoked in current smokers.
Association between Air Pollution Exposure and Genome-Wide DNA Methylation
NO2 exposure was genome-wide significantly associated with differential DNA methylation at seven CpG sites (mapped to seven different genes) at the Bonferroni corrected threshold p–value<1.19×10−7 and with 4,980 CpGs at the False Discovery Rate (FDR) p–value<0.05 (Table 2, see also Excel Table S1 and Figure S1). Among these top signals, three CpG sites showed a negative association with NO2 exposure: cg04908668 (PSMB9, chr6), cg00344801 (TTC38, chr22), and cg02234653 (AP1S3, chr2); four showed a positive association: cg14938677 (ARF5, chr7), cg18379295 (GNG2, chr14), cg25769469 (PTCD2, chr5), and cg08500171 (BAT2, chr6). The results of the sensitivity analyses on these 7 CpG sites are presented in Tables S2, S3, and S4. Importantly, after removal of outliers in the methylation values 1 CpG (i.e., cg02234653) was no longer significant at the Bonferroni corrected threshold although the effect estimate remained similar (Table S2). None of the genome-wide significant CpG sites associated with NO2 exposure was successfully replicated either in the KORA F3 or in the KORA F4 cohort (Tables 3 and 4). The results of the pathway analyses are presented in Excel Tables S2 and S3. A look-up of these 7 CpG sites in the eQTM table provided at https://www.genenetwork.nl/biosqtlbrowser/ showed that 2 CpGs were associated with gene expression of 3 genes [i.e., cg04908668 was associated with lower expression of Proteasome Subunit Beta 9 (PSMB9) and of Transporter 1, ATP Binding Cassette Subfamily B Member (TAP1) genes, and cg00344801 was associated with higher expression of Tetratricopeptide Repeat Domain 38 (TTC38)] (Table S5). PM10, PM2.5, and PM2.5absorbance exposures were not genome-wide significantly associated with DNA methylation, either at the Bonferroni corrected threshold or at the FDR-threshold (see Table S6 and Excel Table S4 and Table S7 for CpG sites associated with a p–value<1×10−5). Given that only NO2 exposure was genome-wide significantly associated with DNA methylation, the subsequent mediation analyses were restricted to NO2.
|CpG site||B±SEa||p-Valueb||Chr||Bp position||Gene||Location in gene||Relation to island|
aEffect estimates±standard error (SE) of DNA methylation per 10–μg/m3 increase in NO2 concentration adjusted for sex, age, BMI, current smoking, pack-years, technical variance, and blood cell composition. Chr, chromosome.
bBonferroni corrected threshold p–value<1.19×10−7.
|Characteristic||Discovery cohort||Replication cohorts|
|KORA F3||KORA F4|
|Male||587 (57.7)||261 (51.2)||383 (39.4)|
|Never smoking||574 (56.4)||205 (48.6)||721 (74.3)|
|Current smokinga||443 (43.6)||217 (51.4)||250 (25.7)|
Note: Data are presented as mean±standard deviation (SD) for continuous variables or N (%) for categorical variables. BMI, body mass index; NO2, nitrogen dioxide.
aCurrent smoking is defined as smoking in the last month and only current smokers with a smoking history greater than five pack-years were included.
bCumulative smoking defined by pack-years of cigarettes smoked in current smokers.
|CpG||Discovery cohort (n=1,017)||KORA F3 (n=422)||KORA F4 (n=971)|
Note: Effect estimate per 10–μg/m3 increase in NO2 concentration. Robust linear regression analysis adjusted for sex, age, BMI, current smoking, pack-years, technical variance. and blood cell composition.
Association between Air Pollution Exposure and Lung Function
Table 5 shows the association between NO2 exposure and lung function levels (see Table S8 for the associations between all pollutants and lung function). NO2 exposure was borderline significantly associated with FVC (B per 10 μg/m3 NO2=−106.3, 95% CI=−219.1−6.6, p=0.065) and with FEV1/FVC (B=1.5, 95% CI=−0.1−3.0, p=0.060). FEV1 was not significantly associated with NO2 exposure, indicating that the positive association between NO2 and FEV1/FVC is driven by a stronger negative association with FVC than FEV1. Given that NO2 exposure was associated with FVC and with FEV1/FVC, we examined the mediation by DNA methylation for FEV1, FVC and FEV1/FVC.
|B (95% CI)a||p-Value|
|FEV1 (mL)b||2.4 (−94.8, 99.6)||0.962|
|FVC (mL)b||−106.3 (−219.1, 6.6)||0.065|
|FEV1/FVC (%)c||1.5 (−0.1, 3.0)||0.06|
|FEF25–75 (mL/s)d||128.5 (−69.8, 326.8)||0.204|
aEffect estimates and 95% confidence interval (95% CI) for NO2 are given per 10–μg/m3 increase.
bFor FEV1 and FVC, robust regression analysis adjusted for sex, age, height, BMI, sex*age interaction, sex*height interaction, current-smoking, and pack-years.
cFor FEV1/FVC, robust regression analysis adjusted for sex, age, BMI, sex*age interaction, current-smoking, and pack-years.
dFor FEF25–75, robust regression analysis adjusted for sex, age, height, BMI, sex*age interaction, sex*height interaction, current-smoking, pack-years, and FVC.
Mediation analysis showed that one of the seven top CpG sites significantly mediated the association between NO2 exposure and FVC (cg14938677), and 2 CpG sites significantly mediated the association between NO2 and FEV1/FVC (cg14938677 and cg18379295) (Table S9).
We performed a cross-sectional genome-wide methylation study in blood to investigate whether long-term air pollution exposure is associated with DNA methylation in the LifeLines cohort study. We further investigated whether the association between air pollution exposure and lung function was mediated by DNA methylation. In our genome-wide methylation study, we identified differential DNA methylation at seven CpG sites to be genome-wide significantly associated with NO2 exposure. After removal of outliers in the methylation values, six CpG sites remained significantly associated with NO2 levels. Unfortunately, none of these associations could be significantly replicated in two independent cohorts. Further, higher levels of NO2 exposure were borderline significantly associated with lower FVC and higher FEV1/FVC levels. Finally, we found one out of seven CpG sites (cg14938677 in ARF5) was a significant mediator between NO2 exposure and FVC, and two CpG sites (cg14938677 in ARF5 and cg18379295 in GNG2) were significant mediators of the association between NO2 exposure and FEV1/FVC.
The top-significant CpG site (cg04908668) identified in our genome-wide methylation study on NO2 maps to PSMB9 (chromosome 6) and is associated with lower gene expression of PSMB9 and TAP1 (https://www.genenetwork.nl/biosqtlbrowser). PSMB9 and TAP1 are suggested to be involved in the pathophysiological mechanisms underlying COPD. Fujino et al. (2012) report both PSMB9 and TAP1 to be differentially expressed in alveolar epithelial type II cells isolated from COPD patients, in comparison with healthy subjects. The putative function of all genes identified in our study is presented in the Supplemental Material (Table S10). Interestingly, 2 of the 7 genome-wide significant CpG sites (i.e., cg14938677 and cg00344801) were also described by Joehanes et al. (2016) in relation to smoking habits, which might indicate they are general markers of inhaled particle exposure.
To date, genome-wide DNA methylation analyses of NO2 allowing a hypothesis-free assessment of epigenetic modifications are scarce. However, relevant evidence comes from a study in children by Gruzieva et al. (2017). In this epigenome-wide meta-analysis of methylation, prenatal NO2 exposure was associated with differential DNA methylation of genes involved in mitochondria and antioxidant defense pathways. Interestingly, in our genome-wide methylation study on NO2, we also identified a CpG (cg25769469) in PTCD2 that is reported to be involved in the mitochondrial RNA metabolism.
The positive association between NO2 exposure and FEV1/FVC found in our study is in line with findings reported in a larger sample of the LifeLines cohort (n=51,855 subjects) (De Jong et al. 2016). In this larger sample, NO2 had a stronger negative association with FVC than with FEV1 resulting in a higher FEV1/FVC. In our current smaller sample, the lack of significant association between NO2 and FEV1 may be the result of low study power (due to smaller sample size and smaller air pollution ranges). FEV1 and FVC are considered early indicators of chronic respiratory disease and predictors for cardiorespiratory mortality (Lee et al. 2011). Clinically, a reduced FVC along with FEV1 within a normal range is indicative (but not specific) of restrictive ventilatory abnormalities (Pellegrino et al. 2005). A comparison with existing studies shows that this restrictive effect is not universally seen. For example, in the ESCAPE study, the negative association between NO2 exposure and FEV1 and FVC are of equal magnitude (Adam et al. 2015). Because the main parameter for the diagnosis of restriction is a low total lung capacity (TLC), further studies including TLC are warranted to better elucidate whether the observed ventilatory pattern associated with NO2 exposure corresponds to a restrictive, obstructive or both types of disorders.
We tested mediation by DNA methylation to confirm our hypothesis that NO2 exposure may affect lung function through effects on DNA methylation. Among the seven differentially methylated CpG sites, two showed suggestive evidence for mediation (cg14938677 in ARF5 and cg18379295 in GNG2). ARF5 is a member of the human ADP-ribosylation factor (ARF) gene family that encodes small guanine nucleotide binding proteins. These proteins activate the phospholipase D (PLD), a critical enzyme involved in various endothelial and epithelial cell functions, such as actin cytoskeleton, vesicle trafficking for secretion, and endocytosis and receptor signaling (Jenkins and Frohman 2005). A family member, PLA1, was found to be significantly increased in plasma membrane of NO2–exposed pulmonary artery endothelial cells (Bhat et al. 1990; Sekharam et al. 1991). Furthermore, the redox regulation of bleomycin-induced PLD activation was reported to play a crucial role in the cytotoxicity underlying the idiopathic pulmonary fibrosis (Patel et al. 2011). The GNG2 (G protein subunit gamma 2) gene belongs to the heterotrimeric G protein family that underlies important pathways involved in cell migration, proliferation, differentiation, apoptosis, and responses to external signals (Olate and Allende 1991). Its distinct isoform subunits α, β, and γ are selectively expressed and enriched in different tissues including white blood cells and lung (Modarressi et al. 2000). To date, we do not know whether differential DNA methylation at this particular CpG site (cg18379295), located in the transcription start site of the gene, results in any functional variation in lung function. However, GNG2 was reported to be involved in airway hyper-responsiveness and inflammation elicited by an antigen challenge in a rabbit model of asthma (Nino et al. 2012). Furthermore, upon activation by G protein-coupled receptors (GPCRs), both free Gα and Gβγ subunits regulate important signaling pathways like the MAPK kinase cascade. This MAPK kinase cascade is involved in various immune and inflammatory cell functions and is a plausible mechanism linking air pollution exposure and respiratory and cardiovascular outcomes (Carmona et al. 2014).
A large number of studies have linked short- and mid-term PM exposure to global and gene-specific DNA methylation (Baccarelli et al. 2009; Bellavia et al. 2013; Chen et al. 2016; Peng et al. 2016; Wang et al. 2016). A genome-wide meta-analysis of DNA methylation and PM2.5 identified twelve genes regulating pathways involved in tumor development, inflammatory stimuli, pulmonary disorders and glucose metabolism (Panni et al. 2016). However, few studies have examined this association in the context of a long-term exposure window (Chi et al. 2016; Ward-Caviness et al. 2016). Although we found no genome-wide significant effect of PM exposure (considering all different size fractions) on DNA methylation, many CpG sites had suggestive effects, especially in response to PM2.5 (Table S8). Possibly, the relatively small range of PM levels and consequently a modest exposure contrast in LifeLines cohort may explain this lack of association. Future genome-wide methylation studies conducted in cohorts with a broader range of PM exposure is needed to clarify this association.
Our study is the largest genome-wide methylation study of air pollution exposure in adults, and the first study to assess the mediation effect of DNA methylation in the association between air pollution and the FEV1/FVC ratio. However, this study has some limitations. We used the individual’s home address as basis for the air pollution exposure estimates, ignoring the fact that a person could spend time in another environment (e.g., while traveling or working), which might lead to some degree of exposure misclassification at the individual level (Sunyer 2009). Interestingly, this exposure misclassification may lead to overestimation of the mediation effect (Valeri et al. 2017) when the methylation levels at our identified CpG sites are better biomarkers of personal NO2 exposure than the estimated NO2 exposure using land-use-regression models. The results of the mediation analyses should thus be interpreted with caution. In addition, because our study was cross-sectional in design, the inference of causality from these measures could be questionable.
We also recognize that ambient air pollution is a complex mixture and the effects attributed to some specific component might be influenced by the underlying toxicity of the full mixture of all pollutants. In this study, we estimated the association between various pollutants and DNA methylation, but only found genome-wide significant associations with NO2. The moderate to high correlation between NO2 and other pollutants prohibits the use of multipollutant models, and thus we cannot completely disentangle the independent pollutant effect. However, the top CpG sites differ for the different pollutants, indicating that each pollutant may have its own specific methylation target sites.
Another potential limitation of this study is the use of DNA methylation in blood samples when the outcome of interest is lung function. To what extent these epigenetic changes that we observe in peripheral blood cells reflect changes in DNA methylation in target tissues like the lung merits further investigation. Finally, the identified associations between NO2 exposure and DNA methylation did not replicate in two independent cohorts from the German KORA study. This lack of replication could be explained by the differences in age, gender, BMI, and smoking habits between the cohorts (see Table 3), and therefore more replication studies should be performed to validate these findings.
In the largest genome-wide methylation study to date, long-term NO2 exposure was associated with differential DNA methylation in blood in 1,017 subjects from the LifeLines cohort study. Among the significant NO2–associated DNA methylation sites, 2 CpGs can be considered potential mediators of the association between NO2 exposure and lung function. In this perspective, replication of these findings in other cohorts is necessary to elucidate the suggested role of epigenetic variability in the pathogenesis of NO2–exposure-related respiratory disease.
This study was funded by the Dutch Lung Foundation (grant number 4.1.13.007) and the Science Without Borders Brazilian program (grant number 234331/2014-3), as well as the São Paulo Research Foundation (FAPESP), (grant number 2016/13384-0) to AJFC Lichtenfels. The LifeLines Biobank initiative has been possible by funds from FES (Fonds Economische Structuurversterking), SNN (Samenwerkingsverband Noord Nederland), and REP (Ruimtelijk Economisch Programma).
Ackermann-Liebrich U, Leuenberger P, Schwartz J, Schindler C, Monn C, Bolognini G, et al. 1997. Lung function and long term exposure to air pollutants in Switzerland. Study on air pollution and lung diseases in adults (SAPALDIA) team. Am J Respir Crit Care Med 155(1):122–129, PMID: 9001300, 10.1164/ajrccm.155.1.9001300.
Adam M, Schikowski T, Carsin AE, Cai Y, Jacquemin B, Sanchez M, et al. 2015. Adult lung function and long-term air pollution exposure. ESCAPE: a multicentre cohort study and meta-analysis. Eur Respir J 45(1):38–50, PMID: 25193994, 10.1183/09031936.00130014.
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, et al. 2014. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 30(10):1363–1369, PMID: 24478339, 10.1093/bioinformatics/btu049.
Aulchenko YS, Ripatti S, Lindqvist I, Boomsma D, Heid IM, Pramstaller PP, et al. 2009. Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nat Genet 41(1):47–55, PMID: 19060911, 10.1038/ng.269.
Baccarelli A, Wright RO, Bollati V, Tarantini L, Litonjua AA, Suh HH, et al. 2009. Rapid DNA methylation changes after exposure to traffic particles. Am J Respir Crit Care Med 179(7):572–578, PMID: 19136372, 10.1164/rccm.200807-1097OC.
Barone-Adesi F, Dent JE, Dajnak D, Beevers S, Anderson HR, Kelly FJ, et al. 2015. Long-term exposure to primary traffic pollutants and lung function in children: cross-sectional study and meta-analysis. PLoS One 10(11):e0142565, PMID: 26619227, 10.1371/journal.pone.0142565.
Beelen R, Hoek G, Vienneau D, Eeftens M, Dimakopoulou K, Pedeli X, et al. 2013. Development of NO2 and NOx land use regression models for estimating air pollution exposure in 36 study areas in Europe — The ESCAPE project. Atmospheric Environment 72:10–23, 10.1016/j.atmosenv.2013.02.037.
Bellavia A, Urch B, Speck M, Brook RD, Scott JA, Albetti B, et al. 2013. DNA hypomethylation, ambient particulate matter, and increased blood pressure: findings from controlled human exposure experiments. J Am Heart Assoc 2(3):e000212, PMID: 23782920, 10.1161/JAHA.113.000212.
Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, et al. 2011. High density DNA methylation array with single CpG site resolution. Genomics 98(4):288–295, PMID: 21839163, 10.1016/j.ygeno.2011.07.007.
Bind MA, Lepeule J, Zanobetti A, Gasparrini A, Baccarelli A, Coull BA, et al. 2014. Air pollution and gene-specific methylation in the Normative Aging Study: association, effect modification, and mediation analysis. Epigenetics 9(3):448–458, PMID: 24385016, 10.4161/epi.27584.
Boezen HM. 2009. Genome-wide association studies: what do they teach us about asthma and chronic obstructive pulmonary disease? Proc Am Thorac Soc 6(8):701–703, PMID: 20008879, 10.1513/pats.200907-058DP.
Carmona JJ, Sofer T, Hutchinson J, Cantone L, Coull B, Maity A, et al. 2014. Short-term airborne particulate matter exposure alters the epigenetic landscape of human genes associated with the mitogen-activated protein kinase network: a cross-sectional study. Environ Health 13:94, PMID: 25395096, 10.1186/1476-069X-13-94.
Chen R, Meng X, Zhao A, Wang C, Yang C, Li H, et al. 2016. DNA hypomethylation and its mediation in the effects of fine particulate air pollution on cardiovascular biomarkers: a randomized crossover trial. Environ Int 94:614–619, PMID: 27397927, 10.1016/j.envint.2016.06.026.
Chi GC, Liu Y, MacDonald JW, Barr RG, Donohue KM, Hensley MD, et al. 2016. Long-term outdoor air pollution and DNA methylation in circulating monocytes: results from the Multi-Ethnic Study of Atherosclerosis (MESA). Environ Health 15(1):119, PMID: 27903268, 10.1186/s12940-016-0202-4.
Cyrys J, Heinrich J, Hoek G, Meliefste K, Lewné M, Gehring U, et al. 2003. Comparison between different traffic-related particle indicators: elemental carbon (EC), PM2.5 mass, and absorbance. J Expo Anal Environ Epidemiol 13(2):134–143, PMID: 12679793, 10.1038/sj.jea.7500262.
De Jong K, Vonk JM, Zijlema WL, Stolk RP, van der Plaat DA, Hoek G, et al. 2016. Air pollution exposure is associated with restrictive ventilatory patterns. Eur Respir J 48(4):1221–1224, PMID: 27492831, 10.1183/13993003.00556-2016.
De Prins S, Koppen G, Jacobs G, Dons E, Van de Mieroop E, Nelen V, et al. 2013. Influence of ambient air pollution on global DNA methylation in healthy adults: a seasonal follow-up. Environ Int 59:418–424, PMID: 23917442, 10.1016/j.envint.2013.07.007.
Ding R, Jin Y, Liu X, Zhu Z, Zhang Y, Wang T, et al. 2016. Characteristics of DNA methylation changes induced by traffic-related air pollution. Mutat Res Genet Toxicol Environ Mutagen 796:46–53, PMID: 26778509, 10.1016/j.mrgentox.2015.12.002.
Eeftens M, Beelen R, de Hoogh K, Bellander T, Cesaroni G, Cirach M, et al. 2012. Development of Land Use Regression models for PM(2.5), PM(2.5) absorbance, PM(10) and PM(coarse) in 20 European study areas; results of the ESCAPE project. Environ Sci Technol 46(20):11195–11205, PMID: 22963366, 10.1021/es301948k.
Forbes LJ, Kapetanakis V, Rudnicka AR, Cook DG, Bush T, Stedman JR, et al. 2009. Chronic exposure to outdoor air pollution and lung function in adults. Thorax 64(8):657–663, PMID: 19359266, 10.1136/thx.2008.109389.
Fujino N, Ota C, Takahashi T, Suzuki T, Suzuki S, Yamada M, et al. 2012. Gene expression profiles of alveolar type II cells of chronic obstructive pulmonary disease: a case-control study. BMJ Open 2(6):pii: e001553, PMID: 23117565, 10.1136/bmjopen-2012-001553.
Gehring U, Gruzieva O, Agius RM, Beelen R, Custovic A, Cyrys J, et al. 2013. Air pollution exposure and lung function in children: the ESCAPE project. Environ Health Perspect 121(11–12):1357–1364, PMID: 24076757, 10.1289/ehp.1306770.
Griffiths AJF, Wessler SR, Carroll SB, Doebley J. 2011. Regulation of gene expression in eukaryotes. In: Introduction to Genetic Analysis, 10th revised edition. New York, NY:W.H. Freeman & Co., 455–456.
Gruzieva O, Xu CJ, Breton CV, Annesi-Maesano I, Antó JM, Auffray C, et al. 2017. Epigenome-wide meta-analysis of methylation in children related to prenatal NO2 air pollution exposure. Environ Health Perspect 125(1):104–110, PMID: 27448387, 10.1289/EHP36.
Hayes AF. 2009. Beyond Baron and Kenny: statistical mediation analysis in the new millennium. Communication Monographs Volume 76 (4):408–420, 10.1080/03637750903310360, [accessed 8 November 2016].
Hobbs BD, de Jong K, Lamontagne M, Bossé Y, Shrine N, Artigas MS, et al. 2017. Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis. Nat Genet 49(3):426–432, PMID: 28166215, 10.1038/ng.3752.
Holloway JW, Savarimuthu Francis S, Fong KM, Yang IA. 2012. Genomics and the respiratory effects of air pollution exposure. Respirology 17(4):590–600, PMID: 22404320, 10.1111/j.1440-1843.2012.02164.x.
Hou L, Zhang X, Zheng Y, Wang S, Dou C, Guo L, et al. 2014. Altered methylation in tandem repeat element and elemental component levels in inhalable air particles. Environ Mol Mutagen 55(3):256–265, PMID: 24273195, 10.1002/em.21829.
Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, et al. 2012. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 13:86, PMID: 22568884, 10.1186/1471-2105-13-86.
Joehanes R, Just AC, Marioni RE, Pilling LC, Reynolds LM, Mandaviya PR, et al. 2016. Epigenetic Signatures of Cigarette Smoking. Circ Cardiovasc Genet 9(5):436–447, PMID: 27651444, 10.1161/CIRCGENETICS.116.001506.
Lehne B, Drong AW, Loh M, Zhang W, Scott WR, Tan ST, et al. 2015. A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. Genome Biol 16:37, PMID: 25853392, 10.1186/s13059-015-0600-x.
Lepeule J, Bind MA, Baccarelli AA, Koutrakis P, Tarantini L, Litonjua A, et al. 2014. Epigenetic influences on associations between air pollutants and lung function in elderly men: the normative aging study. Environ Health Perspect 122(6):566–572, PMID: 24602767, 10.1289/ehp.1206458.
LifeLines Cohort Study. 2016 Home page. http://www.lifelines.net [accessed 8 November 2016].
Madrigano J, Baccarelli A, Mittleman MA, Wright RO, Sparrow D, Vokonas PS, et al. 2011. Prolonged exposure to particulate pollution, genes associated with glutathione pathways, and DNA methylation in a cohort of older men. Environ Health Perspect 119(7):977–982, PMID: 21385671, 10.1289/ehp.1002773.
Mayer A, Thoemmes F, Rose N, Steyer R, West SG. 2014. Theory and analysis of total, direct, and indirect causal effects. Multivariate Behav Res 49(5):425–442. PMID: 26732357, http://www.tandfonline.com/doi/abs/10.1080/00273171.2014.931797 [accessed 8 November 2016].
Modarressi MH, Taylor KE, Wolfe J. 2000. Cloning, characterization, and mapping of the gene encoding the human G protein gamma 2 subunit. Biochem Biophys Res Commun 272(2):610–615, PMID: 10833460, 10.1006/bbrc.2000.2832.
Nino G, Hu A, Grunstein JS, McDonough J, Kreiger PA, Josephson MB, et al. 2012. G protein βγ-subunit signaling mediates airway hyperresponsiveness and inflammation in allergic asthma. PLoS One 7(2):e32078, PMID: 22384144, 10.1371/journal.pone.0032078.
Nitschke M, Appleton SL, Li Q, Tucker GR, Shah P, Bi P, et al. 2016. Lung function reductions associated with motor vehicle density in chronic obstructive pulmonary disease: a cross-sectional study. Respir Res 17(1):138, PMID: 27776510, 10.1186/s12931-016-0451-3.
Panni T, Mehta AJ, Schwartz JD, Baccarelli AA, Just AC, Wolf K, et al. 2016. Genome-wide analysis of DNA methylation and fine particulate matter air pollution in three study populations: KORA F3, KORA F4, and the Normative Aging Study. Environ Health Perspect 124(7):983–990, PMID: 26731791, 10.1289/ehp.1509966.
Patel RB, Kotha SR, Sherwani SI, Sliman SM, Gurney TO, Loar B, et al. 2011. Pulmonary fibrosis inducer, bleomycin, causes redox-sensitive activation of phospholipase D and cytotoxicity through formation of bioactive lipid signal mediator, phosphatidic acid, in lung microvascular endothelial cells. Int J Toxicol 30(1):69–90, PMID: 21131602, 10.1177/1091581810388850.
Pellegrino R, Viegi G, Brusasco V, Crapo RO, Burgos F, Casaburi R, et al. 2005. Interpretative strategies for lung function tests. Eur Respir J 26(5):948–968, PMID: 16264058, 10.1183/09031936.05.00035205.
Peng C, Bind MC, Colicino E, Kloog I, Byun HM, Cantone L, et al. 2016. Particulate air pollution and fasting blood glucose in nondiabetic individuals: associations and epigenetic mediation in the Normative Aging Study, 2000-2011. Environ Health Perspect 124(11):1715–1721, PMID: 27219535, 10.1289/EHP183.
Pidsley R, Y Wong CC, Volta M, Lunnon K, Mill J, Schalkwyk LC. 2013. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genomics 14:293, PMID: 23631413, 10.1186/1471-2164-14-293.
Pitchika A, Hampel R, Wolf K, Kraus U, Cyrys J, Babisch W, et al. 2017. Long-term associations of modeled and self-reported measures of exposure to air pollution and noise at residence on prevalent hypertension and blood pressure. Sci Total Environ 593-594:337–346, PMID: 28346907, 10.1016/j.scitotenv.2017.03.156.
Rückert IM, Heier M, Rathmann W, Baumeister SE, Döring A, Meisinger C. 2011. Association between markers of fatty liver disease and impaired glucose regulation in men and women from the general population: the KORA-F4-study. PLoS One 6(8):e22932, PMID: 21850244, 10.1371/journal.pone.0022932.
Sanchez-Guerra M, Zheng Y, Osorio-Yanez C, Zhong J, Chervona Y, Wang S, et al. 2015. Effects of particulate matter exposure on blood 5-hydroxymethylation: results from the Beijing truck driver air pollution study. Epigenetics 10(7):633–642, PMID: 25970091, 10.1080/15592294.2015.1050174.
Scholtens S, Smidt N, Swertz MA, Bakker SJ, Dotinga A, Vonk JM, et al. 2015. Cohort profile: LifeLines, a three-generation cohort study and biobank. Int J Epidemiol 44(4):1172–1180, PMID: 25502107, 10.1093/ije/dyu229.
Sekharam KM, Patel JM, Block ER. 1991. Plasma membrane-specific phospholipase A1 activation by nitrogen dioxide in pulmonary artery endothelial cells. Toxicol Appl Pharmacol 107(3):545–554, PMID: 2000640, 10.1016/0041-008X(91)90317-8.
Tarantini L, Bonzini M, Apostoli P, Pegoraro V, Bollati V, Marinelli B, et al. 2009. Effects of particulate matter on genomic DNA methylation content and iNOS promoter methylation. Environ Health Perspect 117(2):217–222. Erratum in: Environ Health Perspect 2009. 117(4):A143, PMID: 19270791, 10.1289/ehp.11898.
Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, et al. 2012. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics 29(2):189–196, PMID: 23175756, 10.1093/bioinformatics/bts680.
Urman R, McConnell R, Islam T, Avol EL, Lurmann FW, Vora H, et al. 2014. Associations of children’s lung function with ambient air pollution: joint effects of regional and near-roadway pollutants. Thorax 69(6):540–547, PMID: 24253832, 10.1136/thoraxjnl-2012-203159.
Valeri L, Reese SL, Zhao S, Page CM, Nystad W, Coull BA, et al. 2017. Misclassified exposure in epigenetic mediation analyses. Does DNA methylation mediate effects of smoking on birthweight? Epigenomics 9(3):253–265, PMID: 28234025, 10.2217/epi-2016-0145.
Wang C, Chen R, Cai J, Shi J, Yang C, Tse LA, et al. 2016. Personal exposure to fine particulate matter and blood pressure: a role of angiotensin converting enzyme and its DNA methylation. Environ Int 94:661–666, PMID: 27397929, 10.1016/j.envint.2016.07.001.
Ward-Caviness CK, Nwanaji-Enwerem JC, Wolf K, Wahl S, Colicino E, Trevisi L, et al. 2016. Long-term exposure to air pollution is associated with biological aging. Oncotarget 7(46):74510–74525, PMID: 27793020, 10.18632/oncotarget.12903.
Wichmann HE, Gieger C, Illig T. 2005. KORA-gen–resource for population genetics, controls and a broad spectrum of disease phenotypes. Gesundheitswesen 67 (Suppl 1):S26–S30, PMID: 16032514, 10.1055/s-2005-858226.
Zeilinger S, Kühnel B, Klopp N, Baurecht H, Kleinschmidt A, Gieger C, et al. 2013. Tobacco smoking leads to extensive genome-wide changes in DNA methylation. PloS one 8(5):e63812, PMID: 23691101, 10.1371/journal.pone.0063812.
Zijlema WL, Smidt N, Klijs B, Morley DW, Gulliver J, de Hoogh K, et al. 2016. The LifeLines cohort study: a resource providing new opportunities for environmental epidemiology. Arch Public Health 74:32, PMID: 27482379, 10.1186/s13690-016-0144-x.