1. INTRODUCTION
Air pollution exposure is estimated to contribute to approximately seven million early deaths every year worldwide and more than 3% of disability-adjusted life years lost. Air pollution has numerous harmful effects on health and contributes to the development and morbidity of cardiovascular disease, metabolic disorders, and a number of lung pathologies, including asthma and chronic obstructive pulmonary disease (COPD). Emerging data indicate that air pollution exposure modulates the epigenetic mark, DNA methylation (DNAm), and that these changes might in turn influence inflammation, disease development, and exacerbation risk.
Understanding the complex relationship between environmental factors, the epigenome, and the effects of air pollutant exposure has the potential to lead to the identification of transformative biomarkers of susceptibility and effect that will drive the next generation of risk assessment. While promising, moving forward will require that critical questions be addressed and that challenges be overcome.
2. CONTEXT (FINDINGS)
Studying various biological mechanisms – such as single-nucleotide polymorphisms (SNPs), epigenetic modifications (methylation of genes), gene expression (transcriptome), and microRNA regulation – can enhance our understanding of how air pollutants harm the lungs (Fig. 10.1). Genome-wide association studies (GWAS) have linked specific SNPs respiratory conditions, while air pollution exposure alters DNA methylation, gene expression and microRNA (short non-coding RNA that regulate gene expression) activity. Research using cell and animal models shows distinct gene expression changes due to pollutants like particulate matter and ozone. To mitigate lung damage, especially in those with or at risk of chronic lung disease, strategies must address both pollution control and protective interventions. Genomic research can aid in developing treatments for pollution-related lung injury.
Figure 10.1 ‘Omics’ approaches to studying the respiratory effects of air pollutant exposure (source: Holloway et al., 2012)
Extensive research has shown that differing types of air pollution (e.g. particulates, ozone and nitrogen dioxide) trigger distinct biological responses. For instance, particulate matter (PM) is proven to damage lung and respiratory cells, induce inflammation, and generate reactive oxygen species (ROS), leading to oxidative stress and cytokine release. Sequencing-based approaches, such as DNA methylation profiling and histone modification analysis, hold great promise in unraveling the epigenetic alterations induced by PM exposure.
Individual responses to air pollution exposure vary due to extrinsic (e.g., diet, prior exposure, climate, pre-existing disease) and intrinsic (e.g., age, gender) factors with genetic and epigenetic differences playing a key role. Studies in inbred animal strains highlight genetic influences on pollutant responses. Identifying genetic determinants of variability in humans is essential for understanding lung disease mechanisms, recognizing at-risk populations, and developing targeted prevention strategies, while also informing public health policies on safe exposure levels based on population sensitivity.
2.1. Biological response to air pollutants exposure
The two main approaches to the study of the genetics of disease are:
- Candidate gene approach– It assumes that genetic variation in a trait is largely due to functional mutations in specific genes known to influence development. It is widely used in gene-disease research, genetic association studies, and drug target identification. The candidate gene approach is a powerful and cost-effective method for studying complex traits and discovering genes directly. However, its effectiveness is limited by reliance on existing biological knowledge, which remains incomplete for many traits. Despite identifying many candidate genes, new strategies are needed to overcome this information bottleneck and advance genetic research.
- Hypothesis-independent approaches– In recent years, the study of the genetic basis of complex disease has been revolutionized by technological advances in array-based SNP genotyping technologies and the characterization of millions of SNP variants in the human genome. Genome-wide association studies (GWAS) now allow hypothesis-independent analysis of genetic factors in case-control and population-based samples. GWAS have identified statistically significant associations for numerous phenotypes, including common diseases and physiological traits, providing valuable insight into the biological processes underlying these conditions. Genome-wide scanning usually proceeds without any presuppositions regarding the importance of specific functional features of the investigated traits, but of which the principal disadvantage is expensive and resource intensive.
Learn: How to perform array-based SNP genotyping (video)
Learn: Genome-wide association studies (video)
Table 10.1 summarizes key findings investigating the genetic determinants of responses to air pollution exposure. It highlights how genetic variations influence susceptibility to pollutants such as ozone, PM and sulphur dioxide, as well as their impact on oxidative stress, inflammation and lung function. Understanding these genetic factors can help identify at-risk population and guide future research on preventive strategies and personalized interventions.
Table 10.1 Genetic Determinants of Response to Air Pollution: Key Findings from Candidate Gene and GWAS Studies
| Study type | Key findings | Implications | Reference |
| Ozone exposure study | Susceptible genotypes showed excessive DNA damage and higher oxidative stress under ozone exposure | Highlights need for targeted prevention in genetically susceptible individuals. Suggests potential biomarkers for identifying high-risk individuals | Bergamaschi et al., 2001 |
| PM and allergic response | Low antioxidant genotypes had enhanced nasal IgE and histamine responses, worsened by second-hand smoke | Indicated genetic predisposition to stronger allergic reactions in polluted environments | Gilliland et al., 2004 |
| Inflammatory response & TNF polymorphisms | TNF-308G genotype linked to greater FEV1 decline with ozone exposure | Identifies inflammatory-related genetic factors in pollution susceptibility | Yang et al., 2005 |
| Controlled exposure approach / GWAS in radiation response | A study using 277 lymphoblastoid cell lines identified 50 SNPs in 14 loci affecting radiation sensitivity, validated through siRNA knockdowns | Offers precise control of exposure levels and conditions, allowing measurements of lung function, inflammation, and gene expression changes | Nie et al., 2010 |
| SPIROMETA & CHARGE consortium study | Identified loci associated with lung function | Provide genetic targets for further research into lung function decline | Repapi et al., 2010 |
2.2. Epigenome-wideapproaches for study epigenetic processes
Epigenetics is the process where changes occur in gene functions without changing their underline DNA sequences. Such changes, which may get reflected in cellular and physiological traits, can be generated by environmental factors, besides being a part of the normal developmental phenomena. DNA methylation and histone modifications are two key processes which alter gene functions without changing the DNA sequences (Fig. 10.2).
Figure 10.2 Epigenetic alterations in the mammalian system. (a) DNA methylation at the DNA bases, (b) different types of modifications at the histone tails, and (c) interference of the non-coding RNAs (ncRNAs) with the gene expression process (Mukherjee et al., 2021)
DNA methylation (DNAm)
DNAm describes the attachment of methyl groups to DNA by DNA methyltransferases (DNMT), usually at the fifth carbon of cytosines, leading to the formation of 5-methylcytosine (5-mC). DNA demethylation occurs passively through a lack of maintenance during cell division or by the activity of enzymes. In mammals, DNAm predominantly occurs at C-G dinucleotides, referred to as CpGs. DNAm in the promoter regions of genes may contribute, along with histone variants, histone modifications, and non-coding RNAs, to the regulation of gene expression. DNAm of CpG sites located in gene bodies may be related to transcription initiation, elongation efficiency, and alternative splicing.
The effects of air pollution on DNAm can be investigated using several different study designs:
- Epidemiological-land use regression study design– Epidemiological studies estimate air pollution exposure using land use regression (LUR) models based on geography and sensor data. Volunteers provide samples (e.g., blood), and pollutant levels at their home addresses are averaged over different time windows. These estimates are correlated with DNA methylation data to assess health effects. While this method captures real-world exposure, limitations include controlling personal factors, selecting time windows, and limited population variation during the study period.
- Population study design– This approach compares people living in high- and low-pollution areas, such as industrial vs. rural regions. After adjusting for population differences, this method estimates the health effects of increased pollution exposure. However, challenges include matching participant characteristics, as socioeconomic and healthcare disparities often exist between these areas.
- Controlled crossover exposure studies– Those studies expose volunteers to set air pollution levels in a facility, followed by a control exposure after a washout period. This design reduces confounding factors since individuals serve as their own controls. However, these studies are costly, challenging to implement, and may be affected by carryover effects if washout periods are too short.
DNAm data from different studies is measurable using standardized platforms and is reflective of transcription factor binding and gene expression. DNAm is, therefore, a logical tool for trying to understand air pollution’s effect on genomic function and downstream measures of interest to health. Combining multiple study methods can provide a more comprehensive understanding of air pollution’s effects on DNA methylation.
Histone modification and air pollution exposure
Histones can also be modified by several ways, such as acetylation, methylation, phosphorylation, and ubiquitination. Air pollution affects histone modifications, but large population studies on this topic are limited. Studies show that exposure to pollutants like nickel, arsenic, iron, and polyaromatic hydrocarbons alters histone methylation and acetylation, impacting gene expression and inflammatory responses. Benzo[a]pyrene exposure also modifies histones and reduces DNA methylation. Sirt1, a member of class III histone deacetylase (HDAC), helps regulate PM-induced inflammation in the lungs, while cigarette smoke alters DNMT and HDAC expression, leading to inflammation. PM10 and diesel exhaust particles can disrupt histone acetylation balance in bronchial epithelial cells, contributing to respiratory inflammation.
3. ALTERNATIVES (DISCUSSION)
3.1. Genome-wideinteraction studies (GWIS)
The candidate-gene approach described above is not capable of identifying novel genes, contributing to the phenotype being analysed, thus, limiting its insight into disease mechanisms. While the GWAS approach has successfully identified genetic variants for respiratory diseases, it explains only a small portion of heritability, possibly due to gene–environment (GxE) interactions or more complex pathways involving multiple genes and exposures. There has therefore been considerable interest in exploring GxE interactions in a genome-wide hypothesis independent manner in studies where exposure information is available. Such studies have been termed genome-wide interaction studies (GWIS). However, GWIS faces some challenges as well, those include: accurate exposure assessment, large sample requirements, and heterogeneity between studies.
Despite these challenges, investigators have begun to utilize GWIS to identify genetic variants underlying complex diseases. For example, Beaty et al. conducted a GWAS on non-syndromic cleft palate, a common birth defect influenced by both genetic and environmental factors. Although no single SNP achieved genome-wide significance on its own, several gene markers became significant when GxE interaction with three common maternal exposures (maternal smoking, alcohol consumption, and multivitamin supplementation) were considered. This underscores the importance of incorporating GxE interactions in genetic studies, as many genetic effects may only become apparent in exposed populations.
3.2. Airpollution exposures and epigenome alterations
Environmental epigenetics studies, often based on simple epidemiological models (Fig. 10.3A), have demonstrated links between air pollution exposures and changes in the epigenome. However, in order to determine whether the epigenetic changes play a causal role in air pollution-related health effects, a more integrated approach combining mechanistic, clinical, and epidemiologic research is needed. As our understanding of epigenetic gene regulation deepens, researchers recognize that the relationship between environmental exposure and epigenetic modification is highly complex. The Seed and Soil model suggests that instead of playing a single role, epigenetic changes may act as effects, effect modifiers, or mediators at different points in time (Fig. 10.3B). For instance, a study by Gregory et al. demonstrated that maternal exposure to diesel at one time point (t=1) could alter the newborn’s epigenetic state (t=2) which might later interact with environmental factors to trigger an allergic response (t=3). Rather than viewing these stages separately, linking them provides greater insight into risk assessment, potential health interventions, and future research directions. An ideal study of air pollution and epigenetics would track exposure, biological effects (such as inflammation markers), and epigenetic modifications over time in a longitudinal design. Yet, analysing such complex interactions requires sophisticated statistical techniques and the study design would benefit from input from biostatisticians or systems biologists to ensure accurate interpretation.
Figure 10.3 Conceptual diagram of hypothesized roles of epigenetic modification in the exposure to effect relationship (McCullough et al., 2017)
4. SOLUTION
4.1. Genes– environment interaction study
The development and severity of lung disease like asthma and COPD are influenced by genetic and epigenetic susceptibility interaction with environmental exposures, including air pollution. Some genetic polymorphisms only influence disease outcomes in exposed individuals, while in some cases, their effects may even reverse depending on environmental conditions, a phenomenal known as “flip-flop” effects. Therefore, studying GxE interactions is essential for improving population risk estimates, identifying genetically susceptible individuals, inferring causality using Mendelian randomization, and understanding biological pathways involved in pollutant response, aiding in targeted therapy development.
Research has extensively explored how genetic variations, particularly in antioxidant genes, influence susceptibility to respiratory diseases when combined with air pollution exposure. Several polymorphisms in genes like GSTM1, GSTP1, GSTT1, NQO1, SOD2 (MnSOD), and GPX1 have been linked to asthma and COPD, with studies showing interactions between these genes and exposure to ozone, NO and PM. Furthermore, a systematic review by Minelli et al. identified 12 epidemiological studies and three controlled exposure studies, supporting the presence of GxE interactions. Multiple studies linked GST gene polymorphisms to asthma and childhood wheezing in polluted environments. A clinical trial in Mexico City revealed that asthmatic children with a low-antioxidant GSTM1 genotype experienced lung function decline with rising ozone levels, but supplementation with vitamins C and E helped mitigate this effect. This finding highlights the potential for targeted interventions to protect genetically susceptible individuals from air-pollution related respiratory harm.
4.2. Epigenomic modifications in air pollution research
DNA methylation is one of many epigenetic modifications and is unlikely to be the sole driver of exposure-related effects. The complexity of studying epigenetic modifications can be challenging due to technological limitations and limited sample material. Additionally, recent discoveries about the varied roles of DNA methylation derivatives in gene expression regulation add another layer of complexity. Standard bisulfite conversion methods cannot differentiate these, making accurate detection difficult. Newer techniques like oxidative bisulfite arrays improve accuracy but are costly and require more sample material.
Advancements in epigenome mapping have led to publicly available epigenome browsers, which help visualize histone modifications across cell types thus facilitating the selection of target histone modifications. Improved ChIP-seq techniques with enhanced efficiency, reproducibility and normalization, have made histone modification analysis more feasible for toxicoepigenetic studies. However, detecting exposure-related epigenetic changes is only the first step – establishing a causal link between air pollution, the epigenome, and adverse health outcomes requires more fundamental research.
Traditional methods for modifying epigenetic marks, such as using small molecule inhibitors or small interfering RNAs (siRNAs) tend to produce widespread effects across the genome, making it difficult to pinpoint the role of specific modifications at individual loci. CRISPR-based epigenetic editing overcomes this by using deactivated Cas9 to precisely target loci with transcription factors, histone-modifying enzymes, or DNA methyltransferases/demethylases. This allows controlled epigenetic modifications in cell and animal models, elucidating the role of epigenetic changes observed in human studies. The development and implication of these tools will be crucial in reinforcing and expanding findings from large-scale studies and will help to establish causal relationships between air pollution, epigenetic alterations, and health outcomes.
5. RECOMMENDATIONS (CONCLUSION)
Air pollution continues to pose a significant global health challenge, with widespread impacts on respiratory health. Advances in ‘omics’ technologies have opened new avenues for systematically investigating how air pollution affects the lungs at a molecular level. Researchers are now able to examine the interplay between air pollution and genetic variations, chemical modifications (epigenome), gene expression patterns (transcriptome), and the role of microRNAs in gene regulation.
While reducing air pollution levels remains a critical public health goal, it is equally important to develop strategies that protect vulnerable populations – such as individuals with chronic respiratory conditions or those at risk of developing lung disease due to prolonged pollutant exposure. By exploring genomic responses to air pollution, researchers can deepen their understanding of disease mechanisms and pave the way for future clinical trials aimed at mitigating the harmful effects of pollutants. These insights will be essential for developing targeted interventions to minimize lung damage and improve public health outcomes.
6. REFERENCES
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