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Genomics and the respiratory effects of air pollution exposure
Abstract
Adverse health effects from air pollutants remain important, despite improvement in air quality in the past few decades. The exact mechanisms of lung injury from exposure to air pollutants are not yet fully understood. Studying the genome (e.g. single-nucleotide polymorphisms (SNP) ), epigenome (e.g. methylation of genes), transcriptome (mRNA expression) and microRNAome (microRNA expression) has the potential to improve our understanding of the adverse effects of air pollutants. Genome-wide association studies of SNP have detected SNP associated with respiratory phenotypes; however, to date, only candidate gene studies of air pollution exposure have been performed. Changes in epigenetic processes, such DNA methylation that leads to gene silencing without altering the DNA sequence, occur with air pollutant exposure, especially global and gene-specific methylation changes. Respiratory cell line and animal models demonstrate distinct gene expression signatures in the transcriptome, arising from exposure to particulate matter or ozone. Particulate matter and other environmental toxins alter expression of microRNA, which are short non-coding RNA that regulate gene expression. While it is clearly important to contain rising levels of air pollution, strategies also need to be developed to minimize the damaging effects of air pollutant exposure on the lung, especially for patients with chronic lung disease and for people at risk of future lung disease. Careful study of genomic responses will improve our understanding of mechanisms of lung injury from air pollution and enable future clinical testing of interventions against the toxic effects of air pollutants.
... GSTs have been studied as possible effect modifiers of the association between air pollution exposure and respiratory and allergic diseases [17]. Among the numerous GST polymorphisms, three isozymes, glutathione S-transferase theta 1 (GSTT1), glutathione S-transferase mu 1 (GSTM1), and glutathione S-transferase pi 1 (GSTP1), have gained special interest due to their involvement in biological pathways and their role in detoxification of endogenous agents, such as tobacco smoke and air pollution. ...
... Among the numerous GST polymorphisms, three isozymes, glutathione S-transferase theta 1 (GSTT1), glutathione S-transferase mu 1 (GSTM1), and glutathione S-transferase pi 1 (GSTP1), have gained special interest due to their involvement in biological pathways and their role in detoxification of endogenous agents, such as tobacco smoke and air pollution. The null variants of GSTT1 and GSTM1 and ile/val alleles of GSTP1 have been widely studied, and it has been shown that individuals with these variants have different susceptibility to environmental toxicants, including smoke and air pollution exposure [17,18]. ...
... Identifying how genetic factors modify the relationship between TRAP exposure and respiratory diseases and allergies helps in understanding the underlying biological mechanisms, disease pathogenesis, and, most importantly, in identifying individuals at high risk of allergic and respiratory diseases. Identification of high-risk groups provides a better focus for new preventive and/ or therapeutic approaches [17,18]. The last review on this topic was published in 2011 [19••]. ...
Purpose of review:
The purpose of this review is to summarize the evidence from recently published original studies investigating how glutathione S-transferase (GST) gene polymorphisms modify the impact of air pollution on asthma, allergic diseases, and lung function.
Recent findings:
Current studies in epidemiological and controlled human experiments found evidence to suggest that GSTs modify the impact of air pollution exposure on respiratory diseases and allergies. Of the nine articles included in this review, all except one identified at least one significant interaction with at least one of glutathione S-transferase pi 1 (GSTP1), glutathione S-transferase mu 1 (GSTM1), or glutathione S-transferase theta 1 (GSTT1) genes and air pollution exposure. The findings of these studies, however, are markedly different. This difference can be partially explained by regional variation in the exposure levels and oxidative potential of different pollutants and by other interactions involving a number of unaccounted environment exposures and multiple genes. Although there is evidence of an interaction between GST genes and air pollution exposure for the risk of respiratory disease and allergies, results are not concordant. Further investigations are needed to explore the reasons behind the discordancy.
... However, it is likely that the association between air pollution and respiratory health is influenced by individual genetic susceptibility [17][18][19]. Genetic variation in single nucleotide polymorphisms (SNPs) contributes to some variability in the individual response to air pollutants and the probability to develop respiratory impairment [20,21]. SNPs acting along with environmental factors on respiratory health have already been reported in gene-environment interaction (GxE) studies [17,18]. ...
... The association between chronic air pollution and respiratory health on airway inflammation is likely to be influenced by individual genetic susceptibility [17,18,20]. To the best of our knowledge, there is only one GxE study of air pollution-induced airway inflammation. ...
Background
Air pollutants can activate low-grade subclinical inflammation which further impairs respiratory health. We aimed to investigate the role of polygenic susceptibility to chronic air pollution-induced subclinical airway inflammation.
Methods
We used data from 296 women (69–79 years) enrolled in the population-based SALIA cohort (Study on the influence of Air pollution on Lung function, Inflammation and Aging). Biomarkers of airway inflammation were measured in induced-sputum samples at follow-up investigation in 2007–2010. Chronic air pollution exposures at residential addresses within 15 years prior to the biomarker assessments were used to estimate main environmental effects on subclinical airway inflammation. Furthermore, we calculated internally weighted polygenic risk scores based on genome-wide derived single nucleotide polymorphisms. Polygenic main and gene-environment interaction (GxE) effects were investigated by adjusted linear regression models.
Results
Higher exposures to nitrogen dioxide (NO2), nitrogen oxides (NOx), particulate matter with aerodynamic diameters of ≤ 2.5 μm, ≤ 10 μm, and 2.5–10 µm significantly increased the levels of leukotriene (LT)B4 by 19.7% (p-value = 0.005), 20.9% (p = 0.002), 22.1% (p = 0.004), 17.4% (p = 0.004), and 23.4% (p = 0.001), respectively. We found significant effects of NO2 (25.9%, p = 0.008) and NOx (25.9%, p-value = 0.004) on the total number of cells. No significant GxE effects were observed. The trends were mostly robust in sensitivity analyses.
Conclusions
While this study confirms that higher chronic exposures to air pollution increase the risk of subclinical airway inflammation in elderly women, we could not demonstrate a significant role of polygenic susceptibility on this pathway. Further studies are required to investigate the role of polygenic susceptibility.
Graphical Abstract
... This epimutation is thought to involve mitochondrial DNA, allele imprinting, histone withholding, and non-coding RNAs, and the harmful changes may be passed down across generations, resulting in transgenerational epigenomic inheritance [129]. In addition, respiratory cell lines and animal models have also demonstrated distinct gene expression signatures in the transcriptome when exposed to particulate matter or ozone [130]. Particulate matter such as diesel exhaust particles and other environmental toxins also alter the expression of microRNA (short non-coding RNA that regulates gene expression), subsequently altering cellular processes leading to disease pathogenesis [130,131]. ...
... In addition, respiratory cell lines and animal models have also demonstrated distinct gene expression signatures in the transcriptome when exposed to particulate matter or ozone [130]. Particulate matter such as diesel exhaust particles and other environmental toxins also alter the expression of microRNA (short non-coding RNA that regulates gene expression), subsequently altering cellular processes leading to disease pathogenesis [130,131]. ...
Multiple myeloma (MM) is a malignant hematological disease. The disease is characterized by the clonal proliferation of malignant plasma cells in the bone marrow. MM accounts for 1.3% of all malignancies and has been increasing in incidence all over the world. Various genetic abnormalities, mutations, and translocation, including epigenetic modifications, are known to contribute to the disease’s pathophysiology. The prognosis is good if detected early, or else the outcome is very bad if distant metastasis has already occurred. Conventional treatment with drugs poses a challenge when there is drug resistance. In the present review, we discuss multiple myeloma and its treatment, drug resistance, the molecular basis of epigenetic regulation, the role of natural products in epigenetic regulators, diet, physical activity, addiction, and environmental pollutants, which may be beneficial for clinicians and researchers.
... Transcriptomic studies utilizing in vitro and animal models have shown that pathways associated with fatty acid metabolism, cell proliferation, stress response, adhesion molecules, host defense, and metal binding are perturbed by ozone exposure (Holloway et al., 2012). Rodent proteomics studies have associated ozone exposure with oxidative stress response, and inflammation (Grantziotis et al., 2016;Haque et al., 2007;Kierstein et al., 2008;Wattiez et al., 2003). ...
... Threonate is a metabolite of ascorbic acid, and increased levels of threonate are consistent with a shift to ascorbate for oxidant defense given a deficit in the ability use glutathione. Similarly, the elevated levels of glucose and glutamine in GSTM1 null but not in the GSTM1 positive subjects are consistent with increased sensitivity to the oxidative stress caused by ozone (Peng et al., 2016;Holloway et al., 2012;Zhang et al., 2014) Lipid Metabolites Fatty acids in lung surfactant and epithelial cell membranes are important targets for inhaled ozone. Ozone reacts with fatty acids to form relatively stable lipid peroxides. ...
Controlled human exposure to the oxidant air pollutant ozone causes decrements in lung function and increased inflammation as evidenced by neutrophil influx into the lung and increased levels of proinflammatory cytokines in the airways. Here we describe a targeted metabolomics evaluation of human bronchioalveolar lavage fluid (BALF) following controlled in vivo exposure to ozone to gain greater insight into its pulmonary effects. In a two-arm cross-over study, each healthy adult human volunteer was randomly exposed to filtered air (FA) and to 0.3 ppm ozone for 2 hr while undergoing intermittent exercise with a minimum of 4 weeks between exposures. Bronchoscopy was performed and BALF obtained at 1 (n = 9) or 24 (n = 23) h post-exposure. Metabolites were detected using ultrahigh performance liquid chromatography-tandem mass spectroscopy. At 1-hour post-exposure, a total of 28 metabolites were differentially expressed (DE) (p < 0.05) following ozone exposure compared to FA-exposure. These changes were associated with increased glycolysis and antioxidant responses, suggesting a rapid increased energy utilization as part of the cellular response to oxidative stress. At 24-hour post-exposure, 41 metabolites were DE. Many of the changes were in amino acids and linked with enhanced proteolysis. Changes associated with increased lipid membrane turnover were also observed. These later-stage changes were consistent with ongoing repair of airway tissues. There were 1.37 times as many metabolites were differentially expressed at 24 hour compared to 1-hour post-exposure. The changes at 1 hour reflect responses to oxidative stress while the changes at 24 hour indicate a broader set of responses consistent with tissue repair. These results illustrate the ability of metabolomic analysis to identify mechanistic features of ozone toxicity and aspects of the subsequent tissue response.
... Several components of air pollution are associated with asthma. In addition to major air pollutants (including sulfur dioxide, nitrogen dioxide, and ozone), diesel exhaust particles (DEPs) and diesel exhaust play an effective role in allergic diseases (11)(12)(13). The coarse particulate matter decreased in the atmosphere in the last years, but the (21,22). ...
Background: Cadmium (Cd) is a heavy metal and an important part of diesel exhaust particles (DEPs). Cadmium in high concentrations exhibits detrimental effects and increases the allergenicity of pollen grains. Objectives: The research aimed to study the effects of Cd on the proteins and allergenicity of Petunia hybrida pollen. Methods: Petunia plants were cultured in a greenhouse and treated with various concentrations of cadmium chloride (CdCl2) (400, 800, and 1200 μmol/L). The pollen was collected daily from the flowers of both experimental and control plants. Pollen extracts were prepared in phosphate-buffered saline (PBS) from control and Cd-treated plants, and changes in protein banding profiles were compared by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Mice were sensitized by the treatment of pollen extracts and aluminum hydroxide (Al(OH)3) as an adjuvant 3 times. The allergenicity of pollen extracts was evaluated by the skin test and the amount of immunoglobulin E (IgE) in the experimental animals. Results: The gel electrophoresis results revealed that in the Cd-treated pollen grains, two new protein bands, 46 and 51 kilodaltons (kDa), were observed that may have allergenicity. The results of serological tests showed that the mean of wheal diameter and IgE level were higher in animals sensitized by Cd-treated pollen grains than in control ones. Conclusions: In recent years, pollinosis has increased in polluted areas, especially DEP-polluted areas; the reason may be that Cd, as an important part of DEP, acts as an effective agent in the induction of the formation of detoxifying proteins which can also act as new allergens.
... Research has shown an association between telomere shortening, and age-related diseases and mitochondrial dysfunction [60]. Although more studies are needed, air pollutants may have an epigenetic impact, with changes in histone acetylation, global DNA methylation, candidate gene methylation, and microRNA expression [61][62][63]. These epigenetic alterations can affect embryonic development of multiple organ systems, and have long-term, even multi-generational, health effects [64]. ...
Common outdoor air pollutants present threats to fetal and neonatal health, placing neonatal-perinatal clinical specialists in an important role for harm reduction through patient counseling and advocacy. Climate change is intertwined with air pollution and influences air quality. There is increasing evidence demonstrating the unique vulnerability in the development of adverse health consequences from exposures during the preconception, prenatal, and early postnatal periods, as well as promising indications that policies aimed at addressing these toxicants have improved birth outcomes. Advocacy by neonatal-perinatal providers articulating the potential impact of pollutants on newborns and mothers is essential to promoting improvements in air quality and reducing exposures. The goal of this review is to update neonatal-perinatal clinical specialists on the key ambient air pollutants of concern, their sources and health effects, and to outline strategies for protecting patients and communities from documented adverse health consequences.
... In addition to cytogenetic instability, air pollution can trigger epigenetic alterations, resulting in modifications in genomic structure, such as DNA methylation and gene expression. The epigenetic modification is associated with carcinogenesis and lung dysfunction (Cao, 2015;Carr e et al., 2017;Holloway et al., 2012;Lepeule et al., 2014). ...
Mining plays a prominent role in the economy worldwide since human efforts have been more concentrated in extraction than reusing resources. The ore consists of unique earth minerals that vary according to geological evolution. These compounds are raw materials for the conventional industries, can also be used in new technologies, as fossil fuels are burned to generate energy in power plants. The mining industry triggers intense environmental impacts. Human exposure to multiple small particles from mining effluent, such as dust, uranium, iron, lead, zinc, silicon, titanium, sulfur, nitrogen, platinum, chromium, vanadium, manganese, and mercury, is a health risk. Such elements can have several pathological effects, such as respiratory and cardiovascular, multiple chronic inflammation, and neurodegenerative diseases. Additionally, mining results in severe soil, water (surface and aquifer), and air contamination, reaching large areas miles away from the source. Negligence of mining companies, with the recovery of ancient mined areas during the early development of environmental laws and regulations, compromises environmental integrity for more extended periods, increasing coverage of the affected areas. This review reports the toxicological effects of humans exposed to the mining of common minerals wastes and the impact of these compounds on the ecosystem. This review may be used as an instrument by the government, manufacturers, scientists, private environmental organizations, decision-makers, and readers from different areas of knowledge to explore the potential risk of mining to the ecosystem and human health.
... Ultimately, the pipelines of clinical data convergence lie in the ability of AI to unlock multidimensional complex interactions (e.g., gene-environment or gene-behavioral interactions) beyond simply studying gene-gene interactions or host-gut microbiome interactions [147]. For example, air pollutant exposure could lead to changes in DNA methylation and gene silencing without altering the actual DNA sequence [148]. AI could potentially identify relationships between air pollution or zip codes and genes related to detoxification (GSTM1 and GSTT1) or iron processing (HFE), and then generate individualized healthcare recommendations [149]. ...
Polygenic diseases, which are genetic disorders caused by the combined action of multiple genes, pose unique and significant challenges for the diagnosis and management of affected patients. A major goal of cardiovascular medicine has been to understand how genetic variation leads to the clinical heterogeneity seen in polygenic cardiovascular diseases (CVDs). Recent advances and emerging technologies in artificial intelligence (AI), coupled with the ever-increasing availability of next generation sequencing (NGS) technologies, now provide researchers with unprecedented possibilities for dynamic and complex biological genomic analyses. Combining these technologies may lead to a deeper understanding of heterogeneous polygenic CVDs, better prognostic guidance, and, ultimately, greater personalized medicine. Advances will likely be achieved through increasingly frequent and robust genomic characterization of patients, as well the integration of genomic data with other clinical data, such as cardiac imaging, coronary angiography, and clinical biomarkers. This review discusses the current opportunities and limitations of genomics; provides a brief overview of AI; and identifies the current applications, limitations, and future directions of AI in genomics.
... Respirable pollution is deposited along the airway and is known to exert a variety of effects on airway epithelial cells in a process that results in significant changes in gene expression (6,7). This has been investigated directly in human exposure studies (8), however, these processes are more frequently modeled using cell culture systems and standardized sources of pollution. ...
The heterogeneity of respirable particulates and compounds complicates our understanding of transcriptional responses to air pollution. Here, we address this by applying precision nuclear run-on sequencing (PRO-seq) and the assay for transposase-accessible chromatin sequencing (ATAC-seq) to measure nascent transcription and chromatin accessibility in airway epithelial cells after wood smoke particle (WSP) exposure. We used transcription factor enrichment analysis to identify temporally distinct roles for ternary response factor-serum response factor (TCF-SRF) complexes, the aryl hydrocarbon receptor (AHR), and NFκB in regulating transcriptional changes induced by WSP. Transcription of canonical targets of the AHR, such as CYP1A1 and AHRR, was robustly increased after just 30 minutes of WSP exposure, and we discovered novel AHR-regulated pathways and targets including the DNA methyltransferase, DNMT3L. Transcription of these genes and associated enhancers rapidly returned to near baseline by 120 minutes after exposure. The kinetics of AHR- and NFκB-regulated responses to WSP were distinguishable based on the timing of both transcriptional responses and chromatin remodeling, with induction of several cytokines implicated in maintaining NFκB-mediated responses through 120 minutes of exposure. In aggregate, our data establish a direct and primary role for AHR in mediating airway epithelial responses to WSP and identify crosstalk between AHR and NFκB signaling in controlling pro-inflammatory gene expression. This work also defines an integrated genomics-based strategy for deconvoluting multiplexed transcriptional responses to heterogeneous environmental exposures.
... Primarily, smoking has been identified as the leading risk factor for lung cancer (Sun et al., 2007). However, its incidence is also higher among non-smokers including second-hand smoking, radiation exposures, air pollution and genetic susceptibility (Holloway et al., 2012). On the basis of histology, prognosis and therapeutic indications, lung cancer is categorized into small-cell lung cancer and non-small cell lung cancer. ...
The chitosan-folate conjugate was synthesized initially and confirmed by FTIR and NMR spectroscopic studies. Following, docetaxel (DXL) loaded non-targeted, single receptor and dual receptor (folate and EGFR) targeted chitosan nanoparticles were prepared and their shape, particle size, zeta-potential, surface morphology and texture were screened by SEM, TEM, AFM analyses. Surface chemistry analysis by XPS indeed confirmed the successful conjugation of folate and cetuximab on the targeted formulations. In-vitro analysis of dual-targeted chitosan nanoparticles has revealed their superior cytotoxicity against A-549 cells. The IC50 of dual receptor-targeted chitosan NP was almost 34 times lower than DXL control. In-vivo pharmacokinetic study on Wistar rats has demonstrated improved relative bioavailability of all NP in comparison to DXL control. The results illustrated that EGFR and folate dual targeted NP enhanced the cytotoxicity of DXL towards A-549 lung cancer cells and substantially improved DXL pharmacokinetics in rats.
... Based on toxicological and epidemiological evidence, researchers have proposed potential mechanisms for biological responses to air pollution exposure , which remain largely unclarified, partly due to the complexity of the biological responses and the lack of comprehensive and sensitive indicators (Kim et al., 2015;Rajagopalan et al., 2018;Rückerl et al., 2011). Previous studies have focused on differences in clinical and subclinical indicators of air pollution exposure between COPD patients and other populations (Chi et al., 2019;Lagorio et al., 2006;Shao et al., 2017;Sinharay et al., 2018), but the results were inconsistent and insufficient to explain the role COPD plays in air pollution-associated adverse effects (Holloway et al., 2012). ...
Ambient air pollution is a major risk factor for the prevalence and exacerbation of chronic obstructive pulmonary disease (COPD). Based on the COPDB (COPD in Beijing) panel study, whole-blood transcriptomes were repeatedly measured in 48 COPD patients and 62 healthy participants. Ambient mass concentrations of fine particulate matter (PM2.5), temperature, and relative humidity were continuously monitored at a monitoring station. The linear mixed-effects models were applied to estimate the associations between logarithmically transformed transcript levels and 1-day (d), 7-d, and 14-d average concentrations of PM2.5 before the start of follow-up visits. MetaCoreTM was used to conduct the pathway enrichment analyses. Exposure to 1-, 7-, and 14-d average concentrations of PM2.5 was significantly associated with the transcriptome responses in both groups. The top 10, top 100, and top 1000 PM2.5-associated transcripts differed greatly between the two groups. Among COPD patients, role of alpha-6/beta-4 integrins in carcinoma progression, Notch signaling in breast cancer, and ubiquinone metabolism were the most significantly enriched PM2.5-associated biological pathways in the three time windows, respectively. In healthy participants, pro-opiomelanocortin processing was the most significant PM2.5-associated biological pathway in all three time windows. Our findings provide novel insights into the adverse health effects of air pollution exposure.
... Exposure to polycyclic aromatic hydrocarbons (PAHs) associated with ambient air particulate matter (PM) poses significant health concerns. 1,2 According to the World Health Organization (WHO) ambient air pollution database, it is the fifth leading risk factor for mortality worldwide and continues to be a global problem affecting people in urban areas. 3 Polycyclic aromatic hydrocarbons, mainly from incomplete combustion of fossil fuels and coals, 4 can bind to particulate matter to enter into the human body through the respiratory system, 5 and accumulate in the tracheobronchial and alveolar epithelium, through which they can enter the circulatory system. ...
Purpose
Exposure to polycyclic aromatic hydrocarbons (PAHs) associated with ambient air particulate matter (PM) poses significant health concerns. Increased acute exacerbation (AE) frequency in asthmatic patients has been associated with ambient PAHs, but which subgroup of patients are particularly susceptible to ambient PAHs is uncertain. We developed a new model to simulate grid-scale PM2.5-PAH levels in order to evaluate whether the severity of asthma as measured by the Global Initiative of Asthma (GINA) levels of treatment is related to cumulative exposure of ambient PAHs.
Methods
Patients with asthma residing in the northern Taiwan were reviewed retrospectively from 2014 to 2017. PM2.5 were sampled and analysed for PAHs twice a month over a 72-hour period, in addition to collecting the routinely monitored air pollutant data from an established air quality monitoring network. In combination with correlation analysis and principal component analysis, multivariate linear regression models were performed to simulate hourly grid-scale PM2.5-PAH concentrations (ng/m³). A geographic information system mapping approach with ordinary kriging interpolation method was used to calculate the annual exposure of PAHs (ng/m).
Results
Among the 387 patients with asthma aged 18 to 93 (median 62), 97 subjects were treated as GINA step 5 (24%). Asthmatics in GINA 5 subgroup with high annual PAHs exposure were likely to have a higher annual frequency of any AE (1 (0–12), p<0.0001). Annual PAHs exposure was correlated with the annual frequency of any exacerbation (r=0.11, p=0.02). This was more significant in the GINA 5 subgroup (r=0.29, p=0.005) and in the GINA 5 subgroup with severe acute exacerbations (r=0.51, p=0.002). Annual PAHs exposure, severe acute exacerbation and GINA steps were independent variables that predict annual frequency of any exacerbation.
Conclusion
Asthmatic patients in the GINA 5 subgroup with acute exacerbations were more susceptible to the effect of environmental PAHs on their exacerbation frequency. Reducing environmental levels of PAHs will have the greatest impact on the more severe asthma patients.
... Several possible biologic mechanisms have been proposed supporting the association between exposure to indoor air pollution and adverse health symptoms. Previous studies have reported associations between VOCs and respiratory and allergic symptoms through different pathways such as oxidative stress and coagulation factors and genomics (Holloway et al., 2012). Inflammation may be another mechanism behind a number of self-reported health population among schoolchildren, such as upper-lower airways symptoms and systemic disorders. ...
... Several possible biologic mechanisms have been proposed supporting the association between exposure to indoor air pollution and adverse health symptoms. Previous studies have reported associations between VOCs and respiratory and allergic symptoms through different pathways such as oxidative stress and coagulation factors and genomics (Holloway et al., 2012). Inflammation may be another mechanism behind a number of self-reported health population among schoolchildren, such as upper-lower airways symptoms and systemic disorders. ...
Substantial knowledge is available on the association of the indoor school environment and its effect among
schoolchildren. In the same context, the SINPHONIE (School indoor pollution and health: Observatory network in Europe) conducted a study to collect data and determine the distribution of several indoor air pollutants (IAPs), physical and thermal parameters and their association with eye, skin, upper-, lower
respiratory and systemic disorder symptoms during the previous three months. Finally, data from 115
schools in 54 European cities from 23 countries were collected and included 5175 schoolchildren using a
harmonized and standardized protocol. The association between exposures and the health outcomes
were examined using logistic regression models on the environmental stressors assessed in classroom while adjusting for several confounding factors; a VOC (volatile organic compound) score defined as the
sum of the number of pollutants to which the children were highly exposed (concentration N median of
the distribution) in classroom was also introduced to evaluate the multiexposure – outcome association.
Schoolchildren while adjusting for several confounding factors. Schoolchildren exposed to above or equal
median concentration of PM2.5, benzene, limonene, ozone and radon were at significantly higher odds of
suffering from upper, lower airways, eye and systemic disorders. Increased odds were also observed for
any symptom (sick school syndrome) among schoolchildren exposed to concentrations of limonene and
ozone above median values. Furthermore, the risks for upper and lower airways and systemic disorders significantly increased with the VOCs score. Results also showed that increased ventilation rate was significantly associated with decreased odds of suffering from eye and skin disorders whereas similar
association was observed between temperature and upper airways symptoms. The present study provides
evidence that exposure to IAPs in schools is associated with various health problems in children. Further investigations are needed to confirm our findings.
... Several possible biologic mechanisms have been proposed supporting the association between exposure to indoor air pollution and adverse health symptoms. Previous studies have reported associations between VOCs and respiratory and allergic symptoms through different pathways such as oxidative stress and coagulation factors and genomics (Holloway et al., 2012). Inflammation may be another mechanism behind a number of self-reported health population among schoolchildren, such as upper-lower airways symptoms and systemic disorders. ...
... We selected 35 genes along potential mechanistic pathways relevant to associations between air pollution and adverse health outcomes (Wittkopp et al., 2016) and 6 more genes based on recent reviews (Ward-Caviness, 2019; Zanobetti et al., 2011;Holloway et al., 2012). Details of selected genes and relevant references were included in Tables S1 and S2. ...
Background:
Epidemiological studies have linked air pollutant to adverse health effects even at low exposure levels, but limited evidence is available on its associations with gene expression levels.
Aim:
To investigate associations between air pollutants and gene expression levels.
Methods:
We collected data from Brisbane System Genetics Study (BSGS) - a family-based system genetics study. Expression levels of candidate genes were obtained for whole blood from 266 pairs of twins (192 monozygotic and 74 dizygotic pairs) and 165 parents. Data on individual phenotypes were also obtained, including age, sex, Body Mass Index and exposure to smoke. Daily data on mean temperature and air pollutants, including particulate matter with aerodynamic diameter ≤2.5 μm (PM2.5), ozone (O3), nitrogen dioxide (NO2) and sulfur dioxide (SO2), were collected from seven monitoring stations for the day when the blood samples were collected. The association between each air pollutant and expression level of each gene was analyzed by using generalized linear models with adjustment for temperature and individual phenotypes, and its difference between monozygotic and dizygotic twins was investigated.
Results:
The mean value for daily concentration of air pollutants were 5.9 µg/m3 for PM2.5, 16.3 ppb for O3, 6.5 ppb for NO2, and 1.4 ppb for SO2, respectively. All air pollutants' levels in Brisbane during our study period were well under the National Air Quality Standard Air pollutant levels. We observed positive associations (false discovery rate [FDR]<0.1) among twins between PM2.5 and expression levels of HSPA8 and SOD1 and also between SO2 and AHR expression level. Negative associations were observed between SO2 and 11 genes among twins, including AHR, DUSP1, GEMIN4, GPX1, KLF2, PTGS2, TLR4, TNF, TNFRSF1B, TXNRD1, and XBP1, with most of them found at lag 0-7 days (FDR < 0.1). Furthermore, the association between SO2 and DUSP1 expression level was stronger among monozygotic twins than dizygotic twins (FDR < 0.1). We did not find strong evidence linking air pollutants to gene expression levels among parents.
Conclusion:
Our findings require confirmation but suggest potential associations of expression levels at several genes with air pollutants at low exposure level and an individual's genetic background modifies the association between SO2 and DUSP1 gene, which may help bridge the gap of epidemiological studies with both in vivo and in vitro toxicological experiments and provide some insights into the role of nature-nurture of an individual in gene expression response to air pollutants.
... Another house-dust-mite exposure animal experiment also showed reduced global DNA methylation level of lung (Cheng et al., 2014). Exposure to air pollutants and cigarette smoke had also been proved to alter DNA methylation pattern and induce hypo-methylation of lung (Holloway et al., 2012). The global DNA methylation level of lung after acute PM exposure. ...
DNA methylation (5-mc)is one of the several epigenetic markers, and is generally associated with the inhibition of gene expression. Both hyper and hypo DNA methylation are associated with the diseases. Exposure to fine particles with a diameter of 2.5 μm or less (PM 2.5 )is a pervasive risk factor for cardiopulmonary mortality, metabolic disorders, cognition damage, and etc. Recent reports pointed toward that these diseases were associated with the altered DNA methylation level of some specific-gene, potentially suggesting that the DNA methylation alteration was involved in the health hazard derived from the PM 2.5 exposure. In this study, we systematically investigated the global DNA methylation level of most tissues, including lung, heart, testis, thymus, spleen, epididymal fat, hippocampus, kidney, live, after short and long term PM 2.5 exposure. After acute PM 2.5 exposure, the global hypo-methylation in DNA was observed in lung and heart. Notably, after chronic PM 2.5 exposure, level of global DNA methylation decreased in most organs which included lung, testis, thymus, spleen, epididymal fat, hippocampus and blood. The present study systematically demonstrated the global DNA methylation changes by PM 2.5 exposure, and put forward a possible orientation for further exploring the effects of ambient air particles exposure on the specific organs.
... Single nucleotide polymorphisms (SNP) have also been associated with respiratory phenotypes (Holloway et al., 2012). Genetic association studies have identified SNPs that raise COPD and lung cancer risk (Xiao et al., 2017;Young et al., 2009) suggested that genetic factors can influence the mechanisms of lung injury caused by air pollutants (Xiao et al., 2017). ...
Background:
Chronic obstructive pulmonary disease (COPD) is one of the leading causes of death in the world. Not much is known regarding the influence of non-smoking-related risk factors on COPD in Taiwan. We examined the relationship between exposure to particulate matter <2.5 μm (PM2.5) and COPD among nonsmokers in Taiwan.
Methods:
This population-based study involved 3941 nonsmoking Taiwanese adults who were recruited in the Taiwan Biobank project between 2008 and 2015. Air pollution data between 2006 and 2011 were obtained from the air quality monitoring database (AQMD). COPD was the outcome of interest and was identified using the National health insurance Research Database (NHIRD). The data were analyzed using multiple logistic regression models.
Results:
Compared with the lowest quartile (PM2.5 = 29.38), exposure to PM2.5 in the highest quartile (>38.98 μg/m3) was significantly associated with COPD (OR, 1.29; CI 1.01-1.65) after multivariate adjustments. However, exposures to concentrations of 32.07-38.98 μg/m3 (OR, 1.12 CI 0.88-1.44) and 29.38-32.07 μg/m3 (OR, 1.09 CI 0.84-1.41) showed positive but non-significant associations. However, the test for trend was significant (Ptrend = 0.043). The ORs for exposure to sulfur dioxide (SO2), ozone (O3), carbon monoxide (CO) and NOx (nitrogen monoxide (NO were not significant.
Conclusions:
Based on our data, exposure to PM2.5 at concentrations greater than 38.98 μg/m3 increased susceptibility to COPD among Taiwanese nonsmokers. Combatting COPD would involve integrating tobacco control and pollution management strategies.
... [100][101][102] Interestingly, the susceptibility towards the adverse effects of PM inhalation can be dependent on genetic factors. 103 Polymorphisms in genes encoding for enzymes that regulate oxidative stress, GSTM1, GSTP1 and NQO1, are identified as risk factors for allergic diseases in response to DEPs. 104 High DEPs exposure during infancy, for instance, could be related to an increased risk of wheezing among carriers with GSTP1 polymorphism (GSTP1 Val 105 ). ...
Outdoor air pollution is a major environmental health problem throughout the world. In particular, exposure to particulate matter (PM) has been associated with the development and exacerbation of several respiratory diseases, including asthma. Although the adverse health effects of PM have been demonstrated for many years, the underlying mechanisms have not been fully identified. In this review, we focus on the role of the lung epithelium and specifically highlight multiple cytokines in PM‐induced respiratory responses. We describe the available literature on the topic including in vitro studies, findings in humans (i.e. observations in human cohorts, human controlled exposure and ex vivo studies), and in vivo animal studies. In brief, it has been shown that exposure to PM modulates the airway epithelium and promotes the production of several cytokines, including IL‐1, IL‐6, IL‐8, IL‐25, IL‐33, TNF‐α, TSLP and GM‐CSF. Further, we propose that PM‐induced type‐2 promoting cytokines are important mediators in the acute and aggravating effects of PM on airway inflammation. Targeting these cytokines could therefore be a new approach in the treatment of asthma.
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... 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 De Prins et al. 2013), occupational (Sanchez-Guerra et al. 2015;Tarantini et al. 2009), and experimental settings (Ding et al. 2016). ...
Background:
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.
Objectives:
Our main aim was to study the association between long-term air pollution exposure and DNA methylation.
Methods:
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 ≤2.5μm; PM10, particulate matter with aerodynamic diameter ≤10μm) 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).
Results:
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.
Conclusions:
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.
... Epigenetic modifications, notably changes in DNA methylation, can lead to abnormal gene expression. These abnormalities have been implicated in the effect of air pollution on carcinogenesis [104] and respiratory failure [105,106]. In rats exposed to PM2.5, PM10 and NO 2 , Ding et al. have demonstrated both hypomethylation and hypermethylation of certain genes [107]. ...
Background
Air pollution is involved in many pathologies. These pollutants act through several mechanisms that can affect numerous physiological functions, including reproduction: as endocrine disruptors or reactive oxygen species inducers, and through the formation of DNA adducts and/or epigenetic modifications. We conducted a systematic review of the published literature on the impact of air pollution on reproductive function.Eligible studies were selected from an electronic literature search from the PUBMED database from January 2000 to February 2016 and associated references in published studies. Search terms included (1) ovary or follicle or oocyte or testis or testicular or sperm or spermatozoa or fertility or infertility and (2) air quality or O3 or NO2 or PM2.5 or diesel or SO2 or traffic or PM10 or air pollution or air pollutants. The literature search was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We have included the human and animal studies corresponding to the search terms and published in English. We have excluded articles whose results did not concern fertility or gamete function and those focused on cancer or allergy. We have also excluded genetic, auto-immune or iatrogenic causes of reduced reproduction function from our analysis. Finally, we have excluded animal data that does not concern mammals and studies based on results from in vitro culture. Data have been grouped according to the studied pollutants in order to synthetize their impact on fertility and the molecular pathways involved. Conclusion
Both animal and human epidemiological studies support the idea that air pollutants cause defects during gametogenesis leading to a drop in reproductive capacities in exposed populations. Air quality has an impact on overall health as well as on the reproductive function, so increased awareness of environmental protection issues is needed among the general public and the authorities.
... miRNAs and air pollution. Changes in the expression of miRNAs have also been investigated as biomarkers of air pollution exposure (70,83,113,146,204) (Table 2). Susceptibility to particle health effects, microRNAs and exo-somes (SPHERE) study (15) is focused on evaluating the adverse health effects of air pollution on obese subjects. ...
Significance:
MicroRNAs (miRNAs) are important regulators of gene expression and define part of the epigenetic signature. Their influence on every realm of biomedicine is established and progressively increasing. The impact of environment on human health is enormous. Among environmental risk factors impinging on quality of life are those of chemical nature (toxic chemicals, heavy metals, pollutants, pesticides) as well as those related to everyday life such as exposure to noise or mental and psychosocial stress. Recent Advances: This review elaborates on the relationship between miRNAs and these environmental risk factors.
Critical issues:
The most relevant facts underlying the role of miRNAs in the response to these environmental stressors, including redox regulatory changes and oxidative stress are highlighted and discussed. In the cases where miRNA mutations are relevant for this response the pertinent literature is also reviewed.
Future directions:
We conclude that, even though in some cases important advances have been made regarding close correlations between specific miRNAs and biological responses to environmental risk factors, a need for prospective large-cohort studies is likely necessary to establish causative roles.
... Located in the spacer regions between protein-coding genes or in the introns of protein-encoding genes, miRNA coding sequences are transcribed as primary miRNAs in the same manner as the mRNAs of the protein-coding genes (6). miRNAs are important mediators of biological functions, and their dysregulation has been implicated in a wide range of diseases, including malignancies, heart diseases, inflammation and lung diseases (7)(8)(9). ...
MicroRNAs serve important roles in various diseases, particularly cancer. microRNA-106a (miR-106a) exhibits abnormal expression and oncogenic activity in carcinogenesis. The clinical significance of the abnormal expression of miR-106a in colorectal cancer is poorly understood. In the present study, miR-106a expression from colorectal cancer tissues was quantified using the reverse transcription-quantitative polymerase chain reaction. The overexpression or knockdown of miR-106a was performed by transfection with microRNA mimic or inhibitor in human colorectal carcinoma HCT116 cells. The overexpression of miR-106a promoted viability and inhibited apoptosis in colorectal cancer cells. The association between miR-106a expression and clinicopathological factors was analyzed, and it was identified that miR-106a exhibited significantly increased expression in adenocarcinoma tissues compared with in mucinous carcinoma tissues, and the expression of miR-106a was identified to be associated with the depth of invasion and differentiation. The expression of miR-106a in plasma was also determined and it was identified that increased expression of miR-106a, as a characteristic of patients with colorectal cancer, may be distinguished from that of other patients by digitization of the areas under the receiver operating characteristic curves. These data suggested that miR-106a is a potential biomarker in the diagnosis of colorectal carcinoma. However, the underlying molecular mechanism of miR-106a-promoted viability and inhibition of apoptosis requires further investigation.
... For example, high DEP exposure is associated with more frequent asthma symptoms in children with allergic asthma 7 . Interestingly, co-exposure to allergen and DE(P) increases allergen specific IgE, asthma severity, air inflammation, and airway responsiveness in humans or in mouse models [7][8][9] . ...
Background:
Allergic disease affects 30% to 40% of the world's population, and its development is determined by the interplay between environmental and inherited factors. Air pollution, primarily consisting of diesel exhaust emissions, has increased at a similar rate to allergic disease. Exposure to diesel exhaust may play a role in the development and progression of allergic disease, in particular allergic respiratory disease. One potential mechanism underlying the connection between air pollution and increased allergic disease incidence is DNA methylation, an epigenetic process with the capacity to integrate gene-environment interactions.
Objective:
We sought to investigate the effect of allergen and diesel exhaust exposure on bronchial epithelial DNA methylation.
Methods:
We performed a randomized crossover-controlled exposure study to allergen and diesel exhaust in humans, and measured single-site (CpG) resolution global DNA methylation in bronchial epithelial cells.
Results:
Exposure to allergen alone, diesel exhaust alone, or allergen and diesel exhaust together (coexposure) led to significant changes in 7 CpG sites at 48 hours. However, when the same lung was exposed to allergen and diesel exhaust but separated by approximately 4 weeks, significant changes in more than 500 sites were observed. Furthermore, sites of differential methylation differed depending on which exposure was experienced first. Functional analysis of differentially methylated CpG sites found genes involved in transcription factor activity, protein metabolism, cell adhesion, and vascular development, among others.
Conclusions:
These findings suggest that specific exposures can prime the lung for changes in DNA methylation induced by a subsequent insult.
... The impact of air pollution on health and disease has been well recognized, and the adverse effects of particulate matter (PM) and PAHs on cardiovascular mortality and respiratory diseases (e.g., asthma and lung cancer), particularly for the at-risk subsets of the population [1][2][3][4][5][6][7], have been well documented. The risk is particularly high when exposed to fine and ultrafine particles (UFP) with an aerodynamic diameter <2.5 m, PM2.5 and <100 nm, UFP, respectively [8][9][10][11]. ...
Exposure to polycyclic aromatic hydrocarbons (PAHs) associated with ambient air particulate matter (PM) poses significant health concerns. Several modeling approaches have been developed for simulating ambient PAHs, but no hourly intra-urban spatial data are currently available. The aim of this study is to develop a new modeling strategy in simulating, on an hourly basis, grid-scale PM2.5-PAH levels. PM and PAHs were collected over a one-year time frame through an established air quality monitoring network within a metropolitan area of Taiwan. Multivariate linear regression models, in combination with correlation analysis and PAH source identification by principal component analysis (PCA), were performed to simulate hourly grid-scale PM2.5-PAH concentrations, taking criteria pollutants and meteorological variables selected as possible predictors. The simulated levels of 72-h personal exposure were found to be significantly (R=0.729**, p<0.01) correlated with those analyzed from portable personal monitors. A geographic information system (GIS) was used to visualize spatially distributed PM2.5-PAH concentrations of the modeling results. This new grid-scale modeling strategy, incorporating the output of simulated data by GIS, provides a useful and versatile tool in personal exposure analysis and in the health risk assessment of air pollution.
... LOSS et al. [11] conclude that the 17q21 locus might be related both to environmental susceptibility and to progression from wheeze to asthma. The associations between traffic-related air pollution (TRAP), asthma and allergies in children are heterogeneous; possibly due to genetic polymorphisms that modify the response to oxidative stress [12]. BOWATTE et al. [13] investigated if variants in the glutathione pathway alter associations between early life TRAP exposure and childhood asthma and allergies in a high risk birth cohort of children in Australia. ...
The Paediatric Assembly of the European Respiratory Society (ERS) maintained its high profile at the 2015 ERS International Congress in Amsterdam. There were symposia on preschool wheeze, respiratory sounds and cystic fibrosis; an educational skills workshop on paediatric respiratory resuscitation; a hot topic session on risk factors and early origins of respiratory diseases; a meet the expert session on paediatric lung function test reference values; and the annual paediatric grand round. In this report the Chairs of the Paediatric Assembly's Groups highlight the key messages from the abstracts presented at the Congress.
... In bronchial epithelial cells exposed to diesel exhaust particles, histone deacetylase 1 exhibited degradation while histone acetyltransferase p300 showed increased activation [56]. Combined with the increased acetylation of histone H4 in the promotor site of cyclooxygenase-2, a gene involved in inflammatory processes, these histone modifications appear to have led to an inflammatory response in the bronchial epithelial cells upon exposure to PM [57]. ...
This Editorial refers to the article by Brown et al. (10.1093/jtm/tav005) of this issue.
Accurate quantification of travel-associated risk of tuberculosis (TB) has been a challenging aspect of travel medicine, particularly relevant in contexts where those from low-incidence settings travel to areas where TB is more common. These difficulties arise from factors including the very long latent periods prior to clinical illness, the lack of a gold-standard test for latent TB infection (LTBI) and the large studies that are needed to quantify risk for this uncommon disease in travellers.1 Although not all of these elements are readily soluble, this cohort study of TB risk in Peace Corps volunteers provides important longitudinal data in the largest group of international travellers yet reported.2 This work is itself an updated analysis of a previously published cohort, … justin.denholm{at}mh.org.au
... In bronchial epithelial cells exposed to diesel exhaust particles, histone deacetylase 1 exhibited degradation while histone acetyltransferase p300 showed increased activation [56]. Combined with the increased acetylation of histone H4 in the promotor site of cyclooxygenase-2, a gene involved in inflammatory processes, these histone modifications appear to have led to an inflammatory response in the bronchial epithelial cells upon exposure to PM [57]. ...
Preterm birth is a major cause of infant morbidity and mortality and a potential risk factor for adult chronic disease. With over 15 million infants born preterm worldwide each year, preterm birth poses a global health concern. There is a possible association between air pollution and preterm birth, though studies have been inconsistent, likely due to variation in study design. How air pollution induces health effects is uncertain; however, studies have repeatedly demonstrated the effects of air pollution on epigenetic modifications. More recent evidence suggests that epigenetics may, in turn, be linked to preterm birth. Discovery of environmentally modifiable epigenetic processes connected to preterm birth may help to identify women at risk of preterm birth, and ultimately lead to development of new preterm birth prevention measures.
... Therefore, nanosized metal particles might also act through an epigenetic mechanism, for instance, by directly interacting with subcellular components of the mitotic machineries, giving rise to aneuploidy (Colognato et al. 2007). Investigations making use of in vitro, animal and human studies have identified air pollutants (particulate matter, black carbon and benzene) modifying epigenetic markers (Holloway et al. 2012). Most studies conducted to date have addressed DNA methylation (Szyf 2011), whereas only a few investigations have studied histone modifications or microRNA expression (Cheng & Cho 2012). ...
... Clinical (Brown et al. 2008;Hernandez et al. 2010) and epidemiological (Jia et al. 2011;Wood et al. 2010) studies of acute and chronic effects of ambient air exposures have long had important roles in quantifying human variability in the risks of exposures to widespread toxicants such as ozone and airborne particulates. The addition of GWAS to these established tools has the potential to widen the capability for quantification of effects on susceptibility of many individual genotypic variants that individually have rela tively modest effects (Holloway et al. 2012). Establishing the roles of individual pathways in affecting susceptibility via genetic analysis, in turn, has the potential to advance the assess ment of effects of other exposures during life that also affect the same pathways. ...
Differences in sensitivity to the effects of potentially toxic substances complicate risk assessments for the general population. After describing numerous aspects of biological variability, this article presents new data to improve the existing approaches.
... Although studies that report results of gene expression profiling in human subjects exposed to polluted air have recently been published , they are usually small and deal with exposure to tobacco smoke or inhalation exposure to air pollutants, rather than real exposure to environmental PM [23] [24] [25] [26] [27]. Thus, a larger study that involves human subjects from a highly-polluted environment is still required [28]. ...
We analyzed the ability of particulate matter (PM) and chemicals adsorbed onto it to induce diverse gene expression profiles in subjects living in two regions of the Czech Republic differing in levels and sources of the air pollution. A total of 312 samples from polluted Ostrava region and 154 control samples from Prague were collected in winter 2009, summer 2009 and winter 2010. The highest concentrations of air pollutants were detected in winter 2010 when the subjects were exposed to: PM of aerodynamic diameter <2.5μm (PM2.5) (70 vs. 44.9μg/m(3)); benzo[a]pyrene (9.02 vs. 2.56ng/m(3)) and benzene (10.2 vs. 5.5μg/m(3)) in Ostrava and Prague, respectively. Global gene expression analysis of total RNA extracted from leukocytes was performed using Illumina Expression BeadChips microarrays. The expression of selected genes was verified by quantitative real-time PCR (qRT-PCR). Gene expression profiles differed by locations and seasons. Despite lower concentrations of air pollutants a higher number of differentially expressed genes and affected KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways was found in subjects from Prague. In both locations immune response pathways were affected, in Prague also neurodegenerative diseases-related pathways. Over-representation of the latter pathways was associated with the exposure to PM2.5. The qRT-PCR analysis showed a significant decrease in expression of APEX, ATM, FAS, GSTM1, IL1B and RAD21 in subjects from Ostrava, in a comparison of winter 2010 and summer 2009. In Prague, an increase in gene expression was observed for GADD45A and PTGS2. In conclusion, high concentrations of pollutants in Ostrava were not associated with higher number of differentially expressed genes, affected KEGG pathways and expression levels of selected genes. This observation suggests that chronic exposure to air pollution may result in reduced gene expression response with possible negative health consequences.
Air pollution causes a huge number of fatalities every year around the world. It has been suggested that air pollution contributes to approximately 8.8 million extra deaths worldwide every year, and about 40–80% of these deaths have been linked to various cardiovascular diseases (CVD). Recent epidemiological studies have provided extensive evidence linking air pollution with a wide variety of adverse health conditions and diseases pertaining to respiratory and cardiovascular systems, especially among vulnerable demographic groups such as the children, the elderly, and those with preexisting compromised cardiopulmonary conditions such as asthma. These adverse effects predominantly include reduced functionality of the lung, chronic respiratory and cardiovascular inflammation, chronic obstructive pulmonary disease (COPD), stroke and heart attacks, and lung cancer. All these effects have been associated with exposure to at least one major air pollutant that is routinely found in the ambient air in large cities around the world. These air pollutants include suspended particulate matter (PM), ozone (O3), nitrogen oxides (NOx), sulphur dioxide (SO2), carbon monoxide (CO), volatile organic carbon compounds including polyaromatic hydrocarbons (PAHs), and trace metals such as lead (Pb) (Cohen et al. 2017). Although each of these air pollutants can induce serious health implications for humans, exposure to fine (diameter ≤ 2.5 μm) and ultrafine (diameter ≤ 0.1 μm) particles are believed to be the leading cause of cardiorespiratory illnesses in the developing world. However, the current understanding of the health effects of PM is limited, and most of the epidemiological evidence of linking adverse health effects to PM exposure is not conclusive. Moreover, the cellular and molecular mechanisms by which PM, exclusively and in mixture with other air pollutants, elicit toxic effects in humans are yet to be fully understood. Nevertheless, the use of conventional biochemical and novel molecular biomarker assessments can provide important insights into the cellular perturbations that lead to the onset of adverse health effects during chronic exposure to air pollutants. Furthermore, the advent of next generation, systems biology molecular techniques (e.g., omics technologies) provides exciting new avenues to study the effects of air pollution on human health. These new tools can provide new knowledge on the interactions of air pollutants with genes, proteins and other biomolecules that are currently unknown, and thus, develop a more holistic and in-depth mechanistic understanding of the toxicity of these pollutants. Ultimately, this advanced understanding can then be used to develop toxicity models that can predict potential future adverse health outcomes early during exposure, enabling preventive interactions and implementation of effective mitigation strategies.
Particulate matter (PM) exposure could alter the risk of tuberculosis, but the underlying mechanism is still unclear. We enrolled 132 pulmonary tuberculosis (PTB) patients and 30 controls. Bronchoalveolar lavage fluid samples were collected from all participants to detect organochlorine pesticides, polycyclic aromatic hydrocarbons, metal elements, and DNA methylation of immunity-related genes. We observed that γ-HCH, Bap, Sr, Ag, and Sn were related to an increased risk of PTB, while Cu and Ba had a negative effect. IFN-γ, IL-17A, IL-2, and IL-23 had a higher level in the PTB group, while IL-4 was lower. The methylation of 18 CpG sites was statistically associated with PTB risk. The methylation at the IL-4_06_121 site showed a significant mediating role on γ-HCH, Sr, and Sn. Our study suggests that PM exposure can increase the risk of tuberculosis by affecting DNA methylation and cytokine expression.
Purpose: Cadmium is a heavy metal and is an important part of Diesel Exhaust Particles (DEPs). Cd in high concentrations exhibited detrimental effects and cause also increase the allergenicity of pollen grains. The aim of the research was to study the effects of Cd on the proteins and allergenicity of Petunia hybrida pollens. Methods: Petunia planets were cultured in a greenhouse and treated with various concentrations of Cadmium Chloride (400, 800 & 1200 µmol/L). The pollen was daily collected from the flowers of both experimental and control plants. Pollen extracts were prepared in PBS from control and Cd-treated plants and changes in protein banding profiles were compared by SDS-PAGE. Mice were sensitized by treatment of pollen extracts and AlOH3, as an adjuvant, three times. The allergenicity of pollen extracts was evaluated by skin test and the amount of IgE in the experimental animals. Results: Gel electrophoretic studies revealed that in the Cd-treated pollen grains, two new protein bands, 46 and 51 kDa, were observed that may have allergenicity. Results of serological tests showed the mean of wheal diameter and IgE level in animals that were sensitized to Cadmium chloride-treated pollen grains are more than the control. Conclusion: In recent years pollinosis is increased in polluted areas, especially DEP-polluted areas; the reason may be that Cadmium, as an important part of DEP, acts as an effective agent in the induction of the formation of detoxifying proteins which can also act as new allergens.
Background and aim:
The fractional exhaled nitric oxide (FeNO) concentration in the exhaled breath is a biomarker for eosinophilic airway inflammation. We explored the interplay between chronic air pollution exposure and polygenic susceptibility to airway inflammation at different critical age stages.
Methods:
Adolescents (15 yr) enrolled in the GINIplus/LISA birth cohorts (n = 2434) and 220 elderly women (75 yr on average) enrolled in the SALIA cohort with FeNO measurements available were investigated. Environmental main effects of the mean of ESCAPE land-use regression air pollutant concentrations within a time window of 15 years and main effects of the polygenic risk scores (PRS) using internal weights from elastic net regression of genome-wide derived single nucleotide polymorphisms were investigated. Furthermore, we examined gene-environment interaction (GxE) effects on natural log-transformed FeNO levels by adjusted linear regression models.
Results:
While we observed no significant environmental and polygenic main effects on airway inflammation in either age group, we found robust harmful effects of chronic nitrogen dioxide (NO2) exposure in the GxE models for elderly women (16.2 % increase in FeNO, p-value = 0.027). Stratified analyses found GxE effects between the PRS and chronic NO2 exposure in never-smoker elderly women and in adolescents without any inflammatory respiratory conditions.
Conclusions:
FeNO measurement is a useful biomarker to detect higher risk of NO2-induced eosinophilic airway inflammation in the elderly. There was limited evidence for GxE effects on airway inflammation in adolescents or the elderly. Further GxE studies in subpopulations should be conducted to investigate the assumption that susceptibility to airway inflammation differs between age stages.
Autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and systemic vasculitis are caused by the body's immune response to autoantigens. The pathogenesis of autoimmune diseases is complex. RNA methylation is known to play a key role in disease progression as it regulates almost all aspects of RNA processing, including RNA nuclear export, translation, splicing, and noncoding RNA processing. This review summarizes the mechanisms, molecular structures of RNA methylations and their roles in biological functions. Similar to the roles of RNA methylation in cancers, RNA methylation in RA and SLE involves “writers” that deposit methyl groups to form N6-methyladenosine (m6A) and 5-methylcytosine (m5C), “erasers” that remove these modifications, and “readers” that further affect mRNA splicing, export, translation, and degradation. Recent advances in detection methods have identified N1-methyladenosine (m1A), N6,2-O-dimethyladenosine (m6Am), and 7-methylguanosine (m7G) RNA modifications, and their roles in RA and SLE need to be further studied. The relationship between RNA methylation and other autoimmune diseases has not been reported, and the roles and mechanisms of RNA modifications in these diseases need to be explored in the future.
Ambient air pollution is produced by sources including vehicular traffic, coal-fired power plants, hydraulic fracturing, agricultural production, and forest fires. It consists of primary pollutants generated by combustion and secondary pollutants formed in the atmosphere from precursor gases. Air pollution causes and exacerbates climate change, and climate change worsens health effects of air pollution. Infants and children are uniquely sensitive to air pollution, because their organs are developing and they have higher air per body weight intake. Health effects linked to air pollution include not only exacerbations of respiratory diseases but also reduced lung function development and increased asthma incidence. Additional outcomes of concern include preterm birth, low birth weight, neurodevelopmental disorders, IQ loss, pediatric cancers, and increased risks for adult chronic diseases. These effects are mediated by oxidative stress, chronic inflammation, endocrine disruption, and genetic and epigenetic mechanisms across the life span. Natural experiments demonstrate that with initiatives such as increased use of public transportation, both air quality and community health improve. Similarly, the Clean Air Act has improved air quality, although exposure inequities persist. Other effective strategies for reducing air pollution include ending reliance on coal, oil, and gas; regulating industrial emissions; reducing exposure with attention to proximity of residences, schools, and child care facilities to traffic; and a greater awareness of the Air Quality Index. This policy reviews both short- and long-term health consequences of ambient air pollution, especially in relation to developmental exposures. It examines individual, community, and legislative strategies to mitigate air pollution.
Attempts to secure more energy, food, and infrastructure leave a trail of environmental contamination and human health hazards. Coal is a fossil fuel and nonrenewable energy source that is combusted and used to generate electricity. A coal-fired power plant is a prodigious generator of environmental pollution, releasing large quantities of particles as aerosols in the atmosphere. The inhalation of hazardous substances such as coal micro-particles, nanoparticles, and its by-products constitutes an invisible risk to human health. Although coal is predominantly composed of carbon, there are many other constituents including sulfur, nitrogen, organometallic compounds, and minerals, that contribute to the formation of extremely toxic secondary compounds that come in contact with the atmosphere. The continuous inhalation of these hazardous substances triggers many diseases such respiratory and cardiovascular disease, systemic inflammation, and neurodegeneration. Due to coal heterogeneity, it is extremely complex to establish all the effects of the molecules in the organism. Each cell can undergo different modifications depending on the stressing molecule. On that account, inhaling air contaminated with these particles can be highly dangerous and unpredictable. This review covers the impact of coal inhalation on the lungs, immune system, heart, reproductive system, brain, DNA, and, in general, the human health. For this review, Medline and Scopus databases were accessed, including human epidemiological, review studies, and coal characterization studies over the years. Coal as an energy source must be utilized with appropriate measures of environmental protection and to safeguard human health.
Introduction:
Limited evidence suggests that epigenetic mechanisms may partially mediate the adverse effects of air pollution on health. Our aims were to identify new genomic loci showing differential DNA methylation associated with long-term exposure to air pollution and to replicate loci previously identified in other studies.
Methods:
A two-stage epigenome-wide association study was designed: 630 individuals from the REGICOR study were included in the discovery and 454 participants of the EPIC-Italy study in the validation stage. DNA methylation was assessed using the Infinium HumanMethylation450 BeadChip. NOX, NO2, PM10, PM2.5, PMcoarse, traffic intensity and traffic load exposure were measured according to the ESCAPE protocol. A systematic review was undertaken to identify those cytosine-phosphate-guanine (CpGs) associated with air pollution in previous studies and we screened for them in the discovery study.
Results:
In the discovery stage of the epigenome-wide association study, 81 unique CpGs were associated with air pollution (p-value <10-5) but none of them were validated in the replication sample. Furthermore, we identified 15 CpGs in the systematic review showing differential methylation with a p-value fulfilling the Bonferroni criteria and 1673 CpGs fulfilling the false discovery rate criteria, all of which were related to PM2.5 or NO2. None of them was replicated in the discovery study, in which the top hits were located in an intergenic region on chromosome 1 (cg10893043, p-value = 6.79·10-5) and in the LRRC45 and PXK genes (cg05088605, p-value = 2.15·10-04; cg16560256, p-value = 2.23·10-04).
Conclusions:
Neither new genomic loci associated with long-term air pollution were identified, nor previously identified loci were replicated. Continued efforts to test this potential association are warranted.
Background: Limited evidence suggests that epigenetic mechanisms may partially mediate the adverse effects of air pollution on health. Our aims were to identify new genomic loci showing differential DNA methylation associated with long-term exposure to air pollution and to replicate loci previously identified in other studies.
Methods: A two-stage epigenome-wide association study was designed: 630 individuals from the REGICOR study were included in the discovery and 454 participants of the EPIC-Italy study in the validation stage. DNA methylation was assessed using the Infinium HumanMethylation450 BeadChip. NOX, NO2, PM10, PM2.5, PMcoarse, traffic intensity and traffic load exposure were measured according to the ESCAPE protocol. A systematic review was undertaken to identify those cytosine-phosphate-guanine (CpGs) associated with air pollution in previous studies and we screened for them in the discovery study.
Results: In the discovery stage of the epigenome-wide association study, 81 unique CpGs were associated with air pollution (p-value <10-5) but none of them were validated in the replication sample. Furthemore, we identified 12 CpGs in the systematic review showing differential methylation with a p-value fulfilling the Bonferroni criteria and 1642 CpGs fulfilling the false discovery rate criteria, all of which were related to PM2.5 or NO2. None of them was replicated in the discovery study, in which the top hits were located in an intergenic region on chromosome 1 (cg10893043, p-value=6.79*10-5) and in the PXK and ARSA genes (cg16560256, p-value=2.23*10-04; cg11953250, p-value=3.64*10-04).
Conclusions: Neither new genomic loci associated with long-term air pollution were identified, nor previously identified loci were replicated. Continued efforts to test this potential association are warranted.
Rationale:
Epidemiological studies have demonstrated that exposure to particulate matter ambient pollution has adverse effects on lung health, exacerbated by cigarette smoking. Fine air-borne particles <2.5 μm (PM2.5) are among the most harmful urban pollutants, and are closely linked to respiratory disease.
Objectives:
Based on the knowledge that the small airway epithelium (SAE) plays a central role in the pathogenesis of smoking-related lung disease, we hypothesized that elevated PM2.5 levels are associated with dysregulation of SAE gene expression.
Methods:
From 2009-2012, healthy nonsmoker (n=29) and smoker (n=129) residents of New York City (NYC) underwent bronchoscopy with SAE brushing (2.6 ± 1.3 samples/subject, total of 405 samples). SAE gene expression was assessed by Affymetrix HG-U133 Plus 2.0 microarray. NYC PM2.5 levels (Environmental Protection Agency data) were averaged for the 30 days prior to bronchoscopy. A linear mixed model was used to assess PM2.5-related gene dysregulation accounting for multiple clinical and methodologic variables with multiple test correction to assess significance.
Measurements and main results:
Thirty-day mean PM2.5 levels varied from 6.2-18 µg/m3. In nonsmokers, there was no dysregulation of SAE gene expression associated with ambient PM2.5 levels. In marked contrast, n=219 genes were significantly dysregulated in association with PM2.5 levels in the SAE of smokers. Many of these genes relate to cell growth and transcription regulation. Interestingly, 11% of genes were mitochondria-associated.
Conclusions:
PM2.5 exposure contributes to significant dysregulation of the SAE transcriptome of smokers, linking pollution and airway epithelial biology in the risk of development of respiratory disease in susceptible individuals.
In COPD, or chronic obstructive pulmonary disease, the lungs are damaged which makes it difficult to breathe. Smoking is the most important risk factor for developing COPD, but remarkably, 25-45% of all COPD patients worldwide have never smoked. Within this PhD project we aimed to assess the mechanisms that play a role in COPD in never-smokers. What is the role of genetic variants, epigenetic alterations (DNA-methylation) and environmental exposures, like air pollution and occupational exposures, herein? DNA-methylation can change the activity and functionality of the DNA and can be affected by exposures. It might therefore be the underlying mechanism relating exposures to lung function. The studies described in the thesisshowed that genes, DNA-methylation and environmental exposures indeed play a role in COPD in never-smokers. We have identified several (novel) genes for the development of large or small airway obstruction in specifically never-smokers. However, we found no significant differences in DNA-methylation levels between subjects with and without COPD. On the other hand, we showed that air pollution as well as occupational exposures were associated with DNA-methylation levels. For most identified DNA-methylation sites, our data suggests thatDNA-methylation induces changes in gene expression, which indicates that they may regulate the activity of these genes . In turn, this might lead to COPD depending on the function of the affected genes. Together, the information provided may ultimately lead to new therapies for treatment or prevention of COPD. Hopefully, other researchers will give more attention to never-smokers in their studies on COPD as well.
The seasonal variability of certain non-allergic respiratory diseases is not clearly understood. Analysis of the breath condensate, the liquid that can be collected by breathing into a cold tube, has been proposed to bring closer to the understanding of airway pathologies. It has been assumed, that (1) airway lining fluid was a stable body liquid and (2) the breath condensate samples were representative of the airway lining fluid. Research was focussed on the identification of biomarkers indicative of respiratory pathologies. Despite 30 years of extended investigations breath condensate analysis has not gained any clinical implementation so far. The pH of the condensate is the characteristic that can be determined with the highest reproducibility. The present paper shows, that contrary to the initial assumptions, breath condensate is not a representative of the airway lining fluid, and the airway lining fluid is not a stable body liquid. Condensate pH shows baseline variability and it is influenced by drinking and by the ambient temperature. The changes in condensate pH are linked to changes in airway lining fluid pH. The variability of airway lining fluid pH may explain seasonal incidence of certain non-allergic respiratory diseases such as the catching of a common cold and the increased incidence of COPD exacerbations and exercise-induced bronchoconstriction in cold periods.
Air pollution is a consequential global threat to overall biodiversity, affecting different biological levels – from cellular to ecosystem level. The dust pollution has always been essential environmental issue in Estonia since over the years the large part of industrial pollution was formed by alkaline dust. The current thesis is focused on alkaline coarse dust particles, which are released to the environment through cement industry, limestone quarries and directly from unpaved gravel roads by traffic. In order to monitor and mitigate damages caused by dust pollution, the influence of pollution on different levels of biodiversity should be estimated and the potential sources of pollution and their extension detected. Therefore, the aim of the thesis was to study the response of pine forest ecosystems, epiphytic communities (algae, lichens, bryophytes) on pines, and genetic diversity of populations of a common lichen-forming fungus to changed environmental conditions induced by a long-term alkaline pollution. The results showed that long-term dust pollution had a neutralizing effect on soil properties, pine and spruce barks: the pH value of soil and tree barks decreased along an increasing distance from the sources of pollution. The alkaline pollution has caused destruction of natural communities and formation of novel communities in the vicinity of pollution sources, for example invasion of non-typical and pollution-tolerant species for local communities occurred, including calcicolous species and species characteristic for nutrient-rich habitats. Interestingly, dust pollution revealed a kind of ‘parapositive’ impact on natural communities, suggesting that pollution might, besides disturbing communities, temporarily also contribute to the distribution of rare and protected species. Finally, alkaline pollution had a negative impact on the genetic variation of Usnea subfloridana populations, a common species of lichen-forming fungi.
Purpose: Genetic polymorphisms in antioxidant defense and detoxification genes may modulate the levels of oxidative stress biomarkers. Methods: A total of 301 healthy preschool-aged children in the Seoul and Kyung-gi areas were recruited. DNA was extracted from blood for genotyping of manganese superoxide dismutase (Mn-SOD) Val16Ala, glutathione S-transferase (GST) P1 Ile105Val, GSTT1 present/null, and GSTM1 present/null polymorphisms by PCR-restriction fragment length polymorphism or multiplex PCR analyses. In addition to a questionnaire survey, the levels of urinary 8-hydroxyl-2-deoxiguanosine (8-OHdG) and plasma malondialdehyde (MDA) were measured by ELISA. Results: Significantly higher urinary 8-OHdG concentrations were observed in GSTP1 Ile/Val + Val/Val genotype (p = 0.030), and tended to be higher in Mn-SOD Val/Val genotype (p = 0.065). On the other hand, exposure to environmental tobacco smoking (ETS) and interaction between ETS and gene polymorphisms did not significantly influence either urinary 8-OHdG concentrations or serum MDA. Conclusion: Based on our findings, GSTP1 Ile/Val gene polymorphisms might modulate the levels of oxidative stress biomarkers in healthy preschool children.
BACKGROUND:
Susceptibility to asthma is influenced by genes and environment; implicated genes may indicate pathways for therapeutic intervention. Genetic risk factors may be useful in identifying subtypes of asthma and determining whether intermediate phenotypes, such as elevation of the total serum IgE level, are causally linked to disease.
METHODS:
We carried out a genomewide association study by genotyping 10,365 persons with physician-diagnosed asthma and 16,110 unaffected persons, all of whom were matched for ancestry. We used random-effects pooled analysis to test for association in the overall study population and in subgroups of subjects with childhood-onset asthma (defined as asthma developing before 16 years of age), later-onset asthma, severe asthma, and occupational asthma.
RESULTS:
We observed associations of genomewide significance between asthma and the following single-nucleotide polymorphisms: rs3771166 on chromosome 2, implicating IL1RL1/IL18R1 (P=3×10(−9)); rs9273349 on chromosome 6, implicating HLA-DQ (P=7×10(−14)); rs1342326 on chromosome 9, flanking IL33 (P=9×10(−10)); rs744910 on chromosome 15 in SMAD3 (P=4×10(−9)); and rs2284033 on chromosome 22 in IL2RB (P=1.1×10(−8)). Association with the ORMDL3/GSDMB locus on chromosome 17q21 was specific to childhood-onset disease (rs2305480, P=6×10(−23)). Only HLA-DR showed a significant genomewide association with the total serum IgE concentration, and loci strongly associated with IgE levels were not associated with asthma.
CONCLUSIONS:
Asthma is genetically heterogeneous. A few common alleles are associated with disease risk at all ages. Implicated genes suggest a role for communication of epithelial damage to the adaptive immune system and activation of airway inflammation. Variants at the ORMDL3/GSDMB locus are associated only with childhood-onset disease. Elevation of total serum IgE levels has a minor role in the development of asthma. (Funded by the European Commission and others.)
Background:
Microsomal epoxide hydrolase (EPHX1) metabolises xenobiotics including polyaromatic hydrocarbons (PAHs). Functional variants at this locus have been associated with respiratory diseases. The effects of EPHX1 variants may depend upon exposures from tobacco smoke and traffic emissions that contain PAHs as well as variants in other enzymes in the PAH metabolic pathway such as glutathione S-transferase (GST) genes. A study was undertaken to investigate associations of variants in EPHX1, GSTM1, GSTP1 and GSTT1 with asthma and the relationships between asthma, EPHX1 metabolic phenotypes and exposure to sources of PAHs.
Methods:
Odds ratios (ORs) and 95% confidence intervals (CIs) were computed to estimate the associations of genetic variants and exposures with asthma phenotypes using data from 3124 children from the Children's Health Study.
Results:
High EPHX1 activity was associated with an increased risk for lifetime asthma (OR 1.51, 95% CI 1.14 to 1.98) which varied by GSTP1 Ile105Val genotype and by residential proximity to major roads (p for interaction = 0.006 and 0.03, respectively). Among children with GSTP1 105Val/Val genotype, those who had high EPHX1 phenotype had a fourfold (95% CI 1.97 to 8.16) increased risk of lifetime asthma than children with low/intermediate EPHX1 phenotype. Among children living within 75 metres of a major road, those with high EPHX1 activity had a 3.2-fold (95% CI 1.75 to 6.00) higher lifetime asthma risk than those with low/intermediate activity. The results were similar for current, early persistent and late onset asthma. Children with high EPHX1 phenotype, GSTP1 Val/Val genotype who lived <75 metres from a major road were at the highest asthma risk.
Conclusion:
EPHX1 and GSTP1 variants contribute to the occurrence of childhood asthma and increase asthma susceptibility to exposures from major roads.
Summary During our daily activities including working, running, talking, eating and even sleeping, cells of the body are active. A person consumes oxygen and produces carbon dioxide during such activities. Lungs are air pumping stations of our body which transfer atmospheric oxygen into our body and expel carbon dioxide in the atmosphere, through a process called respiration. Air passes through airways during respiration. The average human being consumes about 12 Kg of air each day to form carbon dioxide. It is about twelve times higher than the food we consume. Hence, even a small concentration of pollutants in the air play a significant role in the deterioration of respiratory health. Man-made vehicles consume nearly 15 Kg of air in the burning of 1 litre of fuel resulting in the emission of harmful pollutants. Combustion of fuel is one of the most significant sources of air pollution. The constantly increasing need for fuel combustion for transportation and in order to produce energy and power industry, we deplete the atmosphere of oxygen and increase the concentration of air borne pollutants. Carbon monoxide, lead and hydrocarbons are emitted in high quantities in petrol combustion. These can cause loss of visual accuracy and mental alertness. Diesel combustion emits considerably higher amounts of Nitrogen dioxide, particulate matter and sulphur dioxide. Air pollution has been associated with a variety of detrimental effects on the respiratory system, including the aggravation of bronchial asthma or the appearance of new onset asthma. Also, increased mortality from respiratory disease especially in high risk groups (elderly people, children) resulting from the exacerbation of underlying cardiopulmonary disorders and increased susceptibility due to the deleterious effects of air pollutants on immunity has a tremendous economic toll on health care systems around the world.
Pulmonary function measures reflect respiratory health and are used in the diagnosis of chronic obstructive pulmonary disease. We tested genome-wide association with forced expiratory volume in 1 second and the ratio of forced expiratory volume in 1 second to forced vital capacity in 48,201 individuals of European ancestry with follow up of the top associations in up to an additional 46,411 individuals. We identified new regions showing association (combined P < 5 x 10(-8)) with pulmonary function in or near MFAP2, TGFB2, HDAC4, RARB, MECOM (also known as EVI1), SPATA9, ARMC2, NCR3, ZKSCAN3, CDC123, C10orf11, LRP1, CCDC38, MMP15, CFDP1 and KCNE2. Identification of these 16 new loci may provide insight into the molecular mechanisms regulating pulmonary function and into molecular targets for future therapy to alleviate reduced lung function.
Pulmonary function measures reflect respiratory health and are used in the diagnosis of chronic obstructive pulmonary disease. We tested genome-wide association with forced expiratory volume in 1 second and the ratio of forced expiratory volume in 1 second to forced vital capacity in 48,201 individuals of European ancestry with follow up of the top associations in up to an additional 46,411 individuals. We identified new regions showing association (combined P < 5 × 10(-8)) with pulmonary function in or near MFAP2, TGFB2, HDAC4, RARB, MECOM (also known as EVI1), SPATA9, ARMC2, NCR3, ZKSCAN3, CDC123, C10orf11, LRP1, CCDC38, MMP15, CFDP1 and KCNE2. Identification of these 16 new loci may provide insight into the molecular mechanisms regulating pulmonary function and into molecular targets for future therapy to alleviate reduced lung function.
In this study, we examined the role of neprilysin (NEP), a key membrane-bound endopeptidase, in the inflammatory response induced by diesel exhaust emissions (DEE) in the airways through a number of approaches: in vitro, animal, and controlled human exposure. Our specific aims were (1) to examine the role of NEP in inflammatory injury induced by diesel exhaust particles (DEP) using Nep-intact (wild-type) and Nep-null mice; (2) to examine which components of DEP are associated with NEP downregulation in vitro; (3) to determine the molecular impact of DEP exposure and decreased NEP expression on airway epithelial cells' gene expression in vitro, using a combination of RNA interference (RNAi) and microarray approaches; and (4) to evaluate the effects on NEP activity of human exposure to DEE. We report four main results: First, we found that exposure of normal mice to DEP consisting of standard reference material (SRM) 2975 via intratracheal installation can downregulate NEP expression in a concentration-dependent manner. The changes were accompanied by increases in the number of macrophages and epithelial cells, as well as proinflammatory cytokines, examined in bronchoalveolar lavage (BAL) fluid and cells. Nep-null mice displayed increased and/or additional inflammatory responses when compared with wild-type mice, especially in response to exposure to the higher dose of DEP that we used. These in vivo findings suggest that loss of NEP in mice could cause increased susceptibility to injury or exacerbate inflammatory responses after DEP exposure via release of specific cytokines from the lungs. Second, we found evidence, using in vitro studies, that downregulation of NEP by DEP in cultured human epithelial BEAS-2B cells was mostly attributable to DEP-adsorbed organic compounds, whereas the carbonaceous core and transition metal components of DEP had little or no effect on NEP messenger RNA (mRNA) expression. This NEP downregulation was not a specific response to DEP or its contents because the change also occurred after exposure to urban dust (SRM 1649a), which differs in physical and chemical composition from DEP. Third, we also collected the transcriptome profiles of the concentration-effects of SRM 2975 in cultured BEAS-2B cells through a 2 X 3 factorial design. DEP exposure upregulated 151 genes and downregulated 59 genes. Cells with decreased NEP expression (accomplished by transfecting an NEP-specific small interfering RNA [siRNA]) substantially altered the expression of genes (upregulating 17 and downregulating 14) associated with DNA/protein binding, calcium channel activities, and the cascade of intracellular signaling by cytokines. Data generated from the combined RNAi and microarray approaches revealed that there is a complex molecular cascade mediated by NEP in different subcellular compartments, possibly influencing the inflammatory response. Fourth, in a controlled human exposure study, we observed significant increases in soluble NEP in sputum after acute exposure to DEE, with an average net increase of 31%. We speculate that the change in NEP activity in sputum, if confirmed in larger epidemiologic investigations at ambient exposure levels to DEE, may provide a useful endpoint and promote insight into the mechanism of DEE-induced airway alterations.
Despite the success of genome-wide association studies (GWASs) in identifying loci associated with common diseases, a substantial proportion of the causality remains unexplained. Recent advances in genomic technologies have placed us in a position to initiate large-scale studies of human disease-associated epigenetic variation, specifically variation in DNA methylation. Such epigenome-wide association studies (EWASs) present novel opportunities but also create new challenges that are not encountered in GWASs. We discuss EWAS design, cohort and sample selections, statistical significance and power, confounding factors and follow-up studies. We also discuss how integration of EWASs with GWASs can help to dissect complex GWAS haplotypes for functional analysis.
Chronic obstructive pulmonary disease (COPD) is characterized by systemic and local chronic inflammation and oxidative stress. The sources of the increased oxidative stress in COPD patients derive from the increased burden of inhaled oxidants such as cigarette smoke and other forms of particulate or gaseous air pollution and from the increase in reactive oxygen species (ROS) generated by several inflammatory, immune, and structural airways cells. There is increasing evidence that genetic factors may also contribute to the pathogenesis if COPD, particularly antioxidant genes, which may confer a susceptibility to environmental insults such as cigarette smoke and thereafter development of COPD. Consequently, heme oxygenase-1 (HO-1), superoxide dismutase (SOD), catalase (CAT), glutathione S-transferase (GST), microsomal epoxide hydrolase (EPHX1), and cytochrome P450 (CYP) genetic polymorphisms may have an important role in COPD pathogenesis. In this review the authors summarized the most recent findings dealing with these antioxidant genes contributing to the free radical neutralization and xenobiotic enzymes playing a role in different phases of cell detoxification reactions related to the redox status imbalance in COPD, with an emphasis on their possible roles in disease progression.
Toll-like receptor 4 (TLR4) is involved in ozone (O3)-induced pulmonary hyperpermeability and inflammation, although the downstream signaling events are unknown.
The aims of our study were to determine the mechanism through which TLR4 modulates O3-induced pulmonary responses and to use transcriptomics to determine potential TLR4 effector molecules.
C3H/HeJ (HeJ; Tlr4 mutant) and C3H/HeOuJ (OuJ; Tlr4 normal) mice were exposed continuously to 0.3 ppm O3 or filtered air for 6, 24, 48, or 72 hr. We assessed inflammation using bronchoalveolar lavage and molecular analysis by mRNA microarray, quantitative RT-PCR (real-time polymerase chain reaction), immunoblots, immunostaining, and ELISAs (enzyme-linked immunosorbent assays). B6-Hspa1a/Hspa1btm1Dix/NIEHS (Hsp70-/-) and C57BL/6 (B6; Hsp70+/+ wild-type control) mice were used for candidate gene validation studies.
O3-induced TLR4 signaling occurred through myeloid differentiation protein 88 (MyD88)-dependent and -independent pathways in OuJ mice and involved multiple downstream pathways. Genomewide transcript analyses of lungs from air- and O3-exposed HeJ and OuJ mice identified a cluster of genes that were significantly up-regulated in O3-exposed OuJ mice compared with O3-exposed HeJ mice or air-exposed controls of both strains; this cluster included genes for heat-shock proteins (e.g., Hspa1b, Hsp70). Moreover, O3-induced inflammation, MyD88 up-regulation, extracellular-signal-related kinase-1/2 (ERK1/2) and activator protein-1 (AP-1) activation, and kerotinocyte-derived chemokine (KC) protein content were significantly reduced in Hspa1a/Hspa1btm1Dix (Hsp70-/-) compared with Hsp70+/+ mice (p < 0.05).
These studies suggest that HSP70 is an effector molecule downstream of TLR4 and is involved in the regulation of O3-induced lung inflammation by triggering similar pathways to TLR4. These novel findings may have therapeutic and preventive implications for inflammatory diseases resulting from environmental exposures.
Chronic obstructive pulmonary disease (COPD) is a major public health problem with increasing prevalence worldwide. The primary aim of this study was to identify genes and gene ontologies associated with COPD severity. Gene expression profiling was performed on total RNA extracted from lung tissue of 18 former smokers with COPD. Class comparison analysis on mild (n = 9, FEV(1) 80-110% predicted) and moderate (n = 9, FEV(1) 50-60% predicted) COPD patients identified 46 differentially expressed genes (p<0.01), of which 14 genes were technically confirmed by quantitative real-time-PCR. Biological replication in an independent test set of 58 lung samples confirmed the altered expression of ten genes with increasing COPD severity, with eight of these genes (NNMT, THBS1, HLA-DPB1, IGHD, ETS2, ELF1, PTGDS and CYRBD1) being differentially expressed by greater than 1.8 fold between mild and moderate COPD, identifying these as candidate determinants of COPD severity. These genes belonged to ontologies potentially implicated in COPD including angiogenesis, cell migration, proliferation and apoptosis. Our secondary aim was to identify gene ontologies common to airway obstruction, indicated by impaired FEV(1) and KCO. Using gene ontology enrichment analysis we have identified relevant biological and molecular processes including regulation of cell-matrix adhesion, leukocyte activation, cell and substrate adhesion, cell adhesion, angiogenesis, cell activation that are enriched among genes involved in airflow obstruction. Exploring the functional significance of these genes and their gene ontologies will provide clues to molecular changes involved in severity of COPD, which could be developed as targets for therapy or biomarkers for early diagnosis.
DNA methylation is a potential pathway linking environmental exposures to disease. Exposure to particulate air pollution has been associated with increased cardiovascular morbidity and mortality, and lower blood DNA methylation has been found in processes related to cardiovascular morbidity.
We hypothesized that prolonged exposure to particulate pollution would be associated with hypomethylation of repetitive DNA elements and that this association would be modified by genes involved in glutathione metabolism and other host characteristics.
DNA methylation of the long interspersed nucleotide element-1 (LINE-1) and the short interspersed nucleotide element Alu were measured by quantitative polymerase chain reaction pyrosequencing in 1,406 blood samples from 706 elderly participants in the Normative Aging Study. We estimated changes in repetitive element DNA methylation associated with ambient particles (particulate matter ≤ 2.5 µm in aerodynamic diameter), black carbon (BC), and sulfates (SO₄), with mixed models. We examined multiple exposure windows (1-6 months) before DNA methylation measurement. We investigated whether this association was modified by genotype and phenotype.
An interquartile range (IQR) increase in BC over a 90-day period was associated with a decrease of 0.31% 5-methylcytosine (5mC) (95% confidence interval, 0.12-0.50%) in Alu. An IQR increase in SO₄ over a 90-day period was associated with a decrease of 0.27% 5mC (0.02-0.52%) in LINE-1. The glutathione S-transferase mu-1-null genotype strengthened the association between BC and Alu hypomethylation.
Prolonged exposure to BC and SO₄ particles was associated with hypomethylation of two types of repetitive elements.
Susceptibility to the respiratory effects of air pollution varies between individuals. Although some evidence suggests higher susceptibility for subjects carrying variants of antioxidant genes, findings from gene-pollution interaction studies conflict in terms of the presence and direction of interactions. The authors conducted a systematic review on antioxidant gene-pollution interactions which included 15 studies, with 12 supporting the presence of interactions. For the glutathione S-transferase M1 gene (GSTM1) (n=10 studies), only 1 study found interaction with the null genotype alone, although 5 observed interactions when GSTM1 was evaluated jointly with other genes (mainly NAD(P)H dehydrogenase [quinone] 1 (NQO1)). All studies on the glutathione S-transferase P1 (GSTP1) Ile105Val polymorphism (n=11) provided some evidence of interaction, but findings conflicted in terms of risk allele. Results were negative for glutathione S-transferase T1 (GSTT1) (n=3) and positive for heme oxygenase 1 (HMOX-1) (n=2). Meta-analysis could not be performed because there were insufficient data available for any specific gene-pollutant-outcome combination. Overall the evidence supports the presence of gene-pollution interactions, although which pollutant interacts with which gene is unclear. However, issues regarding multiple testing, selective reporting, and publication bias raise the possibility of false-positive findings. Larger studies with greater accuracy of pollution assessment and improved quality of conduct and reporting are required.
Introduction:
Lung cancer and COPD commonly coexist in smokers, and the presence of COPD increases the risk of developing lung cancer. In addition to smoking cessation and preventing smoking initiation, understanding the shared mechanisms of these smoking-related lung diseases is critical, in order to develop new methods of prevention, diagnosis and treatment of lung cancer and COPD.
Areas covered:
This review discusses the common mechanisms for susceptibility to lung cancer and COPD, which in addition to cigarette smoke, may involve inflammation, epithelial-mesenchymal transition, abnormal repair, oxidative stress, and cell proliferation. Furthermore, we discuss the underlying genomic and epigenomic changes (single nucleotide polymorphisms (SNPs), copy number variation, promoter hypermethylation and microRNAs) that are likely to alter biological pathways, leading to susceptibility to lung cancer and COPD (e.g., altered nicotine receptor biology).
Expert opinion:
Strategies to study genomics, epigenomics and gene-environment interaction will yield greater insight into the shared pathogenesis of lung cancer and COPD, leading to new diagnostic and therapeutic modalities.
Titanium dioxide nanoparticles (nanoTiO(2) ) are used in various applications including in paints. NanoTiO(2) inhalation may induce pulmonary toxicity and systemic effects. However, the underlying molecular mechanisms are poorly understood. In this study, the effects of inhaled surface-coated nanoTiO(2) on pulmonary global messenger RNA (mRNA) and microRNA (miRNA) expression in mouse were characterized to provide insight into the molecular response. Female C57BL/6BomTac mice were exposed for 1 hr daily to 42.4 ± 2.9 (SEM) mg surface-coated nanoTiO(2) /m(3) for 11 consecutive days by inhalation and were sacrificed 5 days following the last exposure. Physicochemical properties of the particles were determined. Pulmonary response to nanoTiO(2) was characterized using DNA microarrays and pathway-specific PCR arrays and related to data on pulmonary inflammation from bronchial lavages. NanoTiO(2) exposure resulted in increased levels of mRNA for acute phase markers serum amyloid A-1 (Saa1) and serum amyloid A-3 (Saa3), several C-X-C and C-C motif chemokines, and cytokine tumor necrosis factor genes. Protein analysis of Saa1 and 3 showed selective upregulation of Saa3 in lung tissues. Sixteen miRNAs were induced by more than 1.2-fold (adjusted P-value < 0.05) following exposure. Real time polymerase chain reaction confirmed the upregulation of miR-1, miR-449a and revealed dramatic induction of miR-135b (60-fold). Thus, inhalation of surface-coated nanoTiO(2) results in changes in the expression of genes associated with acute phase, inflammation and immune response 5 days post exposure with concomitant changes in several miRNAs. The role of these miRNAs in pulmonary response to inhaled particles is unknown and warrants further research.
Exposure to formaldehyde, a known air toxic, is associated with cancer and lung disease. Despite the adverse health effects of formaldehyde, the mechanisms underlying formaldehyde-induced disease remain largely unknown. Research has uncovered microRNAs (miRNAs) as key posttranscriptional regulators of gene expression that may influence cellular disease state. Although studies have compared different miRNA expression patterns between diseased and healthy tissue, this is the first study to examine perturbations in global miRNA levels resulting from formaldehyde exposure.
We investigated whether cellular miRNA expression profiles are modified by formaldehyde exposure to test the hypothesis that formaldehyde exposure disrupts miRNA expression levels within lung cells, representing a novel epigenetic mechanism through which formaldehyde may induce disease.
Human lung epithelial cells were grown at air-liquid interface and exposed to gaseous formaldehyde at 1 ppm for 4 hr. Small RNAs and protein were collected and analyzed for miRNA expression using microarray analysis and for interleukin (IL-8) protein levels by enzyme-linked immunosorbent assay (ELISA).
Gaseous formaldehyde exposure altered the miRNA expression profiles in human lung cells. Specifically, 89 miRNAs were significantly down-regulated in formaldehyde-exposed samples versus controls. Functional and molecular network analysis of the predicted miRNA transcript targets revealed that formaldehyde exposure potentially alters signaling pathways associated with cancer, inflammatory response, and endocrine system regulation. IL-8 release increased in cells exposed to formaldehyde, and results were confirmed by real-time polymerase chain reaction.
Formaldehyde alters miRNA patterns that regulate gene expression, potentially leading to the initiation of a variety of diseases.
To date, at least 900 different microRNA (miRNA) genes have been discovered in the human genome. These short, single-stranded RNA molecules originate from larger precursor molecules that fold to produce hairpin structures, which are subsequently processed by ribonucleases Drosha/Pasha and Dicer to form mature miRNAs. MiRNAs play role in the posttranscriptional regulation of about one third of human genes, mainly via degradation of target mRNAs. Whereas the target mRNAs are often involved in the regulation of diverse physiological processes ranging from developmental timing to apoptosis, miRNAs have a strong potential to regulate fundamental biological processes also in the lung compartment. However, the knowledge of the role of miRNAs in physiological and pathological conditions in the lung is still limited. This review, therefore, summarizes current knowledge of the mechanism, function of miRNAs and their contribution to lung development and homeostasis. Besides the involvement of miRNAs in pulmonary physiological conditions, there is evidence that abnormal miRNA expression may lead to pathological processes and development of various pulmonary diseases. Next, the review describes current state-of-art on the miRNA expression profiles in smoking-related diseases including lung cancerogenesis, in immune system mediated pulmonary diseases and fibrotic processes in the lung. From the current research it is evident that miRNAs may play role in the posttranscriptional regulation of key genes in human pulmonary diseases. Further studies are, therefore, necessary to explore miRNA expression profiles and their association with target mRNAs in human pulmonary diseases.
Background:
Susceptibility to asthma is influenced by genes and environment; implicated genes may indicate pathways for therapeutic intervention. Genetic risk factors may be useful in identifying subtypes of asthma and determining whether intermediate phenotypes, such as elevation of the total serum IgE level, are causally linked to disease.
Methods:
We carried out a genomewide association study by genotyping 10,365 persons with physician-diagnosed asthma and 16,110 unaffected persons, all of whom were matched for ancestry. We used random-effects pooled analysis to test for association in the overall study population and in subgroups of subjects with childhood-onset asthma (defined as asthma developing before 16 years of age), later-onset asthma, severe asthma, and occupational asthma.
Results:
We observed associations of genomewide significance between asthma and the following single-nucleotide polymorphisms: rs3771166 on chromosome 2, implicating IL1RL1/IL18R1 (P=3×10(−9)); rs9273349 on chromosome 6, implicating HLA-DQ (P=7×10(−14)); rs1342326 on chromosome 9, flanking IL33 (P=9×10(−10)); rs744910 on chromosome 15 in SMAD3 (P=4×10(−9)); and rs2284033 on chromosome 22 in IL2RB (P=1.1×10(−8)). Association with the ORMDL3/GSDMB locus on chromosome 17q21 was specific to childhood-onset disease (rs2305480, P=6×10(−23)). Only HLA-DR showed a significant genomewide association with the total serum IgE concentration, and loci strongly associated with IgE levels were not associated with asthma.
Conclusions:
Asthma is genetically heterogeneous. A few common alleles are associated with disease risk at all ages. Implicated genes suggest a role for communication of epithelial damage to the adaptive immune system and activation of airway inflammation. Variants at the ORMDL3/GSDMB locus are associated only with childhood-onset disease. Elevation of total serum IgE levels has a minor role in the development of asthma. (Funded by the European Commission and others.)
Chronic obstructive pulmonary disease (COPD) is characterized by progressive inflammation in the airways and lungs combined with disturbed homeostatic functions of pulmonary cells. MicroRNAs (miRNAs) have the ability to regulate these processes by interfering with gene transcription and translation.
We aimed to identify miRNA expression in induced sputum and examined whether the expression of miRNAs differed between patients with COPD and subjects without airflow limitation.
Expression of 627 miRNAs was evaluated in induced sputum supernatant of 32 subjects by stem-loop reverse transcription-quantitative polymerase chain reaction. Differentially expressed miRNAs were validated in an independent replication cohort of 41 subjects. Enrichment of miRNA target genes was identified by in silico analysis. Protein expression of target genes was determined by ELISA.
Thirty-four miRNAs were differentially expressed between never-smokers and current smokers without airflow limitation in the screening cohort. Eight miRNAs were expressed at a significantly lower level in current-smoking patients with COPD compared with never-smokers without airflow limitation. Reduced expression of let-7c and miR-125b in patients with COPD compared with healthy subjects was confirmed in the validation cohort. Target genes of let-7c were significantly enriched in the sputum of patients with severe COPD. The concentration of tumor necrosis factor receptor type II (TNFR-II, implicated in COPD pathogenesis and a predicted target gene of let-7c) was inversely correlated with the sputum levels of let-7c .
let-7c is significantly reduced in the sputum of currently smoking patients with COPD and is associated with increased expression of TNFR-II.
MicroRNAs ( miRNAs) are small non-protein-coding RNAs that function as endogenous negative gene regulators. Dysfunctions of miRNAs are frequently found in malignancies, including lung cancer. In this review, we summarise the current understanding of miRNAs in lung cancer tumourigenesis, and highlight their potential in overcoming drug resistance, abetting histological sub-classification techniques, and serving as biomarkers for lung cancer risk stratification and outcome prediction. British Journal of Cancer ( 2010) 103, 1144-1148. doi:10.1038/sj.bjc.6605901 www.bjcancer.com Published online 21 September 2010 (C) 2010 Cancer Research UK
MicroRNAs (miRNAs) are a family of small, non-coding RNA species functioning as negative regulators of multiple target genes including tumour suppressor genes and oncogenes. Many miRNA gene loci are located within cancer-associated genomic regions. To identify potential new amplified oncogenic and/or deleted tumour suppressing miRNAs in lung cancer, we inferred miRNA gene dosage from high dimensional arrayCGH data. From miRBase v9.0 (http://microrna.sanger.ac.uk), 474 human miRNA genes were physically mapped to regions of chromosomal loss or gain identified from a high-resolution genome-wide arrayCGH study of 132 primary non-small cell lung cancers (NSCLCs) (a training set of 60 squamous cell carcinomas and 72 adenocarcinomas). MiRNAs were selected as candidates if their immediately flanking probes or host gene were deleted or amplified in at least 25% of primary tumours using both Analysis of Copy Errors algorithm and fold change (≥ ± 1.2) analyses. Using these criteria, 97 miRNAs mapped to regions of aberrant copy number. Analysis of three independent published lung cancer arrayCGH datasets confirmed that 22 of these miRNA loci showed directionally concordant copy number variation. MiR-218, encoded on 4p15.31 and 5q35.1 within two host genes (SLIT2 and SLIT3), in a region of copy number loss, was selected as a priority candidate for follow-up as it is reported as underexpressed in lung cancer. We confirmed decreased expression of mature miR-218 and its host genes by qRT-PCR in 39 NSCLCs relative to normal lung tissue. This downregulation of miR-218 was found to be associated with a history of cigarette smoking, but not human papilloma virus. Thus, we show for the first time that putative lung cancer-associated miRNAs can be identified from genome-wide arrayCGH datasets using a bioinformatics mapping approach, and report that miR-218 is a strong candidate tumour suppressing miRNA potentially involved in lung cancer.
Asthma, a chronic inflammatory disorder of the airway, is influenced by interplay between genetic and environmental factors now known to be mediated by epigenetics. Aberrant DNA methylation, altered histone modifications, specific microRNA expression, and other chromatin alterations orchestrate a complex early-life reprogramming of immune T-cell response, dendritic cell function, macrophage activation, and a breach of airway epithelial barrier that dictates asthma risk and severity in later life. Adult-onset asthma is under analogous regulation. The sharp increase in asthma prevalence over the past 2 or 3 decades and the large variations among populations of similar racial/ethnic background but different environmental exposures favors a strong contribution of environmental factors. This review addresses the fundamental question of whether environmental influences on asthma risk, severity, and steroid resistance are partly due to differential epigenetic modulations. Current knowledge on the epigenetic effects of tobacco smoke, microbial allergens, oxidants, airborne particulate matter, diesel exhaust particles, polycyclic aromatic hydrocarbons, dietary methyl donors and other nutritional factors, and dust mites is discussed. Exciting findings have been generated by rapid technological advances and well-designed experimental and population studies. The discovery and validation of epigenetic biomarkers linked to exposure, asthma, or both might lead to better epigenotyping of risk, prognosis, treatment prediction, and development of novel therapies.
Glutathione plays an important role in antioxidant and inflammatory processes in the lung. Alterations in glutathione metabolism are a central feature of several chronic lung diseases.
To determine whether sequence variation in genes in the glutathione synthesis pathway alters susceptibility to air pollution effects on lung function.
In this prospective study, 14,821 lung function measurements were taken on 2,106 children from 12 Southern California cities. Tagging single-nucleotide polymorphisms in glutathione metabolism pathway genes GSS, GSR, GCLM, and GCLC were genotyped by GoldenGate assay (Illumina, San Diego, CA). Mixed regression models were used to determine whether particular haplotypes were associated with FEV(1), maximal mid-expiratory flow rate, and FVC and whether any of the genetic associations varied with levels of exposure to air pollutants.
We found that variation in the GSS locus was associated with differences in susceptibility of children for lung function growth deficits associated with NO(2), PM(10), PM(2.5), elemental carbon, organic carbon, and O(3). The negative effects of air pollutants were largely observed within participants who had a particular GSS haplotype. The effects ranged from -124.2 to -149.1 for FEV(1), from -92.9 to -126.7 for FVC, and from -193.9 to -277.9 for maximal mid-expiratory flow rate for all pollutants except O(3), which showed a larger decrease in lung function in children without this haplotype.
Variation in GSS was associated with differences in susceptibility to adverse effects of pollutants on lung function growth.
Wood smoke-associated chronic obstructive pulmonary disease (COPD) is common in women in developing countries but has not been adequately described in developed countries.
Our objective was to determine whether wood smoke exposure was a risk factor for COPD in a population of smokers in the United States and whether aberrant gene promoter methylation in sputum may modify this association.
For this cross-sectional study, 1,827 subjects were drawn from the Lovelace Smokers' Cohort, a predominantly female cohort of smokers. Wood smoke exposure was self-reported. Postbronchodilator spirometry was obtained, and COPD outcomes studied included percent predicted FEV₁, airflow obstruction, and chronic bronchitis. Effect modification of wood smoke exposure with current cigarette smoke, ethnicity, sex, and promoter methylation of lung cancer-related genes in sputum on COPD outcomes were separately explored. Multivariable logistic and poisson regression models were used for binary and rate-based outcomes, respectively.
Self-reported wood smoke exposure was independently associated with a lower percent predicted FEV₁ (point estimate [± SE] -0.03 ± 0.01) and a higher prevalence of airflow obstruction and chronic bronchitis (odds ratio, 1.96; 95% confidence interval, 1.52-2.52 and 1.64 (95% confidence interval, 1.31-2.06, respectively). These associations were stronger among current cigarette smokers, non-Hispanic whites, and men. Wood smoke exposure interacted in a multiplicative manner with aberrant promoter methylation of the p16 or GATA4 genes on lower percent predicted FEV₁.
These studies identify a novel link between wood smoke exposure and gene promoter methylation that synergistically increases the risk for reduced lung function in cigarette smokers.
Complex trait variation is likely to be explained by the combined effects of genes, environmental factors, and gene x environment (G x E) interaction. The authors introduce a novel 2-step method for detecting a G x E interaction in a genome-wide association study (GWAS) of case-parent trios. The method utilizes 2 sources of G x E information in a trio sample to construct a screening step and a testing step. Across a wide range of models, this 2-step procedure provides substantially greater power to detect G x E interaction than a standard test of G x E interaction applied genome-wide. For example, for a disease susceptibility locus with minor allele frequency of 15%, a binary exposure variable with 50% prevalence, and a GWAS scan of 1 million markers in 1,000 case-parent trios, the 2-step method provides 87% power to detect a G x E interaction relative risk of 2.3, as compared with only 25% power using a standard G x E test. The method is easily implemented using standard software. This 2-step scan for G x E interaction is independent of any prior scan that may have been conducted for genetic main effects, and thus has the potential to uncover new genes in a GWAS that have not been previously identified.
Despite the yield of recent genome-wide association (GWA) studies, the identified variants explain only a small proportion of the heritability of most complex diseases. This unexplained heritability could be partly due to gene--environment (G×E) interactions or more complex pathways involving multiple genes and exposures. This Review provides a tutorial on the available epidemiological designs and statistical analysis approaches for studying specific G×E interactions and choosing the most appropriate methods. I discuss the approaches that are being developed for studying entire pathways and available techniques for mining interactions in GWA data. I also explore methods for marrying hypothesis-driven pathway-based approaches with 'agnostic' GWA studies.
Reduced exposure to particulate matter with a 50% cut-off aerodynamic diameter of 10 microm (PM(10)) attenuated age-related lung function decline in our cohort, particularly in the small airways. We hypothesised that polymorphisms in glutathione S-transferase (GST) and haem oxygenase-1 (HMOX1) genes, important for oxidative stress defence, modify these beneficial effects. A population-based sample of 4,365 adults was followed up after 11 yrs, including questionnaire, spirometry and DNA blood sampling. PM(10) exposure was estimated by dispersion modelling and temporal interpolation. The main effects on annual decline in forced expiratory flow at 25-75% of forced vital capacity (FEF(25-75%)) and interactions with PM(10) reduction were investigated for polymorphisms HMOX1 rs2071746 (T/A), rs735266 (T/A) and rs5995098 (G/C), HMOX1 (GT)(n) promoter repeat, GSTM1 and GSTT1 deletions, and GSTP1 p.Ile105Val, using mixed linear regression models. HMOX1 rs5995098, HMOX1 haplotype TTG and GSTP1 showed significant genetic main effects. Interactions with PM(10) reduction were detected: a 10 microg.m(-3) reduction significantly attenuated annual FEF(25-75%) decline by 15.3 mL.s(-1) only in the absence of HMOX1 haplotype ATC. Similarly, carriers of long (GT)(n) promoter repeat alleles or the GSTP1 Val/Val genotype profited significantly more from a 10 microg.m(-3) reduction (26.5 mL.s(-1) and 27.3 mL.s(-1) respectively) than non-carriers. Benefits of a reduction in PM(10) exposure are not equally distributed across the population but are modified by the individual genetic make-up determining oxidative stress defence.
Despite the considerable enthusiasm about the yield of novel and replicated discoveries of genetic associations from the new generation of genome-wide association studies (GWAS), the proportion of the heritability of most complex diseases that have been studied to date remains small. Some of this "dark matter" could be due to gene-environment (G x E) interactions or more complex pathways involving multiple genes and exposures. We review the basic epidemiologic study design and statistical analysis approaches to studying G x E interactions individually and then consider more comprehensive approaches to studying entire pathways or GWAS data. In addition to the usual issues in genetic association studies, particular care is needed in exposure assessment, and very large sample sizes are required. Although hypothesis-driven, pathway-based and agnostic GWA study approaches are generally viewed as opposite poles, we suggest that the two can be usefully married using hierarchical modeling strategies that exploit external pathway knowledge in mining genome-wide data.
Altered patterns of gene expression mediate the effects of particulate matter (PM) on human health, but mechanisms through which PM modifies gene expression are largely undetermined. MicroRNAs (miRNAs) are highly conserved, noncoding small RNAs that regulate the expression of broad gene networks at the posttranscriptional level.
We evaluated the effects of exposure to PM and PM metal components on candidate miRNAs (miR-222, miR-21, and miR-146a) related with oxidative stress and inflammatory processes in 63 workers at an electric-furnace steel plant.
We measured miR-222, miR-21, and miR-146a expression in blood leukocyte RNA on the first day of a workweek (baseline) and after 3 days of work (postexposure). Relative expression of miRNAs was measured by real-time polymerase chain reaction. We measured blood oxidative stress (8-hydroxyguanine) and estimated individual exposures to PM1 (< 1 microm in aerodynamic diameter), PM10 (< 10 microm in aerodynamic diameter), coarse PM (PM10 minus PM1), and PM metal components (chromium, lead, cadmium, arsenic, nickel, manganese) between the baseline and postexposure measurements.
Expression of miR-222 and miR-21 (using the 2-DeltaDeltaCT method) was significantly increased in postexposure samples (miR-222: baseline = 0.68 +/- 3.41, postexposure = 2.16 +/- 2.25, p = 0.002; miR-21: baseline = 4.10 +/- 3.04, postexposure = 4.66 +/- 2.63, p = 0.05). In postexposure samples, miR-222 expression was positively correlated with lead exposure (beta = 0.41, p = 0.02), whereas miR-21 expression was associated with blood 8-hydroxyguanine (beta = 0.11, p = 0.03) but not with individual PM size fractions or metal components. Postexposure expression of miR-146a was not significantly different from baseline (baseline = 0.61 +/- 2.42, postexposure = 1.90 +/- 3.94, p = 0.19) but was negatively correlated with exposure to lead (beta = -0.51, p = 0.011) and cadmium (beta = -0.42, p = 0.04).
Changes in miRNA expression may represent a novel mechanism mediating responses to PM and its metal components.
Particulate matter (PM) is associated with adverse airway health effects; however, the underlying mechanism in disease initiation is still largely unknown. Recently, microRNAs (miRNAs; small noncoding RNAs) have been suggested to be important in maintaining the lung in a disease-free state through regulation of gene expression. Although many studies have shown aberrant miRNA expression patterns in diseased versus healthy tissue, little is known regarding whether environmental agents can induce such changes.
We used diesel exhaust particles (DEP), the largest source of emitted airborne PM, to investigate pollutant-induced changes in miRNA expression in airway epithelial cells. We hypothesized that DEP exposure can lead to disruption of normal miRNA expression patterns, representing a plausible novel mechanism through which DEP can mediate disease initiation.
Human bronchial epithelial cells were grown at air-liquid interface until they reached mucociliary differentiation. After treating the cells with 10 microg/cm(2) DEP for 24 hr, we analyzed total RNA for miRNA expression using microarray profile analysis and quantitative real-time polymerase chain reaction.
DEP exposure changed the miRNA expression profile in human airway epithelial cells. Specifically, 197 of 313 detectable miRNAs (62.9%) were either up-regulated or down-regulated by 1.5-fold. Molecular network analysis of putative targets of the 12 most altered miRNAs indicated that DEP exposure is associated with inflammatory responses pathways and a strong tumorigenic disease signature.
Alteration of miRNA expression profiles by environmental pollutants such as DEP can modify cellular processes by regulation of gene expression, which may lead to disease pathogenesis.
Pulmonary function measures are heritable traits that predict morbidity and mortality and define chronic obstructive pulmonary disease (COPD). We tested genome-wide association with forced expiratory volume in 1 s (FEV1) and the ratio of FEV1 to forced vital capacity (FVC) in the SpiroMeta consortium (n = 20,288 individuals of European ancestry). We conducted a meta-analysis of top signals with data from direct genotyping (n ? 32,184 additional individuals) and in silico summary association data from the CHARGE Consortium (n = 21,209) and the Health 2000 survey (n ? 883). We confirmed the reported locus at 4q31 and identified associations with FEV1 or FEV1/FVC and common variants at five additional loci: 2q35 in TNS1 (P = 1.11 × 10?12), 4q24 in GSTCD (2.18 × 10?23), 5q33 in HTR4 (P = 4.29 × 10?9), 6p21 in AGER (P = 3.07 × 10?15) and 15q23 in THSD4 (P = 7.24 × 10?15). mRNA analyses showed expression of TNS1, GSTCD, AGER, HTR4 and THSD4 in human lung tissue. These associations offer mechanistic insight into pulmonary function regulation and indicate potential targets for interventions to alleviate respiratory disease
Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.
Ozone is a common photochemical air pollutant which is present in the ambient air of many urban areas at concentrations sufficient to produce acute respiratory effects in humans. Because individuals vary considerably in the magnitude of their responses to ozone exposure, it is difficult to estimate the number of individuals in a given population who are experiencing adverse effects. Consequently risk and benefits analysis for various regulatory scenarios cannot be carried out with precision. As an aid to risk assessment this paper presents a method of predicting the proportion of individuals in the population who experience a particular health effect. Risk equations predicting the proportion of individuals experiencing lung function decrements as a function of ozone concentration, duration of exposure, and age are presented.
Outdoor air pollution at levels occurring in many urban areas around the world has substantial adverse effects on health. Children in general, and children with asthma in particular, are sensitive to the adverse effects of outdoor air pollutants, including ozone, nitrogen oxides, and respirable particulate matter. A growing number of studies also show that children living in environments near traffic have increased risks of new-onset asthma, asthma symptoms, exacerbations, school absences, and asthma-related hospitalizations. The large population of children exposed to high levels of outdoor air pollutants and the substantial risks for adverse health effects present unexploited opportunities to reduce the burden of asthma. Because the evidence indicates significant adverse effects of air pollution at current levels, there is clearly a need to reduce levels of regulated pollutants such as ozone, as well as unregulated pollutants in tailpipe emissions from motor vehicles. Achieving this long-term goal requires the active involvement of physicians and medical providers to ensure that the health of children is at the top of the list of competing priorities for regulatory policy decision-making. Clinical approaches include treatment to control asthma and patient education to reduce adverse effects of the disease. Reduction in exposures also can be approached at a policy level through changes in schools and school bus operations. Beyond clinical and public health approaches to reduce exposure, another strategy to be used before clean air goals are met is to decrease the susceptibility of children to air pollution. Emerging research indicates that dietary supplementation for individuals with low antioxidant levels is one promising approach to reducing susceptibility to air pollution. A second approach involves induction of enzymatic antioxidant defenses, especially for individuals with at-risk genetic variants of key antioxidant enzymes.
Cyclooxygenase-2 (COX-2) plays an important role in the inflammatory response induced by physiologic and stress stimuli. Exposure to diesel exhaust particulate matter (DEP) has been shown to induce pulmonary inflammation and exacerbate asthma and chronic obstructive pulmonary disease. DEP is a potent inducer of inflammatory reponses in human airway epithelial cells. The mechanism through which DEP inhalation induces inflammatory mediator expression is not understood. In this report, we demonstrate that DEP can induce the expression of COX-2 gene in a human bronchial epithelial cell line (BEAS-2B) at both transcriptional and protein levels. The induction of COX-2 gene expression involves chromatin modification, in particular acetylation and deacetylation of histones. We show that exposure to DEP increases the acetylation of histone H4 associated with the COX-2 promoter and causes degradation of histone deacetylase 1 (HDAC1). Further, we establish that HDAC1 plays a pivotal role in mediating the transcriptional activation of the COX-2 gene in BEAS-2B cells exposed to DEP, supported by evidence that the down-regulation of HDAC1 using siRNA leads to activation of COX-2 gene expression, whereas overexpression of HDAC1 results in its repression. Finally, DEP exposure induced recruitment of histone acetyltransferase (HAT) p300 to the promoter of the COX-2 gene, suggesting that acetylation is also important in regulating its expression in response to DEP exposure. These results show for the first time acetylation via selective degradation of HDAC1, and that recruitment of HAT plays an important role in DEP-induced expression of the COX-2 gene.
Nonsyndromic cleft palate (CP) is a common birth defect with a complex and heterogeneous etiology involving both genetic and environmental risk factors. We conducted a genome-wide association study (GWAS) using 550 case-parent trios, ascertained through a CP case collected in an international consortium. Family-based association tests of single nucleotide polymorphisms (SNP) and three common maternal exposures (maternal smoking, alcohol consumption, and multivitamin supplementation) were used in a combined 2 df test for gene (G) and gene-environment (G × E) interaction simultaneously, plus a separate 1 df test for G × E interaction alone. Conditional logistic regression models were used to estimate effects on risk to exposed and unexposed children. While no SNP achieved genome-wide significance when considered alone, markers in several genes attained or approached genome-wide significance when G × E interaction was included. Among these, MLLT3 and SMC2 on chromosome 9 showed multiple SNPs resulting in an increased risk if the mother consumed alcohol during the peri-conceptual period (3 months prior to conception through the first trimester). TBK1 on chr. 12 and ZNF236 on chr. 18 showed multiple SNPs associated with higher risk of CP in the presence of maternal smoking. Additional evidence of reduced risk due to G × E interaction in the presence of multivitamin supplementation was observed for SNPs in BAALC on chr. 8. These results emphasize the need to consider G × E interaction when searching for genes influencing risk to complex and heterogeneous disorders, such as nonsyndromic CP.
Epigenetics is traditionally defined as the study of heritable changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence. There are three main classes of epigenetic marks--DNA methylation, modifications of histone tails, and noncoding RNAs--each of which may be influenced by the environment, diet, diseases, and ageing. Importantly, epigenetic marks have been shown to influence immune cell maturation and are associated with the risk of developing various forms of cancer, including lung cancer. Moreover, there is emerging evidence that these epigenetic marks affect gene expression in the lung and are associated with benign lung diseases, such as asthma, chronic obstructive pulmonary disease, and interstitial lung disease. Technological advances have made it feasible to study epigenetic marks in the lung, and it is anticipated that this knowledge will enhance our understanding of the dynamic biology in the lung and lead to the development of novel diagnostic and therapeutic approaches for our patients with lung disease.
The purpose of this review is to provide an update of the current understanding on the role of microRNAs in mediating genetic responses to air pollutants and to contemplate on how these responses ultimately control susceptibility to ambient air pollution. Morbidity and mortality attributable to air pollution continues to be a growing public health concern worldwide. Despite several studies on the health effects of ambient air pollution, underlying molecular mechanisms of susceptibility and disease remain elusive. In the last several years, special attention has been given to the role of epigenetics in mediating, not only genetic and physiological responses to certain environmental insults, but also in regulating underlying susceptibility to environmental stressors. Epigenetic mechanisms control the expression of gene products, both basally and as a response to a perturbation, without affecting the sequence of DNA itself. These mechanisms include structural regulation of the chromatin structure, such as DNA methylation and histone modifications, and post-transcriptional gene regulation, such as microRNA mediated repression of gene expression. microRNAs are small noncoding RNAs that have been quickly established as key regulators of gene expression. As such, miRNAs have been found to control several cellular processes including apoptosis, proliferation and differentiation. More recently, research has emerged suggesting that changes in the expression of some miRNAs may be critical for mediating biological, and ultimately physiological, responses to air pollutants. Although the study of microRNAs, and epigenetics as a whole, has come quite far in the field of cancer, the understanding of how these mechanisms regulate gene-environment interactions to environmental exposures in everyday life is unclear. This article does not necessarily reflect the views and policies of the US EPA.
Tobacco smoking is responsible for substantial morbidity and mortality worldwide, in particular through cardiovascular, pulmonary, and malignant pathology. CpG methylation might plausibly play a role in a variety of smoking-related phenomena, as suggested by candidate gene promoter or global methylation studies. Arrays allowing hypothesis-free searches on a scale resembling genome-wide studies of SNPs have become available only very recently. Methylation extents in peripheral-blood DNA were assessed at 27,578 sites in more than 14,000 gene promoter regions in 177 current smokers, former smokers, and those who had never smoked, with the use of the Illumina HumanMethylation 27K BeadChip. This revealed a single locus, cg03636183, located in F2RL3, with genome-wide significance for lower methylation in smokers (p = 2.68 × 10(-31)). This was similarly significant in 316 independent replication samples analyzed by mass spectrometry and Sequenom EpiTyper (p = 6.33 × 10(-34)). Our results, which were based on a rigorous replication approach, show that the gene coding for a potential drug target of cardiovascular importance features altered methylation patterns in smokers. To date, this gene had not attracted attention in the literature on smoking.
Asthma is caused by both heritable and environmental factors. It has become clear that genetic studies do not adequately explain the heritability and susceptibility to asthma. The study of epigenetics, heritable non-coding changes to DNA may help to explain the heritable component of asthma. Additionally, epigenetic modifications can be influenced by the environment, including pollution and cigarette smoking, which are known asthma risk factors. These environmental trigger-induced epigenetic changes may be involved in skewing the immune system towards a Th2 phenotype following in utero exposure and thereby enhancing the risk of asthma. Alternatively, they may directly or indirectly modulate the immune and inflammatory processes in asthmatics via effects on treatment responsiveness. The study of epigenetics may therefore play an important role in our understanding and possible treatment of asthma and other allergic diseases. This article is part of a Special Issue entitled: Biochemistry of Asthma.
Many complex diseases are likely to be a result of the interplay of genes and environmental exposures. The standard analysis in a genome-wide association study (GWAS) scans for main effects and ignores the potentially useful information in the available exposure data. Two recently proposed methods that exploit environmental exposure information involve a two-step analysis aimed at prioritizing the large number of SNPs tested to highlight those most likely to be involved in a GE interaction. For example, Murcray et al. ([2009] Am J Epidemiol 169:219–226) proposed screening on a test that models the G-E association induced by an interaction in the combined case-control sample. Alternatively, Kooperberg and LeBlanc ([2008] Genet Epidemiol 32:255–263) suggested screening on genetic marginal effects. In both methods, SNPs that pass the respective screening step at a pre-specified significance threshold are followed up with a formal test of interaction in the second step. We propose a hybrid method that combines these two screening approaches by allocating a proportion of the overall genomewide significance level to each test. We show that the Murcray et al. approach is often the most efficient method, but that the hybrid approach is a powerful and robust method for nearly any underlying model. As an example, for a GWAS of 1 million markers including a single true disease SNP with minor allele frequency of 0.15, and a binary exposure with prevalence 0.3, the Murcray, Kooperberg and hybrid methods are 1.90, 1.27, and 1.87 times as efficient, respectively, as the traditional case-control analysis to detect an interaction effect size of 2.0.
Despite their widespread roles as regulators of gene expression, important questions remain about target regulation by microRNAs. Animal microRNAs were originally thought to repress target translation, with little or no influence on mRNA abundance, whereas the reverse was thought to be true in plants. Now, however, it is clear that microRNAs can induce mRNA degradation in animals and, conversely, translational repression in plants. Recent studies have made important advances in elucidating the relative contributions of these two different modes of target regulation by microRNAs. They have also shed light on the specific mechanisms of target silencing, which, although it differs fundamentally between plants and animals, shares some common features between the two kingdoms.
Many environmental risk factors for common, complex human diseases have been revealed by epidemiologic studies, but how genotypes at specific loci modulate individual responses to environmental risk factors is largely unknown. Gene-environment interactions will be missed in genome-wide association studies and could account for some of the 'missing heritability' for these diseases. In this review, we focus on asthma as a model disease for studying gene-environment interactions because of relatively large numbers of candidate gene-environment interactions with asthma risk in the literature. Identifying these interactions using genome-wide approaches poses formidable methodological problems, and elucidating molecular mechanisms for these interactions has been challenging. We suggest that studying gene-environment interactions in animal models, although more tractable, might not be sufficient to shed light on the genetic architecture of human diseases. Lastly, we propose avenues for future studies to find gene-environment interactions.
Asthma is a disease in which both genetic and environmental factors play important roles. The farming environment has consistently been associated with protection from childhood asthma and atopy, and interactions have been reported with polymorphisms in innate immunity genes.
To detect gene-environment interactions for asthma and atopy in the farming environment.
We performed a genome-wide interaction analysis for asthma and atopy by using 500,000 genotyped single nucleotide polymorphisms (SNPs) and farm-related exposures in 1708 children from 4 rural regions of Central Europe. We also tested selectively for interactions between farm exposures and 7 SNPs that emerged as genome-wide significant in a large meta-analysis of childhood asthma and 5 SNPs that had been reported previously as interacting with farm exposures for asthma or atopy.
Neither the asthma-associated SNPs nor the SNPs previously published for interactions with asthma showed significant interactions. The genome-wide interaction study did not reveal any significant interactions with SNPs within genes in the range of interacting allele frequencies from 30% to 70%, for which our study was well powered. Among rarer SNPs, we identified 15 genes with strong interactions for asthma or atopy in relation to farming, contact with cows and straw, or consumption of raw farm milk.
Common genetic polymorphisms are unlikely to moderate the protective influence of the farming environment on childhood asthma and atopy, but rarer variants, particularly of the glutamate receptor, metabotropic 1 gene, may do so. Given the limited statistical power of our study, these findings should be interpreted with caution before being replicated in independent farm populations.
Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels and 1.3 million genome-wide single nucleotide polymorphism (SNP) markers from both Affymetrix and Illumina platforms were assayed for all 277 human LCLs. MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assays for radiation cytotoxicity were also performed to obtain area under the curve (AUC) as a radiation response phenotype for use in the association studies. Functional validation of candidate genes, selected from an integrated analysis that used SNP, expression, and AUC data, was performed with multiple cancer cell lines using specific siRNA knockdown, followed by MTS and colony-forming assays. A total of 27 loci, each containing at least two SNPs within 50 kb with P-values less than 10(-4) were associated with radiation AUC. A total of 270 expression probe sets were associated with radiation AUC with P < 10(-3). The integrated analysis identified 50 SNPs in 14 of the 27 loci that were associated with both AUC and the expression of 39 genes, which were also associated with radiation AUC (P < 10(-3)). Functional validation using siRNA knockdown in multiple tumor cell lines showed that C13orf34, MAD2L1, PLK4, TPD52, and DEPDC1B each significantly altered radiation sensitivity in at least two cancer cell lines. Studies performed with LCLs can help to identify novel biomarkers that might contribute to variation in response to radiation therapy and enhance our understanding of mechanisms underlying that variation.
Characterizing structural variants in the human genome is of great importance, but a genome wide analysis to detect interspersed repeats has not been done. Thus, the degree to which mobile DNAs contribute to genetic diversity, heritable disease, and oncogenesis remains speculative. We perform transposon insertion profiling by microarray (TIP-chip) to map human L1(Ta) retrotransposons (LINE-1 s) genome-wide. This identified numerous novel human L1(Ta) insertional polymorphisms with highly variant allelic frequencies. We also explored TIP-chip's usefulness to identify candidate alleles associated with different phenotypes in clinical cohorts. Our data suggest that the occurrence of new insertions is twice as high as previously estimated, and that these repeats are under-recognized as sources of human genomic and phenotypic diversity. We have just begun to probe the universe of human L1(Ta) polymorphisms, and as TIP-chip is applied to other insertions such as Alu SINEs, it will expand the catalog of genomic variants even further.