Epigenome-wide association study of lung function level and its change.

Previous reports link differential DNA methylation (DNAme) to environmental exposures that are associated with lung function. Direct evidence on lung function DNAme is, however, limited. We undertook an agnostic epigenome-wide association study (EWAS) on pre-bronchodilation lung function and its change in adults.In a discovery-replication EWAS design, DNAme in blood and spirometry were measured twice, 6-15 years apart, in the same participants of three adult population-based discovery cohorts (n=2043). Associated DNAme markers (p<5×10-7) were tested in seven replication cohorts (adult: n=3327; childhood: n=420). Technical bias-adjusted residuals of a regression of the normalised absolute ß-values on control probe-derived principle components were regressed on level and change of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and their ratio (FEV1/FVC) in the covariate-adjusted discovery EWAS. Inverse-variance-weighted meta-analyses were performed on results from discovery and replication samples in all participants and never-smokers.EWAS signals were enriched for smoking-related DNAme. We replicated 57 lung function DNAme markers in adult, but not childhood samples, all previously associated with smoking. Markers not previously associated with smoking failed replication. cg05575921 (AHRR (aryl hydrocarbon receptor repressor)) showed the statistically most significant association with cross-sectional lung function (FEV1/FVC: pdiscovery=3.96×10-21 and pcombined=7.22×10-50). A score combining 10 DNAme markers previously reported to mediate the effect of smoking on lung function was associated with lung function (FEV1/FVC: p=2.65×10-20).Our results reveal that lung function-associated methylation signals in adults are predominantly smoking related, and possibly of clinical utility in identifying poor lung function and accelerated decline. Larger studies with more repeat time-points are needed to identify lung function DNAme in never-smokers and in children.

Inhaled corticosteroids may prevent lung cancer in asthma patients.

BACKGROUND: It is unclear whether inhaled corticosteroids (ICS) have chemopreventive effect on lung cancer (LC) development in humans. We investigated the association between the ICS use in asthma patients and the risk of LC. METHODS: We conducted a nationwide, population-based retrospective cohort study using the National Health Insurance database. We identified 4210 asthmatics who were initially free of LC and regularly used ICS between 2001 and 2005 and 37,228 asthmatics without regular ICS use. Patients with documented history of tobacco use were excluded from the analyses. Asthmatics were categorized into a mild and a severe asthma group. Each patient was tracked until the end of 2010 to identify incident cases of LC. Cox proportional hazards models were used to evaluate the effect of ICS on the risk of LC, further stratifying by asthma severity and comorbidities. RESULTS: During follow-up, we identified 747 incident cases of LC diagnosed in the asthma cohort. Compared with severe asthmatics without regular ICS use, the risk of LC for those with mild asthma with regular ICS use was lower (adjusted hazard ratio = 0.42, 95% confidence interval = 0.31-0.56, P < 0.0001). The risk of LC was calculated among the following rankings of risk severe asthma without regular ICS use, low severity without regular ICS, high severity with regular ICS, and low severity with regular ICS group showed a decreasing trend of LC incidence (P = 0.041). Analyses stratified by comorbidities revealed that the protective effect of ICS was assessed with better precision and more pronounced in those with renal diseases, stroke, and hyperlipidemia. CONCLUSIONS: For patients with asthma, regular ICS use might have a protective effect against LC. Further studies are required to assess this potential association from both immunohistopathological and clinical aspects.

The Effects of Pleural Plaques on Longitudinal Lung Function in Vermiculite Miners of Libby, Montana.

BACKGROUND: This study was conducted to assess associations of pleural plaques (PP) and longitudinal lung function in vermiculite miners of Libby, Montana who are occupationally exposed to asbestos. High-resolution computed tomography (HRCT) was used to identify asbestos-related findings in former Libby vermiculite miners. We investigated annual lung function decline in miners with PP only and compared them to miners with normal HRCT findings. MATERIALS AND METHODS: HRCTs from 128 miners were categorized into the following 4 diagnostic groups: (1) normal computed tomography scan (n = 9); (2) PP only (n = 72); (3) PP and interstitial fibrosis (n = 26) and (4) additional HRCT abnormalities (n = 21) such as rounded atelectasis, diffuse pleural thickening, pleural effusions or pulmonary nodules or tumor >1cm in diameter. Random intercept and slope linear mixed-effect regression models identified differences in lung function decline between miners with asbestos-associated outcomes and those with normal HRCT. Models were adjusted for follow-up time, body mass index, smoking status, latent exposure period and employment years. Interactions for smoking status with age and smoking status with pleural plaque severity were examined. RESULTS: Miners with PP only did not have an accelerated decline in lung function between 40 and 80 years. Miners with PP and additional HRCT abnormalities displayed significantly accelerated declines in forced expiratory volume in 1 second and diffusing capacity of the lungs for carbon monoxide (P = 0.05 and P < 0.01, respectively). Plaque severity did not affect lung function decline. However, smokers with extensive plaques displayed accelerated loss in diffusing capacity of the lungs for carbon monoxide and forced expiratory volume in 1 second when compared to nonsmoking miners with mild plaque formation. CONCLUSIONS: PP alone did not significantly affect lung function decline in vermiculite miners of Libby, Montana.

Comparison of different cell type correction methods for genome-scale epigenetics studies.

BACKGROUND: Whole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. These associations can be confounded by cellular heterogeneity. Algorithms have been developed to measure or adjust for this heterogeneity, and some have been compared in the literature. However, with new methods available, it is unknown whether the findings will be consistent, if not which method(s) perform better. RESULTS: Methods: We compared eight cell-type correction methods including the method in the minfi R package, the method by Houseman et al., the Removing unwanted variation (RUV) approach, the methods in FaST-LMM-EWASher, ReFACTor, RefFreeEWAS, and RefFreeCellMix R programs, along with one approach utilizing surrogate variables (SVAs). We first evaluated the association of DNA methylation at each CpG across the whole genome with prenatal arsenic exposure levels and with cancer status, adjusted for estimated cell-type information obtained from different methods. We then compared CpGs showing statistical significance from different approaches. For the methods implemented in minfi and proposed by Houseman et al., we utilized homogeneous data with composition of some blood cells available and compared them with the estimated cell compositions. Finally, for methods not explicitly estimating cell compositions, we evaluated their performance using simulated DNA methylation data with a set of latent variables representing "cell types". RESULTS: Results from the SVA-based method overall showed the highest agreement with all other methods except for FaST-LMM-EWASher. Using homogeneous data, minfi provided better estimations on cell types compared to the originally proposed method by Houseman et al. Further simulation studies on methods free of reference data revealed that SVA provided good sensitivities and specificities, RefFreeCellMix in general produced high sensitivities but specificities tended to be low when confounding is present, and FaST-LMM-EWASher gave the lowest sensitivity but highest specificity. CONCLUSIONS: Results from real data and simulations indicated that SVA is recommended when the focus is on the identification of informative CpGs. When appropriate reference data are available, the method implemented in the minfi package is recommended. However, if no such reference data are available or if the focus is not on estimating cell proportions, the SVA method is suggested.

Polycyclic aromatic hydrocarbons exposure, oxidative stress, and asthma in children.

PURPOSE: Polycyclic aromatic hydrocarbons (PAHs) are known for their carcinogenic and teratogenic properties. However, little is known about the effect of PAH on our immune and respiratory systems. Hence, we investigated associations (1) between PAH exposure and IgE levels and asthma in children and (2) between PAH exposure and the oxidative stress marker 8OHdG potentially involved in disease pathogenesis stratifying by (3) sex-based differences. METHODS: A total of 453 kindergarten children were recruited and provided samples. Urine biomarker of PAH exposure (1-OHP levels) was measured by UPLC-MS/MS and a marker of oxidative stress (8OHdG) was measured by ELISA. Serum IgE were assessed and information on asthma was collected. Associations between 1-OHP levels, 8OHdG, IgE and asthma were analyzed by multivariate linear and logistic regression. A mediation analysis was conducted to evaluate whether the risk of increased IgE and asthma related to PAH exposure is explained by 8OHdG changes. RESULTS: Urine 1-OHP levels were positively related to 8OHdG levels (per ln-unit: ß = 0.30kU/l, p = 0.002). Similar results were also found for 1-OHP levels with IgE levels (per ln-unit: ß = 0.27 kU/l, p = 0.027). 1-OHP levels (per ln-unit) were significantly associated with asthma, with an OR (95% CI) of 1.42 (1.18-1.70). In addition, 1-OHP levels were associated with asthma. It is estimated that 35% of the effect of PAH exposure on asthma is mediated by 8OHdG levels. CONCLUSION: Exposure to PAH may enhance oxidative stress and may induce asthma. The effect of PAH exposure on asthma may be mediated by oxidative stress.

An Efficient Approach to Screening Epigenome-Wide Data.

Screening cytosine-phosphate-guanine dinucleotide (CpG) DNA methylation sites in association with some covariate(s) is desired due to high dimensionality. We incorporate surrogate variable analyses (SVAs) into (ordinary or robust) linear regressions and utilize training and testing samples for nested validation to screen CpG sites. SVA is to account for variations in the methylation not explained by the specified covariate(s) and adjust for confounding effects. To make it easier to users, this screening method is built into a user-friendly R package, ttScreening, with efficient algorithms implemented. Various simulations were implemented to examine the robustness and sensitivity of the method compared to the classical approaches controlling for multiple testing: the false discovery rates-based (FDR-based) and the Bonferroni-based methods. The proposed approach in general performs better and has the potential to control both types I and II errors. We applied ttScreening to 383,998 CpG sites in association with maternal smoking, one of the leading factors for cancer risk.

Lung Function before and after a Large Chlorine Gas Release in Graniteville, South Carolina.

RATIONALE: On January 6, 2005 a train derailment led to an estimated 54,915-kg release of chlorine at a local textile mill in Graniteville, South Carolina. OBJECTIVES: We used the employee health spirometry records of the textile to identify enduring effects of chlorine gas exposure resulting from the incident on the lung function of workers employed at the textile mill. METHODS: Spirometry records from 1,807 mill workers (7,332 observations) were used from 4 years before and 18 months after the disaster. Longitudinal analysis using marginal regression models produced annual population mean estimates for FEV1, FVC, and FEV1/FVC ratio. Covariate adjustment was made for sex, age, smoking, height, season tested, technician, obesity, season × year interactions, and smoker × year interactions. The increased prevalence of mill workers having accelerated FEV1 decline was also evaluated after the chlorine spill. MEASUREMENTS AND MAIN RESULTS: In the year of the accident, we observed a significant reduction in mean FEV1 (-4.2% predicted; P = 0.019) when compared with the year before the incident. In the second year, partial recovery in the mean FVC % predicted level was seen, but the cohort's average FEV1/FVC ratio continued to decrease over time. Severe annual FEV1 decline was most prevalent in the year of the accident, and independent of mill worker smoking status. CONCLUSIONS: The Graniteville mill worker cohort revealed significant reductions in lung function immediately after the chlorine incident. Improvement was seen in the second year; but the proportion of mill workers experiencing accelerated FEV1 annual decline significantly increased in the 18 months after the chlorine incident.

Early-life antibiotic use is associated with wheezing among children with high atopic risk: a prospective European study.

BACKGROUND: Little is known about the relationship between antibiotic use and asthma in the children with a higher risk of allergic sensitization. We examine the association between the use of specific therapeutic antibiotics in the first year of life and development of wheezing by 36 months among children with a higher risk of allergic sensitization. METHODS: A multi-center prospective cohort study was conducted among children at high risk for allergic sensitization. A validated questionnaire was used to prospectively collect information on antibiotic use and potential risk factors for wheezing from parents or guardians of 606 children from three European countries at 6, 12, 24 and 36 months of age. Multivariate linear and logistic regression models were used to adjust for potential confounders and effect modifiers and to estimate the association of antibiotic use with the development of early childhood wheezing. RESULTS: Of the antibiotics assessed, only macrolide use in the first year of life was associated with increasing risk for wheezing by 36 months, after adjusting for gender, socioeconomic status, breast feeding >6 months, tobacco smoke exposure, family history of asthma, and respiratory infection (RR = 1.09; 95% CI 1.05-1.13). To avoid a bias by indication, we analyzed children with and without respiratory infection separately. Similar associations were observed for macrolides use in children who had no respiratory infection. CONCLUSIONS: In European children with a familial risk for allergic sensitization, we found a positive association between macrolide use in the first year of life and wheezing until 36 months old which was independent of the effect of respiratory infection.

Pleural plaques and their effect on lung function in Libby vermiculite miners.

BACKGROUND: Multiple studies have investigated the relationship between asbestos-related pleural plaques (PPs) and lung function, with disparate and inconsistent results. Most use chest radiographs to identify PPs and simple spirometry to measure lung function. High-resolution CT (HRCT) scanning improves the accuracy of PP identification. Complete pulmonary function tests (PFTs), including spirometry, lung volumes, and diffusing capacity of the lung for carbon monoxide, provide a more definitive assessment of lung function. The goal of this study was to determine, using HRCT scanning and complete PFTs, the effect of PPs on lung function in Libby vermiculite miners. METHODS: The results of HRCT scanning and complete PFTs performed between January 2000 and August 2012 were obtained from the medical records of 166 Libby vermiculite miners. Multivariate regression analyses with Tukey multivariate adjustment were used to assess statistical associations between the presence of PPs and lung function. Adjustments were made for age, BMI, smoking history, duration of employment, and years since last occupational asbestos exposure. RESULTS: Nearly 90% of miners (n = 149) had evidence of PPs on HRCT scan. No significant differences in spirometry results, lung volumes, or diffusing capacity of the lung for carbon monoxide were found between miners with PPs alone and miners with normal HRCT scans. Miners with both interstitial fibrosis and the presence of PPs had a significantly decreased total lung capacity in comparison with miners with normal HRCT scans (P = .02). Age, cumulative smoking history, and BMI were significant covariates that contributed to abnormal lung function. CONCLUSIONS: Asbestos-related PPs alone have no significant effect on lung function in Libby vermiculite miners.

137Cesium exposure and spirometry measures in Ukrainian children affected by the Chernobyl nuclear incident.

BACKGROUND: After the Chernobyl accident in 1986, children of the contaminated Narodichesky region of Ukraine were obliged to participate in a yearly medical screening. They have been exposed to 137cesium (137Cs; half-life = 30 years) in contaminated soils, air, and food. OBJECTIVE: Using a "natural experiment" approach and a longitudinal prospective cohort study design, we investigated the association of soil 137Cs and spirometry measures for 415 children using 1,888 repeated measurements from 1993 to 1998. METHODS: Mean baseline village soil 137Cs measurements, which varied from 29.0 to 879 kBq/m2, were used as exposure indicators. A standardized spirometry protocol and prediction equations specific to Ukrainian children were used by the same pulmonologist in all screenings. RESULTS: Children living in villages with the highest quintile of soil 137Cs were 2.60 times more likely to have forced vital capacity (FVC) < 80% of predicted [95% confidence interval (CI), 1.07-6.34] and 5.08 times more likely to have a ratio of forced expiratory volume in 1 sec (FEV1) to FVC% < 80% (95% CI, 1.02-25.19). We found statistically significant evidence of both airway obstruction (FEV1/FVC%, peak expiratory flow, and maximum expiratory flow at 25%, 50%, and 75% of FVC) and restriction (FVC) with increasing soil 137Cs. CONCLUSIONS: These findings are unique and suggest significant airway obstruction and restriction consequences for children chronically exposed to low-dose radioactive contaminants such as those found downwind of the Chernobyl Nuclear Power Plant.