Pathway analysis of a genome-wide gene by air pollution interaction study in asthmatic children

Identification of potential diagnostic biomarkers and therapeutic targets in patients with hypoxia pulmonary hypertension

BACKGROUND

Pulmonary hypertension is a serious disease. Emerging studies have shown that M2 macrophages play an essential role in pulmonary hypertension; however, their mechanism of action is uncertain.

METHODS

Four GEO datasets were downloaded. The differentially expressed genes (DEGs) were obtained using the limma package. Simultaneously, the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) algorithm and weighted gene co-expression network analysis (WGCNA) were used to get the information about M2 macrophage-related modules. Potential key genes were obtained by intersecting DEGs with M2 macrophage-related module genes (M2MRGs), and finally the area under the curve (AUC) was calculated. Rats were exposed to hypoxia condition (10 % O2) for 4 weeks to induce PH. Subsequently, potential key genes with AUC>0.7 were analyzed by quantitative real-time polymerase chain reaction and Western blot using normoxia and hypoxia rat lungs. We knocked down EPHA3 in Raw264.7 cells and detected the protein expression of M2 macrophage markers including arginase 1 (ARG1) and interleukin 10 (IL-10), phospho-protein kinase B (P-Akt), and protein kinase B (Akt) to explore the downstream pathways of EPHA3.

RESULTS

Seven potential hub genes were detected by intersecting M2MRGs and DEGs. Six genes with AUC values above 0.7 were used for further exploration. The expression of EPHA3 mRNA and protein was significantly more upregulated in rats with hypoxia than in rats with normoxia. The expression levels of IL10, ARG1, and P-Akt/Akt decreased after knocking down EPHA3.

CONCLUSIONS

This study suggested that the activation of the P-Akt/Akt signaling pathway promoted by EPHA3 played an essential role in the progression of pulmonary hypertension.

Ambient air pollution sensitivity and severity of pediatric asthma

BACKGROUND

Ambient air pollution exposure increases the incidence and severity of pediatric asthma. Despite this, we lack effective therapies to protect patients from the impact of ambient air pollution exposure. A roadblock is the inability to identify patients that are affected by air pollution.

OBJECTIVE

To examine the association between AAP sensitivity determined by individual exposure prior to asthma exacerbations and the severity of asthma in pediatric patients.

METHODS

We assess the association between spikes in ambient air pollution and asthma exacerbations. Patients were considered sensitive to a specific pollutant if they experienced an asthma exacerbation immediately following a spike in the concentration of that pollutant. Cut off values for these spikes were determined as two standard deviations above the mean concentration two weeks prior and two weeks post the days leading up to an asthma exacerbation.

RESULTS

We included 8129 pediatric patients with over 34,346 associated asthma exacerbations. In a multinomial log-linear logistic regression model comparing patients with mild asthma to patients with moderate or severe asthma, sensitivity to Ozone, SO2, PM2.5 and PM10 was significantly associated to severe as opposed to mild asthma (OR 1.39 with CI 1.08-1.78, 1.58 with CI 1.12-2.23, 1.37 with CI 1.07-1.76, and 1.63 with CI 1.12-2.37 respectively). Furthermore, moderate as opposed to mild asthma was significantly associated with sensitivity to SO2 and PM2.5 (OR 1.24 with CI 1.06-1.44 and 1.26 with CI 1.12-1.43, respectively).

IMPACT STATEMENT

There is a subpopulation of pediatric asthma patients that experience asthma exacerbations just following spikes in ambient air pollution. This subgroup of patients has more severe asthma despite correction for significant confounders. The presented work is the first to reveal the clinically significant impact of variation in ambient air pollution sensitivity in pediatric asthma, highlighting the importance of accounting for variable sensitivity in the study of the effects of ambient air pollution exposure on pediatric asthma.

Experimental study on the purification capacity of potted plants on low-concentration carbon monoxide in indoor environment

Indoor low-concentration carbon monoxide (CO) exposure is widespread worldwide, and potted plants may be a potential means for CO purification. The objective is to evaluate common indoor plants' CO purification and tolerance capacities. Epipremnum aureum (Linden ex André) G.S.Bunting, Chlorophytum comosum (Thunb.) Jacques, Spathiphyllum kochii Engl. & K.Krause, and Sansevieria trifasciata Hort. ex Prain with similar sizes were tested in the glass chamber with initial CO concentrations of 10, 25, 50, 100, 200, and 400 ppm, respectively. (1) The CO purification capacity of the four potted plants is ranked as Epipremnum aureum (Linden ex André) G.S.Bunting > Chlorophytum comosum (Thunb.) Jacques > Spathiphyllum kochii Engl. & K.Krause > Sansevieria trifasciata Hort. ex Prain. Under the purification effect of each plant, the CO concentration in the chamber decreases linearly and significantly (p < 0.05), and within a specific time period, the time-weighted average (TWA) CO concentrations can be reduced to below the corresponding permissible exposure limits specified by some countries and organizations. (2) With the increase of the stomatal number of each plant and the increase in CO concentration, the hourly and cumulative absorbed CO of each plant increase linearly and significantly (p < 0.05). (3) With the increase in CO concentration, the CO purification efficiency of each plant decreases exponentially and significantly (p < 0.05). (4) When the CO concentration was ≤ 50 ppm, all plants could effectively purify CO without damage. When the CO concentration was in the range of 100 ~ 400 ppm, within 2 weeks after the 48-h experiment, the leaf tips of Chlorophytum comosum (Thunb.) Jacques and Epipremnum aureum (Linden ex André) G.S.Bunting were damaged one after another, and the damaged leaf area increased with the increase of CO concentration. However, each plant as a whole still survived. This study demonstrated that different species of potted plants can effectively absorb low concentrations of CO to varying degrees, but higher concentrations of CO will damage the survival of specific species of potted plants.

Associations between outdoor air pollutants and non-viral asthma exacerbations and airway inflammatory responses in children and adolescents living in urban areas in the USA: a retrospective secondary analysis

BACKGROUND

Asthma prevalence and severity have markedly increased with urbanisation, and children in low-income urban centres have among the greatest asthma morbidity. Outdoor air pollution has been associated with adverse respiratory effects in children with asthma. However, the mechanisms by which air pollution exposure exacerbates asthma, and how these mechanisms compare with exacerbations induced by respiratory viruses, are poorly understood. We aimed to investigate the associations between regional air pollutant concentrations, respiratory illnesses, lung function, and upper airway transcriptional signatures in children with asthma, with particular focus on asthma exacerbations occurring in the absence of respiratory virus.

METHODS

We performed a retrospective analysis of data from the MUPPITS1 cohort and validated our findings in the ICATA cohort. The MUPPITS1 cohort recruited 208 children aged 6-17 years living in urban areas across nine US cities with exacerbation-prone asthma between Oct 7, 2015, and Oct 18, 2016, and monitored them during reported respiratory illnesses. The last MUPPITS1 study visit occurred on Jan 6, 2017. The ICATA cohort recruited 419 participants aged 6-20 years with persistent allergic asthma living in urban sites across eight US cities between Oct 23, 2006, and March 25, 2008, and the last study visit occurred on Dec 30, 2009. We included participants from the MUPPITS1 cohort who reported a respiratory illness at some point during the follow-up and participants from the ICATA cohort who had nasal samples collected during respiratory illness or at a scheduled visit. We used air quality index values and air pollutant concentrations for PM2·5, PM10, O3, NO2, SO2, CO, and Pb from the US Environmental Protection Agency spanning the years of both cohorts, and matched values and concentrations to each illness for each participant. We investigated the associations between regional air pollutant concentrations and respiratory illnesses and asthma exacerbations, pulmonary function, and upper airway transcriptional signatures by use of a combination of generalised additive models, case crossover analyses, and generalised linear mixed-effects models.

FINDINGS

Of the 208 participants from the MUPPITS1 cohort and 419 participants from the ICATA cohort, 168 participants in the MUPPITS1 cohort (98 male participants and 70 female participants) and 189 participants in the ICATA cohort (115 male participants and 74 female participants) were included in our analysis. We identified that increased air quality index values, driven predominantly by increased PM2·5 and O3 concentrations, were significantly associated with asthma exacerbations and decreases in pulmonary function that occurred in the absence of a provoking viral infection. Moreover, individual pollutants were significantly associated with altered gene expression in coordinated inflammatory pathways, including PM2·5 with increased epithelial induction of tissue kallikreins, mucus hypersecretion, and barrier functions and O3 with increased type-2 inflammation.

INTERPRETATION

Our findings suggest that air pollution is an important independent risk factor for asthma exacerbations in children living in urban areas and is potentially linked to exacerbations through specific inflammatory pathways in the airway. Further investigation of these potential mechanistic pathways could inform asthma prevention and management approaches.

FUNDING

National Institutes of Health, National Institute of Allergy and Infectious Diseases.

The role of gene-ambient air pollution interactions in paediatric asthma

Globally, asthma prevention and treatment remain a challenge. Ambient air pollution (AAP) is an environmental risk factor of special interest in asthma research. AAP is poorly defined and has been subdivided either by the origin of the air pollution or by the specific bioactive compounds. The link between AAP exposure and asthma exacerbations is well established and has been extensively reviewed. In this narrative review, we discuss the specific genetic variants that have been associated with increased AAP sensitivity and impact in paediatric asthma. We highlight the relative importance of variants associated with genes with a role in oxidant defences and the nuclear factor-κB pathway supporting a potential central role for these pathways in AAP sensitivity.

One genome, many cell states: epigenetic control of innate immunity

A hallmark of the innate immune system is its ability to rapidly initiate short-lived or sustained transcriptional programs in a cell-specific and pathogen-specific manner that is dependent on dynamic chromatin states. Much of the epigenetic landscape is set during cellular differentiation; however, pathogens and other environmental cues also induce changes in chromatin that can either promote tolerance or 'train' innate immune cells for amplified secondary responses. We review chromatin processes that enable innate immune cell differentiation and functional transcriptional responses in naive or experienced cells, in concert with signal transduction and cellular metabolic shifts. We discuss how immune chromatin mechanisms are maladapted in disease and novel therapeutic approaches for cellular reprogramming.

Single Nucleotide Polymorphisms (SNPs) in PRKG1 & SPATA13-AS1 are associated with bronchodilator response: a pilot study during acute asthma exacerbations in African American children

OBJECTIVE

Inhaled bronchodilators are the first-line treatment for asthma exacerbations, but individual bronchodilator response (BDR) varies by race and ethnicity. Studies have examined BDR's genetic underpinnings, but many did not include children or were not conducted during an asthma exacerbation. This pilot study tested single-nucleotide polymorphisms' (SNPs') association with pediatric African American BDR during an acute asthma exacerbation.

METHODS

This was a study of pediatric asthma patients in the age group 2-18 years treated in the emergency department for an asthma exacerbation. We measured BDR before and after inhaled bronchodilator treatments using both the Pediatric Asthma Severity Score (PASS) and asthma severity score. We collected genomic DNA and examined whether 21 candidate SNPs from a review of the literature were associated with BDR using crude odds ratios (OR) and adjusted analysis.

RESULTS

The final sample population was 53 children, with an average age of 7.2 years. The average initial PASS score (scale of ascending severity from 0 to 6) was 2.5. After adjusting for BMI, age category, gender and smoke exposure, rs912142 was associated with decreased odds of having low BDR (OR, 0.20; 95% confidence interval (CI), 0.02-0.92), and rs7081864 and rs7903366 were associated with decreased odds of having high BDR (OR, 0.097; 95% CI, 0.009-0.62).

CONCLUSIONS

We found three SNPs significantly associated with pediatric African American BDR that provide information regarding a child's potential response to emergency asthma exacerbation treatment. Once validated in larger studies, such information could guide pharmacogenomic evidence-based emergency asthma treatment to improve patient outcomes.

Analyzing Genome-Wide Association Study Dataset Highlights Immune Pathways in Lip Bone Mineral Density

Osteoporosis is a common complex human disease. Until now, large-scale genome-wide association studies (GWAS) using single genetic variant have reported some novel osteoporosis susceptibility variants. However, these risk variants only explain a small proportion of osteoporosis genetic risk, and most genetic risk is largely unknown. Interestingly, the pathway analysis method has been used in investigation of osteoporosis mechanisms and reported some novel pathways. Until now, it remains unclear whether there are other risk pathways involved in BMD. Here, we selected a lip BMD GWAS with 301,019 SNPs in 5,858 Europeans, and conducted a gene-based analysis (SET SCREEN TEST) and a pathway-based analysis (WebGestalt). On the gene level, BMD susceptibility genes reported by previous GWAS were identified to be the top 10 significant signals. On the pathway level, we identified 27 significant KEGG pathways. Three immune pathways including T cell receptor signaling pathway (hsa04660), complement and coagulation cascades (hsa04610), and intestinal immune network for IgA production (hsa04672) are ranked the top three significant signals. Evidence from the PubMed and Google Scholar databases further supports our findings. In summary, our findings provide complementary information to these nine risk pathways.

Short-term associations between daily mortality and ambient particulate matter, nitrogen dioxide, and the air quality index in a Middle Eastern megacity

There is limited evidence for short-term association between mortality and ambient air pollution in the Middle East and no study has evaluated exposure windows of about a month prior to death. We investigated all-cause non-accidental daily mortality and its association with fine particulate matter (PM_2.5), nitrogen dioxide (NO₂), and the Air Quality Index (AQI) from March 2011 through March 2014 in the megacity of Tehran, Iran. Generalized additive quasi-Poisson models were used within a distributed lag linear modeling framework to estimate the cumulative effects of PM_2.5, NO₂, and the AQI up to a lag of 45 days. We further conducted multi-pollutant models and also stratified the analyses by sex, age group, and season. The relative risk (95% confidence interval (CI)) for all seasons, both sexes and all ages at lag 0 for PM_2.5, NO₂, and AQI were 1.004 (1.001, 1.007), 1.003 (0.999, 1.007), and 1.004 (1.001, 1.007), respectively, per inter-quartile range (IQR) increment (18.8 μg/m³ for PM_2.5, 12.6 ppb for NO₂, and 31.5 for AQI). In multi-pollutant models, the PM_2.5 associations were almost independent from NO₂. However, the RRs for NO₂ were slightly attenuated after adjustment for PM_2.5 but they were still largely independent from PM_2.5. The cumulative relative risks (95% CI) per IQR increment reached maximum during the cooler months, including: 1.13 (1.06, 1.20) for PM_2.5 at lag 0-31 (for females, all ages); 1.17 (1.10, 1.25) for NO₂ at lag 0-45 (for males, all ages); and 1.13 (1.07, 1.20) for the AQI at lag 0-30 (for females, all ages). Generally, the RRs were slightly larger for NO₂ than PM_2.5 and AQI. We found somewhat larger RRs in females, age group >65 years of age, and in cooler months. In summary, positive associations were found in most models. This is the first study to report short-term associations between all-cause non-accidental mortality and ambient PM_2.5 and NO₂ in Iran.