Genes and pathways underlying susceptibility to impaired lung function in the context of environmental tobacco smoke exposure

miR449 Protects Airway Regeneration by Controlling AURKA/HDAC6-Mediated Ciliary Disassembly

Airway mucociliary regeneration and function are key players for airway defense and are impaired in chronic obstructive pulmonary disease (COPD). Using transcriptome analysis in COPD-derived bronchial biopsies, we observed a positive correlation between cilia-related genes and microRNA-449 (miR449). In vitro, miR449 was strongly increased during airway epithelial mucociliary differentiation. In vivo, miR449 was upregulated during recovery from chemical or infective insults. miR0449−/− mice (both alleles are deleted) showed impaired ciliated epithelial regeneration after naphthalene and Haemophilus influenzae exposure, accompanied by more intense inflammation and emphysematous manifestations of COPD. The latter occurred spontaneously in aged miR449−/− mice. We identified Aurora kinase A and its effector target HDAC6 as key mediators in miR449-regulated ciliary homeostasis and epithelial regeneration. Aurora kinase A is downregulated upon miR449 overexpression in vitro and upregulated in miR449−/− mouse lungs. Accordingly, imaging studies showed profoundly altered cilia length and morphology accompanied by reduced mucociliary clearance. Pharmacological inhibition of HDAC6 rescued cilia length and coverage in miR449−/− cells, consistent with its tubulin-deacetylating function. Altogether, our study establishes a link between miR449, ciliary dysfunction, and COPD pathogenesis.

Toxicological Mechanism of Individual Susceptibility to Formaldehyde-Induced Respiratory Effects

Understanding the mechanisms of individual susceptibility to exposure to environmental pollutants has been a challenge in health risk assessment. Here, an integrated approach combining a CRISPR screen in human cells and epidemiological analysis was developed to identify the individual susceptibility to the adverse health effects of air pollutants by taking formaldehyde (FA) and the associated chronic obstructive pulmonary disease (COPD) as a case study. Among the primary hits of CRISPR screening of FA in human A549 cells, HTR4 was the only gene genetically associated with COPD susceptibility in global populations. However, the association between HTR4 and FA-induced respiratory toxicity is unknown in the literature. Adverse outcome pathway (AOP) network analysis of CRISPR screen hits provided a potential mechanistic link between activation of HTR4 (molecular initiating event) and FA-induced lung injury (adverse outcome). Systematic toxicology tests (in vitro and animal experiments) were conducted to reveal the HTR4-involved biological mechanisms underlying the susceptibility to adverse health effects of FA. Functionality and enhanced expression of HTR4 were required for susceptibility to FA-induced lung injury, and FA-induced epigenetic changes could result in enhanced expression of HTR4. Specific epigenetic and genetic characteristics of HTR4 were associated with the progression and prevalence of COPD, respectively, and these genetic risk factors for COPD could be potential biomarkers of individual susceptibility to adverse respiratory effects of FA. These biomarkers could be of great significance for defining subpopulations susceptible to exposure to FA and reducing uncertainty in the next-generation health risk assessment of air pollutants. Our study delineated a novel toxicological pathway mediated by HTR4 in FA-induced lung injury, which could provide a mechanistic understanding of the potential biomarkers of individual susceptibility to adverse respiratory effects of FA.

Chronic obstructive pulmonary disease in never-smokers: risk factors, pathogenesis, and implications for prevention and treatment

Chronic obstructive pulmonary disease (COPD) was traditionally thought to be caused by tobacco smoking. However, recognition of the importance of non-smoking-related risk factors for COPD has increased over the past decade, with evidence on the burden, risk factors, and clinical presentations of COPD in never-smokers. About half of all COPD cases worldwide are due to non-tobacco-related risk factors, which vary by geographical region. These factors include air pollution, occupational exposures, poorly controlled asthma, environmental tobacco smoke, infectious diseases, and low socioeconomic status. Impaired lung growth during childhood, caused by a range of early-life exposures, is associated with an increased risk of COPD. Potential mechanisms for the pathogenesis of COPD in never-smokers include inflammation, oxidative stress, airway remodelling, and accelerated lung ageing. Compared with smokers who develop COPD, never-smokers with COPD have relatively mild chronic respiratory symptoms, little or no emphysema, milder airflow limitation, and fewer comorbidities; however, exacerbations can still be frequent. Further research-including epidemiological, translational, clinical, and implementation studies-is needed to address gaps in understanding and to advance potential solutions to reduce the burden of COPD in never-smokers.

CRISPR screen identified that UGT1A9 was required for bisphenols-induced mitochondria dyshomeostasis

Exposure to bisphenols chemicals could cause various adverse health effects, including non-alcoholic fatty liver disease (NAFLD), which have been associated with cellular mitochondria stress. However, the biological mechanism underlying the mitochondria stress-mediated cell death by bisphenols was poorly understood. Here, CRISPR screens were performed to identify the critical genes which were involved in cell death caused by exposure to four bisphenols (BPA, BPB, BPE and BPS). Results of CRISPR screens showed that UGT1A9 was the primary genetic factor facilitating cell death induced by all of the four bisphenols. Systematic toxicological tests demonstrated that UGT1A9 was required for BPA-induced mitochondria dyshomeostasis in vitro and in vivo, and UGT1A9-mediated mitochondria dyshomeostasis was an important cause of facilitating cell death. Liver injury caused by exposure to BPA in wild-type mice was accompanied with suppression of mitophagy and increased expression of C-Caspase 3, but UGT1A9 knockout attenuated these adverse effects induced by BPA. Finally, molecular epidemiology analysis suggested that the five genetic variants of UGT1A9 could be potential genetic risk factors of NAFLD when people were exposed to BPA. The biological mechanism uncovered here provided mechanistic evidence for identification of susceptible populations of liver injury associated with exposure to BPA.

Multigenerational Epigenetic Regulation of Allergic Diseases: Utilizing an Experimental Dust Mite-Induced Asthma Model

Environmental exposures have been linked to increased asthma risk, particularly during pregnancy and in early life. Here we use a mouse model of allergic lung disease to examine the effects of pre- and perinatal house dust mite (HDM) allergen exposure on offspring phenotypic and transcriptional outcomes in three generations. We show that maternal HDM exposure (F0) acts synergistically with adult HDM exposure, leading to enhanced airway hyperresponsiveness (AHR) and lung inflammation when compared to mice exposed solely in adulthood. Additionally, a subset of F1 males were not challenged in adulthood, and used to generate F2 progeny, which was then used to generate F3 progeny. Upon adult challenge to HDM, F2, and F3 males generated from the maternal HDM (F0) exposure lineage displayed increased airway reactivity and inflammation when compared to mice exposed solely in adulthood. These findings indicate that maternal allergen exposure is capable of enhancing either susceptibly to or severity of allergic airway disease. To examine the role of epigenetic inheritance of asthma susceptibility induced by maternal HDM exposure, we utilized a genome-wide MeDIP-seq and hMeDIP-seq analysis to identify genes differentially methylated (DMG) and hydroxymethylated (DHG), and their association with the enhanced AHR. In addition, we validated the relationship between DNA methylation and mRNA expression of the DMGs and DHGs in the male sub-generations (F1-F3). We found the expression of Kchn1, Nron, and Spag17 to be differentially hydroxymethylated and upregulated in the F1 exposed to HDM both in early life and in adulthood when compared to F1 mice exposed solely in adulthood. Kcnh1 remained upregulated in the F2 and F3 from the maternal HDM (F0) exposure lineage, when compared to F1 mice exposed solely in adulthood. In summary, we demonstrated that maternal HDM exposure in early life can alter the gene expression and phenotype of offspring upon adult HDM exposure, resulting in more severe disease. These effects persist at least two generations past the initial insult, transmitted along the paternal line.

Eurotium cristatum Fermented Loose Dark Tea Ameliorates Cigarette Smoke-Induced Lung Injury by MAPK Pathway and Enhances Hepatic Metabolic Detoxification by PXR/AhR Pathway in Mice

Cigarette smoke- (CS-) induced oxidative stress and inflammation in the lung are serious health problems. Primary and reprocessed tea products contain multiple antioxidants that have been reported to protect the lung against CS-induced injury. However, the beneficial effects of Eurotium cristatum fermented loose dark tea (ECT) and Eurotium cristatum particle metabolites (ECP) on CS-induced lung injury and its potential hepatic metabolic detoxification are still unclear. Therefore, sixty mice were randomly divided into six equal groups. CS-exposed mice were prevented or treated with ECP or ECT infusions for 12 or 8 weeks to determine the antioxidative stress, anti-inflammatory and potential metabolic detoxification of ECT and ECP. Thirty-six mice were randomly divided into six equal groups to observe the effects on hepatic metabolic detoxification by replacing daily drinking water with ECT. Results showed that CS significantly decreased the activities of glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD) and upregulated the expressions of malondialdehyde (MDA), tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), IL-8, and IL-1β in serum. These adverse effects were modulated by ECP and ECT. In addition, ECT upregulated the mRNA expression of pregnane X receptor (PXR) and cytochrome P450 (CYP450) in the liver on daily free drinking ECT mice group. Western blot analysis further revealed that in CS-exposed mice, ECP and ECT significantly decreased the phosphorylation of mitogen-activated protein kinase (MAPK) in the lung but upregulated the protein expressions of PXR and aryl hydrocarbon receptor (AhR) in the liver. Overall, our findings demonstrated that ECT and ECP protected against lung injury induced by CS via MAPK pathway and enhanced hepatic metabolic detoxification via PXR and AhR pathways. Therefore, daily intake of ECT and ECP can potentially protect against CS-induced oxidative and inflammatory injuries.

Genetic regulation of gene expression of MIF family members in lung tissue

Macrophage migration inhibitory factor (MIF) is a cytokine found to be associated with chronic obstructive pulmonary disease (COPD). However, there is no consensus on how MIF levels differ in COPD compared to control conditions and there are no reports on MIF expression in lung tissue. Here we studied gene expression of members of the MIF family MIF, D-Dopachrome Tautomerase (DDT) and DDT-like (DDTL) in a lung tissue dataset with 1087 subjects and identified single nucleotide polymorphisms (SNPs) regulating their gene expression. We found higher MIF and DDT expression in COPD patients compared to non-COPD subjects and found 71 SNPs significantly influencing gene expression of MIF and DDTL. Furthermore, the platform used to measure MIF (microarray or RNAseq) was found to influence the splice variants detected and subsequently the direction of the SNP effects on MIF expression. Among the SNPs found to regulate MIF expression, the major LD block identified was linked to rs5844572, a SNP previously found to be associated with lower diffusion capacity in COPD. This suggests that MIF may be contributing to the pathogenesis of COPD, as SNPs that influence MIF expression are also associated with symptoms of COPD. Our study shows that MIF levels are affected not only by disease but also by genetic diversity (i.e. SNPs). Since none of our significant eSNPs for MIF or DDTL have been described in GWAS for COPD or lung function, MIF expression in COPD patients is more likely a consequence of disease-related factors rather than a cause of the disease.

Interactions between environmental pollutants and genetic susceptibility in asthma risk

Exposure to air pollution is associated with enhanced risk of developing asthma, notably in the presence of genetic risk factors. Interaction analyses have shown that both outdoor and indoor air pollution interact with genetic variability to increase the incidence of asthma. In this review, we summarize recent progress in candidate gene-based studies, as well as genome-wide gene-air pollution interaction studies. Advances in epigenetics have provided evidence for DNA methylation as a mediator in gene-air pollution interactions. Emerging strategies for study design and statistical analyses may improve power in future studies. Improved air pollution exposure assessment methods and asthma endo-typing can also be expected to increase the ability to detect biologically driven gene-air pollution interaction effects.

RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

BACKGROUND

Multiple gene expression studies have been performed separately in peripheral blood, lung, and airway tissues to study COPD. We performed RNA-sequencing gene expression profiling of large-airway epithelium, alveolar macrophage and peripheral blood samples from the same subset of COPD cases and controls from the COPDGene study who underwent bronchoscopy at a single center. Using statistical and gene set enrichment approaches, we sought to improve the understanding of COPD by studying gene sets and pathways across these tissues, beyond the individual genomic determinants.

METHODS

We performed differential expression analysis using RNA-seq data obtained from 63 samples from 21 COPD cases and controls (includes four non-smokers) via the R package DESeq2. We tested associations between gene expression and variables related to lung function, smoking history, and CT scan measures of emphysema and airway disease. We examined the correlation of differential gene expression across the tissues and phenotypes, hypothesizing that this would reveal preserved and private gene expression signatures. We performed gene set enrichment analyses using curated databases and findings from prior COPD studies to provide biological and disease relevance.

RESULTS

The known smoking-related genes CYP1B1 and AHRR were among the top differential expression results for smoking status in the large-airway epithelium data. We observed a significant overlap of genes primarily across large-airway and macrophage results for smoking and airway disease phenotypes. We did not observe specific genes differentially expressed in all three tissues for any of the phenotypes. However, we did observe hemostasis and immune signaling pathways in the overlaps across all three tissues for emphysema, and amyloid and telomere-related pathways for smoking. In peripheral blood, the emphysema results were enriched for B cell related genes previously identified in lung tissue studies.

CONCLUSIONS

Our integrative analyses across COPD-relevant tissues and prior studies revealed shared and tissue-specific disease biology. These replicated and novel findings in the airway and peripheral blood have highlighted candidate genes and pathways for COPD pathogenesis.

[Association of cytoplasmic phospholipase A2 gene polymorphism with bronchial asthma and response to montelukast in children]

OBJECTIVE

To study the association of cytoplasmic phospholipase A2 (PLA2G4) rs932476 polymorphism with the development of bronchial asthma and the response to montelukast, a leukotriene receptor antagonist, in children.

METHODS

A total of 128 children with bronchial asthma were enrolled as case group, and 100 healthy children were enrolled as control group. The genotype and allele frequencies of PLA2G4 rs932476 were compared between the two groups. The children in the case group were administered with montelukast except routine treatment for 2 months, and the changes in serum levels of leukotriene B4 (LTB4), interleukin-4 (IL-4), immunoglobulin E (IgE), and interferon gamma (IFN-γ), pulmonary function and fractional exhaled nitric oxide (FeNO) after treatment were observed.

RESULTS

There were no significant differences in the genotype and allele frequencies of PLA2G4 rs932476 between the case and control groups, as well as between the groups with different severities of asthma (P>0.05). After treatment, the children with AA genotype had a significantly higher overall response rate than those with GG genotype. After treatment, the case group had significant reductions in the serum levels of IgE and IL-4 and a significant increase in the level of IFN-γ (P<0.05). After treatment, the children with GG genotype had a higher serum level of IL-4 and a lower level of IFN-γ than those with AA genotype. After treatment, the case group had significant increases in pulmonary function parameters, and the children with AA genotype had significantly higher parameters than those with GG genotype. The case group had a significant reduction in the level of FeNO, and the children with AA genotype had a significantly lower level than those with GG genotype after treatment. The case group had a significantly higher serum level of LTB4 than the control group before treatment (P<0.05). After treatment the case group had a significant reduction in the serum level of LTB4 (P<0.05). The children with GG genotype had a significantly higher level of LTB4 than those with AA genotype after treatment (P<0.05).

CONCLUSIONS

PLA2G4 rs932476 polymorphism is not associated with the susceptibility and severity of bronchial asthma in children, but it may has certain influence on children's response to the leukotriene receptor antagonist montelukast, possibly by affecting the level of LTB4.

[Association of cytoplasmic phospholipase A2 gene polymorphism with bronchial asthma and response to montelukast in children]

OBJECTIVE

To study the association of cytoplasmic phospholipase A2 (PLA2G4) rs932476 polymorphism with the development of bronchial asthma and the response to montelukast, a leukotriene receptor antagonist, in children.

METHODS

A total of 128 children with bronchial asthma were enrolled as case group, and 100 healthy children were enrolled as control group. The genotype and allele frequencies of PLA2G4 rs932476 were compared between the two groups. The children in the case group were administered with montelukast except routine treatment for 2 months, and the changes in serum levels of leukotriene B4 (LTB4), interleukin-4 (IL-4), immunoglobulin E (IgE), and interferon gamma (IFN-γ), pulmonary function and fractional exhaled nitric oxide (FeNO) after treatment were observed.

RESULTS

There were no significant differences in the genotype and allele frequencies of PLA2G4 rs932476 between the case and control groups, as well as between the groups with different severities of asthma (P>0.05). After treatment, the children with AA genotype had a significantly higher overall response rate than those with GG genotype. After treatment, the case group had significant reductions in the serum levels of IgE and IL-4 and a significant increase in the level of IFN-γ (P<0.05). After treatment, the children with GG genotype had a higher serum level of IL-4 and a lower level of IFN-γ than those with AA genotype. After treatment, the case group had significant increases in pulmonary function parameters, and the children with AA genotype had significantly higher parameters than those with GG genotype. The case group had a significant reduction in the level of FeNO, and the children with AA genotype had a significantly lower level than those with GG genotype after treatment. The case group had a significantly higher serum level of LTB4 than the control group before treatment (P<0.05). After treatment the case group had a significant reduction in the serum level of LTB4 (P<0.05). The children with GG genotype had a significantly higher level of LTB4 than those with AA genotype after treatment (P<0.05).

CONCLUSIONS

PLA2G4 rs932476 polymorphism is not associated with the susceptibility and severity of bronchial asthma in children, but it may has certain influence on children's response to the leukotriene receptor antagonist montelukast, possibly by affecting the level of LTB4.

Precision medicine in COPD: where are we and where do we need to go?

Chronic obstructive pulmonary disease (COPD) was the fourth leading cause of death worldwide in 2015. Current treatments for patients ease discomfort and help decrease disease progression; however, none improve lung function or change mortality. COPD is heterogeneous in its molecular and clinical presentation, making it difficult to understand disease aetiology and define robust therapeutic strategies. Given the complexity of the disease we propose a precision medicine approach to understanding and better treating COPD. It is possible that multiOMICs can be used as a tool to integrate data from multiple fields. Moreover, analysis of electronic medical records could aid in the treatment of patients and in the predictions of outcomes. The Precision Medicine Initiative created in 2015 has made precision medicine approaches to treat disease a reality; one of these diseases being COPD.

Tobacco Smoke Induces and Alters Immune Responses in the Lung Triggering Inflammation, Allergy, Asthma and Other Lung Diseases: A Mechanistic Review

Many studies have been undertaken to reveal how tobacco smoke skews immune responses contributing to the development of chronic obstructive pulmonary disease (COPD) and other lung diseases. Recently, environmental tobacco smoke (ETS) has been linked with asthma and allergic diseases in children. This review presents the most actual knowledge on exact molecular mechanisms responsible for the skewed inflammatory profile that aggravates inflammation, promotes infections, induces tissue damage, and may promote the development of allergy in individuals exposed to ETS. We demonstrate how the imbalance between oxidants and antioxidants resulting from exposure to tobacco smoke leads to oxidative stress, increased mucosal inflammation, and increased expression of inflammatory cytokines (such as interleukin (IL)-8, IL-6 and tumor necrosis factor α ([TNF]-α). Direct cellular effects of ETS on epithelial cells results in increased permeability, mucus overproduction, impaired mucociliary clearance, increased release of proinflammatory cytokines and chemokines, enhanced recruitment of macrophages and neutrophils and disturbed lymphocyte balance towards Th2. The plethora of presented phenomena fully justifies a restrictive policy aiming at limiting the domestic and public exposure to ETS.