Epigenetic mechanisms and the development of asthma

Omics approaches in asthma research: Challenges and opportunities

Asthma, a chronic respiratory disease with a global prevalence of approximately 300 million individuals, presents a significant societal and economic burden. This multifaceted syndrome exhibits diverse clinical phenotypes and pathogenic endotypes influenced by various factors. The advent of omics technologies has revolutionized asthma research by delving into the molecular foundation of the disease to unravel its underlying mechanisms. Omics technologies are employed to systematically screen for potential biomarkers, encompassing genes, transcripts, methylation sites, proteins, and even the microbiome components. This review provides an insightful overview of omics applications in asthma research, with a special emphasis on genetics, transcriptomics, epigenomics, and the microbiome. We explore the cutting-edge methods, discoveries, challenges, and potential future directions in the realm of asthma omics research. By integrating multi-omics and non-omics data through advanced statistical techniques, we aspire to advance precision medicine in asthma, guiding diagnosis, risk assessment, and personalized treatment strategies for this heterogeneous condition.

Integrative analysis identifies gene signatures mediating the effect of DNA methylation on asthma severity and lung function

DNA methylation (DNAm) changes play a key role in regulating gene expression in asthma. To investigate the role of epigenetics and transcriptomics change in asthma, we used publicly available DNAm (asthmatics, n = 96 and controls, n = 46) and gene expression (asthmatics, n = 79 and controls, n = 39) data derived from bronchial epithelial cells (BECs). We performed differential methylation/expression and weighted co-methylation/co-expression network analyses to identify co-methylated and co-expressed modules associated with asthma severity and lung function. For subjects with both DNAm and gene expression data (asthmatics, n = 79 and controls, n = 39), machine-learning technique was used to prioritize CpGs and differentially expressed genes (DEGs) for asthma risk prediction, and mediation analysis was used to uncover DEGs that mediate the effect of DNAm on asthma severity and lung function in BECs. Finally, we validated CpGs and their associated DEGs and the asthma risk prediction model in airway epithelial cells (AECs) dataset. The asthma risk prediction model based on 18 CpGs and 28 DEGs showed high accuracy in both the discovery BEC dataset with area under the receiver operating characteristic curve (AUC) = 0.99 and the validation AEC dataset (AUC = 0.82). Genes in the three co-methylated and six co-expressed modules were enriched in multiple pathways including WNT/beta-catenin signaling and notch signaling. Moreover, we identified 35 CpGs correlated with DEGs in BECs, of which 17 CpGs including cg01975495 (SERPINE1), cg10528482 (SLC9A3), cg25477769 (HNF1A) and cg26639146 (CD9), cg17945560 (TINAGL1) and cg10290200 (FLNC) were replicated in AECs. These DEGs mediate the association between DNAm and asthma severity and lung function. Overall, our study investigated the role of DNAm and gene expression change in asthma and provided an insight into the mechanisms underlying the effects of DNA methylation on asthma, asthma severity and lung function.

Advances in the Delivery and Development of Epigenetic Therapeutics for the Treatment of Cancer

Gene expression at the transcriptional level is altered by epigenetic modifications such as DNA methylation, histone methylation, and acetylation, which can upregulate, downregulate, or entirely silence genes. Pathological dysregulation of epigenetic processes can result in the development of cancer, neurological problems, metabolic disorders, and cardiovascular diseases. It is of promising therapeutic interest to find medications that target these epigenetic alterations. Despite the enormous amount of work that has been done in this area, very few molecules have been approved for clinical purposes. This article provides a comprehensive review of recent advances in epigenetic therapeutics for cancer, with a specific focus on emerging delivery and development strategies. Various delivery systems, including pro-drugs, conjugated molecules, nanoparticles (NPs), and liposomes, as well as remedial strategies such as combination therapies, and epigenetic editing, are being investigated to improve the efficacy and specificity of epigenetic drugs (epi-drugs). Furthermore, the challenges associated with available epi-drugs and the limitations of their translation into clinics have been discussed. Target selection, isoform selectivity, physiochemical properties of synthesized molecules, drug screening, and scalability of epi-drugs from preclinical to clinical fields are the major shortcomings that are addressed. This Review discusses novel strategies for the identification of new biomarkers, exploration of the medicinal chemistry of epigenetic modifiers, optimization of the dosage regimen, and design of proper clinical trials that will lead to better utilization of epigenetic modifiers over conventional therapies. The integration of these approaches holds great potential for improving the efficacy and precision of epigenetic treatments, ultimately benefiting cancer patients.

Anti-S100A4 antibody administration alleviates bronchial epithelial-mesenchymal transition in asthmatic mice

We elucidated the effect of S100A4 on airway remodeling by regulating airway inflammation and epithelial-mesenchymal transition (EMT) in mouse models of asthma. Asthmatic mouse models were established by sensitization and challenged with ovalbumin (OVA). Anti-S100A4 antibody or control IgG antibody was administered daily before the OVA challenge. After the last challenge, airway inflammation and airway hyperresponsiveness were measured; lung tissues and bronchoalveolar lavage fluid (BALF) were harvested. Lung tissue sections were stained and evaluated for pathological changes. Levels of inflammatory cytokines were measured using ELISA. Levels of S100A4 and EMT markers were determined via western blotting analysis. Human bronchial epithelial cells were stimulated with 100 mg/mL house dust mites (HDMs) to evaluate the effect of S100A4 downregulation on EMT in vitro. S100A4 was increased in lung tissues and BALF from asthmatic mice. The asthmatic mice presented airway hyperresponsiveness, airway inflammation, and airway remodeling. After anti-S100A4 antibody administration, pathophysiological signs, including airway hyperresponsiveness and increased infiltration of inflammatory cells, were attenuated. Additionally, anti-S100A4 administration downregulated vimentin and α-SMA expression and upregulated E-cadherin expression in OVA-challenged mice. S100A4 downregulation also inhibited EMT process in HDM-stimulated 16HBE cells. Anti-S100A4 antibody administration alters airway remodeling by preventing EMT in mouse models of asthma.

LncRNA AK089514/miR-125b-5p/TRAF6 axis mediates macrophage polarization in allergic asthma

BACKGROUND

Micro RNA (miRNA) plays important roles in macrophage polarization. However, the manner in which miRNA regulate macrophage polarization in response to dermatophagoides farinae protein 1(Der f1)-induced asthma has not been defined. This study aims to explore the role of miRNAs in regulating macrophages in asthma.

METHODS

The microRNAs which may regulate asthma were selectd by Microarrays. The function of miR-125b-5p in macrophage and Der f1-induced asthma were detected in vivo experiment. The long non coding RNA (lncRNA) AK089514/miR-125b-5p/TRAF6 axis was predicted by bioinformatics and confirmed by dual luciferase reporter assay.

RESULTS

In this study, we found that miR-125b-5p is highly expressed in M2 macrophages and bronchoalveolar lavage fluid (BALF) cells with Der f1-induced asthma. In response to the challenge of Der f1, miR-125b-5p KD attenuated allergic airway inflammation of mice by preventing M2 macrophages polarization. Mechanistic studies indicated that lncRNA AK089514 functioned as a competing endogenous RNA for miR-125b-5p, thereby leading to the depression of its endogenous target TNF receptor associated factor 6 (TRAF6).

CONCLUSIONS

miR-125b-5p is significantly over-expressed in asthma, and AK089514-miR-125b-5p-TRAF6 axis play critical role in asthma by modulating macrophage polarization. Our findings may provide a potential new target for potential therapeutic and diagnostic target in asthma.

Recent progress in the genetic and epigenetic underpinnings of atopy

In the past 2 years, there continue to be advances in our understanding of the genetic and epigenetic underpinnings of atopy pertaining to disease risk and disease severity. The joint role of genetics and the environment has been emphasized in multiple studies. Combining genetics with family history, biomarkers, and comorbidities is further refining our ability to predict the development of individual atopic diseases as well as the advancement of the atopic march. Polygenic risk scores will be an important next step for the field moving toward clinical translation of the genetic findings thus far. A systems biology approach, as illustrated by studies of the microbiome and epigenome, will be necessary to fully understand disease development and to develop increasingly targeted therapeutics.

Air Pollution: Possible Interaction between the Immune and Nervous System?

Exposure to environmental pollutants is a serious and common public health concern associated with growing morbidity and mortality worldwide, as well as economic burden. In recent years, the toxic effects associated with air pollution have been intensively studied, with a particular focus on the lung and cardiovascular system, mainly associated with particulate matter exposure. However, epidemiological and mechanistic studies suggest that air pollution can also influence skin integrity and may have a significant adverse impact on the immune and nervous system. Air pollution exposure already starts in utero before birth, potentially causing delayed chronic diseases arising later in life. There are, indeed, time windows during the life of individuals who are more susceptible to air pollution exposure, which may result in more severe outcomes. In this review paper, we provide an overview of findings that have established the effects of air pollutants on the immune and nervous system, and speculate on the possible interaction between them, based on mechanistic data.

Histone Methyltransferase MLL1 Mediates Oxidative Stress and Apoptosis upon Deoxynivalenol Exposure in the Intestinal Porcine Epithelial Cells

Deoxynivalenol (DON), as a secondary metabolite of fungi, is continually detected in livestock feed and has a high risk to animals and humans. Moreover, pigs are very sensitive to DON. Recently, the role of histone modification has drawn people’s attention; however, few studies have elucidated how histone modification participates in the cytotoxicity or genotoxicity induced by mycotoxins. In this study, we used intestinal porcine epithelial cells (IPEC-J2 cells) as a model to DON exposure in vitro. Mixed lineage leukemia 1 (MLL1) regulates gene expression by exerting the role of methyltransferase. Our studies demonstrated that H3K4me3 enrichment was enhanced and MLL1 was highly upregulated upon 1 μg/mL DON exposure in IPEC-J2 cells. We found that the silencing of MLL1 resulted in increasing the apoptosis rate, arresting the cell cycle, and activating the mitogen-activated protein kinases (MAPKs) pathway. An RNA-sequencing analysis proved that differentially expressed genes (DEGs) were enriched in the cell cycle, apoptosis, and tumor necrosis factor (TNF) signaling pathway between the knockdown of MLL1 and negative control groups, which were associated with cytotoxicity induced by DON. In summary, these current results might provide new insight into how MLL1 regulates cytotoxic effects induced by DON via an epigenetic mechanism.

Epigenetic regulation of immune function in asthma

Asthma is a common complex respiratory disease characterized by chronic airway inflammation and partially reversible airflow obstruction resulting from genetic and environmental determinants. Because epigenetic marks influence gene expression and can be modified by both environmental exposures and genetic variation, they are increasingly recognized as relevant to the pathogenesis of asthma and may be a key link between environmental exposures and asthma susceptibility. Unlike changes to DNA sequence, epigenetic signatures are dynamic and reversible, creating an opportunity for not only therapeutic targets but may serve as biomarkers to follow disease course and identify molecular subtypes in heterogeneous diseases such as asthma. In this review, we will examine the relationship between asthma and 3 key epigenetic processes that modify gene expression: DNA methylation, modification of histone tails, and noncoding RNAs. In addition to presenting a comprehensive assessment of the existing epigenetic studies focusing on immune regulation in asthma, we will discuss future directions for epigenetic investigation in allergic airway disease.

Sigma-1 Receptor Alleviates Airway Inflammation and Airway Remodeling Through AMPK/CXCR4 Signal Pathway

Sigma non-opioid intracellular receptor 1 (Sigma-1R) has been proven to play a major role in inflammation and structural remodeling. However, its role in airway inflammation and airway remodeling remains unclear. The purpose of this study aimed to explore the role and mechanism of Sigma-1R in airway remodeling and epithelial-mesenchymal transition (EMT) process in vivo and in vitro. We observed the decrease of Sigma-1R in lung tissue of asthma model. In the mouse model of allergic airway inflammation (AAI), Sigma-1R agonist RPE-084 significantly relieved airway inflammation and airway remodeling, while Sigma-1R antagonist BD1047 (B8562) had opposite effects. Further research showed that RPE-084 treatment increased the expression of pAMPK and inhibited the expression of CXCR4. Furthermore, RPE-084 treatment suppressed the levels of IL-4, IL-5, and IL-13 in BALF. We found that RPE-084 or Sigma-1R overexpression vector treatment regulated cell cycle and inhibited cell proliferation, migration, and EMT process in TGF-β1-induced 16HBE cells. Finally, we confirmed that AMP-activated protein kinase (AMPK) inhibitor compound C or CXCR4 agonist ATI-2341 both reversed the effects of Sigma-1R on TGF-β1-induced 16 HBE cells. In a word, our research shows that Sigma-1R is helpful to improve airway remodeling of asthma, and emphasizes a new candidate molecular for asthma treatment.

[Immune system and allergies-An unholy alliance]

Various factors affect the maturation of the infantile immune system both prenatally and postnatally, including risk and protective factors from the environment, nutrition, genetics and epigenetics. The microbiome seems to play a substantial role. The complex interaction and regulation of all these factors is ultimately decisive for whether a child develops an allergy during the course of development of the immune system. The genetic components play a decisive role in the development of allergic diseases. The epigenetic regulation could represent a mechanism where environmental influences act upon the immune regulation in the emergence of allergic diseases. The main factors in the pathophysiology of allergic reactions are a dysregulation of various cells of the innate and acquired immune systems as well as their interaction. This review describes the role of various T helper cell types in allergic diseases. The incidence and duration of airway infections are clearly increased in allergic patients compared to nonallergic controls. In addition to functional aspects, the reason for the more frequent infections is an impairment of the immune defence by the allergy-related persisting inflammation of the mucous membranes. These mechanisms must be differentiated from a true immunodeficiency. Allergic rhinitis (AR) and bronchial asthma are nowadays no longer defined as separate diseases but as two forms of expression of an atopic entity with a similar pathology. Both diseases can be mediated by immunoglobulin E and be elicited by identical triggers. A bronchial hyperreactivity is detectable in the majority of patients with AR but without clinical asthma.

miR-144-3p Is a Biomarker Related to Severe Corticosteroid-Dependent Asthma

MicroRNAs are non-coding molecules that act both as regulators of the epigenetic landscape and as biomarkers for diseases, including asthma. In the era of personalized medicine, there is a need for novel disease-associated biomarkers that can help in classifying diseases into phenotypes for treatment selection. Currently, severe eosinophilic asthma is one of the most widely studied phenotypes in clinical practice, as many patients require higher and higher doses of corticosteroids, which in some cases fail to achieve the desired outcome. Such patients may only benefit from alternative drugs such as biologics, for which novel biomarkers are necessary. The objective of the study was to study the expression of miR-144-3p in order to discover its possible use as a diagnostic biomarker for severe asthma. For this purpose, miR-144-3p was evaluated in airway biopsies and serum from asthmatics and healthy individuals. mRNA was studied in asthmatic biopsies and smooth muscle cells transfected with miR-144-3p mimic. An in silico regulation of miR-144-3p was performed using miRSystem, miRDB, STRING, and ShinyGO for pathway analysis. From our experimental procedures, we found that miR-144-3p is a biomarker associated with asthma severity and corticosteroid treatment. MiR-144-3p is increased in asthmatic lungs, and its presence correlates directly with blood eosinophilia and with the expression of genes involved in asthma pathophysiology in the airways. When studied in serum, this miRNA was increased in severe asthmatics and associated with higher doses of corticosteroids, thereby making it a potential biomarker for severe asthma previously treated with higher doses of corticosteroids. Thus, we can conclude that miR-144-3p is associated with severe diseases in both the airways and serum of asthmatics, and this association is related to corticosteroid treatment.

Epigenetic regulation of epithelial dectin-1 through an IL-33-STAT3 axis in allergic disease

Allergic diseases arise in susceptible individuals in part because of decrements in protective pathways. The mechanism by which these anti-inflammatory molecules become repressed remains unclear. We have previously reported that epithelial dectin-1 prevents aberrant type 2 responses and is downregulated in the epithelium of allergic patients. Here, we report that dectin-1 is constitutively expressed by the respiratory epithelium in humans and that IL-33 specifically acts as a repressor of dectin-1. Mechanistically, this occurs via IL-33-dependent STAT3 activation and the subsequent repression of the dectin-1 gene, CLEC7A. We have identified a novel enhancer region upstream of the proximal promoter of CLEC7A that is only accessible in epithelial cells, but not in hematopoietic cells. Epigenetic repression of CLEC7A through this newly identified locus, downstream of an aberrant IL-33-STAT3 axis, occurs in the epithelium of allergic individuals. Collectively, our data identify a mechanism of epigenetic fine-tuning of dectin-1 expression in epithelial cells that may participate in allergenicity.

DNA methylome perturbations: an epigenetic basis for the emergingly heritable neurodevelopmental abnormalities associated with maternal smoking and maternal nicotine exposure†

Maternal smoking during pregnancy is associated with an ensemble of neurodevelopmental consequences in children and therefore constitutes a pressing public health concern. Adding to this burden, contemporary epidemiological and especially animal model research suggests that grandmaternal smoking is similarly associated with neurodevelopmental abnormalities in grandchildren, indicative of intergenerational transmission of the neurodevelopmental impacts of maternal smoking. Probing the mechanistic bases of neurodevelopmental anomalies in the children of maternal smokers and the intergenerational transmission thereof, emerging research intimates that epigenetic changes, namely DNA methylome perturbations, are key factors. Altogether, these findings warrant future research to fully elucidate the etiology of neurodevelopmental impairments in the children and grandchildren of maternal smokers and underscore the clear potential thereof to benefit public health by informing the development and implementation of preventative measures, prophylactics, and treatments. To this end, the present review aims to encapsulate the burgeoning evidence linking maternal smoking to intergenerational epigenetic inheritance of neurodevelopmental abnormalities, to identify the strengths and weaknesses thereof, and to highlight areas of emphasis for future human and animal model research therein.

BMI trajectory in childhood is associated with asthma incidence at young adulthood mediated by DNA methylation

PURPOSE

Body mass index (BMI) is associated with asthma but associations of BMI temporal patterns with asthma incidence are unclear. Previous studies suggest that DNA methylation (DNAm) is associated with asthma status and variation in DNAm is a consequence of BMI changes. This study assessed the direct and indirect (via DNAm) effects of BMI trajectories in childhood on asthma incidence at young adulthood.

METHODS

Data from the Isle of Wight (IoW) birth cohort were included in the analyses. Group-based trajectory modelling was applied to infer latent BMI trajectories from ages 1 to 10 years. An R package, ttscreening, was applied to identify differentially methylated CpGs at age 10 years associated with BMI trajectories, stratified for sex. Logistic regressions were used to further exclude CpGs with DNAm at age 10 years not associated with asthma incidence at 18 years. CpGs discovered via path analyses that mediated the association of BMI trajectories with asthma incidence in the IoW cohort were further tested in an independent cohort, the Avon Longitudinal Study of Children and Parents (ALSPAC).

RESULTS

Two BMI trajectories (high vs. normal) were identified. Of the 442,474 CpG sites, DNAm at 159 CpGs in males and 212 in females were potentially associated with BMI trajectories. Assessment of their association with asthma incidence identified 9 CpGs in males and 6 CpGs in females. DNAm at 4 of these 15 CpGs showed statistically significant mediation effects (p-value < 0.05). At two of the 4 CpGs (cg23632109 and cg10817500), DNAm completely mediated the association (i.e., only statistically significant indirect effects were identified). In the ALSPAC cohort, at all four CpGs, the same direction of mediating effects were observed as those found in the IoW cohort, although statistically insignificant.

CONCLUSION

The association of BMI trajectory in childhood with asthma incidence at young adulthood is possibly mediated by DNAm.

COL4A3 expression in asthmatic epithelium depends on intronic methylation and ZNF263 binding

Background

Reduction of COL4A3, one of the six isoforms of collagen 4, in asthmatic airways results in increased inflammation and angiogenesis, implicating it as a central part of asthma pathogenesis. However, to date, the path underlying these diminished COL4A3 levels has been elusive. This study investigated a possible mechanism underlying the reduction of COL4A3 expression.

Methods

Bronchial biopsies of 76 patients with asthma and 83 controls were subjected to RNA-sequencing and DNA methylation bead arrays to identify expression and methylation changes. The binding of ZNF263 was analysed by chromatin-immunoprecipitation sequencing coupled with quantitative (q)PCR. Effects of ZNF263 silencing, using small interfering RNA, on the COL4A3 expression were studied using qPCR.

Results

COL4A3 expression was significantly reduced in bronchial biopsies compared to healthy controls, whereas DNA methylation levels at cg11797365 were increased. COL4A3 expression levels were significantly low in asthmatics without inhaled corticosteroid (ICS) use, whereas the expression was not statistically different between asthmatics using ICS and controls. Methylation levels at cg11797365 in vitro were increased upon consecutive rhinovirus infections.

Conclusion

Our data indicate an epigenetic modification as a contributing factor for the loss of COL4A3 expression in asthmatic airway epithelium.

An epigenetic modification interrupts ZNF263 binding, which may contribute to the loss of COL4A3 expression in asthmatic airway epitheliumhttps://bit.ly/39cZbyn

Airway hyperresponsiveness development and the toxicity of PM2.5

Airway hyperresponsiveness (AHR) is characterized by excessive bronchoconstriction in response to nonspecific stimuli, thereby leading to airway stenosis and increased airway resistance. AHR is recognized as a key characteristic of asthma and is associated with significant morbidity. At present, many studies on the molecular mechanisms of AHR have mainly focused on the imbalance in Th1/Th2 cell function and the abnormal contraction of airway smooth muscle cells. However, the specific mechanisms of AHR remain unclear and need to be systematically elaborated. In addition, the effect of air pollution on the respiratory system has become a worldwide concern. To date, numerous studies have indicated that certain concentrations of fine particulate matter (PM2.5) can increase airway responsiveness and induce acute exacerbation of asthma. Of note, the concentration of PM2.5 does correlate with the degree of AHR. Numerous studies exploring the toxicity of PM2.5 have mainly focused on the inflammatory response, oxidative stress, genotoxicity, apoptosis, autophagy, and so on. However, there have been few reviews systematically elaborating the molecular mechanisms by which PM2.5 induces AHR. The present review separately sheds light on the underlying molecular mechanisms of AHR and PM2.5-induced AHR.

Profiling of H3K27Ac Reveals the Influence of Asthma on the Epigenome of the Airway Epithelium

Background

Asthma is a chronic airway disease driven by complex genetic–environmental interactions. The role of epigenetic modifications in bronchial epithelial cells (BECs) in asthma is poorly understood.

Methods

We piloted genome-wide profiling of the enhancer-associated histone modification H3K27ac in BECs from people with asthma (n = 4) and healthy controls (n = 3).

Results

We identified n = 4,321 (FDR < 0.05) regions exhibiting differential H3K27ac enrichment between asthma and health, clustering at genes associated predominately with epithelial processes (EMT). We identified initial evidence of asthma-associated Super-Enhancers encompassing genes encoding transcription factors (TP63) and enzymes regulating lipid metabolism (PTGS1). We integrated published datasets to identify epithelium-specific transcription factors associated with H3K27ac in asthma (TP73) and identify initial relationships between asthma-associated changes in H3K27ac and transcriptional profiles. Finally, we investigated the potential of CRISPR-based approaches to functionally evaluate H3K27ac-asthma landscape in vitro by identifying guide-RNAs capable of targeting acetylation to asthma DERs and inducing gene expression (TLR3).

Conclusion

Our small pilot study validates genome-wide approaches for deciphering epigenetic mechanisms underlying asthma pathogenesis in the airways.

Health and Well-Being Outcomes of Adolescents Conceived Through In Vitro Fertilization and Intracytoplasmic Sperm Injection

What is the perception of health and well-being of adolescents from an assisted reproductive technology (ART) cohort? We conducted a survey, from September 2015 to June 2016, through self-completion questionnaires, on 487 singleton or twin ART-conceived 11- to 15-year-old adolescents, followed up since 1994, as part of an ART cohort. Collected data concerned perinatal characteristics, health indicators and perception, eating habits, behavior, and living standards. A total of 60.6% of the questionnaires were returned and could therefore be analyzed. This concerned 295 adolescents who were representative of the 788 remaining adolescents of our cohort, in terms of type of ART, maternal and perinatal characteristics, but not gender (sex ratio = 0.77). Overall, 15.3% reported chronic diseases, and only 13.3% of them considered that their chronic disease had an impact on their school life. Moreover, 94.2% of adolescents perceived that their health was "excellent" or "good"; 97.3% adolescents had normal weight or were underweight; onset of menstruation was 12 years old (± 1) for girls, age usually reported for puberty in girls; 51.9% declared having regular physical activity, boys more frequently than girls. Moreover, 70.6% of the boys had a sedentary behavior compared to 44.8% of the girls. A total of 73.5% of the adolescents were stressed at school, but school demand was considered high only in 12.2% of cases. Finally, 90% declared to have high life satisfaction. Overall, ART does not appear to have particular effect on the health indicators and behavior of adolescents who participated in the survey except for higher family affluence scale.

Sex-specific associations of asthma acquisition with changes in DNA methylation during adolescence

BACKGROUND

Underlying biological mechanisms involved in sex differences in asthma status changes from pre- to post-adolescence are unclear. DNA methylation (DNAm) has been shown to be associated with the risk of asthma.

OBJECTIVE

We hypothesized that asthma acquisition from pre- to post-adolescence was associated with changes in DNAm during this period at asthma-associated cytosine-phosphate-guanine (CpG) sites and such an association was sex-specific.

METHODS

Subjects from the Isle of Wight birth cohort (IOWBC) with DNAm in blood at ages 10 and 18 years (n = 124 females, 151 males) were studied. Using a training-testing approach, epigenome-wide CpGs associated with asthma were identified. Logistic regression was used to examine sex-specific associations of DNAm changes with asthma acquisition between ages 10 and 18 at asthma-associated CpGs. The ALSPAC birth cohort was used for independent replication. To assess functional relevance of identified CpGs, association of DNAm with gene expression in blood was assessed.

RESULTS

We identified 535 CpGs potentially associated with asthma. Significant interaction effects of DNAm changes and sex on asthma acquisition in adolescence were found at 13 of the 535 CpGs in IOWBC (P-values <1.0 × 10^-3 ). In the replication cohort, consistent interaction effects were observed at 10 of the 13 CpGs. At 7 of these 10 CpGs, opposite DNAm changes across adolescence were observed between sexes in both cohorts. In both cohorts, cg20891917, located on IFRD1 linked to asthma, shows strong sex-specific effects on asthma transition (P-values <.01 in both cohorts).

CONCLUSION AND CLINICAL RELEVANCE

Gender reversal in asthma acquisition is associated with opposite changes in DNAm (males vs females) from pre- to post-adolescence at asthma-associated CpGs. These CpGs are potential biomarkers of sex-specific asthma acquisition in adolescence.

Prospects for Use of Single-Cell Sequencing to Assess DNA Methylation in Asthma

Asthma is a complex disease with an increasing prevalence rate caused by the interaction of multiple genetically inherited and environmental factors. Epigenetics link genetic susceptibility and environmental factors. DNA methylation is an epigenetic modification that plays a crucial role in the regulation of growth and development, gene expression, and disease. Relatively little is known about DNA methylation in asthma, with few studies to date using single-cell sequencing to analyze the molecular mechanism by which DNA methylation regulates asthma. Cells with similar phenotypes may be heterogeneous in function and transcription, as may their genetic information. Although multi-omics methods, such as studies of the genome, transcriptome, and epigenome, can be used to evaluate biological processes, these methods are applicable only to groups of cells or tissues and provide averages that may obscure direct correlations among multiple layers of data. Single-cell sequencing technology can clarify the methylation and expression of genes in different populations of cells, in contrast to traditional multi-omics sequencing, which can determine only average values of cell populations. Single-cell sequence can therefore better reflect the pathogenesis of asthma, as it can clarify the function and regulatory mechanism of DNA methylation in asthma, and detect new genes and molecular markers that may become therapeutic targets in this disease.

lnc-BAZ2B promotes M2 macrophage activation and inflammation in children with asthma through stabilizing BAZ2B pre-mRNA

BACKGROUND

Dysregulation of long noncoding RNAs (lncRNAs) is associated with a variety of human diseases; however, whether they have a role in childhood asthma is unknown.

OBJECTIVE

We sought to determine the differential expression profiles of lncRNAs in PBMCs of children with asthma and the mechanisms underlying the effects of lncRNAs on the pathogenesis of asthma.

METHODS

The differential expression profiles of lncRNAs were analyzed by transcriptome microarray. The effects and mechanisms by which lncRNAs influence macrophage activation were detected by real-time quantitative PCR, Western blot, RNase protection assay, and chromatin immunoprecipitation assay. The roles played by lncRNAs in asthma were tested in a cockroach allergen extract (CRE)-induced mouse model.

RESULTS

We identified 719 lncRNAs that were differentially expressed in PBMCs of children with asthma, 502 of which were upregulated and 217 were downregulated. An lncRNA of unknown function, lnc-BAZ2B, was dominantly expressed in monocytes and significantly upregulated in children with asthma. lnc-BAZ2B promotes M2 macrophage activation by enhancing BAZ2B expression and exacerbated lung inflammation in an M2 macrophage-associated CRE-induced asthma model. Mechanistically, lnc-BAZ2B promoted the expression of its cis target gene BAZ2B by stabilizing its pre-mRNA. BAZ2B, a reader of H3K14ac modification, enhanced the transcription of IRF4 and promoted M2 macrophage activation. lnc-BAZ2B expression was correlated with that of BAZ2B in PBMCs from children with asthma. Baz2b knockdown could alleviate asthma severity in a CRE-induced asthma model.

CONCLUSION

lnc-BAZ2B promotes M2 macrophage activation and inflammation in children with asthma and may serve as a potential therapeutic and diagnostic target in children with asthma.

Differences in serum markers of oxidative stress in well controlled and poorly controlled asthma in Sri Lankan children: a pilot study

Background

Asthma is a disease characterised by hyper responsiveness and bronchoconstriction of airways, and is a major health burden globally. A dysfunction of the oxidant-antioxidant balance, termed oxidative stress, has been implicated in the pathophysiology of asthma. The present study aims to assess the changes in oxidative stress markers, namely nitric oxide metabolites and antioxidant capacity, in children with poorly controlled and well controlled asthma, in comparison to healthy controls.

Methods

The present study enrolled 72 children (ages 5-15 years) classified into three groups: (1) poorly controlled asthma (n = 20), (2) well controlled asthma (n = 24) and (3) healthy controls (n = 27). An interviewer-administered questionnaire was used to record socio-demographic data of the participants. The serum concentrations of the oxidant markers (nitrite, nitrate and total nitric oxide metabolites [NO_x]) were determined using the Griess test, and the total antioxidant capacity (TAOC) was determined using the ABTS decolorisation method. The concentrations of these markers were compared across the three groups.

Results

The three study groups were similar in terms of socio-demographic data. The differences across the three groups were statistically significant for serum concentrations of nitrate and NO_x (but not nitrite) and serum TAOC. Further analyses showed that the disparity for nitrate and NO_x concentrations was greatest between poorly controlled asthma and healthy controls (p = 0.001 and p < 0.001) compared to the well-controlled asthmatics and healthy controls (p = 0.036 and p = 0.049). A significant difference in serum nitrate and NO_x concentrations was not observed between the two asthma groups (p = 0.311 and 0.203). The TAOC were significantly lower in poorly controlled asthmatics as compared to well-controlled asthmatics (p = 0.003) and healthy controls (p < 0.001). However, there was no significant difference in the serum TAOC between healthy controls and well-controlled asthmatics (p = 0.496). These findings may indicate that it is perhaps the higher TAOC that contributes to the well controlled state of asthma.

Conclusions

The present study indicated that an imbalance of oxidants and antioxidants in the serum may have an underlying role in asthma pathophysiology, and how these markers may be effective in asthma management.

Epigenetics and the Environment in Airway Disease: Asthma and Allergic Rhinitis

Asthma and rhinitis are complex, heterogeneous diseases characterized by chronic inflammation of the upper and lower airways. While genome-wide association studies (GWAS) have identified a number of susceptible loci and candidate genes associated with the pathogenesis of asthma and allergic rhinitis (AR), the risk-associated alleles account for only a very small percent of the genetic risk. In allergic airway and other complex diseases, it is thought that epigenetic modifications, including DNA methylation, histone modifications, and non-coding microRNAs, caused by complex interactions between the underlying genome and the environment may account for some of this "missing heritability" and may explain the high degree of plasticity in immune responses. In this chapter, we will focus on the current knowledge of classical epigenetic modifications, DNA methylation and histone modifications, and their potential role in asthma and AR. In particular, we will review epigenetic variations associated with maternal airway disease, demographics, environment, and non-specific associations. The role of specific genetic haplotypes in environmentally induced epigenetic changes are also discussed. A major limitation of many of the current studies of asthma epigenetics is that they evaluate epigenetic modifications in both allergic and non-allergic asthma, making it difficult to distinguish those epigenetic modifications that mediate allergic asthma from those that mediate non-allergic asthma. Additionally, most DNA methylation studies in asthma use peripheral or cord blood due to poor accessibility of airway cells or tissue. Unlike DNA sequences, epigenetic alterations are quite cell- and tissue-specific, and epigenetic changes found in airway tissue or cells may be discordant from that of circulating blood. These two confounding factors should be considered when reviewing epigenetic studies in allergic airway disease.

Sirtuin 6 attenuates epithelial-mesenchymal transition by suppressing the TGF-β1/Smad3 pathway and c-Jun in asthma models

Allergic asthma is a chronic inflammatory airway disease involving airway remodeling. The histone deacetylase sirtuin6 (SIRT6) has protective effects in cardiac and liver fibrosis; however, its role in airway remodeling is unclear. In this study, we investigated the expression of SIRT6 in a rat model of airway remodeling and observed its effects on the epithelial-mesenchymal transition (EMT) in human bronchial epithelial 16HBE cells. Sprague-Dawley rats were sensitized and challenged with ovalbumin to induce airway remodeling or with phosphate-buffered saline as a control for different periods. Morphological changes, cell counts in the bronchoalveolar lavage fluid, and SIRT6 expression were assessed. 16HBE cells were transfected with plasmids to silence or overexpress SIRT6. Western blotting, quantitative polymerase chain reaction, Transwell assays, and cell proliferation assays were performed to examine the transforming growth factor (TGF)-β1-induced changes in EMT indicators and EMT-related cell behaviors. SIRT6 expression was upregulated in bronchial epithelial cells from rats with airway remodeling and in TGF-β1-treated 16HBE cells. SIRT6 overexpression affected TGF-β1-induced changes in EMT markers and EMT-like cell behaviors. In particular, SIRT6 overexpression alleviated the reduction in E-cadherin and the increases in N-cadherin, vimentin, alpha-smooth muscle actin, and metalloproteinase-9 levels in TGF-β1-treated 16HBE cells. Forced expression of SIRT6 also decreased the rates of cell migration and proliferation, reduced activation of phosphorylated Smad3 induced by TGF-β1 treatment, suppressed the acetylation level at histone H3K9, and inhibited the transcriptional activity of the c-Jun promotor. These results suggested that SIRT6 expression is upregulated during airway remodeling and modulates EMT in bronchial epithelial cells targeting Smad3 and c-Jun, highlighting a new therapeutic candidate for improving airway remodeling in asthma.

Low expression and hypermethylation of FOXP3 in regulatory T cells are associated with asthma in children

The aim of the present study was to determine the expression and methylation levels of forkhead transcription factor P3 (FOXP3) in peripheral blood CD4⁺CD25⁺ regulatory T cells (Tregs) harvested from children with asthma, and to explore the pathogenesis of asthma. The percentages of CD4⁺CD25⁺FOXP3⁺ Tregs in CD4⁺ T lymphocytes from 15 children with asthma and 15 healthy controls were measured by flow cytometry, and FOXP3 mRNA expression in the CD4⁺CD25⁺ Tregs was measured by reverse transcriptase-quantitative PCR. In addition, the forced expiratory volume in one second (FEV1) was measured to determine lung function. The methylation statuses of 16 CpG sites in two regions of the FOXP3 gene's exon and intron were analysed with bisulfite-specific PCR and pyrophosphate sequencing. The differences in methylation levels between the asthma and control groups were compared. The percentage of CD4⁺CD25⁺FOXP3⁺ Tregs in CD4⁺ T lymphocytes and FOXP3 mRNA expression were significantly lower in children with asthma than in control children (P<0.05). The FOXP3 mRNA levels in children with asthma were positively correlated with FEV1 (P<0.001; r=0.895). The methylation levels in 12 of the 16 studied CpG loci of the FOXP3 gene, and of the 6th CpG locus in the exon regions, were significantly higher in the asthma group compared with the control group (P<0.05). In summary, low expression and hypermethylation of the FOXP3 gene in the peripheral blood were associated with the pathogenesis of asthma in children. Thus, the FOXP3 mRNA expression level can be used to predict the severity of asthma in children.

Do Current Asthma-Preventive Measures Appropriately Face the World Health Organization's Concerns: A Study Presentation of a New Clinical, Prospective, Multicentric Pediatric Asthma Exacerbation Cohort in Germany

In summer 2017, the World Health Organization published 10 facts on asthma, which is known as a major non-communicable disease of high clinical and scientific importance with currently several hundred million people-with many children among them-suffering from air passages inflammation and narrowing. Importantly, the World Health Organization sees asthma as being underdiagnosed and undertreated. Consequently, much more efforts in clinical disease management and research need to be spent on reducing the asthma-related health burden. Particularly, for young approximately 6 months aged patients presenting recurrent bronchitic respiratory symptoms, many parents anxiously ask the doctors for risk prognosis for their children's future life. Therefore, we urgently need to reevaluate if the current diagnostic and treatment measures are in concordance with our yet incomplete knowledge of pathomechanisms on exacerbation. To contribute to this increasing concern worldwide, we established a multicentric pediatric exacerbation study network, still recruiting acute exacerbated asthmatics (children >6 years) and preschool asthmatics/wheezers (children <6 years) since winter 2018 in Germany. The current study that has a currently population comprising 176 study participants aims to discover novel holistic entry points for achieving a better understanding of the poorly understood plasticity of involved molecular pathways and to define biomarkers enabling improved diagnostics and therapeutics. With this study description, we want to present the study design, population, and few ongoing experiments for novel biomarker research. Clinical Trial Registration: German Clinical Trials Register (Deutsches Register für Klinische Studien, DRKS): DRKS00015738.

Susceptibility Variations in Air Pollution Health Effects: Incorporating Neuroendocrine Activation

Diverse host factors/phenotypes may exacerbate or diminish biological responses induced by air pollutant exposure. We lack an understanding of biological indicators of environmental exposures that culminate in a physiological response versus those that lead to adversity. Variations in response phenotype might arise centrally and/or at the local tissue level. In addition to genetic differences, the current evidence supports the roles of preexisting cardiopulmonary diseases, diabetes, diet, adverse prenatal environments, neurobehavioral disorders, childhood infections, microbiome, sex, and psychosocial stressors in modifying the susceptibility to air pollutant exposures. Animal models of human diseases, obesity, nutritional inadequacies, and neurobehavioral conditions have been compared with healthy controls to understand the causes of variations in susceptibility. Although psychosocial stressors have been associated with increased susceptibility to air pollutant effects, the contribution of neuroendocrine stress pathways in mediating these effects is just emerging. The new findings of neuroendocrine activation leading to systemic metabolic and immunological effects of air pollutants, and the potential contribution to allostatic load, emphasize the consideration of these mechanisms into susceptibility. Variations in susceptibility to air pollution health effects are likely to underlie host genetic and physiological conditions in concert with disrupted neuroendocrine circuitry that alters physiological stability under the influence of stressors.

[Toxic Components of PM2.5 and Their Toxicity Mechanisms-On the Toxicity of Sulfate and Carbon Components]

Recently, the main air pollutant has been fine particulate matter (PM_2.5), which is taken up by the whole body with severe adverse health effects. The main chemical components of PM_2.5 are salts of sulfate (and nitrate) and carbons. However, it remains unknown which components are toxic. Here, the author reviewed the literatures to determine which components are toxic and the main mechanisms underlying their toxicity. Many epidemiological studies have shown that sulfate concentration is strongly related to mortality. However, there is no experimental evidence showing that sulfate at environmental concentrations of PM_2.5 causes cardiovascular disease or other disease. On the other hand, carbon components such as elementary carbon (EC) produces high concentrations of reactive oxygen species (ROS) via its phagocytosis by macrophages, and organic carbon (OC) also produces high concentrations of ROS during its metabolic processes, and the ROS cause acute and chronic inflammation. They cause many diseases including cardiovascular disease, asthma and cancer. Furthermore, there are many lines of evidence showing that epigenetic changes such as DNA methylation or microRNA expression induced by particulate matters also induce the development of many diseases such as those mentioned above. It has been reported that carbon components are incorporated into the brain and produce ROS, and that the ROS cause damage to brain cells and Alzheimer's disease and cognitive disorders in the elderly.From these lines of evidence, the author would like to emphasize that the main toxicity of PM_2.5 is due to carbon components, and it is important to take countermeasures to decrease the concentration of carbon components in ambient air.

p300 mediates the histone acetylation of ORMDL3 to affect airway inflammation and remodeling in asthma

BACKGROUND

Bronchial asthma is affected by both environmental and genetic factors. The orosomucoid 1-like protein 3 (ORMDL3) gene is related to childhood asthma and is involved in airway inflammation and airway remodeling. The ORMDL3 promoter contains binding sites for the histone acetylase p300. Gene expression can be affected by epigenetic modifications. This study aimed to investigate whether the p300-mediated histone acetylation (HAT) of ORMDL3 gene affects airway inflammation and remodeling in asthma.

METHODS

16HBE14o- cells were transfected with various concentrations of a wild-type p300 plasmid or p300HAT-deletion plasmids. A dual luciferase reporter assay was used to examine the effect of p300-mediated HAT on the ORMDL3 promoter. Thirty BALB/c mice were randomly divided into a control group, an ovalbumin (OVA)-induced asthma group and an asthma + C646 (a selective inhibitor of p300) group. Noninvasive lung function tests were conducted to examine airway hyperreactivity (AHR) in the different groups. HE and Masson's trichrome staining was performed to examine airway remodeling and inflammation. Immunohistochemistry, western blotting and real-time PCR were used to analyze ORMDL3 expression in lung tissues. ELISA and western blotting were used to evaluate the HAT status in lung tissue. The ChIP assay was used to determine the relationship of the ORMDL3 promoter to p300 or acetylated histone H3 (aceH3).

RESULTS

p300 activated transcription from the ORMDL3 promoter, resulting in an increase in endogenous ORMDL3 mRNA levels. ORMDL3 promoter activity was reduced when the HAT activity of p300 was lost. ORMDL3 expression was elevated, and HAT activity was high in the lung tissues of asthmatic mice. p300 and aceH3 bound to the promoter region of ORMDL3. In the asthma group, the amounts of p300 and aceH3 recruited to the ORMDL3 promoter were increased. C646 inhibited p300 expression and reduced HAT activity and aceH3 levels in asthmatic mice, thereby reducing ORMDL3 expression and relieving AHR and airway remodeling.

CONCLUSION

p300-mediated HAT modulates the expression of the asthma susceptibility gene ORMDL3, thereby improving the process of airway inflammation and remodeling in asthma.

[Reasons for the development of allergies in children]

Allergies are one of the most common chronic diseases in childhood, contributing to a tremendous medical and economical burden in health care systems of most industrialized countries. The development of allergies is dependent on a complex interaction of-among others-environmental factors, nutrition, genetic and epigenetic mechanisms as well as the microbiome. These diverse factors can influence early life immune regulation including innate and adaptive immune mechanisms in a complex fashion. In case of any Childhood allergies have increased significantly in past decades. In addition to environmental factors and nutrition, genetic and epigenetic mechanisms as well as the microbiome of children play an important role. Of relevance is the way in which these diverse factors influence early immune development of the innate and adaptive immune systems of children. Their complex regulation is decisive for whether or not a child develops an allergy that manifests in most cases as atopic dermatitis, bronchial asthma, or allergic rhino conjunctivitis, or whether a child develops an immune tolerance. These influences can begin prenatally, already setting the course for later immune system development and occurrence of disease.

Dysfunctional ErbB2, an EGF receptor family member, hinders repair of airway epithelial cells from asthmatic patients

BACKGROUND

Genetic and genomic data increasingly point to the airway epithelium as critical to asthma pathogenesis. Epithelial growth factor (EGF) family members play a fundamental role in epithelial differentiation, proliferation, and repair. Although expression of erythroblastosis oncogene B2 (ErbB2) mRNA, an EGF family receptor, was reported to be lower in asthmatic patients, little is understood about its functional role.

OBJECTIVE

We sought to determine whether decreased ErbB2 activation in freshly isolated human airway epithelial cells (HAECs) from asthmatic patients associated with impaired wound closure in vitro.

METHODS

An in vitro scratch-wound model of air-liquid interface cultured and freshly isolated HAECs were compared between HAECs from healthy control subjects (HCs) and asthmatic patients in relation to ErbB2.

RESULTS

Freshly brushed HAECs from asthmatic patients had impaired ErbB2 activation compared with those from HCs. In an in vitro scratch-wound model, HAECs from asthmatic patients showed delayed wound closure compared with HAECs from HCs. Cell proliferation, as assessed based on [3H] thymidine incorporation after wounding, and expression or activation of ErbB2 and cyclin D1 at the leading edge of the wound were lower in HAECs from asthmatic patients and HCs. A selective ErbB2 tyrosine kinase inhibitor, mubritinib, impaired wound closure and decreased cyclin D1 expression in healthy HAECs, with less effect on cells from asthmatic patients, supporting diminished activity in asthmatic patients.

CONCLUSION

These results implicate a primary defect in the ErbB2 pathway as constraining epithelial repair processes in asthmatic patients. Restoration of homeostatic ErbB2 function should be considered a novel asthma therapeutic target.

Epigenome-wide association studies in asthma: A systematic review

OBJECTIVE

Asthma is a common chronic respiratory airway disease influenced by environmental factors and possibly their interaction with the human genome causing epigenetic changes. Epigenome-wide association studies (EWAS) have mainly investigated DNA methylation and its association with disease or traits, exposure factors or gene expression. This systematic review aimed to identify all EWAS assessing differentially methylated sites associated with asthma in humans.

DESIGN

Structured systematic literature search following PRISMA guidelines, Newcastle-Ottawa Scale (NOS) for cohort studies was used for bias assessment.

DATA SOURCES

We searched PubMed and Embase databases from 2005 to 2019.

ELIGIBILITY CRITERIA

Epigenome-wide association studies testing association between differential methylation and asthma in humans.

RESULTS

Overall, we identified 16 EWAS studies complying with our search criteria. Twelve studies were conducted on children, and 10 were conducted on sample sizes <150 subjects. Four hundred and nineteen CpGs were reported in children studies after correction for multiple testing. In the adult studies, thousands of differentially methylated sites were identified. Differential methylation in inflammatory-related genes correlated with higher levels of gene expressions of inflammatory modulators in asthma. Differentially methylated genes associated with asthma included SMAD3, SERPINC1, PROK1, IL13, RUNX3 and TIGIT. Forty-one CpGs were replicated at least once in blood samples, and 28 CpGs were replicated in nasal samples.

CONCLUSION

Although many differentially methylated CpGs in genes known to be involved in asthma have been identified in EWAS to date, we conclude that further studies of larger sample sizes and analyses of differential methylation between different phenotypes are needed in order to comprehensively evaluate the role of epigenetic factors in the pathophysiology and heterogeneity of asthma, and the potential clinical utility to predict or classify patients with asthma.

Blocking histone deacetylase activity as a novel target for epithelial barrier defects in patients with allergic rhinitis

BACKGROUND

A defective epithelial barrier is found in patients with allergic rhinitis (AR) and asthma; however, the underlying mechanisms remain poorly understood. Histone deacetylase (HDAC) activity has been identified as a crucial driver of allergic inflammation and tight junction dysfunction.

OBJECTIVE

We investigated whether HDAC activity has been altered in patients with AR and in a mouse model of house dust mite (HDM)-induced allergic asthma and whether it contributed to epithelial barrier dysfunction.

METHODS

Primary nasal epithelial cells of control subjects and patients with AR were cultured at the air-liquid interface to study transepithelial electrical resistance and paracellular flux of fluorescein isothiocyanate-dextran (4 kDa) together with mRNA expression and immunofluorescence staining of tight junctions. Air-liquid interface cultures were stimulated with different concentrations of JNJ-26481585, a broad-spectrum HDAC inhibitor. In vivo the effect of JNJ-26481585 on mucosal permeability and tight junction function was evaluated in a mouse model of HDM-induced allergic airway inflammation.

RESULTS

General HDAC activity was greater in nasal epithelial cells of patients with AR and correlated inversely with epithelial integrity. Treatment of nasal epithelial cells with JNJ-26481585 restored epithelial integrity by promoting tight junction expression and protein reorganization. HDM-sensitized mice were treated with JNJ-26481585 to demonstrate the in vivo role of HDACs. Treated mice did not have allergic airway inflammation and had no bronchial hyperreactivity. Moreover, JNJ-26481585 treatment restored nasal mucosal function by promoting tight junction expression.

CONCLUSION

Our findings identify increased HDAC activity as a potential tissue-injury mechanism responsible for dysregulated epithelial cell repair, leading to defective epithelial barriers in AR. Blocking HDAC activity is a promising novel target for therapeutic intervention in patients with airway diseases.

Role of epigenetics in the development of childhood asthma

PURPOSE OF REVIEW

Epigenetic marks are emerging as mediators of genetics and the environment on complex disease phenotypes, including childhood asthma and allergy.

RECENT FINDINGS

Epigenome-wide association studies over the past year have added to the growing body of evidence supporting significant associations of epigenetic regulation of gene expression and asthma and allergy. Studies in children have identified signatures of eosinophils in peripheral blood, Th2 cell transcription factors and cytokines in peripheral blood mononuclear cells, and epithelial dysfunction in the respiratory epithelium. Importantly, studies at birth have begun to decipher the contribution of epigenetic marks to asthma inception. Few studies have also begun to address the contribution of genetics and the environment to these associations.

SUMMARY

Next generation of epigenome-wide association studies that will deal with confounders, study the influence of the genetics and environment, and incorporate multiple datasets to provide better interpretation of the findings are on the horizon. Identification of key epigenetic marks that are shaped by genetics and the environment, and impact transcription of specific genes will help us have a better understanding of etiology, heterogeneity and severity of asthma, and will also empower us to develop biologically driven therapeutics and biomarkers for secondary prevention of this disease.

Linking endotypes to omics profiles in difficult-to-control asthma using the diagnostic Chinese medicine syndrome differentiation algorithm

Objective: Patients with difficult-to-control asthma have difficulty breathing almost all of the time, even leading to life-threatening asthma attacks. However, only few diagnostic markers for this disease have been identified. We aimed to take advantage of unique Chinese medicine theories for phenotypic classification and to explore molecular signatures in difficult-to-control asthma. Methods: The Chinese medicine syndrome differentiation algorithm (CMSDA) is a syndrome-scoring classification method based on the Chinese medicine overall observation theory. Patients with difficult-to-control asthma were classified into Cold- and Hot-pattern groups according to the CMSDA. DNA methylation and metabolomic profiles were obtained using Infinium Human Methylation 450 BeadChip and gas chromatography-mass spectrometer. Subsequently, an integrated bioinformatics analysis was performed to compare those two patterns and identify Cold/Hot-associated candidates, followed by functional validation studies. Results: A total of 20 patients with difficult-to-control asthma were enrolled in the study. Ten were grouped as Cold and 10 as Hot according to the CMSDA. We identified distinct whole-genome DNA methylation and metabolomic profiles between Cold- and Hot-pattern groups. ALDH3A1 gene exhibited variations in the DNA methylation probe cg10791966, while two metabolic pathways were associated with those two patterns. Conclusions: Our study introduced a novel diagnostic classification approach, the CMSDA, for difficult-to-control asthma. This is an alternative way to categorize diverse syndromes and link endotypes with omics profiles of this disease. ALDH3A1 might be a potential biomarker for precision diagnosis of difficult-to-control asthma.

Novel cutaneous mediators of chemical allergy

Chemical allergy can manifest into allergic contact dermatitis and asthma and the importance of skin sensitization in both of these diseases is increasingly being recognized. Given the unique characteristics of chemical allergy, coupled with the distinct immunological microenvironment of the skin research is still unraveling the mechanisms through which sensitization and elicitation occur. This review first describes the features of chemical sensitization and the known steps that must occur to develop a chemical allergy. Next, the unique immunological properties of the skin - which may influence chemical sensitization - are highlighted. Additionally, mediators involved with the development of allergy are reviewed, starting with early ones - including the properties of haptens, skin integrity, the microbiome, the inflammasome, and toll-like receptors (TLR). Novel cellular mediators of chemical sensitization are highlighted, including innate lymphoid cells, mast cells, T-helper (T_H) cell subsets, and skin intrinsic populations including γδ T-cells and resident memory T-cells. Finally, this review discusses two epigenetic mechanisms that can influence chemical sensitization, microRNAs and DNA methylation. Overall, this review highlights recent research investigating novel mediators of chemical allergy that are present in the skin. It also emphasizes the need to further explore these mediators to gain a better understanding of what makes a chemical an allergen, and how best to prevent the development of chemical-induced allergic diseases.

Identification of Epigenetic Mechanisms Involved in the Anti-Asthmatic Effects of Descurainia sophia Seed Extract Based on a Multi-Omics Approach

Asthma, a heterogeneous disease of the airways, is common around the world, but little is known about the molecular mechanisms underlying the interactions between DNA methylation and gene expression in relation to this disease. The seeds of Descurainia sophia are traditionally used to treat coughs, asthma and edema, but their effects on asthma have not been investigated by multi-omics analysis. We undertook this study to assess the epigenetic effects of ethanol extract of D. sophia seeds (DSE) in an ovalbumin (OVA)-induced mouse model of asthma. We profiled genome-wide DNA methylation by Methyl-seq and characterized the transcriptome by RNA-seq in mouse lung tissue under three conditions: saline control, OVA-induced, and DSE-treated. In total, 1995 differentially methylated regions (DMRs) were identified in association with anti-asthmatic effects, most in promoter and coding regions. Among them, 25 DMRs were negatively correlated with the expression of the corresponding 18 genes. These genes were related to development of the lung, respiratory tube and respiratory system. Our findings provide insights into the anti-asthmatic effects of D. sophia seeds and reveal the epigenetic targets of anti-inflammatory processes in mice.

Inhibition of H3K27me3 demethylases attenuates asthma by reversing the shift in airway smooth muscle phenotype

BACKGROUND

The shift in airway smooth muscle cells (ASMCs) phenotype between proliferation and contraction during asthma has been reported recently, highlighting a role of ASMCs plasticity in the pathophysiology of asthma. As an event involved in epigenetic post-translational modification, histone H3 lysine27 (H3K27) demethylation has attracted significant attention with respect to the epigenetic changes in diverse cells; however, little is known about its contribution to the switching of ASMCs phenotype in asthma.

OBJECTIVE

To investigate the role of trimethylated H3K27 (H3k27me3) demethylation in ASM remodelling as well as the underling mechanism.

METHODS

Mice were exposed five times a week to house dust mite (HDM) extract for 5 weeks. Lung function was measured following the final HDM challenge. Airway inflammation and remodelling were then assessed in lungs of individual mice. Human ASMCs were purchased from Sciencell Research Laboratories. Proliferation, synthesis, migration and contraction of ASMCs were analysed, respectively.

RESULTS

We observed demethylation at H3k27me3 sites in lungs harvested from mice exposed to HDM extract. Administration of a selective inhibitor of H3K27 demethylase (GSK-J4) could ameliorate the classical hallmarks of asthma, such as airway hyperresponsiveness, airway inflammation and remodelling. We established a proliferative as well as a contractive model of human ASMCs to explore the impacts of H3K27 demethylase inhibition on ASMCs phenotype. Our results indicated that GSK-J4 decreased ASMCs proliferation and migration elicited by PDGF through the Akt/JNK signalling; GSK-J4 also prevented the upregulation of contractile proteins in ASMCs induced by TGF-β through the Smad3 pathway.

CONCLUSIONS

Inhibition of H3K27me3 demethylation alleviated the development of asthmatic airway disease in vivo and modulated ASMCs phenotype in vitro. Collectively, our findings highlight a role of H3K27me3 demethylation in experimental asthma and ASMCs phenotype switch.

Insights in particulate matter-induced allergic airway inflammation: Focus on the epithelium

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 (ie 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.

The MEGA Project: A Study of the Mechanisms Involved in the Genesis and Disease Course of Asthma. Asthma Cohort Creation and Long-Term Follow-Up

The general aim of this study is to create a cohort of asthma patients with varying grades of severity in order to gain greater insight into the mechanisms underlying the genesis and course of this disease. The specific objectives focus on various studies, including imaging, lung function, inflammation, and bronchial hyperresponsiveness, to determine the relevant events that characterize the asthma population, the long-term parameters that can determine changes in the severity of patients, and the treatments that influence disease progression. The study will also seek to identify the causes of exacerbations and how this affects the course of the disease. Patients will be contacted via the outpatient clinics of the 8 participating institutions under the auspices of the Spanish Respiratory Diseases Networking System (CIBER). In the inclusion visit, a standardized clinical history will be obtained, a clinical examination, including blood pressure, body mass index, complete respiratory function tests, and FENO will be performed, and the Asthma Control Test (ACT), Morisky-Green test, Asthma Quality of Life Questionnaire (Mini AQLQ), the Sino-Nasal Outcome Test 22 (SNOT-22), and the Hospital Anxiety and Depression scale (HADS) will be administered. A specific electronic database has been designed for data collection. Exhaled breath condensate, urine and blood samples will also be collected. Non-specific bronchial hyperresponsiveness testing with methacholine will be performed and an induced sputum sample will be collected at the beginning of the study and every 24 months. A skin prick test for airborne allergens and a chest CT will be performed at the beginning of the study and repeated every 5 years.

Prenatal substance exposure and offspring development: Does DNA methylation play a role?

The period of in utero development is one of the most critical windows during which adverse conditions and exposures may influence the growth and development of the fetus as well as its future postnatal health and behavior. Maternal substance use during pregnancy remains a relatively common but nonetheless hazardous in utero exposure. For example, previous epidemiological studies have associated prenatal substance exposure with reduced birth weight, poor developmental and psychological outcomes, and increased risk for diseases and behavioral disorders (e.g., externalizing behaviors like ADHD, conduct disorder, and substance use) later in life. Researchers are now learning that many of the mechanisms whereby adverse in utero exposures may affect key pathways crucial for proper fetal growth and development are epigenetic in nature, with the majority of work in humans considering DNA methylation specifically. This review will explore the research to date on epigenetic alterations tied to maternal substance use during pregnancy and will also discuss the possible role of DNA methylation in the robust relationship between maternal substance use and later behavioral and developmental sequelae in offspring.

Blood and nasal epigenetics correlate with allergic rhinitis symptom development in the environmental exposure unit

BACKGROUND

Epigenetic alterations may represent new therapeutic targets and/or biomarkers of allergic rhinitis (AR). Our aim was to examine genome-wide epigenetic changes induced by controlled pollen exposure in the environmental exposure unit (EEU).

METHODS

38 AR sufferers and eight nonallergic controls were exposed to grass pollen for 3 hours on two consecutive days. We interrogated DNA methylation at baseline and 3 hours in peripheral blood mononuclear cells (PBMCs) using the Infinium Methylation 450K array. We corrected for demographics, cell composition, and multiple testing (Benjamini-Hochberg) and verified hits using bisulfite PCR pyrosequencing and qPCR. To extend these findings to a clinically relevant tissue, we investigated DNA methylation and gene expression of mucin 4 (MUC4), in nasal brushings from a separate validation cohort exposed to birch pollen.

RESULTS

In PBMCs of allergic rhinitis participants, 42 sites showed significant DNA methylation changes of 2% or greater. DNA methylation changes in tryptase gamma 1 (TPSG1), schlafen 12 (SLFN12), and MUC4 in response to exposure were validated by pyrosequencing. SLFN12 DNA methylation significantly correlated with symptoms (P < 0.05), and baseline DNA methylation pattern was found to be predictive of symptom severity upon grass allergen exposure (P = 0.029). Changes in MUC4 DNA methylation in nasal brushings in the validation cohort correlated with drop in peak nasal inspiratory flow (Spearman's r = 0.314, P = 0.034), and MUC4 gene expression was significantly increased (P < 0.0001).

CONCLUSION

This study revealed novel and rapid epigenetic changes upon exposure in a controlled allergen challenge facility, and identified baseline epigenetic status as a predictor of symptom severity.

Epigenome-wide association study of asthma and wheeze in childhood and adolescence

BACKGROUND

Asthma heritability has only been partially explained by genetic variants and is known to be sensitive to environmental factors, implicating epigenetic modifications such as DNA methylation in its pathogenesis.

METHODS

Using data collected in the Avon Longitudinal Study of Parents and Children (ALSPAC), we assessed associations of asthma and wheeze with DNA methylation at 7.5 and 16.5 years, at over 450,000 CpG sites in DNA from the peripheral blood of approx. 1000 participants. We used Mendelian randomization (MR), a method of causal inference that uses genetic variants as instrumental variables, to infer the direction of association between DNA methylation and asthma.

RESULTS

We identified 302 CpGs associated with current asthma status (FDR-adjusted P value < 0.05) and 445 with current wheeze status at 7.5 years, with substantial overlap between the two. Genes annotated to the 302 associated CpGs were enriched for pathways related to movement of cellular/subcellular components, locomotion, interleukin-4 production and eosinophil migration. All associations attenuated when adjusted for eosinophil and neutrophil cell count estimates. At 16.5 years, two sites were associated with current asthma after adjustment for cell counts. The CpGs mapped to the AP2A2 and IL5RA genes, with a - 2.32 [95% CI - 1.47, - 3.18] and - 2.49 [95% CI - 1.56, - 3.43] difference in percentage methylation in asthma cases respectively. Two-sample bi-directional MR indicated a causal effect of asthma on DNA methylation at several CpG sites at 7.5 years. However, associations did not persist after adjustment for multiple testing. There was no evidence of a causal effect of asthma on DNA methylation at either of the two CpG sites at 16.5 years.

CONCLUSION

The majority of observed associations are driven by higher eosinophil cell counts in asthma cases, acting as an intermediate phenotype, with important implications for future studies of DNA methylation in atopic diseases.

Prenatal maternal depression related to allergic rhinoconjunctivitis in the first 5 years of life in children of the EDEN mother-child cohort study

Backgroud: Evidence about the relationship between prenatal maternal depression and the development of childhood asthma and allergies in early life is scarce. We aimed to examine this relationship by using data set of EDEN mother-child cohort study. A total of 1139 children were followed-up until the age of 5 years.

METHODS

Prenatal maternal depression was self-reported by using the Centre for Epidemiological Studies-Depression scale (CES-D) questionnaire and was classified into binary variable (maternal depression [CES-D score of ≥16] and no maternal depression [CES-D score of <16]). Asthma and allergies in the first 5 years were assessed by using the questionnaire of the International Study of Asthma and Allergies in Childhood (ISAAC). Adjusted odds ratio (aOR) was estimated for the relationship between prenatal maternal depression and early life asthma and allergies by marginal models through the method of generalized estimating equation (GEE) when adjusting for the confounders.

RESULTS

In our study population, 13.67 % of the mothers had clinical significant depression (the total scores for CES-D ≥16) during pregnancy. For children ages 5 years, the prevalence of wheezing, physician-diagnosed asthma, physician-diagnosed eczema and allergic rhinoconjunctivitis were 46.78, 20.99, 29.17, and 22.54%, respectively. Prenatal maternal depression was associated with ever allergic rhinoconjunctivitis (aOR 1.87 [95% confidence interval {CI}, 1.33-2.62]). No significant relationships were found between prenatal maternal depression and wheezing, physician-diagnosed asthma and physician-diagnosed eczema (aOR 1.12 [95% CI, 0.91-1.39], aOR 1.23 [95% CI, 0.81-1.85] and aOR 1.17 [95% CI, 0.86-1.61], respecitvely).

CONCLUSION

Prenatal maternal depression was related to ever allergic rhinoconjunctivitis in the first 5 years of life in children of EDEN mother-child cohort study.

The environment, epigenome, and asthma

Asthma prevalence has been on the increase, especially in North America compared with other continents. However, the prevalence of asthma differs worldwide, and in many countries the prevalence is stable or decreasing. This highlights the influence of environmental exposures, such as allergens, air pollution, and the environmental microbiome, on disease etiology and pathogenesis. The epigenome might provide the unifying mechanism that translates the influence of environmental exposures to changes in gene expression, respiratory epithelial function, and immune cell skewing that are hallmarks of asthma. In this review we will introduce the concept of the environmental epigenome in asthmatic patients, summarize previous publications of relevance to this field, and discuss future directions.

Aflatoxin B1-induced epigenetic alterations: An overview

Aflatoxin B1 (AFB1) is widely distributed in nature, especially in a variety of food commodities. It is confirmed to be the most toxic of all the aflatoxins. The toxicity of AFB1 has been well investigated, and it may result in severe health problems including carcinogenesis, mutagenesis, growth retardation, and immune suppression. Epigenetic modifications including DNA methylation, histone modifications and regulation of non-coding RNA play an important role in AFB1-induced disease and carcinogenesis. To better understand the evidence for AFB1-induced epigenetic alterations and the potential mechanisms of the toxicity of AFB1, we conducted a review of published studies of AFB1-induced epigenetic alterations.