Epigenetics and childhood asthma: current evidence and future research directions

Long-term effects of the Hebei Spirit oil spill on the prevalence and incidence of allergic disorders

The Hebei Spirit oil spill accident occurred in December 2007, approximately 10 km off the coast of Taean, South Korea, a location notably close to residential areas. Crude oil substances have been detected in various environmental mediums since the accident, yet previous studies have primarily focused on the acute effects of oil exposure due to the short latency period of allergic diseases. Therefore, this study evaluated the long-term effects of oil spill exposure on allergic disorders. Our study included adult residents who had participated in the Health Effects Research on Hebei Spirit Oil Spill (HEROS) study up to five years post-incident, which was a prospective cohort to monitor the health status of Taean residents. We used two indicators to assess oil spill exposure, namely the distance from the initial contaminated coastline to each participant's residence and the number of days participants had engaged in oil clean-up work. Current symptoms such as asthma, allergic rhinitis, atopic dermatitis, allergic conjunctivitis, and multimorbidity were considered allergic disorders. In the baseline survey, the prevalence of asthma, allergic rhinitis, atopic dermatitis, allergic conjunctivitis, and allergic multimorbidity symptoms was associated with both exposure indicators; however, these associations were not observed in the two consecutive surveys. Significant longitudinal associations between oil spill exposure indicators and the four allergic disorders, as well as multimorbidity incidences, were observed during a five-year follow-up period. Our results suggest that oil spill exposure can affect acute and long-term allergic symptoms in residents near the accident site.

Dietary Acid Load Modulation of Asthma-Related miRNAs in the Exhaled Breath Condensate of Children

Individual nutrients and bioactive compounds have been implicated in the expression of microRNAs (miRNAs), which are related to inflammation and asthma. However, evidence about the impact of diet is scarce. Therefore, we aimed to assess the association between dietary acid load and asthma-related miRNA in the exhaled breath condensate (EBC) of school-aged children. This cross-sectional analysis included 150 participants aged 7 to 12 years (52% girls) from a nested case–control study, which randomly selected 186 children attending 71 classrooms from 20 public schools located in city of Porto, Portugal. Dietary data were collected by one 24 h-recall questionnaire. Dietary acid load was assessed using the potential renal acid load (PRAL) and net endogenous acid production (NEAP) scores. Based on previous studies, eleven asthma-related miRNAs were chosen and analyzed in EBC by reverse transcription-quantitative real-time PCR. PRAL, NEAP and miRNAs were categorized as high or low according to the median. Logistic regression models were performed to assess the association between dietary acid load scores and miRNAs. Children in high dietary acid load groups (PRAL ≥ 14.43 and NEAP ≥ 55.79 mEq/day) have significantly increased odds of having high miR-133a-3p levels. In conclusion, higher dietary acid loads possibly modulate asthma-related miRNAs of school-aged children.

Exposure to traffic-related air pollution and changes in exhaled nitric oxide and DNA methylation in arginase and nitric oxide synthase in children with asthma

BACKGROUND

Traffic-related air pollution (TRAP) has been associated with increased risk of airway inflammation in children with asthma. While epigenetic changes could potentially modulate TRAP-induced inflammatory responses, few studies have assessed the temporal pattern of exposure to TRAP, epigenetic changes and inflammation in children with asthma. Our goal was to test the time-lag patterns of personal exposure to TRAP, airway inflammation (measured as fractional exhaled nitric oxide, FeNO), and DNA methylation in the promoter regions of genes involved in nitric oxide synthesis among children with asthma.

METHODS

We measured personal exposure to black carbon (BC) and FeNO for up to 30 days in a panel of children with asthma. We collected 90 buccal cell samples for DNA methylation analysis from 18 children (5 per child). Methylation in promoter regions of nitric oxide synthase (NOS1, NOS2A, NOS3) and arginase (ARG1, ARG2) was assessed by bisulfite pyrosequencing. Linear-mixed effect models were used to test the associations of BC at different lag periods, percent DNA methylation at each site and FeNO level.

RESULTS

Exposure to BC was positively associated with FeNO, and negatively associated with DNA methylation in NOS3. We found strongest association between FeNO and BC at lag 0-6 h while strongest associations between methylation at positions 1 and 2 in NOS3 and BC were at lag 13-24 h and lag 0-24 h, respectively. The strengths of associations were attenuated at longer lag periods. No significant associations between exposure to TRAP and methylation levels in other NOS and ARG isoforms were observed.

CONCLUSIONS

Exposure to TRAP was associated with higher levels of FeNO and lower levels of DNA methylation in the promoter regions of the NOS3 gene, indicating that DNA methylation of the NOS3 gene could be an important epigenetic mechanism in physiological responses to TRAP in children with asthma.

The Role of Short-Chain Fatty Acids in the Interplay between a Very Low-Calorie Ketogenic Diet and the Infant Gut Microbiota and Its Therapeutic Implications for Reducing Asthma

Gut microbiota is well known as playing a critical role in inflammation and asthma development. The very low-calorie ketogenic diet (VLCKD) is suggested to affect gut microbiota; however, the effects of VLCKD during pregnancy and lactation on the infant gut microbiota are unclear. The VLCKD appears to be more effective than caloric/energy restriction diets for the treatment of several diseases, such as obesity and diabetes. However, whether adherence to VLCKD affects the infant gut microbiota and the protective effects thereof on asthma remains uncertain. The exact mechanisms underlying this process, and in particular the potential role of short chain fatty acids (SCFAs), are still to be unravelled. Thus, the aim of this review is to identify the potential role of SCFAs that underlie the effects of VLCKD during pregnancy and lactation on the infant gut microbiota, and explore whether it incurs significant implications for reducing asthma.

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.

Children's Environmental Health: A Systems Approach for Anticipating Impacts from Chemicals

Increasing numbers of chemicals are on the market and present in consumer products. Emerging evidence on the relationship between environmental contributions and prevalent diseases suggests associations between early-life exposure to manufactured chemicals and a wide range of children’s health outcomes. Using current assessment methodologies, public health and chemical management decisionmakers face challenges in evaluating and anticipating the potential impacts of exposure to chemicals on children’s health in the broader context of their physical (built and natural) and social environments. Here, we consider a systems approach to address the complexity of children’s environmental health and the role of exposure to chemicals during early life, in the context of nonchemical stressors, on health outcomes. By advancing the tools for integrating this more complex information, the scope of considerations that support chemical management decisions can be extended to include holistic impacts on children’s health.

[Asthma and obesity in adults]

Asthma is a chronic inflammatory airway disorder characterized by a multitude of phenotypes. Epidemiological studies show an increase in asthma prevalence in obese patients regardless of age. The association of asthma and obesity is now considered as a phenotype with its own clinical, biological and functional characteristics. Regarding the pathophysiology of asthma and obesity, numerous factors such as nutrition, genetic predisposition, microbiome, ventilatory mechanics and the role of adipose tissue have been identified to explain the heterogeneous characteristics of patients with asthma and obesity. In adult patients with asthma and obesity, respiratory symptoms are particularly prominent and atopy and eosinophilic inflammation is uncommon compared to normal weight asthma patients. Obese asthma patients experience more hospitalizations and use more rescue medications than normal weight asthmatics. Management of asthma in obese patients is complex because these patients have less response to the usual anti-asthmatic treatments. Weight loss through caloric restriction combined with exercise is the main intervention to obtain improvement of asthma outcomes. Bariatric surgery is an invasive procedure with interesting results.

Methylation profiles of IL33 and CCL26 in bronchial epithelial cells are associated with asthma

AIM

This study aimed to characterize DNA methylation (DNA-me) in promoter region of IL33, IL1RL1 and CCL26 in asthma and their impacts on transcriptional activity in bronchial epithelial cells (BECs).

PATIENTS & METHODS

We performed bis-pyrosequencing, quantitative real-time PCR and sequencing in BECs from ten asthmatic and ten control individuals.

RESULTS

We detected lower DNA-me levels of IL33 and CCL26 in asthmatic than control BECs. No correlation was found between methylation and expression levels. Interestingly, carriers of a mutative allele in a haplotype within the promoter of IL33 had a lower IL33 DNA-me level and CCL26 gene expression correlated with eosinophil count.

CONCLUSION

These findings highlight the importance of investigating both epigenetic and genetic mechanisms in understanding the epithelial immune response in asthma.

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.

Air Pollution and the Epigenome: A Model Relationship for the Exploration of Toxicoepigenetics

The field of toxicoepigenetics is rapidly emerging to provide new insights into the relationship between environmental factors, the epigenome, and public health. Toxicoepigenetic data have the potential to revolutionize our understanding of environmental exposure effects and susceptibility. Studies in recent years have demonstrated that exposure to air pollution alters epigenetic modification states; however, continued advancement of the field is limited by the intrinsic complexity of the epigenome and inherent limitations of different types of studies (epidemiological, clinical, and in vitro) that are used in toxicoepigenetics. Overcoming these challenges will require a concerted and collaborative effort between molecular and cellular biologists, toxicologists, epidemiologists, and risk assessors to develop a thorough and practical understanding of the relationship between air pollution exposure, the epigenome, and health effects. Here we review the current state of air pollution epigenetics and discuss perspectives on the necessary steps to move the field forward to determine the role that the epigenome plays in air pollution exposure effects and susceptibility.

DNA methylation-based variation between human populations

Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development. Genetic variations, such as single-nucleotide polymorphisms and environmental factors, such as age, dietary folate, socioeconomic status, and smoking, impacts DNA methylation levels, which reciprocally impacts expression of phenotypes. Studies show that it is necessary to address these external influences when attempting to differentiate between populations since the relative impacts of these factors on the human methylome remain uncertain. The present review summarises several reported attempts to establish the contribution of differential DNA methylation to natural human variation, and shows that DNA methylation could represent new opportunities for risk stratification and prevention of several diseases amongst populations world-wide. Variation of methylation patterns between human populations is an exciting prospect which inspires further valuable research to apply the concept in routine medical and forensic casework. However, trans-generational inheritance needs to be quantified to decipher the proportion of variation contributed by DNA methylation. The future holds thorough evaluation of the epigenome to understand quantification, heritability, and the effect of DNA methylation on phenotypes. In addition, methylation profiling of the same ethnic groups across geographical locations will shed light on conserved methylation differences in populations.

Epigenetics of inflammation, maternal infection, and nutrition

Studies have demonstrated that epigenetic changes such as DNA methylation, histone modification, and chromatin remodeling are linked to an increased inflammatory response as well as increased risk of chronic disease development. A few studies have begun to investigate whether dietary nutrients play a beneficial role by modifying or reversing epigenetically induced inflammation. Results of these studies show that nutrients modify epigenetic pathways. However, little is known about how nutrients modulate inflammation by regulating immune cell function and/or immune cell differentiation via epigenetic pathways. This overview will provide information about the current understanding of the role of nutrients in the epigenetic control mechanisms of immune function.

The role of antioxidants in the chemistry of oxidative stress: A review

This Review Article is focused on the action of the reactive oxygenated species in inducing oxidative injury of the lipid membrane components, as well as on the ability of antioxidants (of different structures and sources, and following different mechanisms of action) in fighting against oxidative stress. Oxidative stress is defined as an excessive production of reactive oxygenated species that cannot be counteracted by the action of antioxidants, but also as a perturbation of cell redox balance. Reactive oxygenated/nitrogenated species are represented by superoxide anion radical, hydroxyl, alkoxyl and lipid peroxyl radicals, nitric oxide and peroxynitrite. Oxidative stress determines structure modifications and function modulation in nucleic acids, lipids and proteins. Oxidative degradation of lipids yields malondialdehyde and 4-hydroxynonenal, but also isoprostanes, from unsaturated fatty acids. Protein damage may occur with thiol oxidation, carbonylation, side-chain oxidation, fragmentation, unfolding and misfolding, resulting activity loss. 8-hydroxydeoxyguanosine is an index of DNA damage. The involvement of the reactive oxygenated/nitrogenated species in disease occurrence is described. The unbalance between the oxidant species and the antioxidant defense system may trigger specific factors responsible for oxidative damage in the cell: over-expression of oncogene genes, generation of mutagen compounds, promotion of atherogenic activity, senile plaque occurrence or inflammation. This leads to cancer, neurodegeneration, cardiovascular diseases, diabetes, kidney diseases. The concept of antioxidant is defined, along with a discussion of the existent classification criteria: enzymatic and non-enzymatic, preventative or repair-systems, endogenous and exogenous, primary and secondary, hydrosoluble and liposoluble, natural or synthetic. Primary antioxidants are mainly chain breakers, able to scavenge radical species by hydrogen donation. Secondary antioxidants are singlet oxygen quenchers, peroxide decomposers, metal chelators, oxidative enzyme inhibitors or UV radiation absorbers. The specific mechanism of action of the most important representatives of each antioxidant class (endogenous and exogenous) in preventing or inhibiting particular factors leading to oxidative injury in the cell, is then reviewed. Mutual influences, including synergistic effects are presented and discussed. Prooxidative influences likely to occur, as for instance in the presence of transition metal ions, are also reminded.

Beyond the genome: epigenetic mechanisms in lung remodeling

The lung develops from a very simple outpouching of the foregut into a highly complex, finely structured organ with multiple specialized cell types that are required for its normal physiological function. During both the development of the lung and its remodeling in the context of disease or response to injury, gene expression must be activated and silenced in a coordinated manner to achieve the tremendous phenotypic heterogeneity of cell types required for homeostasis and pathogenesis. Epigenetic mechanisms, consisting of DNA base modifications such as methylation, alteration of histones resulting in chromatin modification, and the action of noncoding RNA, control the regulation of information "beyond the genome" required for both lung modeling and remodeling. Epigenetic regulation is subject to modification by environmental stimuli, such as oxidative stress, infection, and aging, and is thus critically important in chronic remodeling disorders such as idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD), bronchopulmonary dysplasia (BPD), and pulmonary hypertension (PH). Technological advances have made it possible to evaluate genome-wide epigenetic changes (epigenomics) in diseases of lung remodeling, clarifying existing pathophysiological paradigms and uncovering novel mechanisms of disease. Many of these represent new therapeutic targets. Advances in epigenomic technology will accelerate our understanding of lung development and remodeling, and lead to novel treatments for chronic lung diseases.

Contemporary proteomic strategies for clinical epigenetic research and potential impact for the clinic

Novel proteomic methods are revealing the intricacy of the epigenetic landscape affecting gene regulation and improving our knowledge of the pathogenesis of complex diseases. Despite the enormous amount of data regarding epigenetic modifications present in DNA and histones, deciphering their biological relevance in the context of the disease and health is currently still an ongoing process. Here, we consider the relationship between epigenetic research in tumorigenesis and the prospect of knowledge transfer to clinical use, focusing primarily on the epigenetic histone post-translational modifications, which could be used as biomarkers. We additionally focus on the use of proteomic techniques in research and evaluate their usefulness in clinical setting.

Epigenetic regulation of Newborns' imprinted genes related to gestational growth: patterning by parental race/ethnicity and maternal socioeconomic status

BACKGROUND

Children born to parents with lower income and education are at risk for obesity and later-life risk of common chronic diseases, and epigenetics has been hypothesised to link these associations. However, epigenetic targets are unknown. We focus on a cluster of well-characterised genomically imprinted genes because their monoallelic expression is regulated by DNA methylation at differentially methylated regions (DMRs), are critical in fetal growth, and DNA methylation patterns at birth have been associated with increased risk of birth weight extremes and overweight status or obesity in early childhood.

METHODS

We measured DNA methylation at DMRs regulating genomically imprinted domains (IGF2/H19, DLK1/MEG3, NNAT and PLAGL1) using umbilical cord blood leucocytes from 619 infants recruited in Durham, North Carolina in 2010-2011. We examined differences in DNA methylation levels by race/ethnicity of both parents, and the role that maternal socioeconomic status (SES) may play in the association between race/ethnic epigenetic differences.

RESULTS

Unadjusted race/ethnic differences only were evident for DMRs regulating MEG3 and IGF2; race/ethnic differences persisted in IGF2/H19 and NNAT after accounting for income and education.

CONCLUSIONS

Results suggest that parental factors may not only influence DNA methylation, but also do so in ways that vary by DMR. Findings support the hypothesis that epigenetics may link the observed lower SES during the prenatal period and poor outcomes such as low birth weight; lower birth weight has previously been associated with adult-onset chronic diseases and conditions that include cardiovascular diseases, diabetes, obesity and some cancers.

Childhood asthma: recent developments and update

PURPOSE OF REVIEW

The purpose of this review is to provide an update on childhood asthma specifically related to the underlying genetic background and pathophysiology of asthma and their interaction with environmental stimuli. We will also discuss emerging data in the field of disease phenotyping.

RECENT FINDINGS

The field of genetics is continuously evolving to expand our knowledge on the cause of disease. Childhood onset asthma has been related to atopy and exposure to early-life infections. More recently, phenotypes have been used to classify asthma as transient and persistent, but the association of each phenotype with the genetic origin of asthma is not clearly understood.

SUMMARY

This review covers the topics of genetics, epigenetics, pathophysiology, phenotypes and treatment as they relate to childhood asthma. Overall, it provides a basis for the future of asthma treatment through description of the current research.

Epigenetics of discordant monozygotic twins: implications for disease

Monozygotic (MZ) twins share nearly all of their genetic variants and many similar environments before and after birth. However, they can also show phenotypic discordance for a wide range of traits. Differences at the epigenetic level may account for such discordances. It is well established that epigenetic states can contribute to phenotypic variation, including disease. Epigenetic states are dynamic and potentially reversible marks involved in gene regulation, which can be influenced by genetics, environment, and stochastic events. Here, we review advances in epigenetic studies of discordant MZ twins, focusing on disease. The study of epigenetics and disease using discordant MZ twins offers the opportunity to control for many potential confounders encountered in general population studies, such as differences in genetic background, early-life environmental exposure, age, gender, and cohort effects. Recently, analysis of disease-discordant MZ twins has been successfully used to study epigenetic mechanisms in aging, cancer, autoimmune disease, psychiatric, neurological, and multiple other traits. Epigenetic aberrations have been found in a range of phenotypes, and challenges have been identified, including sampling time, tissue specificity, validation, and replication. The results have relevance for personalized medicine approaches, including the identification of prognostic, diagnostic, and therapeutic targets. The findings also help to identify epigenetic markers of environmental risk and molecular mechanisms involved in disease and disease progression, which have implications both for understanding disease and for future medical research.

Epigenetics in immune-mediated pulmonary diseases

Immune-mediated pulmonary diseases are a group of diseases that resulted from immune imbalance initiated by allergens or of unknown causes. Inflammatory responses without restrictions cause tissue damage and remodeling, which leads to airway hyperactivity, destruction of alveolar architecture, and a resultant loss of lung function. Epigenetic mechanisms have been demonstrated to be involved in inflammation, autoimmunity, and cancer. Recent studies have identified that epigenetic changes also regulate molecular pathways in immune-mediated lung diseases. Aberrant DNA methylation status, dysregulation of histone modifications, as well as altered microRNAs expression could change transcription activity of genes involved in the development of immune-mediated pulmonary diseases, which contributes to skewed differentiation of T cells and proliferation and activation of myofibroblasts, leading to overproduction of inflammatory cytokines and excessive accumulation of extracellular matrix, respectively. Aside from this, epigenetics also explains how environmental exposure influence on gene transcription without genetic changes. It acts as a mediator of the interaction between environmental factors and genetic factors. Identification of the abnormal epigenetic marks in diseases provides novel biomarkers for prediction and diagnosis and affords novel therapeutic targets for those difficult clinical problems, such as steroid-resistance and rapidly progressing fibrosis. In this review, we summarized the latest experimental and translational epigenetic studies in immune-mediated pulmonary diseases, including asthma, idiopathic pulmonary fibrosis, tuberculosis, sarcoidosis, and silicosis.

Effects of antioxidant supplements and nutrients on patients with asthma and allergies

Asthma and allergic diseases have become a worldwide public health concern because of their increased prevalence. Despite decades of research on risk factors, the causes of these disorders are poorly understood. They are thought to develop through complex interactions between genetic and environmental factors. Because pulmonary and systemic oxidative stress increase inflammatory responses relevant to asthma and allergy, dietary or vitamin supplementation with antioxidants (a broad and varied category) has been proposed as an approach to reducing asthma incidence or morbidity. Meta-analyses of observational epidemiologic studies of variable methodological quality suggest associations of relatively low dietary intake of antioxidants and higher asthma and allergy prevalence. However, there have been few longitudinal studies of maternal or child dietary or vitamin/supplement antioxidant intake and asthma/allergy development. Moreover, there are no clinical trial data to support the use of dietary antioxidants or supplements to prevent asthma or allergy. A few small clinical trials suggest that specific antioxidants from diet or vitamin supplements might improve asthma control or lung function in asthmatic children or adults. Studies suggest that responses to antioxidants might be modified by life stage, genetic susceptibility, and environmental sources of oxidative stress. Large trials of antioxidant vitamin supplementation to prevent cancer suggest an increase in overall mortality with antioxidant vitamin supplementation, at least in populations with sufficient dietary antioxidant intake. This cautionary experience suggests that future trials to assess whether antioxidants reduce asthma incidence or improve asthma control should focus on supplementation of dietary sources of antioxidants. The potential benefits and risks of trials of vitamin supplements might be considered in special situations in which vulnerable populations have marked deficiency in dietary antioxidants, poor access to dietary antioxidants, and high exposure to environmental sources of oxidants.