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

Decoding the role of DNA methylation in allergic diseases: from pathogenesis to therapy

Allergic diseases, characterized by a broad spectrum of clinical manifestations and symptoms, encompass a significant category of IgE-mediated atopic disorders, including asthma, allergic rhinitis, atopic dermatitis, and food allergies. These complex conditions arise from the intricate interplay between genetic and environmental factors and are known to contribute to socioeconomic burdens globally. Recent advancements in the study of allergic diseases have illuminated the crucial role of DNA methylation (DNAm) in their pathogenesis. This review explores the factors influencing DNAm in allergic diseases and delves into their mechanisms, offering valuable perspectives for clinicians. Understanding these epigenetic modifications aims to lay the groundwork for improved early prevention strategies. Moreover, our analysis of DNAm mechanisms in these conditions seeks to enhance diagnostic and therapeutic approaches, paving the way for more effective management of allergic diseases in the future.

Overview of Structural and Functional Insights of SLFN12 Associated With Different Diseases

Schlafen12 is a member of the Schlafen gene family where Slfns have been linked to many functions such as anti-proliferation and cell differentiation, viral replication inhibition, migration of cancer cells and invasion prevention, and sensitivity to DNA-damaging medicines. Researchers are interested in studying the biochemical mechanisms that control thymocyte development to extract and describe gene expression and transcriptionally elevated by the process of positive selection that led to the discovery of this novel gene family. This review aims to give adequate knowledge about human SLFN12 by reviewing the most notable papers from five reliable databases regarding SLFN12 milestones and alterations in SLFN12 expression in various disease discoveries from 1997 to the present. In conclusion, SLFN12 seems to be linked with autoimmune diseases such as multiple sclerosis. Furthermore, SLFN12 levels could modify the effects of radiation and chemotherapy.

Methylation-driven mechanisms of allergic rhinitis during pollen and non-pollen seasons using integrated bioinformatics analysis

Background

Allergic rhinitis (AR) is a widespread allergic airway disease that results from a complex interplay between genetic and environmental factors and affects approximately 10%-40% of the global population. Pollen is a common allergen, and exposure to pollen can cause epigenetic changes. However, the mechanism underlying pollen-induced DNA methylation changes and their potential effects on the allergic march are still unclear. The purpose of this study was to explore the methylation-driven mechanisms of AR during the pollen and non-pollen seasons using bioinformatics analysis and to investigate their relationship with asthma.

Methods

We downloaded DNA methylation and gene expression data from the GEO database (GSE50387: GSE50222, GSE50101) and identified differentially methylated positions (DMPs) and differentially expressed genes (DEGs) during the pollen and non-pollen seasons using the CHAMP and limma packages. Through correlation analysis, we identified methylation-driven genes and performed pathway enrichment analysis to annotate their functions. We incorporated external data on AR combined with asthma (GSE101720) for analysis to identify key CpGs that promote the transformation of AR to asthma. We also utilized external data on olive pollen allergy (GSE54522) for analysis to validate the methylation-driven genes. Weighted correlation network analysis (WGCNA) was employed to identify gene modules significantly correlated with pollen allergy. We extracted genes related to the key methylation-driven gene ZNF667-AS1 from the significant module and performed pathway intelligent clustering using KOBAS-i. We also utilized gene set enrichment analysis to explore the potential function of ZNF667-AS1.

Results

We identified 20 and 24 CpG-Gene pairings during the pollen and non-pollen seasons. After incorporating external data from GSE101720, we found that ZNF667-AS1 is a key gene that may facilitate the transformation of AR into asthma during the pollen season. This finding was further validated in another external dataset, GSE54522, which is associated with pollen allergy. WGCNA identified 17 modules, among which the blue module showed significant correlation with allergies. ZNF667-AS1 was located in the blue module. We performed pathway analysis on the genes correlated with ZNF667-AS1 extracted from the blue module and identified a prominent cluster of pathways in the KOBAS-i results, including Toll-like receptor (TLR) family, MyD88, MAPK, and oxidative stress. Gene set enrichment analysis around cg05508084 (paired with ZNF667-AS1) also indicated its potential involvement in initiating and modulating allergic inflammation from the perspective of TLR and MAPK signaling.

Conclusion

We identified methylation-driven genes and their related pathways during the pollen and non-pollen seasons in patients with AR and identified key CpGs that promote the transformation of AR into asthma due to pollen exposure. This study provides new insights into the underlying molecular mechanisms of the transformation of AR to asthma.

Self-Reported Allergic Rhinitis Prevalence and Risk Factors in Employees of the China National Railway

BACKGROUND: Allergic rhinitis (AR) is a common allergic disease globally and its prevalence is increasing year by year. This study aimed to analyze the prevalence and risk factors of self-reported AR among the Chinese National Railway train crew in the China Railway Beijing Group.METHODS: This prospective questionnaire study surveyed 1511 randomly recruited train crewmembers from 20 cities in the China National Railway network, and 494 reported having AR. A structured questionnaire was tailored, designed, and delivered electronically to all subjects. Prevalence of and risk factors for AR were analyzed based on self-reported results.RESULTS: The prevalence of self-reported AR among train crewmembers was 32.6%. Among respondents, 86.03% worked in passenger cars and 64.6% reported having worse AR symptoms while on trains. AR frequencies were 40.15% perennially and 59.85% seasonally. Among the Total Nasal Symptoms Scores (TNSS), significant differences were found between rhinorrhea and sneezing and between nasal itching and sneezing. The Rhino-Conjunctivitis Quality of Life Questionnaire (RQLQ) showed significant correlations between all seven sections. TNSS was significantly associated with the RQLQ. Scores of both the TNSS and RQLQ showed that the severity of AR symptoms (rp = 0.103) and the impact on quality of life (rp = 0.113) correlated significantly with seniority.CONCLUSIONS: The prevalence of self-reported AR among train crew working in passenger cars is higher than that of the general Chinese population. The severity of AR symptoms and the impact on quality of life are associated with seniority, meaning the number of years working on trains.Yu R-L, Ning H-Y, Lan T-F, He H, Zheng C-B, Wang X-Y, Wang H-T, Wang X-Y. Self-reported allergic rhinitis prevalence and risk factors in employees of the China National Railway. Aerosp Med Hum Perform. 2023; 94(11):821-826.

International consensus statement on allergy and rhinology: Allergic rhinitis - 2023

BACKGROUND

In the 5 years that have passed since the publication of the 2018 International Consensus Statement on Allergy and Rhinology: Allergic Rhinitis (ICAR-Allergic Rhinitis 2018), the literature has expanded substantially. The ICAR-Allergic Rhinitis 2023 update presents 144 individual topics on allergic rhinitis (AR), expanded by over 40 topics from the 2018 document. Originally presented topics from 2018 have also been reviewed and updated. The executive summary highlights key evidence-based findings and recommendation from the full document.

METHODS

ICAR-Allergic Rhinitis 2023 employed established evidence-based review with recommendation (EBRR) methodology to individually evaluate each topic. Stepwise iterative peer review and consensus was performed for each topic. The final document was then collated and includes the results of this work.

RESULTS

ICAR-Allergic Rhinitis 2023 includes 10 major content areas and 144 individual topics related to AR. For a substantial proportion of topics included, an aggregate grade of evidence is presented, which is determined by collating the levels of evidence for each available study identified in the literature. For topics in which a diagnostic or therapeutic intervention is considered, a recommendation summary is presented, which considers the aggregate grade of evidence, benefit, harm, and cost.

CONCLUSION

The ICAR-Allergic Rhinitis 2023 update provides a comprehensive evaluation of AR and the currently available evidence. It is this evidence that contributes to our current knowledge base and recommendations for patient evaluation and treatment.

B Lineage Cells and IgE in Allergic Rhinitis and CRSwNP and the Role of Omalizumab Treatment

BACKGROUND

Allergic rhinitis (AR) and chronic rhinosinusitis (CRS) are two prevalent nasal diseases where both type 2 inflammation and immunoglobulin E (IgE) may play important roles. Although they can exist independently or comorbidly, subtle but important differences exist in immunopathogenesis.

OBJECTIVE

To summarize current knowledge of pathophysiological roles of B lineage cells and IgE in AR and CRS with nasal polyps (CRSwNP).

METHODS

Searched PubMed database, reviewed AR and CRSwNP-related literature, and discussed disease diagnosis, comorbidity, epidemiology, pathophysiology, and treatment. Similarities and differences in B-cell biology and IgE are compared in the 2 conditions.

RESULTS

Both AR and CRSwNP have evidence for pathological type 2 inflammation, B-cell activation and differentiation, and IgE production. However, distinctions exist in the clinical and serological profiles at diagnosis, as well as treatments utilized. B-cell activation in AR may more frequently be regulated in the germinal center of lymphoid follicles, whereas CRSwNP may occur via extrafollicular pathways although controversies remain in these initial activating events. Oligoclonal and antigen-specific IgE maybe predominate in AR, but polyclonal and antigen-nonspecific IgE may predominate in CRSwNP. Omalizumab has been shown efficacious in treating both AR and CRSwNP in multiple clinical trials but is the only Food and Drug Administration-approved anti-IgE biologic to treat CRSwNP or allergic asthma. Staphylococcus aureus frequently colonizes the nasal airway and has the ability to activate type two responses including B-cell responses although the extent to which it modulates AR and CRSwNP disease severity is being investigated.

CONCLUSION

This review highlights current knowledge of the roles of B cells and IgE in the pathogenesis of AR and CRSwNP and a small comparison between the 2 diseases. More systemic studies should be done to elevate the understanding of these diseases and their treatment.

DNA methylation regulatory patterns and underlying pathways behind the co-pathogenesis of allergic rhinitis and chronic spontaneous urticaria

Background

Allergic rhinitis (AR) and chronic spontaneous urticaria (CSU) are often concurrent in patients. Changes in DNA methylation affect T cell biological processes, which may explain the occurrence and progression of comorbidity. However, downstream regulatory pathways of DNA methylation in two diseases and the underlying mechanisms have not been fully elucidated.

Methods

The GSE50101, GSE72541, GSE50222 and OEP002482 were mined for the identification of differentially expressed genes (DEGs) or co-expressed genes and differentially methylated genes (DMGs) in AR and CSU patients. We applied GO analysis and consensus clustering to study the potential functions and signal pathways of selected genes in two diseases. GSVA and logistic regression analysis were used to find the regulatory pathway between DNA methylation and activation patterns of CD4+ T cells. Besides, we used the Illumina 850k chip to detect DNA methylation expression profiles and recognize the differentially methylated CpG positions (DMPs) on corresponding genes. Finally, we annotated the biological process of these genes using GO and KEGG pathway analysis.

Result

The AR-related DEGs were found closely related to the differentiation and activation of CD4+ T cells. The DEGs or co-expressed genes of CD4+ T cells in AR and CSU patients were also clustered using GO and KEGG analysis and we got 57 co-regulatory pathways. Furthermore, logistic regression analysis showed that the regulation of cellular component size was closely related to the activation of CD4+ T cells regulated by DNA methylation. We got self-tested data using the Illumina 850k chip and identified 98 CpGs that were differentially methylated in patients. Finally, we mapped the DMPs to 15 genes and found that they were mainly enriched in the same CD4+T cell regulating pathway.

Conclusion

Our study indicated that DNA methylation affected by pollen participated in the activation patterns of CD4 + T cells, providing a novel direction for the symptomatic treatment of the co-occurrence of AR and CSU.

Methylation risk scores for childhood aeroallergen sensitization: Results from the LISA birth cohort

BACKGROUND

Epigenomic (e.g., DNA methylation [DNAm]) changes have been hypothesized as intermediate step linking environmental exposures with allergic disease. Associations between individual DNAm at CpGs and allergic diseases have been reported, but their joint predictive capability is unknown.

METHODS

Data were obtained from 240 children of the German LISA cohort. DNAm was measured in blood clots at 6 (N = 234) and 10 years (N = 227) using the Illumina EPIC chip. Presence of aeroallergen sensitization was measured in blood at 6, 10, and 15 years. We calculated six methylation risk scores (MRS) for allergy-related phenotypes, like total and specific IgE, asthma, or any allergies, based on available publications and assessed their performances both cross-sectionally (biomarker) and prospectively (predictor of the disease). Dose-response associations between aeroallergen sensitization and MRS were evaluated.

RESULTS

All six allergy-related MRS were highly correlated (r > .86), and seven CpGs were included in more than one MRS. Cross-sectionally, we observed an 81% increased risk for aeroallergen sensitization at 6 years with an increased MRS by one standard deviation (best-performing MRS, 95% confidence interval = [43%; 227%]). Significant associations were also seen cross-sectionally at 10 years and prospectively, though the effect of the latter was attenuated when restricted to participants not sensitized at baseline. A clear dose-response relationship with levels of aeroallergen sensitization could be established cross-sectionally, but not prospectively.

CONCLUSION

We found good classification and prediction capabilities of calculated allergy-related MRS cross-sectionally, underlining the relevance of altered gene-regulation in allergic diseases and providing insights into potential DNAm biomarkers of aeroallergen sensitization.

[Genetic aspects involved in asthma]

Asthma is an etiologically heterogeneous disease resulting from a complex interaction between genetic. The genetic aspects involved in asthma, which were analyzed from the perspective of the traditional model of multifactorial inheritance, were susceptibility, host factors, and environmental exposures. In the present paper, studies on their family aggregation, concordance in twins, and heritability were analized; as well as the current knowledge about candidate genes, genome wide association studies, and epigenomics contributions and other omic studies that have increased our knowledge about their pathophysiology and environmental interactions.

Biologic Responses to House Dust Mite Exposure in the Environmental Exposure Unit

Introduction: Allergic rhinitis (AR) is an inflammatory disease of the nasal mucosa that can be modeled using Controlled Allergen Exposure Facilities (CACF). Recently, we clinically validated the house dust mite (HDM) Environmental Exposure Unit (EEU) facility. In the current study, we aimed to assess biological responses in the blood following HDM exposure in the HDM-EEU. Methods: Fifty-five participants passed a screening visit, where they provided consent and completed a skin prick test (SPT), then attended a modest or higher HDM exposure session. Baseline and post-exposure blood samples were collected. Complete blood counts with differentials were measured, and isolated serum was used to determine Dermatophagoides farinae- and Dermatophagoides pteronyssinus-specific IgE (sIgE) and cytokine concentrations (IL-4, IL-5, IL-6, IL-10, IL-13, TNF-α). Results: HDM-allergic participants had significantly greater SPT wheal sizes than healthy controls. sIgE concentrations were significantly greater in allergic participants, with a strong correlation between Dermatophagoides farinae and Dermatophagoides pteronyssinus. Serum eosinophil counts were significantly decreased post-exposure for allergic participants. White blood cell, neutrophil, and lymphocyte counts were significantly increased for both allergic and non-allergic participants post-exposure. Serum IL-13 concentrations were significantly reduced post-exposure in allergics while TNF-α was significantly reduced in non-allergics. Conclusion: The HDM-EEU is a useful model for investigating biologic mechanisms of HDM-induced AR. Allergic participants produced measurable biological changes compared to healthy controls following allergen exposure, specifically with serum expression of eosinophils and related markers, namely IL-5, which promotes the proliferation and differentiation of eosinophils, and IL-13, a cytokine released by eosinophils. The exact mechanisms at play require further investigation.

Genetics and Epigenetics in Allergic Rhinitis

The pathogenesis of allergic rhinitis is associated with genetic, environmental, and epigenetic factors. Genotyping of single nucleotide polymorphisms (SNPs) is an advanced technique in the field of molecular genetics that is closely correlated with genome-wide association studies (GWASs) in large population groups with allergic diseases. Many recent studies have paid attention to the role of epigenetics, including alteration of DNA methylation, histone acetylation, and miRNA levels in the pathogenesis of allergic rhinitis. In this review article, genetics and epigenetics of allergic rhinitis, including information regarding functions and significance of previously known and newly-discovered genes, are summarized. Directions for future genetic and epigenetic studies of allergic rhinitis are also proposed.

Advances and highlights in allergic rhinitis

Allergic rhinitis (AR) is a growing public health, medical and economic problem worldwide. The current review describes the major discoveries related to AR during the past 2 years, including risk factors for the prevalence of AR, the corresponding diagnostic strategy, precise underlying immunological mechanisms, and efficient therapies for AR during the ongoing global "coronavirus disease 2019" (COVID-19) pandemic. The review further attempts to highlight future research perspectives. Increasing evidence suggests that environmental exposures, climate changes, and lifestyle are important risk factors for AR. Consequently, detailed investigation of the exposome and the connection between environmental exposures and health in the future should provide better risk profiles instead of single predictors, and also help mitigate adverse health outcomes in allergic diseases. Although patients with dual AR, a newly defined AR phenotype, display perennial and seasonal allergens-related nasal symptoms, they are only allergic to seasonal allergens, indicating the importance of measuring inflammation at the local sites. Herein, we suggest that a combination of precise diagnosis in local sites and traditional diagnostic methods may enhance the precision medicine-based approach for management of AR; however, this awaits further investigations. Apart from traditional treatments, social distancing, washing hands, and disinfection are also required to better manage AR patients in the ongoing global COVID-19 pandemic. Despite recent advances in understanding the immune mechanisms underlying the effects of allergen immunotherapy (AIT), further understanding changes of cell profiles after AIT and accurately evaluate the efficacy of AIT are required.

Epigenetic Mechanisms in Allergy Development and Prevention

There has been a substantial increase in the incidence and the prevalence of allergic disorders in the recent decades, which seems to be related to rapid environmental and lifestyle changes, such as higher exposure to factors thought to exert pro-allergic effects but less contact with factors known to be associated with protection against the development of allergies. Pollution is the most remarkable example of the former, while less contact with microorganisms, lower proportion of unprocessed natural products in diet, and others resulting from urbanization and westernization of the lifestyle exemplify the latter. It is strongly believed that the effects of environmental factors on allergy susceptibility and development are mediated by epigenetic mechanisms, i.e. biologically relevant biochemical changes of the chromatin carrying transcriptionally-relevant information but not affecting the nucleotide sequence of the genome. Classical epigenetic mechanisms include DNA methylation and histone modifications, for instance acetylation or methylation. In addition, microRNA controls gene expression at the mRNA level. Such epigenetic mechanisms are involved in crucial regulatory processes in cells playing a pivotal role in allergies. Those include centrally managing cells, such as T lymphocytes, as well as specific structural and effector cells in the affected organs, responsible for the local clinical presentation of allergy, e.g. epithelial or airway smooth muscle cells in asthma. Considering that allergic disorders possess multiple clinical (phenotypes) and mechanistic (endotypes) forms, targeted, stratified treatment strategies based on detailed clinical and molecular diagnostics are required. Since conventional diagnostic or therapeutic approaches do not suffice, this gap could possibly be filled out by epigenetic approaches.

Ten-eleven translocation 2 modulates allergic inflammation by 5-hydroxymethylcytosine remodeling of immunologic pathways

Allergic rhinitis (AR) is an allergen specific IgE-mediated inflammatory disease. Both genetic and environmental factors could play a role in the pathophysiology of AR. 5-methylcytosine (5-mC) can be converted to 5-hydroxymethylcytosine (5hmC) by the Ten-Eleven Translocation (TET) family of proteins as part of active DNA de-methylation pathway. 5hmC plays an important role in regulation of gene expression and differentiation in immune cells. Here we show that loss of ten-eleven translocation protein 2 (Tet2) could impact the severity of AR in the ovalbumin-induced mouse model. Genome-wide 5hmC profiling of both wildtype and Tet2 KO mice in response to AR revealed that the loss of Tet2 could lead to 5hmC alteration at specific immune response genes. Both partial loss and complete loss of Tet2 alters the 5hmC dynamic remodeling for the adaptive immune pathway, as well as cytokines. Thus, our results reveal a new role of Tet2 in immunology, and Tet2 may serve as a promising target in regulating the level of immune response.

Maternal atopy and offspring epigenome-wide methylation signature

The increase in the prevalence of allergic diseases is believed to partially depend on environmental changes. DNA methylation is a major epigenetic mechanism, which is known to respond to environmental factors. A number of studies have revealed that patterns of DNA methylation may potentially predict allergic diseases.Here, we examined how maternal atopy is associated with methylation patterns in the cord blood of neonates.We conducted an epigenome-wide association study in a cohort of 96 mother-child pairs. Pregnant women aged not more than 35 years old, not currently smoking or exposed to environmental tobacco smoke, who did not report obesity before conception were considered eligible. They were further tested for atopy. Converted DNA from cord blood was analysed using Infinium MethylationEPIC; for statistical analysis, RnBeads software was applied. Gestational age and sex were included as covariates in the final analysis.83 DM sites were associated with maternal atopy. Within the top DM sites, there were CpG sites which mapped to genes SCD, ITM2C, NT5C3A and NPEPL1. Regional analysis revealed 25 tiling regions, 4 genes, 3 CpG islands and 5 gene promoters, (including PIGCP1, ADAM3A, ZSCAN12P1) associated with maternal atopy. Gene content analysis revealed pointwise enrichments in pathways related to purine-containing compound metabolism, the G1/S transition of the mitotic cell cycle, stem cell division and cellular glucose homoeostasis.These findings suggest that maternal atopy provides a unique intrauterine environment that may constitute the first environment in which exposure is associated with methylation patterns in newborn.

The role of epigenetics in allergy and asthma development

PURPOSE OF REVIEW

Epigenetic mechanisms are known to play a crucial role in the pathogenesis of asthma, allergic rhinitis, atopic dermatitis, food allergy, and other allergic disorders, especially through mediating the effects of the environmental factors, well recognized allergy-risk modifiers. The aim of this work was to provide a concise but comprehensive review of the recent progress in the epigenetics of allergic diseases.

RECENT FINDINGS

Recent few years have substantially expanded our knowledge on the role of epigenetics in the pathogenesis and clinical picture of allergies. Specifically, it has been shown that epigenetic marks, especially DNA methylation, possess a diagnostic potential for atopic sensitization, asthma, allergic rhinitis, and food allergy. DNA methylation can be a predictor of clinical responses in controlled allergen challenges, including oral food challenges. Furthermore, direct or indirect targeting epigenetic mechanisms, this time especially histone modifications, was able to favorably affect expression of the genes underlying allergies and generally improve airway biology in allergic diseases or their animal models.

SUMMARY

Further studies are needed to explore the diagnostic and therapeutic potential of epigenetic modifications in allergies and to develop respective clinical tools.

Interaction between early-life pet exposure and methylation pattern of ADAM33 on allergic rhinitis among children aged 3-6 years in China

Background

Recent research has pointed out the important roles of epigenetic modifications in the development and persistence of allergic rhinitis (AR), especially in relation to DNA methylation of disease-associated genes. We investigated whether AR susceptibility genes were epigenetically regulated, and whether methylation modulation of these genes in response to early-life environment could be a molecular mechanism underlying the risk for AR onset in a cohort of children aged 3–6 years in China.

Methods

Peripheral blood mononuclear cell (PBMC) samples were collected from 130 children patients, aged 3–6 years and diagnosed with AR; and 154 matched controls to detect promoter methylation in 25 AR susceptibility genes with the MethylTarget approach. Methylation levels were compared for each CpG site, each amplified region, and each gene. In addition, the relationship among DNA methylation, early-life environmental risk factors and AR onset were assessed.

Results

Maternal allergic history (P = 0.0390) and pet exposure (P = 0.0339) were significantly associated with increased AR risk. Differential methylation analyses were successfully performed for 507 CpG sites, 34 amplified regions and 17 genes and significant hypomethylation was observed in the promoter region of ADAM33 in AR patients [multiple test-corrected (FDR) P-value < 0.05]. Spearman correlation analysis revealed that the hypomethylation of ADAM33 was significantly associated with higher eosinophil counts (Spearman’s ρ: − 0.187, P-value = 0.037). According to the results of the multiple regression analysis, after adjusting for cofounders, the interaction of early-life pet exposure with methylation level of ADAM33 increased the risk for AR onset 1.423 times more in children (95% CI = 0.0290–4.109, P-value = 0.005).

Conclusion

This study provides evidence that early-life pet exposure and low methylation level of ADAM33 increase AR risk in children, and the interaction between pet exposure and methylation level of ADAM33 may play an important role in the development of AR.

It is no skin off my nose: The relationship between the skin and allergic rhinitis

OBJECTIVE

Evidence supports the relationship between the skin barrier and allergic conditions. This narrative review evaluates what role the cutaneous barrier may play in the pathogenesis, disease course, and management of allergic rhinitis (AR).

DATA SOURCES

A literature review of the MEDLINE (PubMed), Embase, Cochrane, and SCOPUS Sciverse databases was conducted to identify available evidence. Reference lists of pertinent papers were searched using a snowball technique.

STUDY SELECTIONS

Papers published in English from all years until December 2020 were included. Papers that did not address the relationship between AR and the skin and hypothesis papers were excluded.

RESULTS

The cutaneous barrier shares histologic characteristics with the sinonasal epithelial barrier, which may explain commonalities between AR and atopic dermatitis. A disruption in the epithelial barrier could be a common pathway in the development of multiple allergic conditions. The skin is a common target for the treatment of AR. Available data that look at the relationship between the skin and AR often include other topics such as other atopic disorders and the role of the epithelial barrier. Increased understanding of how the cutaneous barrier affects AR may lead to new innovations in its management.

CONCLUSION

The connection between the cutaneous barrier and AR holds possibilities for further investigation, and these may lead to a better understanding and future innovations for all atopic diseases.

Male-specific age estimation based on Y-chromosomal DNA methylation

Although DNA methylation variation of autosomal CpGs provides robust age predictive biomarkers, no male-specific age predictor exists based on Y-CpGs yet. Since sex chromosomes play an important role in aging, a Y-chromosome-based age predictor would allow studying male-specific aging effects and would also be useful in forensics. Here, we used blood-based DNA methylation microarray data of 1,057 males from six cohorts aged 15-87 and identified 75 Y-CpGs with an interquartile range of ≥0.1. Of these, 22 and six were significantly hyper- and hypomethylated with age (p(cor)<0.05, Bonferroni), respectively. Amongst several machine learning algorithms, a model based on support vector machines with radial kernel performed best in male-specific age prediction. We achieved a mean absolute deviation (MAD) between true and predicted age of 7.54 years (cor=0.81, validation) when using all 75 Y-CpGs, and a MAD of 8.46 years (cor=0.73, validation) based on the most predictive 19 Y-CpGs. The accuracies of both age predictors did not worsen with increased age, in contrast to autosomal CpG-based age predictors that are known to predict age with reduced accuracy in the elderly. Overall, we introduce the first-of-its-kind male-specific epigenetic age predictor for future applications in aging research and forensics.

LPCAT2 Methylation, a Novel Biomarker for the Severity of Cedar Pollen Allergic Rhinitis in Japan

BACKGROUND

Recently, the role of the epigenome in allergies has been receiving increasing attention. Although several genes that are methylated in relation to serum immunoglobulin E (IgE) concentration have been reported by epigenome-wide association studies, little is known about the DNA methylation sites associated with the symptoms and severity of cedar pollinosis (CP).

OBJECTIVE

Our aim was to analyze the association between DNA methylation and the symptoms and severity of CP in peripheral blood mononuclear cells (PBMCs) and nasal mucosa scraping cells (NMSCs).

METHODS

We recruited 70 participants during the cedar pollen dispersal season. IgE levels were measured by a fluorescence enzyme immunoassay. We analyzed DNA methylation of acyl-CoA thioesterase 7 (ACOT7), mucin 4 (MUC4), schlafen 12 (SLFN12), lysophosphatidylcholine acyltransferase 2 (LPCAT2), and interleukin-4 (IL4) in PBMCs and NMSCs using bisulfite next-generation sequencing; the correlation of DNA methylation with non-specific IgE and cedar pollen-specific IgE levels in peripheral blood samples was also investigated. Symptom severity and DNA methylation were investigated in 15 untreated CP patients.

RESULTS

Non-specific IgE levels showed a significant negative correlation with average IL4 methylation in PBMCs (r = -0.46, P < 0.0001) but not with methylation of ACOT7, MUC4, SLFN12, and LPCAT2. Cedar pollen-specific IgE levels showed a significant negative correlation with average IL4 and MUC4 methylation in PBMCs (r = -0.31, P = 0.01 and r = -0.241, P = 0.046, respectively) but not with methylation of ACOT7, SLFN12, and LPCAT2. The methylation of some genes in NMSCs was not significantly correlated with IgE levels. The mean methylation of LPCAT2 in NMSCs showed a decreasing trend with increasing severity of CP (P = 0.027).

CONCLUSION

LPCAT2 methylation in NMSCs may reflect the severity of CP and could be used as a novel biomarker to identify suitable treatment options for CP.

Biomarkers for diagnosis and prediction of therapy responses in allergic diseases and asthma

Modern health care requires a proactive and individualized response to diseases, combining precision diagnosis and personalized treatment. Accordingly, the approach to patients with allergic diseases encompasses novel developments in the area of personalized medicine, disease phenotyping and endotyping, and the development and application of reliable biomarkers. A detailed clinical history and physical examination followed by the detection of IgE immunoreactivity against specific allergens still represents the state of the art. However, nowadays, further emphasis focuses on the optimization of diagnostic and therapeutic standards and a large number of studies have been investigating the biomarkers of allergic diseases, including asthma, atopic dermatitis, allergic rhinitis, food allergy, urticaria and anaphylaxis. Various biomarkers have been developed by omics technologies, some of which lead to a better classification of distinct phenotypes or endotypes. The introduction of biologicals to clinical practice increases the need for biomarkers for patient selection, prediction of outcomes and monitoring, to allow for an adequate choice of the duration of these costly and long‐lasting therapies. Escalating healthcare costs together with questions about the efficacy of the current management of allergic diseases require further development of a biomarker‐driven approach. Here, we review biomarkers in diagnosis and treatment of asthma, atopic dermatitis, allergic rhinitis, viral infections, chronic rhinosinusitis, food allergy, drug hypersensitivity and allergen immunotherapy with a special emphasis on specific IgE, the microbiome and the epithelial barrier. In addition, EAACI guidelines on biologicals are discussed within the perspective of biomarkers.

The need for clean air: The way air pollution and climate change affect allergic rhinitis and asthma

Air pollution and climate change have a significant impact on human health and well-being and contribute to the onset and aggravation of allergic rhinitis and asthma among other chronic respiratory diseases. In Westernized countries, households have experienced a process of increasing insulation and individuals tend to spend most of their time indoors. These sequelae implicate a high exposure to indoor allergens (house dust mites, pets, molds, etc), tobacco smoke, and other pollutants, which have an impact on respiratory health. Outdoor air pollution derived from traffic and other human activities not only has a direct negative effect on human health but also enhances the allergenicity of some plants and contributes to global warming. Climate change modifies the availability and distribution of plant- and fungal-derived allergens and increases the frequency of extreme climate events. This review summarizes the effects of indoor air pollution, outdoor air pollution, and subsequent climate change on asthma and allergic rhinitis in children and adults and addresses the policy adjustments and lifestyle changes required to mitigate their deleterious effects.

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.

IgE Levels to Ascaris and House Dust Mite Allergens Are Associated With Increased Histone Acetylation at Key Type-2 Immune Genes

Background

Epigenetic changes in response to allergen exposure are still not well understood. The aim of this study was to evaluate histone acetylation levels in peripheral blood leukocytes from humans naturally infected by intestinal parasites and perennially exposed to house dust mites (HDM).

Methods

Peripheral blood mononuclear cells (PBMCs) were isolated by gradient centrifugation from 20 infected and 21 non-infected individuals living in a rural/village in Colombia. Histone 3 acetylation (H3Ac) and histone 4 acetylation (H4Ac) levels were measured in six immune genes previously associated with helminth immunity by chromatin immunoprecipitation (ChIP)-quantitative PCR. Then we analyzed the association between histone acetylation levels with total parasite egg burden and IgE levels.

Results

We found an inverse correlation between H4Ac levels in the IL13 gene and egg worm burden that remained significant after adjustment by age [−0.20 (−0.32 to −0.09), p < 0.0001]. Moreover, we found significant associations between H4Ac levels in IL4 [0.32 (0.05–0.60), p = 0.02] and CHI3L1 [0.29 (0.08–0.51), p = 0.008] with the IgE levels to Ascaris lumbricoides. In addition, the levels of specific IgE antibodies to HDM were associated with H4Ac levels in the gene TNFSF13B encoding the B cell activating factor (BAFF) [0.51 (0.26–0.76), p < 0.001]. All values are presented as beta (95% CI).

Conclusion

Histone acetylation levels at key type-2 immune genes in humans were modified by nematode infection and HDM allergens and are associated with the intensity of the IgE response.

Genetics and epigenetics of allergy

PURPOSE OF REVIEW

Allergic diseases are prototypic examples for gene × environment-wide interactions. This review considers the current evidence for genetic and epigenetic mechanisms in allergic diseases and highlights barriers and facilitators for the implementation of these novel tools both for research and clinical practice.

RECENT FINDINGS

The value of whole-genome sequencing studies and the use of polygenic risk score analysis in homogeneous well characterized populations are currently being tested. Epigenetic mechanisms are known to play a crucial role in the pathogenesis of allergic disorders, especially through mediating the effects of the environmental factors, well recognized risk modifiers. There is emerging evidence for the immune-modulatory role of probiotics through epigenetic changes. Direct or indirect targeting of epigenetic mechanisms affect expression of the genes favouring the development of allergic diseases and can improve tissue biology. The ability to specifically edit the epigenome, especially using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology, holds the promise of enhancing understanding of how epigenetic modifications function and enabling manipulation of cell phenotype for research or therapeutic purposes.

SUMMARY

Additional research in the role of genetic and epigenetic mechanisms in relation to allergic diseases' endotypes is needed. An international project characterizing the human epigenome in relation to allergic diseases is warranted.

Recent findings in the genetics and epigenetics of asthma and allergy

In asthma and allergy genetics, a trend towards a few main topics developed over the last 2 years. First, a number of studies have been published recently which focus on overlapping and/or very specific phenotypes: within the allergy spectrum but also reaching beyond, looking for common genetic traits shared between different diseases or disease entities. Secondly, an urgently needed focus has been put on asthma and allergy genetics in populations genetically different from European ancestry. This acknowledges that the majority of new asthma patients today are not white and asthma is a truly worldwide disease. In epigenetics, recent years have seen several large-scale epigenome-wide association studies (EWAS) being published and a further focus was on the interaction between the environment and epigenetic signatures. And finally, the major trends in current asthma and allergy genetics and epigenetics comes from the field of pharmacogenetics, where it is necessary to understand the susceptibility for and mechanisms of current asthma and allergy therapies while at the same time, we need to have scientific answers to the recent availability of novel drugs that hold the promise for a more individualized therapy.

Recent developments and highlights in allergic rhinitis

Allergic rhinitis (AR) is a disease with high prevalence all over the world and therefore needs to be thoroughly investigated and treated accordingly. The mechanisms underlying the pathology and treatment of AR have been widely studied, but many aspects remain unclear and warrant further investigations. This review presents an overview of recently published papers highlighting the risk factors, mechanisms, and treatment of AR. Additionally, recent studies discussing the role of single nucleotide polymorphism, DNA methylation, regulatory B cells, group 2 innate lymphoid cells, immunotherapy, and biologics in AR are also covered.

Highlights and recent developments in airway diseases in EAACI journals (2018)

The European Academy of Allergy and Clinical Immunology (EAACI) supports three journals: Allergy, Pediatric Allergy and Immunology, and Clinical and Translational Allergy. EAACI's major goals include supporting the promotion of health, in which the prevention of allergy and asthma plays a critical role, and disseminating the knowledge of allergic disease to all stakeholders. In 2018, the remarkable progress in the identification of basic mechanisms of allergic and respiratory diseases as well as the translation of these findings into clinical practice were observed. Last year's highlights include publication of EAACI guidelines for allergen immunotherapy, many EAACI Position Papers covering important aspects for the specialty, better understanding of molecular and cellular mechanisms, identification of biomarkers for disease prediction and progress monitoring, novel prevention and intervention studies, elucidation of mechanisms of multimorbidities, introduction of new drugs to the clinics, recently completed phase three clinical studies, and publication of a large number of allergen immunotherapy studies and meta-analyses.

Ten-Eleven Translocation (TET) Enzymes Modulate the Activation of Dendritic Cells in Allergic Rhinitis

Background: The prevalence of allergic rhinitis (AR) has increased in recent decades. Accumulating evidence indicates that aberrant DNA demethylation modulated by enzymes of ten-eleven translocation (TET) promotes an imbalanced immune response.

Objective: This study aimed to explore TETs on the activation of dendritic cells (DCs) in AR.

Methods: The levels of TETs in peripheral blood mononuclear cells (PBMCs), peripheral myeloid DCs (mDCs), and plasmacytoid DCs (pDCs) from house dust mite (HDM)-sensitive AR patients and healthy volunteers (HC) were evaluated by qPCR and flow cytometry. The levels of 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) in PBMCs were determined by DNA-5hmC and DNA-5mC ELISA. The major HDM allergen, Dermatophagoides pteronyssinus (Der p 1), was used to stimulate atopic monocyte-derived DCs (moDCs) to assess its effect on the TETs. TET1 knockdown effect on the activation of non-atopic and atopic moDCs was investigated.

Results: TETs and global 5hmC were higher in PBMCs of AR than HC. So was TET1 in peripheral mDCs and pDCs of AR. In vitro, TET1 in atopic moDCs was significantly decreased by allergen challenge. Knockdown of TET1 in moDCs tended to induce CD86, CD80, and CD40 in AR but not in HC. TET1-knockdown moDCs significantly decreased the differentiation of activated regulatory T cells in AR.

Conclusion: DCs from AR patients express higher TET1 and are susceptible to be activated by TET1 decrease, which can be triggered by allergen challenge. Collectively, this suggests a role for TET in the pathogenesis of AR and potential for novel TET1-related, preventive, and therapeutic targets.

The nuts and bolts of omics for the clinical allergist

OBJECTIVE

Omics, aka multi-omics, is an emerging area of research that is advancing the use of personalized medicine in clinical practice and is therefore relevant for the practicing allergist.

DATA SOURCES

We performed a literature search of a selection of scientific findings in omics and allergy, including variants that may be important to allergy outcomes in the genome, transcriptome, metabolome, microbiome, epigenome, and exposome, among others.

STUDY SELECTIONS

Basic science papers and review articles.

RESULTS

The use of multi-omic data in clinical practice is changing how clinicians treat their patients whereby more personalized approaches are becoming standard in medical practice and has the potential to transform the treatment of allergies.

CONCLUSION

Multi-omic data are relevant and will become increasingly important for the clinical allergist.

Epigenetic changes: An emerging potential pharmacological target in allergic rhinitis

The importance of epigenetics has increased due to identification of its role in the pathophysiology of a number of diseases including allergic rhinitis. Amongst the different epigenetic changes in allergic retinitis, deacetylation of histone proteins by histone deacetylase (HDACs), hypermethylation of DNA by DNA methyltransferases (DNMT) and alteration in post-transcriptional process by the changes in the levels of miRNA are widely studied. Studies conducted related to allergic rhinitis have shown the elevation in the levels of HDAC1, 3 and 11 in the nasal epithelia and HDAC inhibitors have shown effectiveness in decreasing the symptoms of rhinitis. Their beneficial effects are attributed to restoration of the expression of TWIK-related potassium channel-1, correction of cytokine profile along with normalization of Th1/Th2 imbalance. Another epigenetic change due to increase in DNMT activity may induce DNA hypermethylation in CpG sites in the airway epithelial cells and CD4⁺ T-cells. The reduction in DNA methylation decreases allergic symptoms and normalizes the over-reactive immune system. Mechanistically, allergens may promote the hypermethylation in the promoter region of IFN-γ gene in CD4⁺ T cells via activation of ERK pathway to decrease the expression of IFN-γ. In allergic rhinitis patients, there is also a downregulation of certain miRNAs including miR-135a, miR-146a, miR-181a, miR-155 and upregulation of miRNA19a. This review discusses the studies describing the epigenetic changes taking place in the host cells in response to allergen along with possible mechanisms.

Increased DNA methylation of SLFN12 in CD4+ and CD8+ T cells from multiple sclerosis patients

DNA methylation is an epigenetic mark that is influenced by environmental factors and is associated with changes to gene expression and phenotypes. It may link environmental exposures to disease etiology or indicate important gene pathways involved in disease pathogenesis. We identified genomic regions that are differentially methylated in T cells of patients with relapsing remitting multiple sclerosis (MS) compared to healthy controls. DNA methylation was assessed at 450,000 genomic sites in CD4+ and CD8+ T cells purified from peripheral blood of 94 women with MS and 94 healthy women, and differentially methylated regions were identified using bumphunter. Differential DNA methylation was observed near four loci: MOG/ZFP57, HLA-DRB1, NINJ2/LOC100049716, and SLFN12. Increased methylation of the first exon of the SLFN12 gene was observed in both T cell subtypes and remained present after restricting analyses to samples from patients who had never been on treatment or had been off treatment for more than 2.5 years. Genes near the regions of differential methylation in T cells were assessed for differential expression in whole blood samples from a separate population of 1,329 women with MS and 97 healthy women. Gene expression of HLA-DRB1, NINJ2, and SLFN12 was observed to be decreased in whole blood in MS patients compared to controls. We conclude that T cells from MS patients display regions of differential DNA methylation compared to controls, and corresponding gene expression differences are observed in whole blood. Two of the genes that showed both methylation and expression differences, NINJ2 and SLFN12, have not previously been implicated in MS. SLFN12 is a particularly compelling target of further research, as this gene is known to be down-regulated during T cell activation and up-regulated by type I interferons (IFNs), which are used to treat MS.

Aeroallergens in Canada: Distribution, Public Health Impacts, and Opportunities for Prevention

Aeroallergens occur naturally in the environment and are widely dispersed across Canada, yet their public health implications are not well-understood. This review intends to provide a scientific and public health-oriented perspective on aeroallergens in Canada: their distribution, health impacts, and new developments including the effects of climate change and the potential role of aeroallergens in the development of allergies and asthma. The review also describes anthropogenic effects on plant distribution and diversity, and how aeroallergens interact with other environmental elements, such as air pollution and weather events. Increased understanding of the relationships between aeroallergens and health will enhance our ability to provide accurate information, improve preventive measures and provide timely treatments for affected populations.