Advances in asthma and allergic disease genetics: Is bigger always better?

Asthma-Genomic Advances Toward Risk Prediction

Asthma is a common complex airway disease whose prediction of disease risk and most severe outcomes is crucial in clinical practice for adequate clinical management. This review discusses the latest findings in asthma genomics and current obstacles faced in moving forward to translational medicine. While genome-wide association studies have provided valuable insights into the genetic basis of asthma, there are challenges that must be addressed to improve disease prediction, such as the need for diverse representation, the functional characterization of genetic variants identified, variant selection for genetic testing, and refining prediction models using polygenic risk scores.

Genetics of chronic respiratory disease

Chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), asthma and interstitial lung diseases are frequently occurring disorders with a polygenic basis that account for a large global burden of morbidity and mortality. Recent large-scale genetic epidemiology studies have identified associations between genetic variation and individual respiratory diseases and linked specific genetic variants to quantitative traits related to lung function. These associations have improved our understanding of the genetic basis and mechanisms underlying common lung diseases. Moreover, examining the overlap between genetic associations of different respiratory conditions, along with evidence for gene-environment interactions, has yielded additional biological insights into affected molecular pathways. This genetic information could inform the assessment of respiratory disease risk and contribute to stratified treatment approaches.

Severe Allergy as a Chronic Inflammatory Condition From a Systems Biology Perspective

Persistent and unresolved inflammation is a common underlying factor observed in several and seemingly unrelated human diseases, including cardiovascular and neurodegenerative diseases. Particularly, in atopic conditions, acute inflammatory responses such as those triggered by insect venom, food or drug allergies possess also a life-threatening potential. However, respiratory allergies predominantly exhibit late immune responses associated with chronic inflammation, that can eventually progress into a severe phenotype displaying similar features as those observed in other chronic inflammatory diseases, as is the case of uncontrolled severe asthma. This review aims to explore the different facets and systems involved in chronic allergic inflammation, including processes such as tissue remodelling and immune cell dysregulation, as well as genetic, metabolic and microbiota alterations, which are common to other inflammatory conditions. Our goal here was to deepen on the understanding of an entangled disease as is chronic allergic inflammation and expose potential avenues for the development of better diagnostic and intervention strategies.

PGAP3 regulates human bronchial epithelial cell mRNAs present in asthma and respiratory virus reference data sets

PGAP3 is a glycosylphosphatidylinositol (GPI) phospholipase gene localized within chromosome 17q12-21, a region highly linked to asthma. Although much is known about the function of other chromosome 17q12-21 genes expressed at increased levels in bronchial epithelium such as ORMDL3 and GSDMB, little is known about the function of increased PGAP3 expression in bronchial epithelium in the context of asthma. The aim of this study was therefore to determine whether increased PGAP3 expression in human bronchial epithelial cells regulated expression of mRNA pathways important to the pathogenesis of asthma by utilizing RNA-sequencing and bioinformatic analysis. We performed RNA-sequencing on normal human bronchial epithelial cells transfected with PGAP3 for 24 and 48 hours. PGAP3 regulated genes were compared to asthma and respiratory virus (influenza A, rhinovirus, respiratory syncytial virus) reference data sets to identify PGAP3 target genes and pathways. Approximately 9% of the upregulated PGAP3-induced genes were found in an asthma reference data set, 41% in a rhinovirus reference data set, 33% in an influenza A reference data set, and 3% in a respiratory syncytial virus reference data set. PGAP3 significantly upregulated the expression of several genes associated with the innate immune response and viral signatures of respiratory viruses associated with asthma exacerbations. Two of the highest expressed genes induced by PGAP3 are RSAD2, OASL, and IFN-λ, which are anti-viral genes associated with asthma. PGAP3 also upregulated the antiviral gene BST2, which like PGAP3 is a GPI-anchored protein. We conclude that PGAP3 expression in human bronchial epithelial cells regulates expression of genes known to be linked to asthma, and also regulates the bronchial epithelial expression of genes pertinent to the pathogenesis of respiratory viral triggered asthma exacerbations.

Precision medicine for asthma treatment: Unlocking the potential of the epigenome and microbiome

Asthma is a leading worldwide biomedical concern. Patients can experience life-threatening worsening episodes (exacerbations) usually controlled by anti-inflammatory and bronchodilator drugs. However, substantial heterogeneity in treatment response exists, and a subset of patients with unresolved asthma carry the major burden of this disease. The study of the epigenome and microbiome might bridge the gap between human genetics and environmental exposure to partially explain the heterogeneity in drug response. This review aims to provide a critical examination of the existing literature on the microbiome and epigenetic studies examining associations with asthma treatments and drug response, highlight convergent pathways, address current challenges, and offer future perspectives. Current epigenetic and microbiome studies have shown the bilateral relationship between asthma pharmacologic interventions and the human epigenome and microbiome. These studies, focusing on corticosteroids and to a lesser extent on bronchodilators, azithromycin, immunotherapy, and mepolizumab, have improved the understanding of the molecular basis of treatment response and identified promising biomarkers for drug response prediction. Immune and inflammatory pathways (eg, IL-2, TNF-α, NF-κB, and C/EBPs) underlie microbiome-epigenetic associations with asthma treatment, representing potential therapeutic pathways to be targeted. A comprehensive evaluation of these omics biomarkers could significantly contribute to precision medicine and new therapeutic target discovery.

Association Between Atopic Dermatitis and Aging: Clinical Observations and Underlying Mechanisms

As one of the most prevalent chronic inflammatory skin diseases, atopic dermatitis (AD) increasingly affects the aging population. Amid the ongoing global aging trend, it's essential to recognize the intricate relationship between AD and aging. This paper reviews existing knowledge, summarizing clinical observations of associations between AD and aging-related diseases in various systems, including endocrine, cardiovascular, and neurological. Additionally, it discusses major theories explaining the correlation, encompassing skin-mucosal barriers, systemic inflammation and stress, genes, signal transduction, and environmental and behavioral factors. The association between AD and aging holds significant importance, both in population and basic perspectives. While further research is warranted, this paper aims to inspire deeper exploration of inflammation/allergy-aging dynamics and the timely management of elderly patients with AD.

5-HTP inhibits eosinophilia via intracellular endothelial 5-HTRs; SNPs in 5-HTRs associate with asthmatic lung function

Background

Previous research showed that 5-hydroxytryptophan (5HTP), a metabolic precursor of serotonin, reduces allergic lung inflammation by inhibiting eosinophil migration across endothelial monolayers.

Objective

It is unknown if serotonin receptors are involved in mediating this 5HTP function or if serotonin receptor (HTR) single nucleotide polymorphisms (SNPs) associate with lung function in humans.

Methods

Serotonin receptor subtypes were assessed by qPCR, western blot, confocal microscopy, pharmacological inhibitors and siRNA knockdown. HTR SNPs were assessed in two cohorts.

Results

Pharmacological inhibition or siRNA knockdown of the serotonin receptors HTR1A or HTR1B in endothelial cells abrogated the inhibitory effects of 5HTP on eosinophil transendothelial migration. In contrast, eosinophil transendothelial migration was not inhibited by siRNA knockdown of HTR1A or HTR1B in eosinophils. Surprisingly, these HTRs were intracellular in endothelial cells and an extracellular supplementation with serotonin did not inhibit eosinophil transendothelial migration. This is consistent with the inability of serotonin to cross membranes, the lack of selective serotonin reuptake receptors on endothelial cells, and the studies showing minimal impact of selective serotonin reuptake inhibitors on asthma. To extend our HTR studies to humans with asthma, we examined the CHIRAH and GALA cohorts for HTR SNPs that affect HTR function or are associated with behavior disorders. A polygenic index of SNPs in HTRs was associated with lower lung function in asthmatics.

Conclusions

Serotonin receptors mediate 5HTP inhibition of transendothelial migration and HTR SNPs associate with lower lung function. These results may serve to aid in design of novel interventions for allergic inflammation.

Update on asthma biology

This is an exciting time to be conducting asthma research. The recent development of targeted asthma biologics has validated the power of basic research to discover new molecules amenable to therapeutic intervention. Advances in high-throughput sequencing are providing a wealth of "omics" data about genetic and epigenetic underpinnings of asthma, as well as about new cellular interacting networks and potential endotypes in asthma. Airway epithelial cells have emerged not only as key sensors of the outside environment but also as central drivers of dysregulated mucosal immune responses in asthma. Emerging data suggest that the airway epithelium in asthma remembers prior encounters with environmental exposures, resulting in potentially long-lasting changes in structure and metabolism that render asthmatic individuals susceptible to subsequent exposures. Here we summarize recent insights into asthma biology, focusing on studies using human cells or tissue that were published in the past 2 years. The studies are organized thematically into 6 content areas to draw connections and spur future research (on genetics and epigenetics, prenatal and early-life origins, microbiome, immune and inflammatory pathways, asthma endotypes and biomarkers, and lung structural alterations). We highlight recent studies of airway epithelial dysfunction and response to viral infections and conclude with a framework for considering how bidirectional interactions between alterations in airway structure and mucosal immunity can lead to sustained lung dysfunction in asthma.

Genome-wide Association Study of Susceptibility Loci for Self-Reported Atopic Dermatitis and Allergic Rhinitis in the Korean Population

BACKGROUND

Allergic diseases include atopic dermatitis (AD) and allergic rhinitis (AR), which are chronic, relapsing inflammatory disorders of the skin or mucosa that usually accompany immunoglobulin E-mediated immune responses. They are complex, multifactorial diseases with an etiology involving interactions between genetic and environmental factors.

OBJECTIVE

We performed a genome-wide association study (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with allergic diseases in the Korean population.

METHODS

A total of 8,840 samples were obtained from the Korean Association Resource Consortium dataset of the Korean Genome and Epidemiology Study Ansan-Anseong cohort. The allergic disease phenotype was determined based on self-reported physician diagnoses. After quality control, 8,823 subjects with 877,242 variants remained for the final analysis. The GWAS was performed using logistic regression analysis in an additive model adjusted for age and sex.

RESULTS

A total of 636 patients with allergic disease and 8,176 controls were analyzed. Three SNPs were associated with allergic disease at a level of genome-wide suggestive significance (p<1.0×10-5) in the Korean population: rs7275360, located in neural cell adhesion molecule 2; rs698195; and rs3750552, located in family with sequence similarity 189, member A2. These polymorphisms were on chromosomes 21q21.1, 7q31.1, and 9q21.12, respectively.

CONCLUSION

We identified 3 novel SNPs significantly associated with allergic diseases in the Korean population. Further research is required to confirm the association between these novel SNPs and allergic disease in the Korean population and in other ethnicities.

Allergic Phenotypes and Sarcopenia: Evidence from Observational Studies and Mendelian Randomization Analysis

Commonly affected in early-life population, the impact of allergic phenotypes on mid- or late-life health is less discussed. This study is to explore the association of allergic phenotypes including atopic dermatitis (AD), asthma, eosinophils count (EC), and sarcopenia. We conducted observational studies and mendelian randomization (MR) analysis based on UK Biobank (UKB), the China Health and Retirement Longitudinal Study (CHARLS) and data from genome-wide association study (GWAS). Based on the UKB data, AD, asthma and EC were positively correlated with pre-sarcopenia and decreased skeletal muscle mass index and hand grip in fully adjusted model. Asthma and EC were significantly associated with sarcopenia while AD was marginally associated (p = 0.095). Based on the CHARLS cohort, asthma significantly added 109.4% risk for pre-sarcopenia in adjusted model (relative risk = 2.094; p = 0.002), respectively. Both asthma (β = 0.100, p = 0.006) and EC (β = 0.023, p = 0.017) exerted significantly casual effects on pre-sarcopenia. However, as for sarcopenia, merely EC exhibited a significantly casual effect (β = 0.005, p = 0.048). Significant casual effects of AD (β = - 0.027, p = 0.003), asthma (β = - 0.029, p = 0.027) and EC (β = - 0.041, p < 0.001) on decreased appendicular lean mass (ALM) were observed using the inverse-variance weighted method and the Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) method. Our results revealed a contributory role of AD, asthma and EC on sarcopenia, especially in terms of decreased ALM, an indicator for sarcopenia diagnosis. The findings of our study will raise the awareness of preventing aging-related disorders or geriatric syndromes among allergic populations.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-023-00110-4.

Investigation of miRNAs that are effective in the pathogenesis of asthma

OBJECTIVES

Asthma is a complex disease characterized by inflammation of the airways, involving epigenetic changes, in which genetic and environmental factors act together. MicroRNAs as candidate biomarkers stand out as target molecules in the diagnosis and treatment of immunological and inflammatory diseases. Our aim of this study is to identify miRNAs that are thought to be effective in the pathogenesis of allergic asthma and to reveal candidate biomarkers associated with the disease.

METHODS

Fifty patients, aged between 18-80 years, who were diagnosed with allergic asthma and 18 healthy volunteers were included in the study. After the collection 2 mL of total blood from volunteers, RNA isolation and cDNA synthesis were performed. For miRNA profile screening, expression analysis was performed by real-time PCR method using miScript miRNA PCR Array. GeneGlobe Data Analysis Center was used to evaluate dysregulated miRNAs.

RESULTS

In the allergic asthma group, 9 (18%) of the patients were male and 41 (82%) of them were female. In the control group, 7 (38.89%) were male and 11 (61.1%) were female (P:0.073). As a result of the research, the expression levels of miR-142-5p, miR-376c-3p and miR-22-3p were down-regulated, while miR-27b-3p, miR-26b-5p, miR-15b-5p and miR-29c-3p detected as up-regulated.

DISCUSSION

The results of our study suggest that miR142-5p, miR376c-3p and miR22-3p promote Ubiquitin-mediated proteolysis by inhibiting TGF-β expression through a mechanism involving the p53 signaling pathway. The deregulated miRNAs may be used as a diagnostic and prognostic biomarker in asthma.

Living in environmental justice areas worsens asthma severity and control: Differential interactions with disease duration, age at onset, and pollution

BACKGROUND

Impoverished and historically marginalized communities often reside in areas with increased air pollution.

OBJECTIVE

We evaluated the association between environmental justice (EJ) track and asthma severity and control as modified by traffic-related air pollution (TRAP).

METHODS

We performed a retrospective study of 1526 adult asthma patients in Allegheny County, Pa, enrolled in an asthma registry during 2007-20. Asthma severity and control were determined using global guidelines. EJ tract designation was based on residency in census tracts with ≥30% non-White and/or ≥20% impoverished populations. TRAP exposures (NO2 and black carbon) for each census tract were normalized into pollution quartiles. Generalized linear model analyses determined the effect of EJ tract and TRAP on asthma.

RESULTS

TRAP exposure in the highest quartile range was more frequent among patients living in an EJ tract (66.4% vs 20.8%, P < .05). Living in an EJ tract increased the odds of severe asthma in later onset asthma. The odds of uncontrolled asthma increased with disease duration in all patients living in EJ tracts (P < .05). Living in the highest quartile of NO2 also increased the odds of uncontrolled asthma in patients with severe disease (P < .05), while there was no effect of TRAP on uncontrolled asthma in patients with less severe disease (P > .05).

CONCLUSIONS

Living in an EJ tract increased the odds of severe and uncontrolled asthma and was influenced by age at onset, disease duration, and potentially by TRAP exposure. This study underscores the need to better understand the complex environmental interactions that affect lung health in groups that have been economically and/or socially marginalized.

A conversation on allergy: recognizing the past and looking to the future

Allergy is an ever-evolving group of disorders, which includes asthma, atopic dermatitis, rhinitis and food allergies and that currently affects over 1 billion people worldwide. This group of disorders has exploded in incidence since around the start of the 20th century, implying that genetics is not solely responsible for its development but that environmental factors have an important role. Here, Fabio Luciani and Jonathan Coquet, in their role as editors at Immunology & Cell Biology, asked nine prominent researchers in the field of allergy to define the term 'allergy', discuss the role of genetics and the environment, nominate the most important discoveries of the past decade and describe the best strategies to combat allergy at the population level going forward.

Investigations of a combination of atopic status and age of asthma onset identify asthma subphenotypes

OBJECTIVE

Subphenotypes of asthma may be determined by age onset and atopic status. We sought to characterize early or late onset atopic asthma with fungal or non-fungal sensitization (AAFS or AANFS) and non-atopic asthma (NAA) in children and adults in the Severe Asthma Research Program (SARP). SARP is an ongoing project involving well-phenotyped patients with mild to severe asthma.

METHODS

Phenotypic comparisons were performed using Kruskal-Wallis or chi-square test. Genetic association analyses were performed using logistic or linear regression.

RESULTS

Airway hyper-responsiveness, total serum IgE levels, and T2 biomarkers showed an increasing trend from NAA to AANFS and then to AAFS. Children and adults with early onset asthma had greater % of AAFS than adults with late onset asthma (46% and 40% vs. 32%; P < 0.00001). In children, AAFS and AANFS had lower % predicted FEV1 (86% and 91% vs. 97%) and greater % of patients with severe asthma than NAA (61% and 59% vs. 43%). In adults with early or late onset asthma, NAA had greater % of patients with severe asthma than AANFS and AAFS (61% vs. 40% and 37% or 56% vs. 44% and 49%). The G allele of rs2872507 in GSDMB had higher frequency in AAFS than AANFS and NAA (0.63 vs. 0.55 and 0.55), and associated with earlier age onset and asthma severity.

CONCLUSIONS

Early or late onset AAFS, AANFS, and NAA have shared and distinct phenotypic characteristics in children and adults. AAFS is a complex disorder involving genetic susceptibility and environmental factors.

Associations between HLA class II alleles and IgE sensitization to allergens in the Qatar Biobank cohort

Background

Allergic disorders are the consequence of IgE sensitization to allergens. Population studies have shown that certain human leukocyte antigen (HLA) alleles are associated with increased or decreased risk of developing allergy.

Objective

We aimed to characterize the relationship between HLA class II allelic diversity and IgE sensitization in an understudied Arab population.

Methods

We explored associations between IgE sensitization to 7 allergen mixes and mesquite (comprising 41 food or aeroallergens) and 45 common classical HLA class II alleles in a well-defined cohort of 797 individuals representing the general adult population of Qatari nationals and long-term residents. To do so, we performed HLA calling from whole genome sequencing data at 2-field resolution using 2 independent algorithms. We then applied 3 different regression models to assess either each allergen mix independently, in the context of IgE sensitization to other allergens tested, or polysensitization.

Results

More than half (n = 447) of the study participants showed IgE sensitization to at least 1 allergen, most of them (n = 400) to aeroallergens (Phadiatop). We identified statistically significant negative and positive associations with 24 HLA class II alleles. These have been reported to confer risk or protection from variety of diseases; however, only a few have previously been associated with allergy in other populations.

Conclusions

Our study reveals several new risk and protective genetic markers for allergen-specific IgE sensitization. This is a first and essential step toward a better understanding of the origins of allergic diseases in this understudied population.

Assessing causal relationships between gut microbiota and asthma: evidence from two sample Mendelian randomization analysis

Background

Accumulating evidence has suggested that gut microbiota dysbiosis is commonly observed in asthmatics. However, it remains unclear whether dysbiosis is a cause or consequence of asthma. We aimed to examine the genetic causal relationships of gut microbiota with asthma and its three phenotypes, including adult-onset asthma, childhood-onset asthma, and moderate-severe asthma.

Methods

To elucidate the causality of gut microbiota with asthma, we applied two sample Mendelian randomization (MR) based on the largest publicly available genome-wide association study (GWAS) summary statistics. Inverse variance weighting meta-analysis (IVW) was used to obtain the main estimates; and Weighted median, MR-Egger, Robust Adjusted Profile Score (MR-RAPS), Maximum likelihood method (ML), and MR pleiotropy residual sum and outlier (MR-PRESSO) methods were applied in sensitivity analyses. Finally, a reverse MR analysis was performed to evaluate the possibility of reverse causation.

Results

In the absence of heterogeneity and horizontal pleiotropy, the IVW method revealed that genetically predicted Barnesiella and RuminococcaceaeUCG014 were positively correlated with the risk of asthma, while the association between genetically predicted CandidatusSoleaferrea and asthma was negative. And for the three phenotypes of asthma, genetically predicted Akkermansia reduced the risk of adult-onset asthma, Collinsella and RuminococcaceaeUCG014 increased the risk of childhood-onset asthma, and FamilyXIIIAD3011group, Eisenbergiella, and Ruminiclostridium6 were correlated with the risk of moderate-severe asthma (all P<0.05). The reverse MR analysis didn't find evidence supporting the reverse causality from asthma and its three phenotypes to the gut microbiota genus.

Conclusion

This study suggested that microbial genera were causally associated with asthma as well as its three phenotypes. The findings deepened our understanding of the role of gut microbiota in the pathology of asthma, which emphasizes the potential of opening up a new vista for the prevention and diagnosis of asthma.

A meta-analysis of genome-wide association studies of childhood wheezing phenotypes identifies ANXA1 as a susceptibility locus for persistent wheezing

Background

Many genes associated with asthma explain only a fraction of its heritability. Most genome-wide association studies (GWASs) used a broad definition of 'doctor-diagnosed asthma', thereby diluting genetic signals by not considering asthma heterogeneity. The objective of our study was to identify genetic associates of childhood wheezing phenotypes.

Methods

We conducted a novel multivariate GWAS meta-analysis of wheezing phenotypes jointly derived using unbiased analysis of data collected from birth to 18 years in 9568 individuals from five UK birth cohorts.

Results

Forty-four independent SNPs were associated with early-onset persistent, 25 with pre-school remitting, 33 with mid-childhood remitting, and 32 with late-onset wheeze. We identified a novel locus on chr9q21.13 (close to annexin 1 [ANXA1], p<6.7 × 10-9), associated exclusively with early-onset persistent wheeze. We identified rs75260654 as the most likely causative single nucleotide polymorphism (SNP) using Promoter Capture Hi-C loops, and then showed that the risk allele (T) confers a reduction in ANXA1 expression. Finally, in a murine model of house dust mite (HDM)-induced allergic airway disease, we demonstrated that anxa1 protein expression increased and anxa1 mRNA was significantly induced in lung tissue following HDM exposure. Using anxa1-/- deficient mice, we showed that loss of anxa1 results in heightened airway hyperreactivity and Th2 inflammation upon allergen challenge.

Conclusions

Targeting this pathway in persistent disease may represent an exciting therapeutic prospect.

Funding

UK Medical Research Council Programme Grant MR/S025340/1 and the Wellcome Trust Strategic Award (108818/15/Z) provided most of the funding for this study.

Asthma Exacerbations: The Genes Behind the Scenes

The clinical and socioeconomic burden of asthma exacerbations (AEs) constitutes a major public health problem. In the last 4 years, there has been an increase in ethnic diversity in candidate-gene and genome-wide association studies of AEs, which in the latter case led to the identification of novel genes and underlying pathobiological processes. Pharmacogenomics, admixture mapping analyses, and the combination of multiple "omics" layers have helped to prioritize genomic regions of interest and/or facilitated our understanding of the functional consequences of genetic variation. Nevertheless, the field still lags behind the genomics of asthma, where a vast compendium of genetic approaches has been used (eg, gene-environment nteractions, next-generation sequencing, and polygenic risk scores). Furthermore, the roles of the DNA methylome and histone modifications in AEs have received little attention, and microRNA findings remain to be validated in independent studies. Likewise, the most recent transcriptomic studies highlight the importance of the host-airway microbiome interaction in the modulation of risk of AEs. Leveraging -omics and deep-phenotyping data from subtypes or homogenous subgroups of patients will be crucial if we are to overcome the inherent heterogeneity of AEs, boost the identification of potential therapeutic targets, and implement precision medicine approaches to AEs in clinical practice.

Decoding the genetic and epigenetic basis of asthma

Asthma is a complex and heterogeneous chronic inflammatory disease of the airways. Alongside environmental factors, asthma susceptibility is strongly influenced by genetics. Given its high prevalence and our incomplete understanding of the mechanisms underlying disease susceptibility, asthma is frequently studied in genome-wide association studies (GWAS), which have identified thousands of genetic variants associated with asthma development. Virtually all these genetic variants reside in non-coding genomic regions, which has obscured the functional impact of asthma-associated variants and their translation into disease-relevant mechanisms. Recent advances in genomics technology and epigenetics now offer methods to link genetic variants to gene regulatory elements embedded within non-coding regions, which have started to unravel the molecular mechanisms underlying the complex (epi)genetics of asthma. Here, we provide an integrated overview of (epi)genetic variants associated with asthma, focusing on efforts to link these disease associations to biological insight into asthma pathophysiology using state-of-the-art genomics methodology. Finally, we provide a perspective as to how decoding the genetic and epigenetic basis of asthma has the potential to transform clinical management of asthma and to predict the risk of asthma development.

Prevalence and Severity Distribution of Type 2 Inflammation-Related Comorbidities Among Patients with Asthma, Chronic Rhinosinusitis with Nasal Polyps, and Atopic Dermatitis

This observational study assessed the prevalence of co-existing type 2 inflammatory conditions [T2Cs; asthma, atopic dermatitis (AD), allergic rhinitis, and chronic rhinosinusitis with nasal polyps (CRSwNP)] in patients with moderate-to-severe (M/S) type 2 asthma, M/S CRSwNP, or M/S AD, in the real-world setting. Data from 761 physicians in the US and EUR5 were sourced from Adelphi Disease-Specific Programmes covering patients with M/S asthma (n = 899), M/S CRSwNP (n = 683), and M/S AD (n = 1497). At least one T2C was identified in 66%, 69%, and 46% of M/S asthma, M/S CRSwNP, and M/S AD cohorts, respectively, and 24%, 36% and 16% had at least two T2Cs; trends were similar in the US and EUR5. In patients with M/S asthma or M/S CRSwNP, T2Cs commonly presented as mild or moderate. The comorbidity burden suggests that an integrated treatment approach is warranted to address underlying type 2 inflammation in patients with M/S type 2 diseases.

Transferability of the PRS estimates for height and BMI obtained from the European ethnic groups to the Western Russian populations

Genetic data plays an increasingly important role in modern medicine. Decrease in the cost of sequencing with subsequent increase in imputation accuracy, and the accumulation of large amounts of high-quality genetic data enable the creation of polygenic risk scores (PRSs) to perform genotype-phenotype associations. The accuracy of phenotype prediction primarily depends on the overall trait heritability, Genome-wide association studies cohort size, and the similarity of genetic background between the base and the target cohort. Here we utilized 8,664 high coverage genomic samples collected across Russia by "Evogen", a Russian biomedical company, to evaluate the predictive power of PRSs based on summary statistics established on cohorts of European ancestry for basic phenotypic traits, namely height and BMI. We have demonstrated that the PRSs calculated for selected traits in three distinct Russian populations, recapitulate the predictive power from the original studies. This is evidence that GWAS summary statistics calculated on cohorts of European ancestry are transferable onto at least some ethnic groups in Russia.

STAT6 gain-of-function variant exacerbates multiple allergic symptoms

BACKGROUND

Allergic diseases were long considered to be complex multifactorial disorders. However, recent findings indicate that severe allergic inflammation can be caused by monogenic immune defects.

OBJECTIVES

We sought to clarify the molecular pathogenesis of a patient with early-onset multiple allergic diseases, a high serum IgE level, hypereosinophilia, treatment-resistant severe atopic dermatitis with increased dermal collagen fiber deposition, and eosinophilic gastrointestinal disorder with numerous polypoid nodules.

METHODS

A missense variant in STAT6 was identified, and its function was examined using peripheral blood, transfected HEK293 cells, lymphoblastoid cell lines, and knock-in mice with the corresponding mutation.

RESULTS

Whole-exome sequencing identified a de novo heterozygous missense variant in signal transducer and activator of transcription 6 (STAT6) (p.Asp419Asn). Luciferase reporter assay revealed that the transcriptional activity of this STAT6 mutant was upregulated even without IL-4 stimulation. Phosphorylation of STAT6 was not observed in either the patient's T_H2 cells or lymphoblastoid cell lines without stimulation, whereas it was induced more strongly in both by IL-4 stimulation compared with healthy controls. STAT6 protein was present in the nuclear fraction of the lymphoblastoid cell lines of the patient even in the absence of IL-4 stimulation. The patient's gastric mucosa showed upregulation of STAT6-, fibrosis-, and germinal center formation-related molecules. Some of the knock-in mice with the corresponding mutation spontaneously developed dermatitis with skin thickening and eosinophil infiltration. Moreover, serum IgE levels and mRNA expression of type 2 cytokines were increased in the knock-in mice-with or without development of spontaneous dermatitis-compared with the wild-type mice.

CONCLUSIONS

A novel STAT6 gain-of-function variant is a potential cause of primary atopic disorders.

Multiancestral polygenic risk score for pediatric asthma

BACKGROUND

Asthma is the most common chronic condition in children and the third leading cause of hospitalization in pediatrics. The genome-wide association study catalog reports 140 studies with genome-wide significance. A polygenic risk score (PRS) with predictive value across ancestries has not been evaluated for this important trait.

OBJECTIVES

This study aimed to train and validate a PRS relying on genetic determinants for asthma to provide predictions for disease occurrence in pediatric cohorts of diverse ancestries.

METHODS

This study applied a Bayesian regression framework method using the Trans-National Asthma Genetic Consortium genome-wide association study summary statistics to derive a multiancestral PRS score, used one Electronic Medical Records and Genomics (eMERGE) cohort as a training set, used a second independent eMERGE cohort to validate the score, and used the UK Biobank data to replicate the findings. A phenome-wide association study was performed using the PRS to identify shared genetic etiology with other phenotypes.

RESULTS

The multiancestral asthma PRS was associated with asthma in the 2 pediatric validation datasets. Overall, the multiancestral asthma PRS has an area under the curve (AUC) of 0.70 (95% CI, 0.69-0.72) in the pediatric validation 1 and AUC of 0.66 (0.65-0.66) in the pediatric validation 2 datasets. We found significant discrimination across pediatric subcohorts of European (AUC, 95% CI, 0.60 and 0.66), African (AUC, 95% CI, 0.61 and 0.66), admixed American (AUC, 0.64 and 0.70), Southeast Asian (AUC, 0.65), and East Asian (AUC, 0.73) ancestry. Pediatric participants with the top 5% PRS had 2.80 to 5.82 increased odds of asthma compared to the bottom 5% across the training, validation 1, and validation 2 cohorts when adjusted for ancestry. Phenome-wide association study analysis confirmed the strong association of the identified PRS with asthma (odds ratio, 2.71, PFDR = 3.71 × 10-65) and related phenotypes.

CONCLUSIONS

A multiancestral PRS for asthma based on Bayesian posterior genomic effect sizes identifies increased odds of pediatric asthma.

Genome-Wide Integration of Genetic and Genomic Studies of Atopic Dermatitis: Insights into Genetic Architecture and Pathogenesis

Atopic dermatitis (AD) is a common heterogeneous, chronic, itching, and inflammatory skin disease. Genetic studies have identified multiple AD susceptibility genes. However, the genetic architecture of AD has not been elucidated. In this study, we conducted a large-scale meta-analysis of AD (35,647 cases and 1,013,885 controls) to characterize the genetic basis of AD. The heritability of AD in different datasets varied from 0.6 to 7.1%. We identified 31 previously unreported genes by integrating multiomics data. Among the 31 genes, MCL1 was identified as a potential treatment target for AD by mediating gene‒drug interactions. Tissue enrichment analyses and phenome-wide association study provided strong support for the role of the hemic and immune systems in AD. Across 1,207 complex traits and diseases, genetic correlations indicated that AD shared links with multiple respiratory phenotypes. The phenome-wide Mendelian randomization analysis (Mendelian randomization‒phenome-wide association study) revealed that the age of onset of diabetes exhibited a positive causal effect on AD (inverse-variance weighted β = 0.39, SEM = 0.09, P = 2.77 × 10^-5). Overall, these results provide important insights into the genetic architecture of AD and will lead to a more thorough and complete understanding of the molecular mechanisms underlying AD.

The priming effect of diesel exhaust on native pollen exposure at the air-liquid interface

Pollen related allergic diseases have been increasing for decades. The reasons for this increase are unknown, but environmental pollution like diesel exhaust seem to play a role. While previous studies explored the effects of pollen extracts, we studied here for the first time priming effects of diesel exhaust on native pollen exposure using a novel experimental setup.

METHODS

Human bronchial epithelial BEAS-2B cells were exposed to native birch pollen (real life intact pollen, not pollen extracts) at the air-liquid interface (pollen-ALI). BEAS-2B cells were also pre-exposed in a diesel-ALI to diesel CAST for 2 h (a model for diesel exhaust) and then to pollen in the pollen-ALI 24 h later. Effects were analysed by genome wide transcriptome analysis after 2 h 25 min, 6 h 50 min and 24 h. Selected genes were confirmed by qRT-PCR.

RESULTS

Bronchial epithelial cells exposed to native pollen showed the highest transcriptomic changes after about 24 h. About 3157 genes were significantly up- or down-regulated for all time points combined. After pre-exposure to diesel exhaust the maximum reaction to pollen had shifted to about 2.5 h after exposure, plus the reaction to pollen was desensitised as only 560 genes were differentially regulated. Only 97 genes were affected synergistically. Of these, enrichment analysis showed that genes involved in immune and inflammatory response were involved.

CONCLUSION

Diesel exhaust seems to prime cells to react more rapidly to native pollen exposure, especially inflammation related genes, a factor known to facilitate the development of allergic sensitization. The marker genes here detected could guide studies in humans when investigating whether modern and outdoor diesel exhaust exposure is still detrimental for the development of allergic disease.

Atopy as Immune Dysregulation: Offender Genes and Targets

Allergic diseases are a heterogeneous group of disorders resulting from exaggerated type 2 inflammation. Although typically viewed as polygenic multifactorial disorders caused by the interaction of several genes with the environment, we have come to appreciate that allergic diseases can also be caused by monogenic variants affecting the immune system and the skin epithelial barrier. Through a myriad of genetic association studies and high-throughput sequencing tools, many monogenic and polygenic culprits of allergic diseases have been described. Identifying the genetic causes of atopy has shaped our understanding of how these conditions occur and how they may be treated and even prevented. Precision diagnostic tools and therapies that address the specific molecular pathways implicated in allergic inflammation provide exciting opportunities to improve our care for patients across the field of allergy and immunology. Here, we highlight offender genes implicated in polygenic and monogenic allergic diseases and list targeted therapeutic approaches that address these disrupted pathways.

DNA methylation signatures in airway cells from adult children of asthmatic mothers reflect subtypes of severe asthma

Maternal asthma is one of the most replicated risk factors for childhood-onset asthma. However, the underlying mechanisms are unknown. We identified DNA methylation signatures in bronchial epithelial cells from adults with asthma that were specific to those with a mother with asthma. These maternal asthma-associated methylation signatures were correlated with distinct gene regulatory pathways and clinical features. Genes in 16 pathways discriminated cases with and without maternal asthma and suggested impaired T cell signaling and responses to viral and bacterial pathogens in asthmatic children of an asthmatic mother. Our findings suggest that the prenatal environment in pregnancies of mothers with asthma alters epigenetically mediated developmental programs that may lead to severe asthma in their children through diverse gene regulatory pathways.

Maternal asthma (MA) is among the most consistent risk factors for asthma in children. Possible mechanisms for this observation are epigenetic modifications in utero that have lasting effects on developmental programs in children of mothers with asthma. To test this hypothesis, we performed differential DNA methylation analyses of 398,186 individual CpG sites in primary bronchial epithelial cells (BECs) from 42 nonasthma controls and 88 asthma cases, including 56 without MA (NMA) and 32 with MA. We used weighted gene coexpression network analysis (WGCNA) of 69 and 554 differentially methylated CpGs (DMCs) that were specific to NMA and MA cases, respectively, compared with controls. WGCNA grouped 66 NMA-DMCs and 203 MA-DMCs into two and five comethylation modules, respectively. The eigenvector of one MA-associated module (turquoise) was uniquely correlated with 85 genes expressed in BECs and enriched for 36 pathways, 16 of which discriminated between NMA and MA using machine learning. Genes in all 16 pathways were decreased in MA compared with NMA cases (P = 7.1 × 10⁻³), a finding that replicated in nasal epithelial cells from an independent cohort (P = 0.02). Functional interpretation of these pathways suggested impaired T cell signaling and responses to viral and bacterial pathogens. The MA-associated turquoise module eigenvector was additionally correlated with clinical features of severe asthma and reflective of type 2 (T2)-low asthma (i.e., low total serum immunoglobulin E, fractional exhaled nitric oxide, and eosinophilia). Overall, these data suggest that MA alters diverse epigenetically mediated pathways that lead to distinct subtypes of severe asthma in adults, including hard-to-treat T2-low asthma.

Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region

BACKGROUND

Genome-wide association studies of asthma have revealed robust associations with variation across the human leukocyte antigen (HLA) complex with independent associations in the HLA class I and class II regions for both childhood-onset asthma (COA) and adult-onset asthma (AOA). However, the specific variants and genes contributing to risk are unknown.

METHODS

We used Bayesian approaches to perform genetic fine-mapping for COA and AOA (n=9432 and 21,556, respectively; n=318,167 shared controls) in White British individuals from the UK Biobank and to perform expression quantitative trait locus (eQTL) fine-mapping in immune (lymphoblastoid cell lines, n=398; peripheral blood mononuclear cells, n=132) and airway (nasal epithelial cells, n=188) cells from ethnically diverse individuals. We also examined putatively causal protein coding variation from protein crystal structures and conducted replication studies in independent multi-ethnic cohorts from the UK Biobank (COA n=1686; AOA n=3666; controls n=56,063).

RESULTS

Genetic fine-mapping revealed both shared and distinct causal variation between COA and AOA in the class I region but only distinct causal variation in the class II region. Both gene expression levels and amino acid variation contributed to risk. Our results from eQTL fine-mapping and amino acid visualization suggested that the HLA-DQA1*03:01 allele and variation associated with expression of the nonclassical HLA-DQA2 and HLA-DQB2 genes accounted entirely for the most significant association with AOA in GWAS. Our studies also suggested a potentially prominent role for HLA-C protein coding variation in the class I region in COA. We replicated putatively causal variant associations in a multi-ethnic cohort.

CONCLUSIONS

We highlight roles for both gene expression and protein coding variation in asthma risk and identified putatively causal variation and genes in the HLA region. A convergence of genomic, transcriptional, and protein coding evidence implicates the HLA-DQA2 and HLA-DQB2 genes and HLA-DQA1*03:01 allele in AOA.

Gene-environment interactions in childhood asthma revisited; expanding the interaction concept

Investigation of gene-environment interactions (GxE) may provide important insights into the gene regulatory framework in response to environmental factors of relevance for childhood asthma. Over the years, different methodological strategies have been applied, more recently using genome-wide approaches. The best example to date is the major asthma locus on the 17q12-21 chromosome region, viral infections, and airway epithelium processes where recent studies have shed much light on mechanisms in childhood asthma. However, there are challenges with the traditional single variant-single exposure interaction models, as they do not encompass the complexity and cumulative effects of multiple exposures or multiple genetic variants. As such, we need to redefine our traditional GxE thinking, and we propose in this review to expand the GxE concept by also evaluating other omics layers, such as epigenetics, transcriptomics, metabolomics, and proteomics. In addition, host factors such as age, gender, and other exposures are very likely to influence GxE effects and need firmly to be considered in future studies.

Association Between Atopic Dermatitis, Asthma, and Serum Lipids: A UK Biobank Based Observational Study and Mendelian Randomization Analysis

Background

Both atopic diseases and dysregulation of serum lipids (SLs) add to significant health burden, but evidences about their association are inconsistent.

Objective

This work is to evaluate the association between asthma/atopic dermatitis (AD) and SLs and investigate the potential causal relationship.

Methods

A large-scale cross-sectional study based on the UK Biobank (UKB) and then examined the casual relationships between SLs with asthma/AD based on a Mendelian randomization (MR) analysis.

Results

A total of 502,505 participants were included in analysis. After full adjustment, AD was associated with lower TG (β = −0.006; 95%CI, −0.010 to −0.002; P = 0.006), lower LDL (β = −0.004; 95%CI, −0.006 to −0.002, P < 0.001), and lower TC (β = −0.004; 95%CI, −0.005 to −0.002; P < 0.001) but insignificantly correlated to HDL (P = 0.794). Asthma was also inversely correlated to TG (β = −0.005; 95%CI, = −0.007 to −0.003; < 0.001), LDL (β = −0.003; 95%CI, −0.004 to −0.002; P < 0.001), and TC (β = −0.002; 95%CI, −0.003 to −0.002; P < 0.001), but was positively correlated to HDL (β = 0.004; 95%CI, 0.003 to 0.005; P < 0.001), respectively. In subsequent MR analysis, both allergic diseases and asthma showed a protective effect on TC. Allergic diseases, asthma, and AD all showed a negative effect on LDL.

Conclusion

Collectively, we identify a protective causal effect of allergic diseases on serum lipids, as well as a potentially positive association of HDL with asthma. Owing to the largest sample size and the application of IVs in causal inference, this study will provide a robust evidence for the management of asthma and AD and the prevention of dyslipidemia.

Association of IL33, IL1RL1, IL1RAP Polymorphisms and Asthma in Chinese Han Children

Background: Genome-wide association studies have identified interleukin 33 (IL33), interleukin 1 receptor-like 1 (IL1RL1), interleukin 1 receptor accessory protein (IL1RAP) as asthma susceptibility loci in Europeans. IL33, IL1RL1, and IL1RAP constitute a ligand-receptor complex.

Objective: We analyzed associations of asthma susceptibility, eosinophilic airway inflammation, and response to inhaled corticosteroid (ICS) with single nucleotide polymorphisms (SNPs) of 3 genes encoding IL33, IL1RL1, and its coreceptor IL1RAP in Chinese Han nationality children.

Methods: A total of 153 non-asthmatic children and 265 asthmatic children who visited the Xiangya Hospital between September 2015 and August 2019 were recruited for this study. Pulmonary function tests, peripheral blood eosinophil counts (PBEC), and fractional exhaled nitric oxide (FeNO) tests were performed before treatment, and 3 months after treatment. Each participant’s DNA was extracted from the peripheral blood, and a Mass ARRAY system was used to genotype the SNPs.

Results: The T allele of rs4742170 in IL33 was associated with a risk of higher FeNO at baseline, and no improvement in FeNO and airway hyperresponsiveness was found after ICS treatment. The A allele of rs10208293 and C allele of rs13424006 in IL1RL1 both were associated with lower susceptibility to asthma and lower FeNO. The TT genotype of rs1420101 and AA genotype of rs4142132 in IL1RL1 were associated with a greater probability of improvement in PBEC after ICS treatment.

Conclusion: IL33-IL1RL1-IL1RAP complex polymorphisms are associated with childhood asthma susceptibility, eosinophilic airway inflammation, and ICS response in Chinese Han children in Hunan. We speculate that IL33-IL1RL1-IL1RAP complex polymorphisms affect the development of asthma, airway inflammation, and subsequent ICS response in childhood.

Genome-wide association study identifies TNFSF15 associated with childhood asthma

BACKGROUND

Genome-wide association studies (GWASs) of asthma have identified several risk alleles and loci, but most have been conducted in individuals with European-ancestry. Studies in Asians, especially children, are still lacking. We aimed to identify susceptibility loci by performing the first GWAS of asthma in Korean children with persistent asthma.

METHODS

We used a discovery set of 741 children with persistent asthma as cases and 589 healthy children and 551 healthy adults as controls to perform a GWAS. We validated our GWAS findings using UK Biobank data. We then used the Genotype-Tissue Expression database to identify expression quantitative trait loci of candidate variants. Finally, we quantified proteins of genes associated with asthma.

RESULTS

Variants at the 17q12-21 locus and SNPs in CYBRD1 and TNFSF15 genes were associated with persistent childhood asthma at genome-wide thresholds of significance. Four SNPs in the TNFSF15 gene were also associated with childhood-onset asthma in British white participants in the UK Biobank data. The asthma-associated rs7856856-C allele, the lead SNP, was associated with decreased TNFSF15 expression in whole blood and in arteries. Korean children with asthma had lower serum TNFSF15 levels than controls, and those with the asthma risk rs7856856-CC genotype exhibited the lowest serum TNFSF15 levels overall, especially asthmatic children.

CONCLUSIONS

Our GWAS of persistent childhood asthma with allergic sensitization identified a new susceptibility gene, TNFSF15, and replicated associations at the 17q12-21 childhood-onset asthma locus. This novel association may be mediated by reduced expression of serum TNFSF15 and loss of suppression of angiogenesis.

Targeted analysis of genomic regions enriched in African ancestry reveals novel classical HLA alleles associated with asthma in Southwestern Europeans

Despite asthma has a considerable genetic component, an important proportion of genetic risks remain unknown, especially for non-European populations. Canary Islanders have the largest African genetic ancestry observed among Southwestern Europeans and the highest asthma prevalence in Spain. Here we examined broad chromosomal regions previously associated with an excess of African genetic ancestry in Canary Islanders, with the aim of identifying novel risk variants associated with asthma susceptibility. In a two-stage cases-control study, we revealed a variant within HLA-DQB1 significantly associated with asthma risk (rs1049213, meta-analysis p = 1.30 × 10^–7, OR [95% CI] = 1.74 [1.41–2.13]) previously associated with asthma and broad allergic phenotype. Subsequent fine-mapping analyses of classical HLA alleles revealed a novel allele significantly associated with asthma protection (HLA-DQA1*01:02, meta-analysis p = 3.98 × 10^–4, OR [95% CI] = 0.64 [0.50–0.82]) that had been linked to infectious and autoimmune diseases, and peanut allergy. HLA haplotype analyses revealed a novel haplotype DQA1*01:02-DQB1*06:04 conferring asthma protection (meta-analysis p = 4.71 × 10^–4, OR [95% CI] = 0.47 [0.29– 0.73]).

Genome-wide association study of asthma, total IgE, and lung function in a cohort of Peruvian children

BACKGROUND

Genetic ancestry plays a role in asthma health disparities.

OBJECTIVE

Our aim was to evaluate the impact of ancestry on and identify genetic variants associated with asthma, total serum IgE level, and lung function.

METHODS

A total of 436 Peruvian children (aged 9-19 years) with asthma and 291 without asthma were genotyped by using the Illumina Multi-Ethnic Global Array. Genome-wide proportions of indigenous ancestry populations from continental America (NAT) and European ancestry from the Iberian populations in Spain (IBS) were estimated by using ADMIXTURE. We assessed the relationship between ancestry and the phenotypes and performed a genome-wide association study.

RESULTS

The mean ancestry proportions were 84.7% NAT (case patients, 84.2%; controls, 85.4%) and 15.3% IBS (15.8%; 14.6%). With adjustment for asthma, NAT was associated with higher total serum IgE levels (P < .001) and IBS was associated with lower total serum IgE levels (P < .001). NAT was associated with higher FEV1 percent predicted values (P < .001), whereas IBS was associated with lower FEV1 values in the controls but not in the case patients. The HLA-DR/DQ region on chromosome 6 (Chr6) was strongly associated with total serum IgE (rs3135348; P = 3.438 × 10-10) and was independent of an association with the haplotype HLA-DQA1∼HLA-DQB1:04.01∼04.02 (P = 1.55 × 10-05). For lung function, we identified a locus (rs4410198; P = 5.536 × 10-11) mapping to Chr19, near a cluster of zinc finger interacting genes that colocalizes to the long noncoding RNA CTD-2537I9.5. This novel locus was replicated in an independent sample of pediatric case patients with asthma with similar admixture from Brazil (P = .005).

CONCLUSION

This study confirms the role of HLA in atopy, and identifies a novel locus mapping to a long noncoding RNA for lung function that may be specific to children with NAT.

Influential Usage of Big Data and Artificial Intelligence in Healthcare

Artificial intelligence (AI) is making computer systems capable of executing human brain tasks in many fields in all aspects of daily life. The enhancement in information and communications technology (ICT) has indisputably improved the quality of people's lives around the globe. Especially, ICT has led to a very needy and tremendous improvement in the health sector which is commonly known as electronic health (eHealth) and medical health (mHealth). Deep machine learning and AI approaches are commonly presented in many applications using big data, which consists of all relevant data about the medical health and diseases which a model can access at the time of execution or diagnosis of diseases. For example, cardiovascular imaging has now accurate imaging combined with big data from the eHealth record and pathology to better characterize the disease and personalized therapy. In clinical work and imaging, cancer care is getting improved by knowing the tumor biology and helping in the implementation of precision medicine. The Markov model is used to extract new approaches for leveraging cancer. In this paper, we have reviewed existing research relevant to eHealth and mHealth where various models are discussed which uses big data for the diagnosis and healthcare system. This paper summarizes the recent promising applications of AI and big data in medical health and electronic health, which have potentially added value to diagnosis and patient care.

Associations between specific IgE sensitization to 26 respiratory allergen molecules and HLA class II alleles in the EGEA cohort

BACKGROUND

Allergy, the most frequent immune disorder affecting 30% of the world's population, is the consequence of immunoglobin E (IgE) sensitization to allergens. Among the genetic factors suspected to be involved in allergy, the HLA class-II genomic region is a strong candidate.

OBJECTIVE

To assess the association between HLA class-II alleles and specific IgE (sIgE) sensitization to a large number of respiratory allergen molecules.

METHODS

The analysis relied on 927 participants of the EGEA cohort, including 497 asthmatics. The study focuses on 26 aeroallergens recognized by sIgE in at least 5% of the study population (determined with the MEDALL chip with sIgE ≥ 0.3 ISU) and 23 imputed HLA class-II alleles. For each sIgE sensitization and HLA class-II allele, we fitted a logistic regression model accounting for familial dependence and adjusted for gender, age, and genetic principal components. p-values were corrected for multiple comparisons (False Discovery Rate).

RESULTS

Most of the 19 statistically significant associations observed regard pollen allergens (mugwort Art v 1, olive tree Ole e 1, timothy grass Phl p 2, Phl p 5 and plantain Pla l 1), three were mold allergen (Alternaria Alt a 1), and a single one regards house dust mite allergen (Der p 7). No association was observed with pet allergens. The strongest associations were found with mugwort Art v 1 (OR = 5.42 (95%CI, 3.30; 8.88), 4.14 (2.65; 6.47), 3.16 (1.88; 5.31) with DQB1*05:01, DQA1*01:01 and DRB1*01:01, respectively).

CONCLUSION

Our results support the important role of HLA class-II alleles as immune response genes predisposing their carriers for sensitization to various major pollen allergens.

Identification of OCA2 as a novel locus for the co-morbidity of asthma-plus-eczema

BACKGROUND

Numerous genes have been associated with the three most common allergic diseases (asthma, allergic rhinitis or eczema) but these genes explain only a part of the heritability. In the vast majority of genetic studies, complex phenotypes such as co-morbidity of two of these diseases, have not been considered. This may partly explain missing heritability.

OBJECTIVE

To identify genetic variants specifically associated with the co-morbidity of asthma-plus-eczema.

METHODS

We first conducted a meta-analysis of four GWAS (Genome-Wide Association Study) of the combined asthma-plus-eczema phenotype (total of 8807 European-ancestry subjects of whom 1208 subjects had both asthma and eczema). To assess whether the association with SNP(s) was specific to the co-morbidity, we also conducted a meta-analysis of homogeneity test of association according to disease status ("asthma-plus-eczema" vs. the presence of only one disease "asthma only or eczema only"). We then used a joint test by combining the two test statistics from the co-morbidity-SNP association and the phenotypic heterogeneity of SNP effect meta-analyses.

RESULTS

Seven SNPs were detected for specific association to the asthma-plus-eczema co-morbidity, two with significant and five with suggestive evidence using the joint test after correction for multiple testing. The two significant SNPs are located in the OCA2 gene (Oculocutaneous Albinism II), a new locus never detected for significant evidence of association with any allergic disease. This gene is a promising candidate gene, because of its link to skin and lung diseases, and to epithelial barrier and immune mechanisms.

CONCLUSION

Our study underlines the importance of studying sub-phenotypes as co-morbidities to detect new susceptibility genes.

Genetics of Asthma and Allergic Diseases

Asthma genes have been identified through a range of approaches, from candidate gene association studies and family-based genome-wide linkage analyses to genome-wide association studies (GWAS). The first GWAS of asthma, reported in 2007, identified multiple markers on chromosome 17q21 as associates of the childhood-onset asthma. This remains the best replicated asthma locus to date. However, notwithstanding undeniable successes, genetic studies have produced relatively heterogeneous results with limited replication, and despite considerable promise, genetics of asthma and allergy has, so far, had limited impact on patient care, our understanding of disease mechanisms, and development of novel therapeutic targets. The paucity of precise replication in genetic studies of asthma is partly explained by the existence of numerous gene-environment interactions. Another important issue which is often overlooked is that of time of the assessment of the primary outcome(s) and the relevant environmental exposures. Most large GWASs use the broadest possible definition of asthma to increase the sample size, but the unwanted consequence of this is increased phenotypic heterogeneity, which dilutes effect sizes. One way of addressing this is to precisely define disease subtypes (e.g. by applying novel mathematical approaches to rich phenotypic data) and use these latent subtypes in genetic studies.

The Association Between Asthma and Risk of Myasthenia Gravis: A Systematic Review and Meta-analysis

PURPOSE

This study aimed to investigate the association between asthma and risk of myasthenia gravis (MG) using the method of systematic review and meta-analysis.

METHODS

Potentially eligible studies were identified from Medline and EMBASE databases from inception to July 2020 using search strategy that comprised terms for "Asthma" and "Myasthenia Gravis". Eligible cohort study must consist of one cohort of individuals with asthma and another cohort of individuals without asthma. Then, the study must report relative risk (RR) with 95% confidence intervals (95% CIs) of incident MG between the groups. Eligible case-control studies must include cases with MG and controls without MG. Then, the study must explore their history of asthma. Odds ratio (OR) with 95% CIs of the association between asthma status and MG must be reported. Point estimates with standard errors were retrieved from each study and were combined together using the generic inverse variance method.

RESULTS

A total of 6,835 articles were identified. After two rounds of independent review by five investigators, two cohort studies and three case-control studies met the eligibility criteria and were included into the meta-analysis. Pooled analysis showed that asthma was significantly associated with risk of MG with the pooled risk ratio of 1.38 (95% CI 1.02-1.86). Funnel plot was symmetric, which was not suggestive of publication bias.

CONCLUSION

The current study found a significant association between asthma and increased risk of MG.

The intersect of genetics, environment, and microbiota in asthma-perspectives and challenges

In asthma, a significant portion of the interaction between genetics and environment occurs through microbiota. The proposed mechanisms behind this interaction are complex and at times contradictory. This review covers recent developments in our understanding of this interaction: the "microbial hypothesis" and the "farm effect"; the role of endotoxin and genetic variation in pattern recognition systems; the interaction with allergen exposure; the additional involvement of host gut and airway microbiota; the role of viral respiratory infections in interaction with the 17q21 and CDHR3 genetic loci; and the importance of in utero and early-life timing of exposures. We propose a unified framework for understanding how all these phenomena interact to drive asthma pathogenesis. Finally, we point out some future challenges for continued research in this field, in particular the need for multiomic integration, as well as the potential utility of asthma endotyping.

Genetics and Epigenetics in Asthma

Asthma is one of the most common respiratory disease that affects both children and adults worldwide, with diverse phenotypes and underlying pathogenetic mechanisms poorly understood. As technology in genome sequencing progressed, scientific efforts were made to explain and predict asthma’s complexity and heterogeneity, and genome-wide association studies (GWAS) quickly became the preferred study method. Several gene markers and loci associated with asthma susceptibility, atopic and childhood-onset asthma were identified during the last few decades. Markers near the ORMDL3/GSDMB genes were associated with childhood-onset asthma, interleukin (IL)33 and IL1RL1 SNPs were associated with atopic asthma, and the Thymic Stromal Lymphopoietin (TSLP) gene was identified as protective against the risk to TH2-asthma. The latest efforts and advances in identifying and decoding asthma susceptibility are focused on epigenetics, heritable characteristics that affect gene expression without altering DNA sequence, with DNA methylation being the most described mechanism. Other less studied epigenetic mechanisms include histone modifications and alterations of miR expression. Recent findings suggest that the DNA methylation pattern is tissue and cell-specific. Several studies attempt to describe DNA methylation of different types of cells and tissues of asthmatic patients that regulate airway remodeling, phagocytosis, and other lung functions in asthma. In this review, we attempt to briefly present the latest advancements in the field of genetics and mainly epigenetics concerning asthma susceptibility.

Sex-specific differences in peripheral blood leukocyte transcriptional response to LPS are enriched for HLA region and X chromosome genes

Sex-specific differences in prevalence are well documented for many common, complex diseases, especially for immune-mediated diseases, yet the precise mechanisms through which factors associated with biological sex exert their effects throughout life are not well understood. We interrogated sex-specific transcriptional responses of peripheral blood leukocytes (PBLs) to innate immune stimulation by lipopolysaccharide (LPS) in 46 male and 66 female members of the Hutterite community, who practice a communal lifestyle. We identified 1217 autosomal and 54 X-linked genes with sex-specific responses to LPS, as well as 71 autosomal and one X-linked sex-specific expression quantitative trait loci (eQTLs). Despite a similar proportion of the 15 HLA genes responding to LPS compared to all expressed autosomal genes, there was a significant over-representation of genes with sex by treatment interactions among HLA genes. We also observed an enrichment of sex-specific differentially expressed genes in response to LPS for X-linked genes compared to autosomal genes, suggesting that HLA and X-linked genes may disproportionately contribute to sex disparities in risk for immune-mediated diseases.

The efficacy of Tuina for asthma: A protocol for a systematic review and meta-analysis

BACKGROUND

Asthma is one of the most common chronic diseases in the world, with ∼100 million asthma patients worldwide. China has become one of the countries with the highest asthma death rate in the world. Asthma is a chronic airway inflammatory disease. Patients with this disease may have symptoms such as cough, wheezing, and difficulty breathing. For many years, Western medicine has mainly used anti-inflammatory, anti-bronchial spasm, asthma, cough, and oxygen to treat this disease, but the effect is not good. Tuina is a common treatment for asthma in China. But at present, there is no systematic evaluation report on its therapeutic effectiveness and safety. This protocol aims to reveal the efficacy and safety of Tuina for treating asthma.

METHODS

The following databases will be searched by electronic methods: PubMed, EBASE, WHO International Clinical Trials Registry Platform, Embase, the Chinese Biomedical Literature Database (CBM), Wan-fang Data (WANFANG), the China National Knowledge Infrastructure (CNKI), and other sources from inception to November 2020. Bias risk, subgroup analysis, data synthesis, and meta-analyses will be assessed with RevMan V.5.3 software if the data is met inclusion conditions.

RESULTS

This study will present a quality evidence of Tuina for the treatment of astma patients.

CONCLUSION

The systematic review will present reliable evidence to judge whether or not Tuina is a safe and effective intervention for asthma patients. International Platform of Registered Systematic Review and Meta-Analysis Protocols (INPLASY) registration number: INPLASY2020110100.

Adult-onset eosinophilic airway diseases

Eosinophilic airway inflammation is one of the cardinal features of allergic airway diseases such as atopic asthma and allergic rhinitis. These childhood-onset conditions are mediated by allergen and allergen-specific IgE and often accompanied by other allergic diseases including food allergy and eczema. They can develop consecutively in the same patient, which is referred to as an allergic march. In contrast, some phenotypes of asthma, nonsteroidal anti-inflammatory drugs-exacerbated airway disease (N-ERD), chronic rhinosinusitis with nasal polyps (CRSwNP)/eosinophilic CRS and allergic bronchopulmonary aspergillosis/mycosis (ABPA/ABPM) are adult-onset airway diseases, which are characterized by prominent peripheral blood eosinophilia. Most of these conditions, except for ABPA/ABPM, are nonatopic, and the coexistence of multiple diseases, including an adult-onset eosinophilic systemic disease, eosinophilic granulomatosis with polyangiitis (EGPA), is common. In this review, we focus on eosinophil biology, genetics and clinical characteristics and the pathophysiology of adult-onset eosinophilic asthma, N-ERD, CRSwNP/eosinophilic CRS, ABPA/ABPM and EGPA, while exploring the common genetic, immunological and pathological conditions among these adult-onset eosinophilic diseases.

Genomics of asthma, allergy and chronic rhinosinusitis: novel concepts and relevance in airway mucosa

Genome wide association studies (GWASs) have revealed several airway disease-associated risk loci. Their role in the onset of asthma, allergic rhinitis (AR) or chronic rhinosinusitis (CRS), however, is not yet fully understood. The aim of this review is to evaluate the airway relevance of loci and genes identified in GWAS studies. GWASs were searched from databases, and a list of loci associating significantly (p < 10-8) with asthma, AR and CRS was created. This yielded a total of 267 significantly asthma/AR-associated loci from 31 GWASs. No significant CRS -associated loci were found in this search. A total of 170 protein coding genes were connected to these loci. Of these, 76/170 (44%) showed bronchial epithelial protein expression in stained microscopic figures of Human Protein Atlas (HPA), and 61/170 (36%) had a literature report of having airway epithelial function. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses were performed, and 19 functional protein categories were found as significantly (p < 0.05) enriched among these genes. These were related to cytokine production, cell activation and adaptive immune response, and all were strongly connected in network analysis. We also identified 15 protein pathways that were significantly (p < 0.05) enriched in these genes, related to T-helper cell differentiation, virus infection, JAK-STAT signaling pathway, and asthma. A third of GWAS-level risk loci genes of asthma or AR seemed to have airway epithelial functions according to our database and literature searches. In addition, many of the risk loci genes were immunity related. Some risk loci genes also related to metabolism, neuro-musculoskeletal or other functions. Functions overlapped and formed a strong network in our pathway analyses and are worth future studies of biomarker and therapeutics.

Immune-microbiota interaction in Finnish and Russian Karelia young people with high and low allergy prevalence

Background

After the Second World War, the population living in the Karelian region was strictly divided by the “iron curtain” between Finland and Russia. This resulted in different lifestyle, standard of living, and exposure to the environment. Allergic manifestations and sensitization to common allergens have been much more common on the Finnish compared to the Russian side.

Objective

The remarkable allergy disparity in the Finnish and Russian Karelia calls for immunological explanations.

Methods

Young people, aged 15‐20 years, in the Finnish (n = 69) and Russian (n = 75) Karelia were studied. The impact of genetic variation on the phenotype was studied by a genome‐wide association analysis. Differences in gene expression (transcriptome) were explored from the blood mononuclear cells (PBMC) and related to skin and nasal epithelium microbiota and sensitization.

Results

The genotype differences between the Finnish and Russian populations did not explain the allergy gap. The network of gene expression and skin and nasal microbiota was richer and more diverse in the Russian subjects. When the function of 261 differentially expressed genes was explored, innate immunity pathways were suppressed among Russians compared to Finns. Differences in the gene expression paralleled the microbiota disparity. High Acinetobacter abundance in Russians correlated with suppression of innate immune response. High‐total IgE was associated with enhanced anti‐viral response in the Finnish but not in the Russian subjects.

Conclusions and clinical relevance

Young populations living in the Finnish and Russian Karelia show marked differences in genome‐wide gene expression and host contrasting skin and nasal epithelium microbiota. The rich gene‐microbe network in Russians seems to result in a better‐balanced innate immunity and associates with low allergy prevalence.

Atopic phenotypes and their implication in the atopic march

INTRODUCTION

Eczema, allergic rhinitis, and asthma are traditionally considered atopic (or allergic) diseases. They are complex, multifactorial, and are caused by a variety of different mechanisms, which result in multiple heterogeneous clinical phenotypes. Atopic march is usually interpreted as the sequential development of symptoms from eczema in infancy, to asthma, and then allergic rhinitis. Areas covered: The authors reviewed the evidence on the multimorbidity of eczema, asthma, and rhinitis, and the implication of results of data-driven analyses on the concept framework of atopic march. A literature search was conducted in the PubMed and Web of Science for peer-reviewed articles published until July 2020. Application of Bayesian machine learning framework to rich phenotypic data from birth cohorts demonstrated that the postulated linear progression of symptoms (atopic march) does not capture the heterogeneity of allergic phenotypes. Expert opinion: Eczema, wheeze, and rhinitis co-exist more often than would be expected by chance, but their relationship can be best understood in a multimorbidity framework, rather than through atopic march sequence. The observation of their co-occurrence does not imply any specific relationship between them, and certainly not a progressive or causal one. It is unlikely that a sngle mechanism such as allergic sensitization underpins different multimorbidity manifestations.