17q12-21 and asthma: interactions with early-life environmental exposures

IKZF3 polymorphisms contribute to the increased risk of acute lymphoblastic leukemia in children

BACKGROUND

Acute lymphoblastic leukemia (ALL) is the most common cancer in children. IKZF3 (IKAROS family zinc finger 3) is a hematopoietic-specific transcription factor, and it has been validated that it is involved in leukemia. However, the role of IKZF3 single-nucleotide polymorphisms (SNPs) remains unclear. In this case-control study, the authors investigated the association of IKZF3 SNPs with ALL in children.

METHODS

Six IKZF3 reference SNPs (rs9635726, rs2060941, rs907092, rs12946510, rs1453559, and rs62066988) were genotyped in 692 patients who had ALL (cases) and in 926 controls. The associations between IKZF3 polymorphisms and ALL risk were determined using odds ratios (ORs) and 95% confidence intervals (CIs). The associations of rs9635726 and rs2060941 with the risk of ALL were further estimated by using false-positive report probability (FPRP) analysis. Functional analysis in silico was performed to evaluate the probability that rs9635726 and rs2060941 might influence the regulation of IKZF3.

RESULTS

The authors observed that rs9635726C>T (adjusted OR, 1.49; 95% CI, 1.06-2.11; p = .023) and rs2060941G>T (adjusted OR, 1.51; 95% CI, 1.24-1.84; p = .001) were related to and increased risk of ALL in the recessive and dominant models, respectively. Furthermore, the associations of both rs9635726 (FPRP = .177) and rs2060941 (FPRP < .001) with ALL were noteworthy in the FPRP analysis. Functional analysis indicated that rs9635726 and rs2060941 might repress the transcription of IKZF3 by disrupting its binding to MLLT1, TAF1, POLR2A, and/or RAD21.

CONCLUSIONS

This study revealed that IKZF3 polymorphisms were associated with increased ALL susceptibility in children and might influence the expression of IKZF3 by disrupting its binding to MLLT1, TAF1, POLR2A, and/or RAD21. IKZF3 polymorphisms were suggested as a biomarker for childhood ALL.

Prevalence and Risk Factors of Childhood Asthma in Jazan Region, Saudi Arabia

Background

The prevalence of asthma among children has been on the rise worldwide, leading to significant morbidity and mortality. Our study was conducted to determine the prevalence of asthma and its related risk factors among school-age children in the Jazan Region, Saudi Arabia.

Materials and Method

The study was a cross-sectional prospective study that used Phase I ISAAC protocol and was conducted from March to June 2023. The sample size was calculated to be 1600 among school-age children in the Jazan Region Saudi Arabia. This study complies with the Declaration of Helsinki. Data was analyzed using SPSS version 23.0, Descriptive statistics were calculated for study variables, and appropriate tests of significance were performed to determine statistical significance.

Results

The total study population was 1368 the majority of them, 96.6% (n=1321), were Saudi nationals, and most of them lived in rural areas (70.6%, n=966). The prevalence of life-long wheezing, wheezing in the last 12 months, and exercise-induced wheezing was 28.0%, 29.2%, and 30.9%, respectively. Risk factors such as having indoor plants, having a pet, and a smoker in the household were reported by 48.0%, 24.6%, and 36.4% of participants, respectively. Living near an industrial area was determined as a risk factor in 98 (7.2%) of the children. Asthma-related symptoms were strongly correlated with all risk factors based on the chi-square test, and some risk factors based on multivariate linear regression.

Conclusion

The prevalence of asthma among children in the Jazan Region is higher than previously reported, and the reported risk factors are significantly correlated with symptoms of asthma.

Dog ownership in infancy is protective for persistent wheeze in 17q21 asthma-risk carriers

BACKGROUND

Asthma-associated single nucleotide polymorphisms from large genome-wide association studies only explain a fraction of genetic heritability. Likely causes of the missing heritability include broad phenotype definitions and gene-environment interactions (GxE). The mechanisms underlying GxE in asthma are poorly understood. Previous GxE studies on pet ownership showed discordant results.

OBJECTIVES

We sought to study the GxE between the 17q12-21 locus and pet ownership in infancy in relation to wheeze.

METHODS

Wheezing classes derived from 5 UK-based birth cohorts (latent class analysis) were used to study GxE between the 17q12-21 asthma-risk variant rs2305480 and dog and cat ownership in infancy, using multinomial logistic regression. A total of 9149 children had both pet ownership and genotype data available. Summary statistics from individual analyses were meta-analyzed.

RESULTS

rs2305480 G allele was associated with increased risk of persistent wheeze (additive model odds ratio, 1.37; 95% CI, 1.25-1.51). There was no evidence of an association between dog or cat ownership and wheeze. We found significant evidence of a GxE interaction between rs2305480 and dog ownership (P = 8.3 × 10-4) on persistent wheeze; among dog owners, the G allele was no longer associated with an increased risk of persistent wheeze (additive model odds ratio, 0.95; 95% CI, 0.73-1.24). For those without pets, G allele was associated with increased risk of persistent wheeze (odds ratio, 1.61; 95% CI, 1.40-1.86). Among cat owners, no such dampening of the genetic effect was observed.

CONCLUSIONS

Among dog owners, rs2305480 G was no longer associated with an increased risk of persistent wheeze (or asthma). Early-life environmental exposures may therefore attenuate likelihood of asthma in those carrying 17q12-21 risk alleles.

Environmental influences on childhood asthma: Allergens

Allergen exposure is associated with the development of allergen-specific sensitization, but their relationship is influenced by other contemporaneous exposures (such as microbial exposure) and the genetic predisposition of the host. Clinical outcomes of the primary prevention studies that tested the effectiveness of allergen avoidance in pregnancy and early life on the subsequent development of sensitization and asthma published to date are inconsistent. Therefore, we cannot provide any evidence-based advice on the use of allergen avoidance for the primary prevention of these conditions. The evidence about the impact of allergen exposure among and among sensitized children with asthma is more consistent, and the combination of sensitization and high exposure to sensitizing allergen increases airway inflammation, triggers symptoms, adversely impacts upon disease control, and is associated with poorer lung function in preschool age. However, there are differing opinions about the role of inhalant allergen avoidance in asthma management, and recommendations differ in different guidelines. Evidence from more recent high-quality trials suggests that mite allergen-impermeable bed encasings reduce hospital attendance with asthma attacks and that multifaceted targeted environmental control improves asthma control in children. We therefore suggest a pragmatic approach to allergen avoidance in the management of childhood asthma for clinical practice, including the recommendations to: (1) tailor the intervention to the patient's sensitization and exposure status by using titer of allergen-specific IgE antibodies and/or the size of the skin test as indicators of potential response; (2) use a multifaceted allergen control regime to reduce exposure as much as possible; and (3) start intervention as early as possible upon diagnosis.

Association between 17q21 variants and asthma predisposition in Pashtun population from Pakistan

OBJECTIVE

Asthma is a heterogeneous and genetically complex respiratory disease, and more than 300 million people are affected worldwide. In this study, frequencies of four SNPs (rs3816470, rs7216389, rs8067378, rs12603332) in chromosome 17q21 region were analyzed and their relationship with the asthma susceptibility, in the Pashtun population of Khyber Pakhtunkhwa province (KPK) of Pakistan were investigated.

METHODS

DNA samples from 500 subjects (asthma cases/controls) were genotyped by Sanger sequencing. Chi-square tests, logistic regression analysis, linkage disequilibrium, and haplotype analysis techniques were applied to study the association of the SNPs with asthma.

RESULTS

Genetic models, including recessive, dominant, co-dominant, over-dominant, and additive, were tested. The frequencies of alleles T/T at rs3816470 (OR = 1.91; 95%CI = 1.15-3.18; p = .011*) and rs7216389 (OR = 2.14; 95%CI = 1.21-3.79; p = .0076*), A/A at rs 8067378 (OR = 1.89; 95%CI = 1.17-3.06; p = .0081*), C/C at rs12603332 (OR = 1.97; 95%CI = 1.18-3.27; p = .008*), under recessive models, respectively, were significantly (p-values < .0125) associated with asthma susceptibility. The frequencies of T/T genotype in rs3816470 (OR = 6.01; 95%CI = 2.48-14.60; p = .000147*), and rs7216389 (OR = 5.05; 95%CI = 1.79-14.21; p = .003296*), and C/C at rs12603332 (OR = 2.64; 95%CI = 1.11-6.32; p = .019063*), were significantly (p-values < .0125) associated with asthma susceptibility in Pashtun women by stratified analysis based on age and gender. Similarly, three unique haplotypes were found associated with disease development and protective effect in female and male subjects. Linkage disequilibrium analysis presented a strong linkage (≥80%) between SNP variants and predicted their co-inheritance in the studied population.

CONCLUSION

The 17q21 variants (rs3816470, rs7216389, rs12603332) were found significantly (p-values < .0125) associated with asthma predisposition in the Pashtun population of KPK exclusively in the female asthmatic cases.

Supplemental data for this article can be accessed.

New Insights Relating Gasdermin B to the Onset of Childhood Asthma

Chromosome 17q12-q21 is the most replicated genetic locus for childhood-onset asthma. Polymorphisms in this locus containing ∼10 genes interact with a variety of environmental exposures in the home and outdoors to modify asthma risk. However, the functional basis for these associations and their linkages to the environment have remained enigmatic. Within this extended region, regulation of GSDMB (gasdermin B) expression in airway epithelial cells has emerged as the primary mechanism underlying the 17q12-q21 genome-wide association study signal. Asthma-associated SNPs influence the abundance of GSDMB transcripts as well as the functional properties of GSDMB protein in airway epithelial cells. GSDMB is a member of the gasdermin family of proteins, which regulate pyroptosis and inflammatory responses to microbial infections. The aims of this review are to synthesize recent studies on the relationship of 17q12-q21 SNPs to childhood asthma and the evidence pointing to GSDMB gene expression or protein function as the underlying mechanism and to explore the potential functions of GSDMB that may influence the risk of developing asthma during childhood.

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.

Joint variable selection and network modeling for detecting eQTLs

In this study, we conduct a comparison of three most recent statistical methods for joint variable selection and covariance estimation with application of detecting expression quantitative trait loci (eQTL) and gene network estimation, and introduce a new hierarchical Bayesian method to be included in the comparison. Unlike the traditional univariate regression approach in eQTL, all four methods correlate phenotypes and genotypes by multivariate regression models that incorporate the dependence information among phenotypes, and use Bayesian multiplicity adjustment to avoid multiple testing burdens raised by traditional multiple testing correction methods. We presented the performance of three methods (MSSL - Multivariate Spike and Slab Lasso, SSUR - Sparse Seemingly Unrelated Bayesian Regression, and OBFBF - Objective Bayes Fractional Bayes Factor), along with the proposed, JDAG (Joint estimation via a Gaussian Directed Acyclic Graph model) method through simulation experiments, and publicly available HapMap real data, taking asthma as an example. Compared with existing methods, JDAG identified networks with higher sensitivity and specificity under row-wise sparse settings. JDAG requires less execution in small-to-moderate dimensions, but is not currently applicable to high dimensional data. The eQTL analysis in asthma data showed a number of known gene regulations such as STARD3, IKZF3 and PGAP3, all reported in asthma studies. The code of the proposed method is freely available at GitHub (https://github.com/xuan-cao/Joint-estimation-for-eQTL).

Role of genomics in asthma exacerbations

PURPOSE OF REVIEW

Asthma exacerbations have been suggested to result from complex interactions between genetic and nongenetic components. In this review, we provide an overview of the genetic association studies of asthma exacerbations, their main results and limitations, as well as future directions of this field.

RECENT FINDINGS

Most studies on asthma exacerbations have been performed using a candidate-gene approach. Although few genome-wide association studies of asthma exacerbations have been conducted up to date, they have revealed promising associations but with small effect sizes. Additionally, the analysis of interactions between genetic and environmental factors has contributed to better understand of genotype-specific responses in asthma exacerbations.

SUMMARY

Genetic association studies have allowed identifying the 17q21 locus and the ADRB2 gene as the loci most consistently associated with asthma exacerbations. Future studies should explore the full spectrum of genetic variation and will require larger sample sizes, a better representation of racial/ethnic diversity and a more precise definition of asthma exacerbations. Additionally, the analysis of important environmental gene-environment analysis and the integration of multiple omics will allow understanding the genetic factors and biological processes underlying the risk for asthma exacerbations.

Early-life inhalant allergen exposure, filaggrin genotype, and the development of sensitization from infancy to adolescence

Background

We hypothesized that filaggrin (FLG) loss-of-function mutations modify the effect of allergen exposure on the development of allergic sensitization.

Objective

We sought to determine whether early-life exposure to inhalant allergens increases the risk of specific sensitization and whether FLG mutations modulate these odds.

Methods

In a population-based birth cohort we measured mite, cat, and dog allergen levels in dust samples collected from homes within the first year of life. Sensitization was assessed at 6 time points between infancy and age 16 years. Genotyping was performed for 6 FLG mutations.

Results

In the longitudinal multivariable model (age 1-16 years), we observed a significant interaction between FLG and Fel d 1 exposure on cat sensitization, with the effect of exposure being significantly greater among children with FLG mutations compared with those without (odds ratio, 1.36; 95% CI, 1.02-1.80; P = .035). The increase in risk of mite sensitization with increasing Der p 1 exposure was consistently greater among children with FLG mutations, but the interaction did not reach statistical significance. Different associations were observed for dogs: there was a significant interaction between FLG and dog ownership, but the risk of sensitization to any allergen was significantly lower among children with FLG mutations who were exposed to a dog in infancy (odds ratio, 0.16; 95% CI, 0.03-0.86; P = .03).

Conclusions

FLG loss-of-function mutations modify the relationship between allergen exposure and sensitization, but effects differ at different ages and between different allergens.

Asthma and obesity in the Middle East region: An overview

This paper aims to cover the current status of asthma and obesity in the Middle East, as well as to introduce the various studies tying the two diseases; further expanding on the proposed mechanisms. Finally, the paper covers recent literature related to sphingolipids and its role in asthma, followed by recommendations and future directions. In preparation of this paper, we searched PubMed and Google Scholar, with no restrictions, using the following terms; asthma, obesity, Middle East, sphingolipids. We also used the reference list of retrieved articles to further expand on the pool of articles that were used for this review.

Interactive effect between ATPase-related genes and early-life tobacco smoke exposure on bronchial hyper-responsiveness detected in asthma-ascertained families

BACKGROUND

A positional cloning study of bronchial hyper-responsiveness (BHR) at the 17p11 locus in the French Epidemiological study on the Genetics and Environment of Asthma (EGEA) families showed significant interaction between early-life environmental tobacco smoke (ETS) exposure and genetic variants located in DNAH9. This gene encodes the heavy chain subunit of axonemal dynein, which is involved with ATP in the motile cilia function.Our goal was to identify genetic variants at other genes interacting with ETS in BHR by investigating all genes belonging to the 'ATP-binding' and 'ATPase activity' pathways which include DNAH9, are targets of cigarette smoke and play a crucial role in the airway inflammation.

METHODS

Family-based interaction tests between ETS-exposed and unexposed BHR siblings were conducted in 388 EGEA families. Twenty single-nucleotide polymorphisms (SNP) showing interaction signals (p≤5.10^-3) were tested in the 253 Saguenay-Lac-Saint-Jean (SLSJ) families.

RESULTS

One of these SNPs was significantly replicated for interaction with ETS in SLSJ families (p=0.003). Another SNP reached the significance threshold after correction for multiple testing in the combined analysis of the two samples (p=10^-5). Results were confirmed using both a robust log-linear test and a gene-based interaction test.

CONCLUSION

The SNPs showing interaction with ETS belong to the ATP8A1 and ABCA1 genes, which play a role in the maintenance of asymmetry and homeostasis of lung membrane lipids.

A decade of research on the 17q12-21 asthma locus: Piecing together the puzzle

Chromosome 17q12–21 remains the most highly replicated and significant asthma locus. Genotypes in the core region defined by the first genome-wide association study correlate with expression of 2 genes, ORM1-like 3 (ORMDL3) and gasdermin B (GSDMB), making these prime candidate asthma genes, although recent studies have implicated gasdermin A (GSDMA) distal to and post-GPI attachment to proteins 3 (PGAP3) proximal to the core region as independent loci. We review 10 years of studies on the 17q12–21 locus and suggest that genotype-specific risks for asthma at the proximal and distal loci are not specific to early-onset asthma and mediated by PGAP3, ORMDL3, and/or GSDMA expression. We propose that the weak and inconsistent associations of 17q single nucleotide polymorphisms with asthma in African Americans is due to the high frequency of some 17q alleles, the breakdown of linkage disequilibrium on African-derived chromosomes, and possibly different early-life asthma endotypes in these children. Finally, the inconsistent association between asthma and gene expression levels in blood or lung cells from older children and adults suggests that genotype effects may mediate asthma risk or protection during critical developmental windows and/or in response to relevant exposures in early life. Thus studies of young children and ethnically diverse populations are required to fully understand the relationship between genotype and asthma phenotype and the gene regulatory architecture at this locus. (J Allergy Clin Immunol 2018;142:749–64.)

Chromosome 17q21 Genes ORMDL3 and GSDMB in Asthma and Immune Diseases

Chromosome 17q21 contains a cluster of genes including ORMDL3 and GSDMB, which have been highly linked to asthma in genome-wide association studies. ORMDL3 is localized to the endoplasmic reticulum and regulates downstream pathways including sphingolipids, metalloproteases, remodeling genes, and chemokines. ORMDL3 inhibits serine palmitoyl-CoA transferase, the rate-limiting enzyme for sphingolipid biosynthesis. In addition, ORMDL3 activates the ATF6α branch of the unfolded protein response which regulates SERCA2b and IL-6, pathways of potential importance to asthma. The SNP-linking chromosome 17q21 to asthma is associated with increased ORMDL3 and GSDMB expression. Mice expressing either increased levels of human ORMDL3, or human GSDMB, have an asthma phenotype characterized by increased airway responsiveness and increased airway remodeling (increased smooth muscle and fibrosis) in the absence of airway inflammation. GSDMB regulates expression of 5-LO and TGF-β1 which are known pathways involved in the pathogenesis of asthma. GSDMB is one of four members of the GSDM family (GSDMA, GSDMB, GSDMC, and GSDMD). GSDMD (located on chromosome 8q24 and not linked to asthma) has emerged as a key mediator of pyroptosis. GSDMD is a key component of the NLPR3 inflammasome and is required for its activation. GSDMD undergoes proteolytic cleavage by caspase-1 to release its N-terminal fragment, which in turn mediates pyroptosis and IL-1β secretion. Chromosome 17q21 has not only been linked to asthma but also to type 1 diabetes, inflammatory bowel disease, and primary biliary cirrhosis suggesting that future insights into the biology of genes located in this region will increase our understanding of these diseases.

Interaction between 25-hydroxyvitamin D and variants at 17q12-21 on respiratory infections

OBJECTIVES

25-hydroxyvitamin D (25[OH]D) deficiency and genetic variants at the 17q12-21 locus are independent risk factors for respiratory tract infections (RTIs). We aimed to investigate whether the effect of 25(OH)D at birth and 1 year of age and the polymorphism at the 17q12-21 locus, or interactions between these two factors, increase susceptibility to RTIs in the first year of life.

METHODS

We tested cord-blood (CB) 25(OH)D at birth and 1 year of age and genotypes of a variant at the 17q12-21 locus for associations with RTIs, particularly lower respiratory tract infections (LRTIs), and determined whether there exist interactions between 25(OH)D and 17q12-21 genotypes in a birth cohort of 473 infants.

RESULTS

The levels of CB 25(OH)D inversely associate with development of RTIs and LRTIs during the first year of life. There exists an inverse association of 25(OH)D at birth, but not at 1 year, with the risk of acquiring LRTIs in early infancy (adjusted odds ratio [aOR], 2.37; 95% confidence interval [CI]: 1.23-4.60; P = 0.010 and aOR, 0.50; 95%CI: 0.23-1.12; P = 0.094). We have also found a significant interaction between CB 25(OH)D and a variant at the 17q12-21 locus with respect to the development of early LRTIs, such that associations between a variant at the 17q12-21 locus and LRTIs are restricted to infants with low CB 25(OH)D concentrations (P for interaction = 0.013). In addition, when infants with a variant at the 17q12-21 locus had been exposed to chronic 25(OH)D deficiency over the first year, their risk of LRTIs was increased.

CONCLUSION

CB 25(OH)D deficiency during fetal life contribute to the development of LRTIs in genetically susceptible infants. Pediatr Pulmonol. 2016; 51:958-967. © 2016 Wiley Periodicals, Inc.

Interaction between the DNAH9 gene and early smoke exposure in bronchial hyperresponsiveness

A previous genome-wide linkage scan of bronchial hyperresponsiveness (BHR) in the French Epidemiological study on the Genetics and Environment of Asthma (EGEA) families, performed in the presence of a gene×early-life environmental tobacco smoke (ETS) exposure interaction, showed the strongest interaction in the 17p11 region where linkage was detected only among unexposed siblings. Our goal was to conduct fine-scale mapping of 17p11 to identify single nucleotide polymorphisms (SNPs) interacting with ETS that influence BHR.Analyses were performed in 388 French EGEA asthmatic families, using a two-step strategy: 1) selection of SNPs displaying family-based association test (FBAT) association signals (p≤0.01) with BHR in unexposed siblings, and 2) a FBAT homogeneity test between exposed and unexposed siblings plus a robust log-linear interaction test.A single SNP reached the threshold (p≤3×10(-3)) for significant interaction with ETS using both interaction tests, after accounting for multiple testing. Results were replicated in 253 French-Canadian families, but not in 341 UK families, probably due in part to differences in phenotypic features between datasets.The SNP showing significant interaction with ETS belongs toDNAH9(dynein, axonemal, heavy chain 9), a promising candidate gene involved in respiratory cilia mobility and associated with primary ciliary dyskinesia, a disease associated with abnormalities of pulmonary function.

To what extent is allergen exposure a risk factor for the development of allergic disease?

The role of allergen exposure in the development of allergic disease has been a matter of considerable debate, and our understanding of the importance of allergens has evolved over the last 25 years. Several observational and primary prevention studies have investigated these relationships, and different studies reported inconsistent, and sometimes opposite findings. It has to be emphasized that a clear understanding of how aeroallergen exposure occurs, and accurate and reproducible measurement of exposure are essential prerequisites for understanding the role of exposure. However, our current understanding of how we get exposed to allergens is not based on solid evidence, but on a number of assumptions, and we urgently need to develop better proxy measures (or indices) of exposure. In addition, the relative importance of the timing of exposure (e.g. early compared to exposure in later life) is unknown. It is also unclear which route of exposure is the most relevant (e.g. inhaled vs. oral vs. transcutaneous). Available data suggest that the dose-response relationship between allergen exposure and allergic disease may differ between different allergens, dose ranges and exposure patterns, and these relationships may further differ between different populations and geographical areas. It is increasingly clear that childhood asthma and atopy are not single phenotypes, and it is likely that allergen exposure has different effect on distinct subgroups under the umbrella terms of 'sensitization' and 'asthma'. Susceptibility to allergen exposure, other environmental exposures and their interactions may also differ between individuals with different genetic predispositions. However, the precise nature of these complex relationships is unclear. We need a holistic approach offered by systems biology, with integration of information on the standardized and reliable measures of exposures (including allergens and other relevant exposures) with genetic and biological data to fully understand the role of allergens in the development of allergic disease.

Pet ownership is associated with increased risk of non-atopic asthma and reduced risk of atopy in childhood: findings from a UK birth cohort

BACKGROUND

Studies have shown an inverse association of pet ownership with allergy but inconclusive findings for asthma.

OBJECTIVE

To investigate whether pet ownership during pregnancy and childhood was associated with asthma and atopy at the age of 7 in a UK population-based birth cohort.

METHODS

Data from the Avon Longitudinal Study of Parents and Children (ALSPAC) were used to investigate associations of pet ownership at six time points from pregnancy to the age of 7 with asthma, atopy (grass, house dust mite, and cat skin prick test) and atopic vs. non-atopic asthma at the age of 7 using logistic regression models adjusted for child's sex, maternal history of asthma/atopy, maternal smoking during pregnancy, and family adversity.

RESULTS

A total of 3768 children had complete data on pet ownership, asthma, and atopy. Compared with non-ownership, continuous ownership of any pet (before and after the age of 3) was associated with 52% lower odds of atopic asthma [odds ratio (OR) 0.48, 95% CI 0.34-0.68]. Pet ownership tended to be associated with increased risk of non-atopic asthma, particularly rabbits (OR 1.61, 1.04-2.51) and rodents (OR 1.86, 1.15-3.01), comparing continuous vs. non-ownership. Pet ownership was consistently associated with lower odds of sensitization to grass, house dust mite, and cat allergens, but rodent ownership was associated with higher odds of sensitization to rodent allergen. Differential effects of pet ownership on atopic vs. non-atopic asthma were evident for all pet types.

CONCLUSIONS AND CLINICAL RELEVANCE

Pet ownership during pregnancy and childhood in this birth cohort was consistently associated with a reduced risk of aeroallergen sensitization and atopic asthma at the age of 7, but tended to be associated (particularly for rabbits and rodents) with an increased risk of non-atopic asthma. The opposing effects on atopy vs. non-atopic asthma might be considered by parents when they are deciding whether to acquire a pet.

Gene-environment interactions in the study of asthma in the postgenomewide association studies era

PURPOSE OF REVIEW

Asthma is a complex disease characterized by an intricate interplay of both heritable and environmental factors. Understanding the mechanisms through which genes and environment interact represents one of the major challenges for pulmonary researchers. This review provides an overview of the recently published literature on gene-environment (G × E) interactions in asthma, with a special focus on the new methodological developments in the postgenomewide association studies (GWAS) era.

RECENT FINDINGS

Most recent studies on G × E interaction in asthma used a candidate-gene approach. Candidate-gene studies considering exposure to outdoor air pollutants showed significant interactions mainly with variants in the GSTP1 gene on asthma in children. G × E studies on passive and active smoking, including one genomewide interaction study, identified novel genes of susceptibility to asthma and a time-dependent effect of maternal smoking. Other recent studies on asthma found interactions between candidate genes and occupational allergen exposure and several domestic exposures such as endotoxin and gas cooking. New methods were developed to efficiently estimate G × E interaction in GWAS, and a pathway-based strategy to select an enriched gene-set for G × E studies has recently been proposed.

SUMMARY

The G × E studies presented in this review offer a good example on how candidate-gene approaches can complement and help in validating GWAS findings.

Associations of Pet Ownership with Wheezing and Lung Function in Childhood: Findings from a UK Birth Cohort

Background

Asthma is a heterogeneous condition and differential effects of pet ownership on non-atopic versus atopic asthma have been reported. The aim of this study was to investigate whether pet ownership during pregnancy and early childhood was associated with wheezing from birth to age 7 years and with lung function at age 8 years in a UK population-based birth cohort.

Methods

Data from the Avon Longitudinal Study of Parents and Children (ALSPAC) were used to investigate associations of pet ownership at six time-points from pregnancy to age 7 years with concurrent episodes of wheezing, wheezing trajectories (phenotypes) and lung function at age 8 years using logistic regression models adjusted for child’s sex, maternal history of asthma/atopy, maternal smoking during pregnancy, and family adversity.

Results

4,706 children had complete data on pet ownership and wheezing. From birth to age 7 years, cat ownership was associated with an overall 6% lower odds of wheezing (OR=0.94 (0.89-0.99)). Rabbit and rodent ownership was associated with 21% (OR=1.21 (1.12-1.31)) and 11% (OR=1.11 (1.02–1.21)) higher odds of wheezing, respectively, with strongest effects evident during infancy. Rabbit and rodent ownership was positively associated with a ‘persistent wheeze’ phenotype. Pet ownership was not associated with lung function at age 8 years, with the exception of positive associations of rodent and bird ownership with better lung function.

Conclusions

Cat ownership was associated with reduced risk, and rabbit and rodent ownership with increased risk, of wheezing during childhood. The mechanisms behind these differential effects warrant further investigation.

Contributing factors to the development of childhood asthma: working toward risk minimization

Asthma is the most common chronic disease in childhood, and considerable research has been undertaken to find ways to prevent its development and reduce its prevalence. For such interventions to be successful, risk factors for asthma emergence should be identified and clearly defined. Data are robust for some of them, including atopy, viral infections and exposure to airborne irritants, whereas it is less conclusive for others, such as aeroallergen exposure and bacterial infections. Several interventions for asthma prevention, including avoidance and pharmacotherapy, have been attempted. However, most of them have furnished equivocal results. Various issues hinder the establishment of risk factors for asthma development and reduce the effectiveness of interventions, including the complexity of the disease and the fluidity of the developing systems in childhood. In this review, we revisit the evidence on pediatric asthma risk factors and prevention and discuss issues that perplex this field.

[Genetic and environmental factors of asthma and allergy: Results of the EGEA study]

INTRODUCTION AND METHODS

The EGEA study (epidemiological study on the genetics and environment of asthma, bronchial hyperresponsiveness and atopy), which combines a case-control and a family-based study of asthma case (n=2120 subjects) with three surveys over 20 years, aims to identify environmental and genetic factors associated with asthma and asthma-related phenotypes. We summarize the results of the phenotypic characterization and the investigation of environmental and genetic factors of asthma and asthma-related phenotypes obtained since 2007 in the EGEA study (42 articles).

RESULTS

Both epidemiological and genetic results confirm the heterogeneity of asthma. These results strengthen the role of the age of disease onset, the allergic status and the level of disease activity in the identification of the different phenotypes of asthma. The deleterious role of active smoking, exposure to air pollution, occupational asthmogenic agents and cleaning products on the prevalence and/or activity of asthma has been confirmed. Accounting for gene-environment interactions allowed the identification of new genetic factors underlying asthma and asthma-related traits and better understanding of their mode of action.

CONCLUSION

The EGEA study is contributing to the advances in respiratory research at the international level. The new phenotypic, environmental and biological data available in EGEA study will help characterizing the long-term evolution of asthma and the factors associated to this evolution.

An ADAM33 polymorphism associates with progression of preschool wheeze into childhood asthma: a prospective case-control study with replication in a birth cohort study

BACKGROUND

The influence of asthma candidate genes on the development from wheeze to asthma in young children still needs to be defined.

OBJECTIVE

To link genetic variants in asthma candidate genes to progression of wheeze to persistent wheeze into childhood asthma.

MATERIALS AND METHODS

In a prospective study, children with recurrent wheeze from the ADEM (Asthma DEtection and Monitoring) study were followed until the age of six. At that age a classification (transient wheeze or asthma) was based on symptoms, lung function and medication use. In 198 children the relationship between this classification and 30 polymorphisms in 16 asthma candidate genes was assessed by logistic regression. In case of an association based on a p<0.10, replication analysis was performed in an independent birth cohort study (KOALA study, n = 248 included for the present analysis).

RESULTS

In the ADEM study, the minor alleles of ADAM33 rs511898 and rs528557 and the ORMDL3/GSDMB rs7216389 polymorphisms were negatively associated, whereas the minor alleles of IL4 rs2243250 and rs2070874 polymorphisms were positively associated with childhood asthma. When replicated in the KOALA study, ADAM33 rs528557 showed a negative association of the CG/GG-genotype with progression of recurrent wheeze into childhood asthma (0.50 (0.26-0.97) p = 0.04) and no association with preschool wheeze.

CONCLUSION

Polymorphisms in ADAM33, ORMDL3/GSDMB and IL4 were associated with childhood asthma in a group of children with recurrent wheeze. The replication of the negative association of the CG/GG-genotype of rs528557 ADAM33 with childhood asthma in an independent birth cohort study confirms that a compromised ADAM33 gene may be implicated in the progression of wheeze into childhood asthma.

Risk of childhood asthma is associated with CpG-site polymorphisms, regional DNA methylation and mRNA levels at the GSDMB/ORMDL3 locus

Single-nucleotide polymorphisms (SNPs) in GSDMB (Gasdermin B) and ORMDL3 (ORMDL sphingolipid biosynthesis regulator 3) are strongly associated with childhood asthma, but the molecular alterations contributing to disease remain unknown. We investigated the effects of asthma-associated SNPs on DNA methylation and mRNA levels of GSDMB and ORMDL3. Genetic association between GSDMB/ORMDL3 and physician-diagnosed childhood asthma was confirmed in the Swedish birth-cohort BAMSE. CpG-site SNPs (rs7216389 and rs4065275) showed differences in DNA methylation depending on carrier status of the risk alleles, and were significantly associated with methylation levels in two CpG sites in the 5′ UTR (untranslated region) of ORMDL3. In the Swedish Search study, we found significant differences in DNA methylation between asthmatics and controls in five CpG sites; after adjusting for lymphocyte and neutrophil cell counts, three remained significant: one in IKZF3 [IKAROS family zinc finger 3 (Aiolos); cg16293631] and two in the CpG island (CGI) of ORMDL3 (cg02305874 and cg16638648). Also, cg16293631 and cg02305874 correlated with mRNA levels of ORMDL3. The association between methylation and asthma was independent of the genotype in rs7216389, rs4065275 and rs12603332. Both SNPs and CpG sites showed significant associations with ORMDL3 mRNA levels. SNPs influenced expression independently of methylation, and the residual association between methylation and expression was not mediated by these SNPs. We found a differentially methylated region in the CGI shore of ORMDL3 with six CpG sites less methylated in CD8⁺ T-cells. In summary, this study supports that there are differences in DNA methylation at this locus between asthmatics and controls; and both SNPs and CpG sites are independently associated with ORMDL3 expression.

Genetic variation in ORMDL3 gene may contribute to the risk of asthma: a meta-analysis

BACKGROUND

Since the first genome-wide association study report of an association between the ORMDL3 rs7216389 polymorphism and asthma, many studies have been carried out to establish its role in asthma susceptibility among different ethnic groups. However, results have not been consistent across all studies, compelling us to conduct the present meta-analysis.

METHODS

A literature search for eligible studies published before January 20, 2014 was conducted in the MEDLINE, EMBASE, and CNKI databases. The association was assessed using pooled crude odds ratios (ORs) with their corresponding 95% confidence intervals (CIs).

RESULTS

A total of 18 individual studies in 15 publications (total 7904 asthma patients and 10,874 healthy controls) were included in the meta-analysis. A meta-analysis of all included studies suggested that there was a highly significant risk effect conferred by the rs7216389*T allele on asthma susceptibility. In addition, we performed stratified analyses to evaluate ethnicity-specific and age-specific effects. Our subgroup analyses based on ethnicity and age-of-onset confirmed the role of the ORMDL3 rs7216389 polymorphism in conferring susceptibility to both childhood- and adult-onset asthma, especially in Caucasians and Asians.

CONCLUSIONS

The results of this meta-analysis firmly established that genetic variation at the rs7216389 locus, which controls the expression of the ORMDL3, may be a major, independent predisposing factor for asthma in ethnically diverse populations. However, further systematic studies are needed to determine the underlying mechanisms of this association.

Trajectories of lung function during childhood

RATIONALE

Developmental patterns of lung function during childhood may have major implications for our understanding of the pathogenesis of respiratory disease throughout life.

OBJECTIVES

To explore longitudinal trajectories of lung function during childhood and factors associated with lung function decline.

METHODS

In a population-based birth cohort, specific airway resistance (sRaw) was assessed at age 3 (n = 560), 5 (n = 829), 8 (n = 786), and 11 years (n = 644). Based on prospective data (questionnaires, skin tests, IgE), children were assigned to wheeze phenotypes (no wheezing, transient, late-onset, and persistent) and atopy phenotypes (no atopy, dust mite, non-dust mite, multiple early, and multiple late). We used longitudinal linear mixed models to determine predictors of change in sRaw over time.

MEASUREMENTS AND MAIN RESULTS

Contrary to the assumption that sRaw is independent of age and sex, boys had higher sRaw than girls (mean difference, 0.080; 95% confidence interval [CI], 0.049-0.111; P < 0.001) and a higher rate of increase over time. For girls, sRaw increased by 0.017 kPa ⋅ s(-1) per year (95% CI, 0.011-0.023). In boys this increase was significantly greater (P = 0.012; mean between-sex difference, 0.011 kPa ⋅ s(-1); 95% CI, 0.003-0.019). Children with persistent wheeze (but not other wheeze phenotypes) had a significantly greater rate of deterioration in sRaw over time compared with never wheezers (P = 0.009). Similarly, children with multiple early, but not other atopy phenotypes had significantly poorer lung function than those without atopy (mean difference, 0.116 kPa ⋅ s(-1); 95% CI, 0.065-0.168; P < 0.001). sRaw increased progressively with the increasing number of asthma exacerbations.

CONCLUSIONS

Children with persistent wheeze, frequent asthma exacerbations, and multiple early atopy have diminished lung function throughout childhood, and are at risk of a progressive loss of lung function from age 3 to 11 years. These effects are more marked in boys.

Association between serotonin transporter gene polymorphisms and childhood asthma

BACKGROUND

Asthma is a common chronic inflammatory disease of the airways in which genetic factors play a major role in its pathogenesis. High serotonin serum levels in patients with asthma suggest that serotonin is involved in the pathophysiology of the disease. Serotonin clearance is mediated by the serotonin reuptake transporter, and functional polymorphisms in this gene lead to altered serotonin reuptake efficiency.

OBJECTIVE

The aim of this study was to investigate the relationship between serotonin transporter gene polymorphisms and asthma.

METHODS

Serotonin transporter gene polymorphisms (5-HTTLPR, rs35521 and STin2.VNTR) were assessed by PCR-based methods in 100 children with mild to moderate persistent asthma and compared with 100 healthy controls.

RESULTS

There were no significant differences in allele, genotype or haplotype frequencies between patients and controls. No association was observed between SERT gene polymorphisms after stratification of patients for sex, age, spirometry indices, family history, passive smoking behavior and concomitant allergic rhinitis. Significant differences were observed in the distribution of 5-HTTLPR alleles (p = 0.025) and genotypes (p = 0.021) between patients with and without atopic dermatitis.

CONCLUSIONS

Despite strong evidence suggesting the role of serotonin in the pathophysiology of asthma, we found no association between serotonin transporter gene polymorphisms and mild to moderate persistent asthma. Further serotonin transporter gene analyses in patients with severe asthma may open up new horizons in the utilization of common serotonin regulators to treat asthma, based on their pharmacogenetic effects. However, serotonin may also be indirectly influenced by emotional stress during asthma attacks.