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

Discriminant analysis and logistic regression on genetic history and environmental factors in children with asthma

BACKGROUND

Asthma is known to be related to genetic and environmental factors, we aimed to identify the predictors discriminating between children with asthma and a control group in order to build typical profiles of these children.

METHODS

A multidimensional analysis covered children (58 with asthma and 217 as control group), under 17 years of age, involving environmental variables and medical history of these children and their families.

RESULTS

Chi-square tests highlighted significant links between variables as rhinitis and conjunctivitis (P<0.001). The results showed, in group of asthmatic children, significant high frequencies of allergies, mainly seasonal (P<0.001), rhinitis, family history more present in mothers (P=0.002) and in maternal aunts and uncles (P<0.02). Allergies were mostly present in mothers of asthmatic children (P=0.03). Children whose father, mother or both had asthma were significantly more numerous in asthmatic group (P=0.0007). A multiple correspondence analysis (MCA) identified two typical profiles of children, a first group of asthmatic children with positive modalities of family history, medical and environmental factors, a second, the control group (nA, non-asthmatic children), with essentially negative modalities of the variables. Logistic regression (LR) resulted in a final model which retained four significant predictors, rhinitis (P=0.01), atopic dermatitis (P=0.04), mother antecedents (P=0.03) and paternal uncle antecedents (P=0.008) with a globally appreciable predictive value (82%) of the Hosmer-Lemeshow Test.

CONCLUSIONS

These results allowed the drafting of a typical profile quantifying through a function of a few predictors, the variation of the probability for a child to develop an asthma.

Sensitization and Clinical Characteristics of Congolese Children with Vernal Keratoconjunctivitis in Kinshasa

BACKGROUND

Data on the sensitization pattern and clinical characteristics of pediatric vernal keratoconjunctivitis (VKC) are scary in Central Africa. This chronic form of allergic conjunctivitis affects the quality of school life and work productivity. There is no study that shows the breadth of vernal keratoconjunctivitis in our setting.

PURPOSE

To describe the clinical characteristics of vernal keratoconjunctivitis in Kinshasa, to evaluate the sensitization profile and associated factors.

METHODS

A total of 400 children with vernal keratoconjunctivitis underwent a clinical examination and a skin prick test (SPT) for 10 allergens. Dermatophagoides pteronyssinus, Blomia tropicalis and cockroach were the most common allergens in 52, 1 %, 18, 8% and 13% respectively among sensitized children and 66, 4% showed polysensitization.

RESULTS

The main symptoms were itchy eyes 45%, brownish discoloration conjunctiva 17%, red eyes 12, 2%, eyelids rubbing 11, 5%, tearing 8, 7% and photophobia 5, 5%.The limbic form was predominant with 54%, followed by palpebral form 26% and mixed form 20%. The most common complications were superficial punctate keratitis 17, 2%, shield ulcer 1, 5%, corneal plaque 1, 3% and corneal erosion 1%.

CONCLUSION

This study outlines that 34, 5% of children attending the outpatient Ophthalmology Department in two hospitals of Kinshasa for vernal keratoconjunctivitis disease had a positive skin prick test to at least one allergen, in particular for Dermatophagoides pteronyssinus, Blomia tropicalis and cockroach.

Identification of novel genes influencing eosinophil-specific protein levels in asthma families

BACKGROUND

Eosinophils play a key role in the asthma allergic response by releasing cytotoxic molecules such as eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) that generate epithelium damages.

OBJECTIVE

To identify genetic variants influencing ECP and EDN levels in asthma-ascertained families.

METHODS

We performed univariate and bivariate genome-wide association analyses of ECP and EDN levels in 1,018 subjects from EGEA study with follow-up in 153 subjects from SLSJ study and combined the results of these two studies through meta-analysis. We then conducted Bayesian statistical fine-mapping together with quantitative trait locus and functional annotation analyses to identify the most likely functional genetic variants and candidate genes.

RESULTS

We identified five genome-wide significant loci (P<5x10^-8) including seven distinct signals associated with ECP and/or EDN levels. The genes targeted by our fine-mapping and functional search include RNASE2 and RNASE3 (14q11) which encode EDN and ECP respectively and four other genes which regulate ECP/EDN levels. These four genes were the following: JAK1 (1p31) a transcription factor with a key role in the immune response and a potential therapeutic target for eosinophilic asthma, ARHGAP25 (2p13) involved in leukocyte recruitment to inflammatory sites, NDUFA4 (7p21) encoding a component of the mitochondrial respiratory chain and involved in cellular response to stress and CTSL (9q22) involved in immune response, extra-cellular remodeling and allergic inflammation.

CONCLUSION

This study demonstrates that the analysis of specific phenotypes produced by eosinophils allows identifying genes with a major role in allergic response and inflammation and offering potential therapeutic targets for asthma.

[Asthma in adults]

L’asthme est une pathologie chronique, hétérogène et fréquente des voies respiratoires, qui peut devenir handicapante et dont le coût socio-économique est important. Les stratégies thérapeutiques sont multiples et complexes. L’adhésion et l’observance du traitement sont souvent faibles. Le pharmacien d’officine peut mener des entretiens pharmaceutiques favorisant l’éducation thérapeutique et donc le contrôle de l’asthme.

Association of RANTES gene polymorphisms with susceptibility to childhood asthma: A meta-analysis

BACKGROUND

Previous investigations have illustrated that regulated upon activation, normal T-cell expressed and secreted (RANTES) polymorphisms are linked to susceptibility to childhood asthma; nevertheless, the findings continue to be controversial. Accordingly, we conducted the present meta-analysis to clarify the impact of RANTES genetic polymorphisms (-403G/A and -28C/G) on childhood asthma vulnerability.

METHODS

A search for published literature was performed using the PubMed, EMBASE, Chinese National Infrastructure, Cochrane Library, Scopus, Web of Science, and WanFang databases and selected in the form of PICOS (participants, interventions, comparisons, outcomes, and study design) to identify all eligible research works. The link between RANTES genetic polymorphisms and childhood asthma susceptibility was evaluated by a pooled odds ratio with a 95% confidence interval.

RESULTS

In total, 14 case-control studies were included in the analysis. No significant association existed between risk of childhood asthma and the -403G/A polymorphism subjected to any genetic framework in the overall population. In the stratified analysis, according to ethnicity, the -403G/A polymorphism was linked to augmented vulnerability to childhood asthma in Caucasians (allelic model: odds ratio [OR] = 1.63, 95% confidence interval [CI] = 1.04-2.57, P = .034; codominant model: OR = 2.20, 95% CI = 1.28-3.78, P = .004; dominant model: OR = 1.78, 95% CI = 1.01-3.13, P = .047; and recessive model: OR = 1.92, 95% CI = 1.11-3.30, P = .019). For the stratified analysis by atopic status, the -403G/A polymorphism was linked to augmented childhood asthma in the codominant (OR = 1.39, 95% CI = 1.02-1.91, P = .037) and dominant models (OR = 1.43, 95% CI = 1.02-2.01, P = .037) in atopic asthma. For the -28C/G polymorphism, there was a significant association between childhood asthma and the -28C/G variant (allelic model: OR = 1.33, 95% CI = 1.08-1.65, P = .009; codominant framework: OR = 2.14, 95% CI = 1.47-3.10, P < .001; dominant model: OR = 1.44, 95% CI = 1.07-1.93, P = .017; and recessive model: OR = 2.08, 95% CI = 1.44-3.02, P < .001). Stratified analysis based on ethnicity and the -28C/G polymorphism was linked to augmented vulnerability to childhood asthma in Asian and Caucasian populations. For the subgroup analysis by atopic status, no association was found in atopic and non-atopic asthma.

CONCLUSION

The present meta-analysis indicated that the RANTES -403G/A and -28C/G polymorphisms contributed to the development of childhood asthma.

Single Nucleotide and Copy-Number Variants in IL4 and IL13 Are Not Associated with Asthma Susceptibility or Inflammatory Markers: A Case-Control Study in a Mexican-Mestizo Population

BACKGROUND

Asthma is a complex and chronic inflammatory airway disease. Asthma's etiology is unknown; however, genetic and environmental factors could affect disease susceptibility. We designed a case-control study aimed to evaluate the role of single-nucleotide polymorphisms (SNP), and copy-number variants (CNV) in the IL4 and IL13 genes in asthma susceptibility and their participation in plasma cytokine levels depending on genotypes Methods: We include 486 subjects, divided into asthma patients (AP, n = 141) and clinically healthy subjects (CHS, n = 345). We genotyped three SNP, two in the IL4 and two in the IL13 gene; also, two CNVs in IL4. The IL-4, IL-13 and IgE plasma levels were quantified.

RESULTS

Biomass-burning smoke exposure was higher in the AP group compared to CHS (47.5% vs. 20.9%; p < 0.01, OR = 3.4). No statistical differences were found in the genetic association analysis. In both CNV, we only found the common allele. For the analysis of IL-4, IL-13, and IgE measures stratified by genotypes, no significant association or correlation was found.

CONCLUSION

In the Mexican-mestizo population, SNPs neither CNVs in IL4 nor IL13 are associated with asthma susceptibility or involved serum cytokine levels. Biomass-burning smoke is a risk factor in asthma susceptibility.

Long-term air pollution exposure is associated with increased severity of rhinitis in 2 European cohorts

BACKGROUND

Very few studies have examined the association between long-term outdoor air pollution and rhinitis severity in adults.

OBJECTIVE

We sought to assess the cross-sectional association between individual long-term exposure to air pollution and severity of rhinitis.

METHODS

Participants with rhinitis from 2 multicenter European cohorts (Epidemiological Study on the Genetics and Environment on Asthma and the European Community Respiratory Health Survey) were included. Annual exposure to NO₂, PM₁₀, PM_2.5, and PM_coarse (calculated by subtracting PM_2.5 from PM₁₀) was estimated using land-use regression models derived from the European Study of Cohorts for Air Pollution Effects project, at the participants' residential address. The score of rhinitis severity (range, 0-12), based on intensity of disturbance due to symptoms reported by questionnaire, was categorized into low (reference), mild, moderate, and high severity. Polytomous logistic regression models with a random intercept for city were used.

RESULTS

A total of 1408 adults with rhinitis (mean age, 52 years; 46% men, 81% from the European Community Respiratory Health Survey) were included. The median (1st quartile-3rd quartile) score of rhinitis severity was 4 (2-6). Higher exposure to PM₁₀ was associated with higher rhinitis severity (adjusted odds ratio [95% CI] for a 10 μg/m³ increase in PM₁₀: for mild: 1.20 [0.88-1.64], moderate: 1.53 [1.07-2.19], and high severity: 1.72 [1.23-2.41]). Similar results were found for PM_2.5. Higher exposure to NO₂ was associated with an increased severity of rhinitis, with similar adjusted odds ratios whatever the level of severity. Adjusted odds ratios were higher among participants without allergic sensitization than among those with, but interaction was found only for NO_2. CONCLUSIONS: People with rhinitis who live in areas with higher levels of pollution are more likely to report more severe nasal symptoms. Further work is required to elucidate the mechanisms of this association.

Does the oxidative stress play a role in the associations between outdoor air pollution and persistent asthma in adults? Findings from the EGEA study

BACKGROUND

Evidences that oxidative stress plays a role in the associations between outdoor air pollution and asthma are growing. We aimed to study the role of plasma fluorescent oxidation products levels (FlOPs; an oxidative stress-related biomarker), as potential mediators, in the associations between outdoor air pollution and persistent asthma.

METHODS

Analyses were conducted in 204 adult asthmatics followed up in the French case-control and family study on asthma (EGEA; the Epidemiological study of the Genetic and Environmental factors of Asthma). Persistent asthma was defined as having current asthma at EGEA2 (baseline, 2003-2007) and EGEA3 (follow-up, 2011-2013). Exposures to nitrogen dioxide, nitrogen oxides, road traffic, particulate matter with a diameter ≤ 10 μm (PM₁₀) and ≤ 2.5 μm were estimated by ESCAPE models (2009-2010), and ozone (O₃) by IFEN models (2004). We used a mediation analysis to assess the mediated effect by FlOPs levels and the interaction between FlOPs levels and air pollution.

RESULTS

FlOPs levels increased with PM₁₀ and O₃ (adjusted β = 0.04 (95%CI 0.001-0.08), aβ = 0.04 (95%CI 0.009-0.07) per 10 μg/m³, respectively), and the risk of persistent asthma increased with FlOPs levels (aOR = 1.81 (95%CI 1.08-3.02)). The risk of persistent asthma decreased with exposures to NO₂, NOx and PM_2.5 (aOR ranging from 0.62 to 0.94), and increased with exposures to PM₁₀, O₃, O_3-summer and road traffic, the greater effect being observed for O₃ (aOR = 1.78, 95% CI 0.73-4.37, per 10 μg/m³). Using mediation analysis, we observed a positive total effect (aOR = 2.16, 95%CI 0.70-11.9), a positive direct effect of O₃ on persistent asthma (OR = 1.68, 95%CI 0.57-7.25), and a positive indirect effect mediated by FIOPs levels (aOR = 1.28 (95%CI 1.01-2.29)) accounting for 41% of the total effect.

CONCLUSIONS

Our results add insights on the role of oxidative stress in the association between air pollution and persistent asthma.

Immunological Factors Associated with Adult Asthma in the Aseer Region, Southwestern Saudi Arabia

Background: The prevalence of asthma is on the rise in Saudi Arabia. Data regarding the immunological profile of asthma in adults in the Aseer region, in southwestern Saudi Arabia, have not been well studied. Objectives: Our aim was to study the immunological factors associated with sensitization to asthma among adults in the Aseer region. Methods: A cross-sectional study with a nested case control design in a 1:1 ratio was conducted on a sample of adults attending primary health care centers in the Aseer region. The study used a validated Arabic version of the International study of asthma and allergies in childhood (ISAAC) questionnaire. The presence of wheezing in the past 12 months was used as a proxy for bronchial asthma. Matched age and sex controls were selected. Both groups were tested for complete blood count (CBC), total and differential white blood cell (WBC) count including eosinophils, total immunoglobulin E (IgE) measurement, allergen-specific immunoglobulin E (IgE), and cytokine levels. Results: The present study included 110 cases and 157 age- and sex-matched controls. Rye wheat was found to be a significant outdoor sensitizing agent ((odds ratio) OR = 5.23, 95% CI: 1.06–25.69). Indoors, house dust mites Dermatophagoides petronyssinus (OR = 2.04, 95% CI: 1.04–3.99) and Dermatophagoides farinae (OR = 2.50, 95% CI: 1.09–5.75) were significant. Higher total IgE (OR = 1.84, 95% CI: 1.10–3.06) and eosinophil levels (OR = 2.85, 95% CI: 1.14–7.15) were significantly associated with adult bronchial asthma in Aseer. On the other hand, the role of cytokines was not significant. Conclusions: In the present study, certain environmental agents were found to be important with regards to sensitization to bronchial asthma in adults. Knowledge about these sensitization agents should be disseminated to health providers and treating physicians in order to enhance preventive environmental control measures and asthma management. Asthma-treating physicians in the region should be alerted to the use of targeted biological therapies in selected asthmatics with difficult-to-control courses.

A meta-analysis of the association between CTLA-4 genetic polymorphism and susceptibility of asthma

BACKGROUND

Numerous studies have reported an association between cytotoxic T-lymphocyte associated antigen 4 gene (CTLA4) polymorphism and susceptibility to asthma, in different populations, but the results have been inconsistent. We performed a meta-analysis of 19 published case-control studies to obtain a reasonably accurate estimation of the relationship between CTLA4 polymorphism and asthma.

METHODS

We searched the Pubmed, EMBASE, Chinese National Knowledge Infrastructure, and Wanfang databases and extracted data from 19 independent, eligible studies. Odds ratios (ORs) with 95% confidence intervals (CIs) and Egger test were separately used to assess the strength of associations and publication bias.

RESULTS

A total of 19 case-control studies involving 4831 cases and 4534 controls were identified. The combined results revealed that there was significant association between the +49A/G polymorphism and asthma (for GG + GA vs. AA: OR = 0.82, 95% CI = 0.70-0.97, P = .02). Stratification by race or age indicated a significant association between the CTLA-4 +49 GA+GG genotype and asthma in Asians (OR = 0.80, 95% CI = 0.68-0.95, P = .01) and children (OR = 0.75, 95% CI = 0.62-0.90, P = .002), but there was no association in whites (OR = 0.94, 95% CI = 0.80-1.10, P = .44) and adults (OR = 0.85, 95% CI = 0.68-1.06, P = .15). Additionally, there was a significant association with atopic asthma under the random-effects model (OR = 0.81, 95% CI = 0.67-0.98, P = .03). In addition, there was no significant association between the -318 C/T polymorphism and asthma risk.

CONCLUSIONS

Our meta-analysis results suggested that the +49A/G polymorphism in CTLA-4 was an important risk factor for asthma susceptibility, especially in Asian individuals, children, and atopic patients.

Association between air pollution and rhinitis incidence in two European cohorts

BACKGROUND

The association between air pollution and rhinitis is not well established.

AIM

The aim of this longitudinal analysis was to study the association between modeled air pollution at the subjects' home addresses and self-reported incidence of rhinitis.

METHODS

We used data from 1533 adults from two multicentre cohorts' studies (EGEA and ECRHS). Rhinitis incidence was defined as reporting rhinitis at the second follow-up (2011 to 2013) but not at the first follow-up (2000 to 2007). Annual exposure to NO₂, PM₁₀ and PM_2.5 at the participants' home addresses was estimated using land-use regression models developed by the ESCAPE project for the 2009-2010 period. Incidence rate ratios (IRR) were computed using Poisson regression. Pooled analysis, analyses by city and meta-regression testing for heterogeneity were carried out.

RESULTS

No association between long-term air pollution exposure and incidence of rhinitis was found (adjusted IRR (aIRR) for an increase of 10 μg·m^-3 of NO_2: 1.00 [0.91-1.09], for an increase of 5 μg·m^-3 of PM_2.5: 0.88 [0.73-1.04]). Similar results were found in the two-pollutant model (aIRR for an increase of 10 μg·m^-3 of NO_2: 1.01 [0.87-1.17], for an increase of 5 μg·m^-3 of PM_2.5: 0.87 [0.68-1.08]). Results differed depending on the city, but no regional pattern emerged for any of the pollutants.

CONCLUSIONS

This study did not find any consistent evidence of an association between long-term air pollution and incident rhinitis.

A novel role for ciliary function in atopy: ADGRV1 and DNAH5 interactions

BACKGROUND

Atopy, an endotype underlying allergic diseases, has a substantial genetic component.

OBJECTIVE

Our goal was to identify novel genes associated with atopy in asthma-ascertained families.

METHODS

We implemented a 3-step analysis strategy in 3 data sets: the Epidemiological Study on the Genetics and Environment of Asthma (EGEA) data set (1660 subjects), the Saguenay-Lac-Saint-Jean study data set (1138 subjects), and the Medical Research Council (MRC) data set (446 subjects). This strategy included a single nucleotide polymorphism (SNP) genome-wide association study (GWAS), the selection of related gene pairs based on statistical filtering of GWAS results, and text-mining filtering using Gene Relationships Across Implicated Loci and SNP-SNP interaction analysis of selected gene pairs.

RESULTS

We identified the 5q14 locus, harboring the adhesion G protein-coupled receptor V1 (ADGRV1) gene, which showed genome-wide significant association with atopy (rs4916831, meta-analysis P value = 6.8 × 10^-9). Statistical filtering of GWAS results followed by text-mining filtering revealed relationships between ADGRV1 and 3 genes showing suggestive association with atopy (P ≤ 10^-4). SNP-SNP interaction analysis between ADGRV1 and these 3 genes showed significant interaction between ADGRV1 rs17554723 and 2 correlated SNPs (rs2134256 and rs1354187) within the dynein axonemal heavy chain 5 (DNAH5) gene (P_meta-int = 3.6 × 10^-5 and 6.1 × 10^-5, which met the multiple-testing corrected threshold of 7.3 × 10^-5). Further conditional analysis indicated that rs2134256 alone accounted for the interaction signal with rs17554723.

CONCLUSION

Because both DNAH5 and ADGRV1 contribute to ciliary function, this study suggests that ciliary dysfunction might represent a novel mechanism underlying atopy. Combining GWAS and epistasis analysis driven by statistical and knowledge-based evidence represents a promising approach for identifying new genes involved in complex traits.

Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome

Background

The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have only been carried out in a limited set of samples.

Results

We describe a large-scale coordinated study of allelic and non-allelic effects on DNA methylation, histone mark deposition, and gene expression, detecting the interrelations between epigenetic and functional features at unprecedented resolution. We use information from whole genome and targeted bisulfite sequencing from 910 samples to perform genotype-dependent analyses of allele-specific methylation (ASM) and non-allelic methylation (mQTL). In addition, we introduce a novel genotype-independent test to detect methylation imbalance between chromosomes. Of the ~2.2 million CpGs tested for ASM, mQTL, and genotype-independent effects, we identify ~32% as being genetically regulated (ASM or mQTL) and ~14% as being putatively epigenetically regulated. We also show that epigenetically driven effects are strongly enriched in repressed regions and near transcription start sites, whereas the genetically regulated CpGs are enriched in enhancers. Known imprinted regions are enriched among epigenetically regulated loci, but we also observe several novel genomic regions (e.g., HOX genes) as being epigenetically regulated. Finally, we use our ASM datasets for functional interpretation of disease-associated loci and show the advantage of utilizing naïve T cells for understanding autoimmune diseases.

Conclusions

Our rich catalogue of haploid methylomes across multiple tissues will allow validation of epigenome association studies and exploration of new biological models for allelic exclusion in the human genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1173-7) contains supplementary material, which is available to authorized users.

Blood granulocyte patterns as predictors of asthma phenotypes in adults from the EGEA study

To what extent blood granulocyte patterns may predict asthma control remains under-studied. Our aim was to study associations between blood neutrophilia and eosinophilia and asthma control outcomes in adults.Analyses were conducted in 474 asthmatics from the first follow-up of the Epidemiological Study on the Genetics and Environment of Asthma (EGEA2), including 242 asthmatics who were adults a decade earlier (EGEA1). At EGEA2, asthma control was assessed using the Global Initiative for Asthma definition (2015), and asthma exacerbations by use of urgent care or courses of oral corticosteroids in the past year. Blood EOS^lo/EOS^hi was defined as </≥250 eosinophils·mm^-3, respectively, and NEU^lo/NEU^hi as </≥5000 neutrophils·mm^-3, respectively. Estimates were adjusted for age, sex and smoking.At EGEA2, NEU^hi was associated with asthma exacerbations and poor asthma control (OR >2.10). EOS^hi was associated with higher bronchial hyperresponsiveness (BHR) (OR (95% CI) 2.21 (1.24-3.97)), poor lung function (p=0.02) and higher total IgE level (p=0.002). Almost 50% of asthmatics had a persistent pattern between surveys. Persistent NEU^hi was associated with poor asthma control at EGEA2 (OR (95% CI) 3.09 (1.18-7.05)). EOS^hi at EGEA1 and persistent EOS^hi were associated with higher BHR (OR (95% CI) 2.36 (1.10-5.07) and 3.85 (1.11-13.34), respectively), poor lung function (p<0.06) and higher immunoglobulin E level (p<10^-4) at EGEA2.Granulocyte patterns were differently associated with asthma outcomes, suggesting specific roles for each one, which could be tested as predictive signatures.