Genomic factors underlying the effect of Respiratory Viruses and Allergens in Asthma – NIRVANA

The project is conducted in the French Epidemiological study on the Genetics and Environment of Asthma (EGEA), an internationally renowned respiratory cohort (https://egeanet.vjf.inserm.fr). Comprehensive data on allergen-specific (>170 allergen components) and RV-specific (130 RV proteins and peptides) immune responses using micro-array technologies developed by a leader group at the international level (R Valenta, Vienna, Austria) are generated to get immune response data for almost all EGEA2 population (n=1350) and EGEA1 samples in children (n=550), totaling 1900 samples.
The project is developping with 4 tasks:
Task-1 is aimed to estimate the association between allergen-specific IgE and RV-specific immune responses on asthma, considering first each immune response independently of the others, and then using patterns of immune responses defined by hypothesis-free clustering approaches.
Task-2 & task-3 are aimed to identify shared and independent genetic factors involved in antibody responses towards respiratory allergens (task-2) and RV (task-3) found associated with asthma-related phenotypes in task-1, through genome-wide association study and by an extensive analysis of the HLA region.
Task-4 is aimed to address the causality using Mendelian Randomization and by integrating genetic and epigenetic data.

Two articles have already been published.
Gheerbrant et al, Allergy 2021: We assessed the association between HLA class-II alleles and specific IgE (sIgE) sensitization to a large number of respiratory allergen molecules. 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 show that 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). In 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.
Siroux et al, Allergy 2021: We aimed to assess trajectories of molecular sIgE sensitization profiles from childhood to adulthood and their associations with respiratory health. IgE reactivity to microarrayed allergen molecules were measured in childhood (EGEA1) and 12 years later in adult life (EGEA2) among 291 EGEA participants (152 with asthma). At each time point, sIgE sensitization profiles were identified by latent class analysis (LCA) by considering IgE-reactivity to the 38 most prevalent respiratory allergens. The LCA-defined profiles were then studied in association with respiratory health. The LCA identified four sIgE sensitization profiles which were very similar at both time points (% at EGEA1 and EGEA2); A: «no/few allergen(s)« (48%, 39%), B: «pollen/ animal allergens« (18%, 21%), C: «most prevalent house dust mite allergens« (22%, 27%) and D: «many allergens« (12%, 13%). Overall, 73% of the participants remained in the same profile from childhood to adulthood. The profiles were associated with asthma and rhinitis phenotypes. Participants of profiles C and D had lower FEV1% and FEF25-75% as compared to profile A. Similar patterns of associations were observed for participants with asthma. In conclusion, using cluster-based statistical methods applied to high-resolution sIgE longitudinal data, we identified four molecular sensitization profiles, mainly stable from childhood to adulthood, that were associated with respiratory health.

As initially planed in the NIRVANA program, The work continues with 1) a study aimed at identifying specific immune responses to respiratory viruses associated with asthma phenotypes, 2) a genetic association study on specific immune responses to allergens and viruses, and 3) a study to assess the causality of the observed associations between specific immune responses to allergens and respiratory viruses and asthma phenotypes, via Mendelian randomization and by integrating genetic and epigenetic data.

1. Gheerbrant H, Guillien A, Vernet R, Lupinek C, Pison C, Pin I, Demenais F, Nadif R, Bousquet J, Pickl WF, Valenta R, Bouzigon E, Siroux V. Associations between specific IgE sensitization to 26 respiratory allergen molecules and HLA class II alleles in the EGEA cohort. Allergy. 2021; 76(8):2575-2586. doi: 10.1111/all.14820
2. Siroux V, Boudier A, Bousquet J, Dumas O, Just J, Le Moual N, Nadif R, Varraso R, Valenta R, Pin I. Trajectories of IgE sensitization to allergen molecules from childhood to adulthood and respiratory health in the EGEA cohort. Allergy. 2021 ; 76(8):2575-2586. doi: 10.1111/all.14820. Epub 2021 Apr 7. PMID: 33742477

Asthma is a frequent disabling chronic respiratory disease associated with high global costs ($81.9 billion in USA). In France, asthma prevalence in children is 11%. Asthma cannot be cured; therefore, prevention is thought to be the long-term solution for the asthma epidemic. Asthma results from interplays between environmental, lifestyle, genetic and epigenetic factors. For two environmental factors, respiratory allergens and respiratory viruses, strong association with asthma incidence or exacerbations is well documented. A few previous observations suggest that the host genotype plays an important role in the immune response of individual allergens and rhinovirus (RV), but these studies were limited in the assessment of allergen-specific and RV-specific immune responses. New technologies based on microarrays allow accurate and comprehensive characterization of hundreds allergen-specific and RV-specific antibody responses, and offer new avenues in the asthma epidemiological research.

Our main objective is to identify allergen-specific and RV-specific antibody responses associated with asthma and the host genomic determinants of these immune responses. The central hypothesis that the host genotype plays an important role in the effects of respiratory allergens and viruses in asthma is supported by several observations, but has still never been deeply addressed.
The project will be conducted in the French Epidemiological study on the Genetics and Environment of Asthma (EGEA), an internationally renowned respiratory cohort (https://egeanet.vjf.inserm.fr). Comprehensive data on allergen-specific (>170 allergen components) and RV-specific (130 RV proteins and peptides) immune responses using micro-array technologies developed by a leader group at the international level (R Valenta, Vienna, Austria) will be generated to get immune response data for almost all EGEA2 population (n=1350) and EGEA1 samples in children (n=550), totaling 1900 samples.

The project will develop with 4 tasks:
- Task-1 is aimed to estimate the association between allergen-specific IgE and RV-specific immune responses on asthma, considering first each immune response independently of the others, and then using patterns of immune responses defined by hypothesis-free clustering approaches.
- Task-2 & task-3 are aimed to identify shared and independent genetic factors involved in antibody responses towards respiratory allergens (task-2) and RV (task-3) found associated with asthma-related phenotypes in task-1, through genome-wide association study and by an extensive analysis of the HLA region.
- Task-4 is aimed to address the causality using Mendelian Randomization and by integrating genetic and epigenetic data.

EGEA will represent a unique cohort with a such comprehensive assessment of both allergen-specific and RV-specific immune responses, both in children and adults for which detailed phenotypic and environmental information for 20-years and whole-genome genetic and epigenetic data are available. The project builds on collaborations between laboratories with world leading expertise in respiratory and environmental epidemiology (Partner 1) and genetic epidemiology (Partner 2), with strong expertise in sophisticated statistical models (i.e. variable selection models, clustering approaches, polygenic risk score, mendelian randomization), which maximizes the success of the study. In each Tasks, replication will be sought in the MeDALL group and a French-Canadian group (SLSJ study).

A detailed knowledge of the most harmful allergens and RV strains is mandatory for an appropriate diagnostic and preventive approach. Through detailed analysis of genetic factors underlying the antibody responses to allergens and RV involved in the development of asthma, the project will have major implications in deepening knowledge of the population at risk for allergic asthma and RV-induced asthma, which in turn will impact on the asthma management and prevention.