Identification of the Mhc region as an asthma susceptibility locus in recombinant congenic mice

Haplotype function score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits

We propose a new framework for human genetic association studies: at each locus, a deep learning model (in this study, Sei) is used to calculate the functional genomic activity score for two haplotypes per individual. This score, defined as the Haplotype Function Score (HFS), replaces the original genotype in association studies. Applying the HFS framework to 14 complex traits in the UK Biobank, we identified 3619 independent HFS-trait associations with a significance of p < 5 × 10-8. Fine-mapping revealed 2699 causal associations, corresponding to a median increase of 63 causal findings per trait compared with single-nucleotide polymorphism (SNP)-based analysis. HFS-based enrichment analysis uncovered 727 pathway-trait associations and 153 tissue-trait associations with strong biological interpretability, including 'circadian pathway-chronotype' and 'arachidonic acid-intelligence'. Lastly, we applied least absolute shrinkage and selection operator (LASSO) regression to integrate HFS prediction score with SNP-based polygenic risk scores, which showed an improvement of 16.1-39.8% in cross-ancestry polygenic prediction. We concluded that HFS is a promising strategy for understanding the genetic basis of human complex traits.

Mouse mast cell protease-6 and MHC are involved in the development of experimental asthma

Allergic asthma is a complex disease with a strong genetic component where mast cells play a major role by the release of proinflammatory mediators. In the mouse, mast cell protease-6 (mMCP-6) closely resembles the human version of mast cell tryptase, β-tryptase. The gene that encodes mMCP-6, Tpsb2, resides close by the H-2 complex (MHC gene) on chromosome 17. Thus, when the original mMCP-6 knockout mice were backcrossed to the BALB/c strain, these mice were carrying the 129/Sv haplotype of MHC (mMCP-6(-/-)/H-2bc). Further backcrossing yielded mMCP-6(-/-) mice with the BALB/c MHC locus. BALB/c mice were compared with mMCP-6(-/-) and mMCP-6(-/-)/H-2bc mice in a mouse model of experimental asthma. Although OVA-sensitized and challenged wild type mice displayed a striking airway hyperresponsiveness (AHR), mMCP-6(-/-) mice had less AHR that was comparable with that of mMCP-6(-/-)/H-2bc mice, suggesting that mMCP-6 is required for a full-blown AHR. The mMCP-6(-/-)/H-2bc mice had strikingly reduced lung inflammation, IgE responses, and Th2 cell responses upon sensitization and challenge, whereas the mMCP-6(-/-) mice responded similarly to the wild type mice but with a minor decrease in bronchoalveolar lavage eosinophils. These findings suggest that inflammatory Th2 responses are highly dependent on the MHC-haplotype and that they can develop essentially independently of mMCP-6, whereas mMCP-6 plays a key role in the development of AHR.

Intermediary quantitative traits--an alternative in the identification of disease genes in asthma?

Intermediary quantitative traits are a possible alternative for the identification of disease genes. This may be particularly relevant when diagnostic criteria are not very well defined as described for asthma. We analyzed serum samples from 944 individuals of 218 asthma families for 17 cytokines (eotaxin, GM-CSF, IFNγ, IL1B, IL1RA, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12(p40), IL-13, IL-17, IL-23, IL-33, TSLP and TNF-α) and determined the heritability. Linked chromosomal regions were identified by a genome-wide analysis using 334 autosomal microsatellite marker and association tested by further 550 SNP marker at genes implicated earlier with immune response. Heritability varied with TNF-α and IL-8 levels having the highest and TSLP having the lowest heritability. Linkage was significantly increased only for IL-12(p40) at D17S949. There were multiple significant single-nucleotide polymorphisms (SNP) associations (P<0.05) as found in the transmission disequilibrium test, whereas only a few replicated in parents or children only. These include SNPs in IL1RN that were associated with IL-33 and TSLP levels, and a SNP in NR3C2 that was associated with eotaxin, IL-13 and IFN-γ levels. Circulating level of serum cytokines exhibits genetic associations with asthma traits that are otherwise not detected using clinical diagnosis or when the clinical details are ambiguous.

TLR-2 activation induces regulatory T cells and long-term suppression of asthma manifestations in mice

Asthma is a chronic inflammatory disease of the airways characterized by variable airway obstruction and airway hyperresponsiveness (AHR). The T regulatory (Treg) cell subset is critically important for the regulation of immune responses. Adoptive transfer of Treg cells has been shown to be sufficient for the suppression of airway inflammation in experimental allergic asthma. Intervention strategies aimed at expanding the Treg cell population locally in the airways of sensitized individuals are therefore of high interest as a potential therapeutic treatment for allergic airway disease. Here, we aim to test whether long-term suppression of asthma manifestations can be achieved by locally expanding the Treg cell subset via intranasal administration of a TLR-2 agonist. To model therapeutic intervention aimed at expanding the endogenous Treg population in a sensitized host, we challenged OVA-sensitized mice by OVA inhalation with concomitant intranasal instillation of the TLR-2 agonist Pam3Cys, followed by an additional series of OVA challenges. Pam3Cys treatment induced an acute but transient aggravation of asthma manifestations, followed by a reduction or loss of AHR to methacholine, depending on the time between Pam3Cys treatment and OVA challenges. In addition, Pam3Cys-treatment induced significant reductions of eosinophils and increased numbers of Treg cells in the lung infiltrates. Our data show that, despite having adverse acute effects, TLR2 agonist treatment as a therapeutic intervention induces an expansion of the Treg cell population in the lungs and results in long-term protection against manifestation of allergic asthma upon subsequent allergen provocation. Our data indicate that local expansion of Tregs in allergic airway disease is an interesting therapeutic approach that warrants further investigation.