Fine Mapping of Lung Function Association in the MHC Region by Haplotype Imputation Reveals an Amino Acid change Underlying SNP Associations

We performed a Genome-wide association study (GWAS) of lung function quantitative traits forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC) and their ratio (FEV1/FVC) in 48,493 samples of European Ancestry (UK BiLEVE study) which, in addition to confirming 4 previously identified lung function signals in the major histocompatibility complex (MHC) on chromosome 6, identified 2 new secondary independent signals.In order to fine map the MHC GWAS signals, we used a published reference panel to impute HLA classical alleles and amino acid changes and tested their association with lung function traits. The new second most significant signal across the MHC region for both FEV1 (P=5.7×10-13) and FEV1/FVC (P=1.2×10‑20) was an association with HLA-DQB1 amino acid 57 Alanine present/absent (Alanine frequency=36.6%). After conditioning on the amino acid variant, 1 of 2 genome-wide significant (P‑8) GWAS signals for FEV1 and 5 of 6 for FEV1/FVC were strongly attenuated (minimum P=2.1×10‑5). Stepwise conditional analyses showed that the majority of the MHC lung function association signal could be explained by just the lead independent GWAS SNP and the amino acid change for both traits.Using haplotype imputation allowed us to build upon lung function GWAS discovery to pinpoint a potential causal variant in the MHC (HLA-DQB1 amino acid change 57, previously linked to type 1 diabetes risk) that explains a substantial proportion of the variance previously attributed to GWAS SNPs in this region.</p

Genome-wide Association Study Combining UK Biobank and GASP Consortium Highlights Novel Loci Associated with Moderate-Severe Asthma

The genetic architecture of asthma to date has been described by the discovery of around 20 loci from genome-wide association studies (GWAS), primarily with cases covering mild-to-moderate asthma. We hypothesised that moderate-to-severe asthma, which is currently difficult to treat, may have a specific genetic architecture, however there have not been large GWAS of moderate-to-severe asthma.Accordingly, we selected 5,135 European ancestry moderate-severe asthma cases (British Thoracic Society criteria 3 or above) and 25,675 controls free from lung disease, allergic rhinitis and atopic dermatitis, from UK Biobank and the Genetics of Asthma Severity & Phenotypes (GASP) cohort (cases only). We tested 33,771,858 SNPs and indels genome-wide (imputation against combined UK10K and 1000 genomes phase 3 panels) for association with moderate-severe asthma.We identified 23 independent signals associated with moderate-to-severe asthma (P -8), including novels signals in or near GATA3, RIC1, ZNF652, RPAP3 and MUC5AC, highlighting regions that harbour variants that effect gene expression or genes that play a role in respiratory disease and immune response. Previously described asthma loci where replicated including signals in or near D2HGDH, CD247, HLA-DQB1, HLA-DQA1, TSLP/WDR36, IL1RL1/IL18R1, CLEC16A, GATA3, IL33, SMAD3, SLC22A5/IL13, C11orf30, ZBTB10, IKZF3-ORMDL3 and IKZF4.This largest GWAS of moderate-severe asthma to date and highlights novel loci that may provide new biological insights relevant to treatment of severe asthma.</p

Preliminary Results from Genome-wide Meta-analysis of Survival Time in Idiopathic Pulmonary Fibrosis

Introduction: Idiopathic pulmonary fibrosis (IPF) is a rare lung disease of unknown cause, with few effective treatments available and poor prognosis (median survival time of 3 years). Genome-wide studies have identified variants associated with susceptibility to IPF. Although the effects of those variants on survival time have been investigated, no study has investigated survival time genome-wide for IPF. We set out to identify novel signals of association with IPF survival time and to replicate previous reports that variants in MUC5B that are associated with increased susceptibility to IPF, are paradoxically associated with an increase in survival time. Methods: We performed genome-wide analyses investigating survival time in a UK IPF study and a USA IPF study and meta-analysed the results. Survival analyses were performed on variants with minor allele frequency (MAF)>0.5% in both studies using a Cox Proportional Hazards model. Independent variants meeting meta-analysis P−6 and P Results: A total of 963 individuals and 7,730,466 variants were included in the final meta-analysis with maximum follow-up of 16.5 years. A total of 79 independent signals (11 with MAF>5%) reached the criteria described above. Consistent with previous reports, the allele in rs35705950 in MUC5B that is associated with increased susceptibility to IPF, shows some association with increased survival time (HR=0.73, 95% CI: [0.61, 0.87], P=5.08×10−4). Conclusions: This details the first analysis to investigate survival time genome-wide in IPF.</p

Mendelian randomization of eosinophils and other cell types in relation to lung function and disease

Rationale Eosinophils are associated with airway inflammation in respiratory disease. Eosinophil production and survival is controlled partly by interleukin-5: anti-interleukin-5 agents reduce asthma and response correlates with baseline eosinophil counts. However, whether raised eosinophils are causally related to chronic obstructive pulmonary disease (COPD) and other respiratory phenotypes is not well understood. Objectives We investigated causality between eosinophils and: lung function, acute exacerbations of COPD, asthma-COPD overlap (ACO), moderate-to-severe asthma and respiratory infections. Methods We performed Mendelian randomisation (MR) using 151 variants from genome-wide association studies of blood eosinophils in UK Biobank/INTERVAL, and respiratory traits in UK Biobank/SpiroMeta, using methods relying on different assumptions for validity. We performed multivariable analyses using eight cell types where there was possible evidence of causation by eosinophils. Measurements and main results Causal estimates derived from individual variants were highly heterogeneous, which may arise from pleiotropy. The average effect of raising eosinophils was to increase risk of ACO (weighted median OR per SD eosinophils, 1.44 (95%CI 1.19 to 1.74)), and moderate-severe asthma (weighted median OR 1.50 (95%CI 1.23 to 1.83)), and to reduce forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) and FEV1 (weighted median estimator, SD FEV1/FVC: −0.054 (95% CI −0.078 to −0.029), effect only prominent in individuals with asthma). Conclusions Broad consistency across MR methods may suggest causation by eosinophils (although of uncertain magnitude), yet heterogeneity necessitates caution: other important mechanisms may be responsible for the impairment of respiratory health by these eosinophil-raising variants. These results could suggest that anti-IL5 agents (designed to lower eosinophils) may be valuable in treating other respiratory conditions, including people with overlapping features of asthma and COPD.</p

Phenotypic and functional translation of IL33 genetics in asthma.

BACKGROUND:Asthma is a complex disease with multiple phenotypes that may differ in disease pathobiology and treatment response. Interleukin 33 (IL33) single nucleotide polymorphisms (SNPs) have been reproducibly associated with asthma. IL33 levels are elevated in sputum, and bronchial biopsies of asthma patients. The functional consequences of IL33 asthma SNPs remain unknown. OBJECTIVE:We studied whether IL33 SNPs associate with asthma-related phenotypes and with IL33 expression in lung or bronchial epithelium. We investigated the effect of increased IL33 expression on human bronchial epithelial cell (HBEC) function. METHODS:Association between IL33 SNPs (Chr9: 5,815,786-6,657,983) and asthma phenotypes (Lifelines/DAG/GASP cohorts) and between SNPs and expression (lung tissue, bronchial brushes, HBECs) was done using regression modelling. Lentiviral overexpression was used to study IL33 effects on HBECs. RESULTS:161 SNPs spanning the IL33 region associated with one or more asthma phenotypes after correction for multiple testing. We report one main independent signal tagged by rs992969 associating with blood eosinophil levels, asthma and eosinophilic asthma. A second, independent signal tagged by rs4008366 presented modest association with eosinophilic asthma. Neither signal associated with FEV1, FEV1/FVC, atopy, and age of asthma onset. The two IL33 signals are expression quantitative loci (eQTLs) in bronchial brushes and cultured HBECs, but not in lung tissue. IL33 overexpression in vitro resulted in reduced viability and ROS-capturing of HBECs, without influencing epithelial cell count, metabolic activity or barrier function. CONCLUSION:We identify IL33 as an epithelial susceptibility gene for eosinophilia and asthma, provide mechanistic insight, and implicate targeting of the IL33 pathway specifically in eosinophilic asthma

Genome-wide association study of preserved ratio impaired spirometry (PRISm)

BACKGROUND: Preserved ratio impaired spirometry (PRISm) is defined as a forced expiratory volume in 1 s (FEV1) <80% predicted and FEV1/forced vital capacity ≥0.70. PRISm is associated with respiratory symptoms and comorbidities. Our objective was to discover novel genetic signals for PRISm and see if they provide insight into the pathogenesis of PRISm and associated comorbidities. METHODS: We undertook a genome-wide association study (GWAS) of PRISm in UK Biobank participants (Stage 1), and selected single nucleotide polymorphisms (SNPs) reaching genome-wide significance for replication in 13 cohorts (Stage 2). A combined meta-analysis of Stage 1 and Stage 2 was done to determine top SNPs. We used cross-trait linkage disequilibrium score regression to estimate genome-wide genetic correlation between PRISm and pulmonary and extrapulmonary traits. Phenome-wide association studies of top SNPs were performed. RESULTS: 22 signals reached significance in the joint meta-analysis, including four signals novel for lung function. A strong genome-wide genetic correlation (rg) between PRISm and spirometric COPD (rg=0.62, p<0.001) was observed, and genetic correlation with type 2 diabetes (rg=0.12, p=0.007). Phenome-wide association studies showed that 18 of 22 signals were associated with diabetic traits and seven with blood pressure traits. CONCLUSION: This is the first GWAS to successfully identify SNPs associated with PRISm. Four of the signals, rs7652391 (nearest gene MECOM), rs9431040 (HLX), rs62018863 (TMEM114) and rs185937162 (HLA-B), have not been described in association with lung function before, demonstrating the utility of using different lung function phenotypes in GWAS. Genetic factors associated with PRISm are strongly correlated with risk of both other lung diseases and extrapulmonary comorbidity