Michael A. Portelli

Genetic risk factors for the development of allergic disease identified by genome‐wide association

An increasing proportion of the worldwide population is affected by allergic diseases such as allergic rhinitis (AR), atopic dermatitis (AD) and allergic asthma and improved treatment options are needed particularly for severe, refractory disease. Allergic diseases are complex and development involves both environmental and genetic factors. Although the existence of a genetic component for allergy was first described almost 100 years ago, progress in gene identification has been hindered by lack of high throughput technologies to investigate genetic variation in large numbers of subjects. The development of Genome‐Wide Association Studies (GWAS), a hypothesis‐free method of interrogating large numbers of common variants spanning the entire genome in disease and non‐disease subjects has revolutionised our understanding of the genetics of allergic disease. Susceptibility genes for asthma, AR and AD have now been identified with confidence, suggesting there are common and distinct genetic loci associated with these diseases, providing novel insights into potential disease pathways and mechanisms. Genes involved in both adaptive and innate immune mechanisms have been identified, notably including multiple genes involved in epithelial function/secretion, suggesting that the airway epithelium may be particularly important in asthma. Interestingly, concordance/discordance between the genetic factors driving allergic traits such as IgE levels and disease states such as asthma have further supported the accumulating evidence for heterogeneity in these diseases. While GWAS have been useful and continue to identify novel genes for allergic diseases through increased sample sizes and phenotype refinement, future approaches will integrate analyses of rare variants, epigenetic mechanisms and eQTL approaches, leading to greater insight into the genetic basis of these diseases. Gene identification will improve our understanding of disease mechanisms and generate potential therapeutic opportunities.

Genetic basis for personalized medicine in asthma

There is heterogeneity in patient responses to current asthma medications. Significant progress has been made identifying genetic polymorphisms that influence the efficacy and potential for adverse effects to asthma drugs, including; β2-adrenergic receptor agonists, corticosteroids and leukotriene modifiers. Pharmacogenetics holds great promise to maximise clinical outcomes and minimize adverse effects. Asthma is heterogeneous with respect to clinical presentation and inflammatory mechanisms underlying the disease, which is likely to contribute to variable results in clinical trials targeting specific inflammatory mediators. Genome-wide association studies have begun to identify genes underlying asthma (e.g., IL1RL1), which represent future therapeutic targets. In this article, we review and update the pharmacogenetics of current asthma therapies and discuss the genetics underlying selected Phase II and future targets.

Genome-wide protein QTL mapping identifies human plasma kallikrein as a post-translational regulator of serum uPAR levels

The soluble cleaved urokinase plasminogen activator receptor (scuPAR) is a circulating protein detected in multiple diseases, including various cancers, cardiovascular disease, and kidney disease, where elevated levels of scuPAR have been associated with worsening prognosis and increased disease aggressiveness. We aimed to identify novel genetic and bio‐molecular mechanisms regulating scuPAR levels. Elevated serum scuPAR levels were identified in asthma (n=514) and chronic obstructive pulmonary disease (COPD; n=219) cohorts when compared to controls (n=96). In these cohorts, a genome‐wide association study of serum scuPAR levels identified a human plasma kallikrein gene (KLKB1) promoter polymorphism (rs4253238) associated with serum scuPAR levels in a control/asthma population (P=1.17 × 10–7), which was also observed in a COPD population (combined P=5.04 × 10–12). Using a fluorescent assay, we demonstrated that serum KLKB1 enzymatic activity was driven by rs4253238 and is inverse to scuPAR levels. Biochemical analysis identified that KLKB1 cleaves scuPAR and negates scuPARs effects on primary human bronchial epithelial cells (HBECs) in vitro. Chymotrypsin was used as a proproteolytic control, while basal HBECs were used as a control to define scuPAR‐driven effects. In summary, we reveal a novel post‐translational regulatory mechanism for scuPAR using a hypothesis‐free approach with implications for multiple human diseases.—Portelli, M. A., Siedlinski, M., Stewart, C. E., Postma, D. S., Nieuwenhuis, M. A., Vonk, J. M., Nurnberg, P., Altmuller, J., Moffatt, M. F., Wardlaw, A. J., Parker, S. G., Connolly, M. J., Koppelman, G. H., Sayers, I. Genome‐wide protein QTL mapping identifies human plasma kallikrein as a post‐translational regulator of serum uPAR levels. FASEB J. 28, 923–934 (2014). www.fasebj.org

Whole Exome Re-Sequencing Implicates CCDC38 and Cilia Structure and Function in Resistance to Smoking Related Airflow Obstruction

Chronic obstructive pulmonary disease (COPD) is a leading cause of global morbidity and mortality and, whilst smoking remains the single most important risk factor, COPD risk is heritable. Of 26 independent genomic regions showing association with lung function in genome-wide association studies, eleven have been reported to show association with airflow obstruction. Although the main risk factor for COPD is smoking, some individuals are observed to have a high forced expired volume in 1 second (FEV1) despite many years of heavy smoking. We hypothesised that these “resistant smokers” may harbour variants which protect against lung function decline caused by smoking and provide insight into the genetic determinants of lung health. We undertook whole exome re-sequencing of 100 heavy smokers who had healthy lung function given their age, sex, height and smoking history and applied three complementary approaches to explore the genetic architecture of smoking resistance. Firstly, we identified novel functional variants in the “resistant smokers” and looked for enrichment of these novel variants within biological pathways. Secondly, we undertook association testing of all exonic variants individually with two independent control sets. Thirdly, we undertook gene-based association testing of all exonic variants. Our strongest signal of association with smoking resistance for a non-synonymous SNP was for rs10859974 (P = 2.34×10−4) in CCDC38, a gene which has previously been reported to show association with FEV1/FVC, and we demonstrate moderate expression of CCDC38 in bronchial epithelial cells. We identified an enrichment of novel putatively functional variants in genes related to cilia structure and function in resistant smokers. Ciliary function abnormalities are known to be associated with both smoking and reduced mucociliary clearance in patients with COPD. We suggest that genetic influences on the development or function of cilia in the bronchial epithelium may affect growth of cilia or the extent of damage caused by tobacco smoke.

Airway and peripheral urokinase plasminogen activator receptor is elevated in asthma, and identifies a severe, nonatopic subset of patients.

Genetic polymorphisms in the asthma susceptibility gene, urokinase plasminogen activator receptor (uPAR/PLAUR) have been associated with lung function decline and uPAR blood levels in asthma subjects. Preliminary studies have identified uPAR elevation in asthma; however, a definitive study regarding which clinical features of asthma uPAR may be driving is currently lacking.

Chapter 28 – Asthma

Abstract Asthma is a common respiratory disease with a complex etiology involving a combination of genetic and environmental components. Current asthma management involves a step-up and step-down approach based on asthma control with a large degree of heterogeneity in responses to the main drug classes currently in use: β2-adrenergic receptor agonists, corticosteroids, and leukotriene modifiers. Importantly, asthma is heterogeneous with respect to clinical presentation and the inflammatory mechanisms that underlie it. This heterogeneity likely contributes to variable results in clinical trials, particularly when targeting specific inflammatory mediators. These factors have motivated a drive toward stratified medicine in asthma based on clinical/cellular outcomes or genetics (i.e., pharmacogenetics). Significant progress has been made in identifying genetic polymorphisms that influence the efficacy and potential for adverse effects of all main classes of asthma drugs. Importantly an emerging role for genetics in phase II development of newer therapies has been demonstrated (e.g., anti-IL4). Similarly, the stratification of patients based on clinical characteristics (e.g., blood and sputum eosinophil levels) has been critical in evaluating newer therapies (e.g., anti-IL5). As a proof of concept, anti-IgE is the latest therapy to be introduced into clinical practice, although only for severe, allergic patients (i.e., in a stratified manner). As new asthma genes are identified using genome-wide association, among other technologies, new targets (e.g., IL33/IL33 receptor (IL1RL1)) will emerge and pharmacogenetics in these development programs will be essential. In this chapter we review the current understanding of asthma pathobiology and its clinical presentation, as well as the use of stratified medicine, which holds great promise for maximizing clinical outcomes and minimizing adverse effects in existing and new therapies. Asthma is a common respiratory disease with a complex etiology involving a combination of genetic and environmental components. Current asthma management involves a step-up and step-down approach based on asthma control with a large degree of heterogeneity in responses to the main drug classes currently in use: β2-adrenergic receptor agonists, corticosteroids, and leukotriene modifiers. Importantly, asthma is heterogeneous with respect to clinical presentation and the inflammatory mechanisms that underlie it. This heterogeneity likely contributes to variable results in clinical trials, particularly when targeting specific inflammatory mediators. These factors have motivated a drive toward stratified medicine in asthma based on clinical/cellular outcomes or genetics (i.e., pharmacogenetics). Significant progress has been made in identifying genetic polymorphisms that influence the efficacy and potential for adverse effects of all main classes of asthma drugs. Importantly an emerging role for genetics in phase II development of newer therapies has been demonstrated (e.g., anti-IL4). Similarly, the stratification of patients based on clinical characteristics (e.g., blood and sputum eosinophil levels) has been critical in evaluating newer therapies (e.g., anti-IL5). As a proof of concept, anti-IgE is the latest therapy to be introduced into clinical practice, although only for severe, allergic patients (i.e., in a stratified manner). As new asthma genes are identified using genome-wide association, among other technologies, new targets (e.g., IL33/IL33 receptor (IL1RL1)) will emerge and pharmacogenetics in these development programs will be essential. In this chapter we review the current understanding of asthma pathobiology and its clinical presentation, as well as the use of stratified medicine, which holds great promise for maximizing clinical outcomes and minimizing adverse effects in existing and new therapies.

Urokinase plasminogen activator receptor polymorphisms and airway remodelling in asthma

In the past decade, several asthma genes have been identified [1]; however, the key challenge is to determine how these genetic changes contribute to the underlying lung biology. We identified the urokinase plasminogen activator receptor (PLAUR) as an asthma susceptibility gene by positional cloning [2]. We showed that the same single nucleotide polymorphisms (SNPs) were associated with soluble PLAUR levels in blood, airway hyperresponsiveness (AHR) and accelerated lung function decline in asthma; a clinical feature linked to airway wall remodelling [2]. Therefore, we hypothesised that PLAUR may contribute to structural changes in asthma via increased levels of the membrane bound or soluble receptor. We subsequently showed that PLAUR levels were elevated in the airway epithelium of asthma patients and that PLAUR has a role in epithelial repair responses [3]. The aim of the current study was to 1) test for association between PLAUR SNPs and markers of airway remodelling using bronchial biopsies from asthma patients; and 2) test for association between SNPs and staining for PLAUR in airway tissue. PLAUR polymorphisms and levels are associated with markers of airway remodelling in lung biopsies of asthma patients http://ow.ly/X5Srl