Precision medicine in asthma: linking phenotypes to targeted treatments

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1 REVIEW C URRENT OPINION Precision medicine in asthma: linking phenotypes to targeted treatments Kian F. Chung a,b Purpose of review Asthma is a heterogeneous disease consisting of different phenotypes that are driven by different mechanistic pathways. The purpose of this review is to emphasize the important role of precision medicine in asthma management. Recent findings Despite asthma heterogeneity, the approach to management has been on the basis of disease severity, with the most severe patients reserved for the maximum treatments with corticosteroids and bronchodilators. At the severe end, the recent availability of biologic therapies in the form of anti-ige (omalizumab) and anti- IL5 therapies (mepolizumab and reslizumab) has driven the adaptation of precision medicine. These therapies are reserved for severe asthma with defined either allergic or eosinophilic background, respectively. Summary Unbiased definition of phenotypes or endotypes (which are phenotypes defined by mechanisms) is an important step towards the use of precision medicine in asthma. Although T2-high asthma has been defined with targets becoming available for treating allergic or eosinophilic asthma, the definition of non-t2 phenotypes remains a priority. Precision medicine is also dependent on the definition of biomarkers that can help differentiate between these phenotypes and pinpoint patients suitable for specific-targeted therapies. Thus, precision medicine links phenotypes (endotypes) to targeted treatments for better outcomes. Keywords asthma, biomarkers, phenotyping, precision medicine INTRODUCTION Asthma is diagnosed by the presence of intermittent symptoms of wheeze, cough and chest tightness that usually resolves spontaneously or with asthma treatments, and under such an umbrella term, would exist different phenotypes of asthma. In fact, the Global Initiative for Asthma (GINA) has now recognized asthma as being a heterogeneous disease with different presentations, outcomes and underlying mechanisms. Clinicians have defined several phenotypes based on the presentation and age of onset of symptoms, the severity of the disease and the presence of other conditions such as allergy and eosinophilia. When these phenotypes have been linked to long-term outcomes or to response to therapy with corticosteroids, these have been used by clinicians to predict the course of asthma. Despite the recognition of these phenotypes of asthma, the approach to the management of asthma continues to be based on the severity of the condition, with drugs added on the basis of asthma control. Inhaled corticosteroid (ICS) therapy remains the cornerstone of treatment of asthma because asthma is recognized as an eosinophilic inflammatory condition; however, those who respond to ICS therapy with an improvement in lung function such as the forced expiratory volume measured in one second (FEV 1 ) are associated with eosinophilia, and these usually represent up 50% of asthmatic patients [1,2]. The use of blood eosinophil count as a biomarker to define responders to ICS is not used. Treatment of patients with asthma based on their sputum eosinophil counts rather than on symptoms results in better control of asthma with less exacerbations using less corticosteroid therapy [3]. There may be many reasons why this approach of using sputum a National Heart and Lung Institute, Imperial College London and b Res- Respiratory Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, Imperial College London, London, UK Correspondence to Professor Kian F. Chung, MD, DSc, FRCP, National Heart and Lung Institute, Imperial College London, Dovehouse St, London SW3 6LY, UK. Tel: ; f.chung@imperial.ac.uk Curr Opin Pulm Med 2017, 23: DOI: /MCP Copyright ß 2017 Wolters Kluwer Health, Inc. All rights reserved.

2 Asthma KEY POINTS Severe asthma is a heterogeneous condition and phenotyping of patients with severe asthma into a T2 and non-t2 category is possible. Precision medicine is being introduced with the availability of biologic therapies targeting IgE and IL-5, because these agents are targeted towards specific phenotypes of severe asthma. The future of precision medicine in asthma will depend on the unbiased recognition of all the molecular phenotypes or endotypes of asthma, and the definition of associated biomarkers. eosinophil counts to improve the therapy of asthma has not been adopted. Most importantly, obtaining sputum samples from patients with asthma is not always successful and the analysis of the samples takes time and effort. Thus, the practice of precision (or personalized) medicine in asthma is lagging behind. However, the introduction of specific biologic therapies such as anti-ige and anti-il5 antibody treatments at the step 5 of the GINA guidelines has opened up the new era of precision medicine in asthma. These therapies are only used in the severe allergic asthma and in the severe eosinophilic phenotypes of asthma, respectively. Although the practice of medicine has always been based on a personalized approach since the dawn of medicine, with the concept of treating each patient as being unique, this delivery has remained very limited mainly as a concept rather than hard practice because of limitations in our understanding of what constitutes asthma. Currently, we recognize a category of asthma as being severe asthma, defined as by poor therapeutic responses of these patients to currently approved asthma medications, particularly inhaled and oral corticosteroid therapies, and approaches to phenotyping have been proposed in the international severe asthma guidelines [4]. The clinical diversity of this group has been recognized and this group of patients has been the subject of unbiased clustering approaches. Phenotypes of asthma have not been well described and there has been a lack of biomarkers developed for identifying different types of asthma. Consequently, the treatment of asthma has remained a one size fits all. Treatments should not only be based on the basis of severity, but on the basis of the driving mechanisms. The introduction of new biologic therapies at step 5 has heralded a new era of precision medicine for asthma. This review will discuss how precision medicine will alter the approach to the management of asthma. WHAT IS PRECISION MEDICINE? Precision medicine can be defined as an approach to treat and prevent disease by taking into consideration the individual variability in genes, environment and lifestyle for each individual and by taking this approach, there is increased likelihood of treating the right patient with the right drug at the right time, with preventive measures and therapies tailored for each individual [5]. Analysis of the genes and proteins is more likely to point towards causative pathways, which would lead to definition of endotypes which are phenotypes defined according to mechanisms. This is more likely to lead to treatments that target the cause of these diseases. Precision medicine is the tailoring of medical management to the individual characteristics not only genetic or genomic but also environmental and psychosocial characteristics, and preferences of each patient. Other terms that are used often synonymously with precision medicine are tailored medicine, stratified medicine or targeted medicine that will ultimately lead to targeted therapeutics. The concept of the P4 medicine that is predictive, preventive, personalized and participatory also falls within a similar definition ( systemsbiology.org/research/p4-medicine/). In order to be able to practise precision medicine with particular reference to asthma, one should understand the different endotypes of asthma and the biomarkers that will be used to help the doctor in determining the right treatment. In addition, because asthma is a disease that changes with time, information on a daily basis about the patient s condition and environment that could influence the course of the disease is needed. Such daily information may be used to predict any future exacerbations of asthma and the influence of potential environmental factors. PHENOTYPING TO ENDOTYPING Description of clinical phenotypes based on clinical variables and inflammatory markers has been made possible by the use of unbiased methods of clustering. The most recent report from the U-BIOPRED cohort described a well-controlled moderate-tosevere asthma phenotype and three other severe phenotypes: late-onset asthma with past or current smoking and chronic airflow obstruction, predominantly eosinophilic inflammation, nonsmoking severe asthma with chronic airflow obstruction and high use of oral corticosteroid therapy and obese female patients with frequent exacerbations but with normal lung function [6 ] (Fig. 1). In the American Severe Asthma Research Project (SARP) cohort, phenotypes of early-onset atopic asthma 2 Volume 23 Number 00 Month 2017

3 Precision medicine for asthma Chung FIGURE 1. Clinical phenotypes of moderate severe asthma derived from U-BIOPRED cohort from a cluster analysis of eight clinico-physiologic parameters. Reproduced from [6 ] (with permission). with mild-to-moderate severity, of obese late-onset nonatopic asthma female patients with frequent exacerbations and of those with severe airflow obstruction with use of oral corticosteroid therapy were identified [7]. In the Leicester cohorts, the use of sputum eosinophilia as a marker of eosinophilic asthma [8] has resulted in the description of two cohorts: a cluster of noneosinophilic inflammation (early-onset, symptom-predominant group in female obese patients) and a cluster of eosinophilic inflammation with late-onset disease, associated with rhinosinusitis, aspirin sensitivity and recurrent exacerbations. This latter eosinophilic phenotype was also described in the SARP cohort with late-onset asthma and nasal polyps with exacerbations despite high systemic corticosteroid use; the other eosinophilic cohort had early-onset allergic asthma with low lung function [9]. This clustering based on clinical, physiological and inflammatory parameters while yielding distinct phenotypes has not in general led to the elaboration of phenotypic biomarkers. DEFINITION OF A SEVERE EOSINOPHILIC ASTHMA PHENOTYPE/ENDOTYPE Molecular phenotyping has allowed us to define the severe eosinophilic asthma phenotype as an endotype, that is a phenotype defined by underlying mechanisms. The clinical phenotype characterized by concomitant high blood and sputum eosinophilia has been associated with very poor asthma control and propensity to asthma exacerbation [9] Copyright ß 2017 Wolters Kluwer Health, Inc. All rights reserved. 3

4 Asthma The unbiased cluster analyses have uncovered a phenotype of patients with late-onset, eosinophilic inflammation-predominant asthma [6,7,8], and adult-onset asthma patients with a high blood eosinophil count with frequent exacerbations and a poor prognosis [10]. Persistent airflow limitation and distal inflammation with air trapping are common in these patients, as is upper airway disease such as chronic rhinosinusitis with nasal polyposis [11]. Molecular support for this endotype was provided by determining the expression of three genes upregulated by exposing airway epithelial cells to the T2 cytokine, interleukin-13 (IL-13), in airway epithelial cells of patients with asthma. A Th2-high molecular phenotype was characterized by more blood and bronchoalveolar lavage eosinophils, increased levels of serum immunoglobulin E (IgE), increased expression of mucin MUC5AC, increased expression of IL5 and IL13 in biopsies, increased bronchial hyperresponsiveness and respond to ICSs by an increase in FEV 1 when compared to those with Th2-low expression [12]. Finally, the recent sputum analysis of U-BIOPRED has defined the molecular shape of this endotype associated with high T2 pathway and also with mast cell activation pathway [13 ]. New targeted treatments such as anti-il5 and anti-il5ra antibody that caused a reduction in the exacerbation rate support the concept that this is a severe eosinophilic asthma endotype [14,15 ]. The major criteria for this endotype have been defined as having severe asthma, with high load eosinophilic disease, having frequent exacerbations and the need for oral corticosteroid therapy to maintain control [16]. UNBIASED MOLECULAR PHENOTYPING The Th2-high phenotype is only found in 37% of patients with severe asthma when analysing genes in the airway epithelium [17]. Therefore, the majority of patients with severe asthma can be considered to be low-t2. In order to elucidate these non-t2 endotypes, an unbiased approach to obtaining molecular phenotypes of asthma was undertaken in U-BIOPRED. A hierarchical clustering of differentially expressed genes between eosinophilic and noneosinophilic inflammatory profiles from an analysis of sputum omics data revealed three molecular phenotypes [13 ]. One cluster was characterized by the immune receptors IL33R, CCR3 and TSLPR with the highest enrichment of gene signatures for IL- 13/T-helper cell type 2 (Th2) and innate lymphoid cell type 2 associated with the highest sputum eosinophilia: this grouped patients with severe asthma with oral corticosteroid dependency, frequent exacerbations and severe airflow obstruction. The second cluster was characterized by interferon-a (IFN-a), tumour necrosis factor-a-associated (TNF-a) and inflammasome-associated genes with the highest sputum neutrophilia, serum C-reactive protein levels and prevalence of eczema. The third phenotype was characterized by genes of metabolic pathways, ubiquitination and mitochondrial function with paucigranulocytic inflammation and little airflow obstruction [13 ]. The second phenotype is in agreement with the report that in neutrophilic asthma, an elevated gene expression of NLRP3, caspase-1 and IL- 1b was seen in sputum macrophages [18]. Thus, this unbiased approach has provided an overall idea of the various pathways associated with these three phenotypes of asthma, with the possibility that each of these phenotypes is underlined by several interacting pathways. Therefore, within this categorization, it has been possible to define an eosinophilic inflammation phenotype, a neutrophilic phenotype and a paucigranulocytic phenotype according to sputum cell measurements. Furthermore, each inflammatory phenotype was observed with several pathways that could contribute to the definition of the phenotype. However, because there has been no validation of these pathways yet, it is not possible to describe these as endotypes yet. One could consider the cluster associated with the highest expression of T2 and ILC2 pathway signature and sputum eosinophilia to be a severe eosinophilic asthma endotype. On the contrary, the neutrophilic cluster associated with inflammasome activation cannot be considered an endotype yet, because the role of the inflammasome in this cluster is yet to be defined. Nevertheless, this remains a potential therapeutic target for this cluster. Similarly, this similar argument can be made for the third cluster that may be driven by mitochondrial oxidative stress pathways. DEVELOPMENT OF TARGETED THERAPIES Recent progress in the therapy of severe asthma has been marked by the introduction of biologic treatments as add-on treatment to step 5 of the GINA guidelines. Such biologic treatments have now been important in defining the target population, not only because these treatments are relatively expensive compared to existing ones but also because such specific targeting needs to be used only in those who have the target abnormality. However, cost-effectiveness analyses will be needed to determine the true costs of these treatments. These biologic treatments being very specific in their actions in targeting single cytokines have opened up the field of precision medicine, placing the emphasis on the application of precision medicine in severe asthma 4 Volume 23 Number 00 Month 2017

5 Precision medicine for asthma Chung as the correct patient needs to be singled out for these specifically targeted treatments. The greatest emphasis has been on the targeted treatments for the T2 pathway, whereas treatments targeted at non-t2 pathways have been less successful [19 & ]. associated with lower rates of clinically significant asthma exacerbations than those who received placebo, independent of baseline blood eosinophil counts in patients with uncontrolled moderateto-severe asthma [27]. TARGETING THE T2 PATHWAY Activation of Th2 and ILC2 cells can occur through the release of innate cytokines, such as thymic stromal lymphopoietin (TSLP), IL-25 and IL-33 from the epithelium, which can be induced by external stimuli such as lipopolysaccharide, pollutants and viruses [20]. These activated Th2 or ILC2 cells release IL4, 5 and 13, which are expressed in the bronchial submucosa of patients with asthma. The new biologic treatments available for patients with severe asthma include anti-ige antibody and anti-il5 antibody. Anti-IgE antibody prevents the binding of free IgE to IgE receptors on mast cells and basophils by binding itself to free IgE. IgE production from B cells is under the control of the T2 cytokines, IL-4 and IL- 13. Anti-IL5 antibody is targeted towards IL-5, produced by Th2 cells and ILC2s and is important for the terminal differentiation and maturation of eosinophils in the bone marrow and for the mobilization of eosinophils and eosinophil precursors into the circulation. Both anti-ige antibody and anti-il5 antibody are targeted for use in patients with severe asthma, the former for allergic asthmatic patients and the latter for eosinophilic asthma. In severe persistent allergic asthma defined by patients with an allergic background with raised serum IgE levels and at step 4 or 5 of GINA guidelines, omalizumab, an anti-ige antibody, as an add-on therapy decreased severe asthma exacerbations by 26%, compared with placebo [21]. Mepolizumab and reslizumab, anti-il5 antibodies, have been shown to benefit allergic and eosinophilic severe asthma, respectively, by reducing asthma exacerbation frequency and also improving baseline airflow obstruction [22,23 ]: the patients chosen for these studies had to show a raised level of blood eosinophil count. Other potential therapies not yet approved targeting T-2 pathway include anti-il5ra antibody (benralizumab) that inhibits the effect of IL5 [24,25 ], and anti-il4ra antibody (dupilumab) [26 ] that blocks the effects of IL-13 and IL-4 together, both showing beneficial effects on exacerbations and lung function, particularly in those with a raised blood eosinophil count. More recently, tezepelumab (AMG 157/ MEDI9929), a human monoclonal antibody specific for the epithelial-cell-derived cytokine TSLP which regulates type 2 immunity through not only Th2 cells but also through ILC2 cells, has been NON-T2 TARGETS There have been descriptions of non-t2 phenotypes previously. Thus, a systemic IL-6 inflammation with clinical features of metabolic dysfunction associated with more severe asthma has been described [28]. In addition, apart from Th2 high, a Th17 high group has been described with the Th2 high being mutually exclusive of Th17 high [29]. However, despite this targeting non-t2 targets, it has not proven to be successful in providing effective therapies for asthma. Brodalumab, a human anti-il-17ra monoclonal antibody, had no effect on asthma control scores, symptom-free days and FEV 1 in patients with inadequately controlled moderate-to-severe asthma who were receiving ICS therapy [30]. Treatment with a selective CXCR2 antagonist, AZD5069, which blocks the effect of CXCL8, did not reduce the frequency of severe exacerbations in patients with uncontrolled severe asthma [31]. Finally, in adults with uncontrolled severe persistent asthma, the anti-tnfa antibody golimumab had no overall beneficial effects [32]. These have raised the issue as to whether a neutrophilic asthma phenotype does exist [33], but it is more likely that the reason for the failure of these therapies is that the right patients were not chosen for these therapies with the lack of the appropriate biomarkers. The molecular phenotypes derived from sputum transcriptomic analysis in U-BIOPRED defined a neutrophilic inflammatory phenotype (sputum neutrophil >73%), with inflammasome, IFN and TNF activation pathways [13 ]. This could be associated with the microbial dysbiosis that is now increasingly being associated with severe asthma [34], but further validation research is needed to definitely determine the mechanism underlying the neutrophilic inflammation. Analysis of transcriptomics in bronchial biopsies and brushings identified the coexpression of high Th2 and high Th1 pathways indicating that more than one pathway may coexist [35 ]. A raised concentration of the gastrotransmitter, hydrogen sulphide, in sputum has also been associated as a potential biomarker of neutrophilic asthma associated with airflow obstruction [36]. BIOMARKERS FOR PRECISION MEDICINE In order to define the phenotypes that constitute the whole range of asthma and to find the patients who Copyright ß 2017 Wolters Kluwer Health, Inc. All rights reserved. 5

6 Asthma will respond to specific therapies, it is important to define the biomarkers that will help the clinician to select the right therapy for the right patient. A biomarker can be defined as a characteristic that can be measured and evaluated as an indicator of normal or pathological biological processes or the biological response to a therapeutic intervention [37]. Biomarkers mostly indicative of T2-high asthma that are easily accessible to the patient are available for the management of asthma; these include blood eosinophil count and serum IgE and also serum periostin levels, levels of nitric oxide in exhaled breath (FeNO) and sputum eosinophil count in some centres. Using sputum eosinophil counts as a response biomarker to treatment with corticosteroid therapy results in better outcome measures mainly in terms of a reduction in exacerbations compared to using symptom severity [38]. FeNO did not perform as well. Responsiveness to corticosteroid therapy particularly in children can be predicted from a blood eosinophil count [39], but validated cut-off levels in different populations still need to be established. Increasingly, biomarkers will be used to select patients who would be suitable for specific biological treatments. Baseline blood eosinophil count is being used as a biomarker that predicts the clinical efficacy of anti-il5 therapy in patients with severe eosinophilic asthma with a history of exacerbations [15,22,40,41]. Total serum IgE level has been used as a response biomarker for the use of anti-ige antibody, omalizumab, in the treatment of severe allergic asthma. High levels of FeNO (>19.5 parts per billion) and blood eosinophil count (>260/ml) significantly predicted those responding to omalizumab with a reduction in exacerbations [42]. There is an increasing need for developing biomarkers that will guide clinicians in the management of asthma. The following areas need further development: definition of molecular phenotypes of asthma, particularly those in the non-t2/th2 pathways, develop more phenotypic and predictive biomarkers to delineate these molecular phenotypes of asthma and obtain specific biomarkers to predict therapeutic outcomes to more specific targeted therapies. An unbiased approach is necessary to define the phenotypes of asthma. Although the use of omics data from multiple platforms including transcriptomics, proteomics, lipidomics or metabolomics in lung tissue compartments holds the best chance of obtaining endotypes [43,44], biomarkers need to be developed in easily accessible compartments, so-called bedside biomarkers, which can be assayed relatively easily. Thus, assays involving exhaled breath, blood or urine would appear more promising. Therefore, one unmet need is how to develop such bedside biomarkers. The other possibility is that composite biomarkers may be another answer to this [45]. CONCLUSION Because of the heterogeneity and complexity of asthma, a different approach from current practice is needed to the management of asthma that takes into account these varied features of the disease. The use of omics data and unbiased clustering together with the use of clinical features, physiological and inflammatory data will provide greater opportunity of phenotyping asthma according to the mechanisms driving the disease thus leading to endotype definition. Biomarkers could be used to define and categorize these endotypes. This will be a tremendous help for the development of precision medicine for asthma that will allow for more precise treatment aims and also provide a source of novel targets and hence new treatments for each defined endotype. Precision medicine should be applied to the whole spectrum of asthma, not just at the more severe end of the disease. Acknowledgements K.F.C. is a Senior Fellow of the National Institute for Health Research, UK. He also acknowledges support from the Medical Research Council and European Union. Financial support and sponsorship K.F.C. reports personal fees from Advisory Board membership with GSK, Boehringer Ingelheim, Novartis, Astra-Zeneca and Teva, personal fees from payments for lectures from Astra-Zeneca, Novartis and Merck, and grants for research to his institution from Merck and GSK, all in relation to asthma, COPD and cough. Conflicts of interest There are no conflicts of interest. REFERENCES AND RECOMMENDED READING Papers of particular interest, published within the annual period of review, have been highlighted as: & of special interest of outstanding interest 1. Green RH, Brightling CE, Woltmann G, et al. Analysis of induced sputum in adults with asthma: identification of subgroup with isolated sputum neutrophilia and poor response to inhaled corticosteroids. Thorax 2002; 57: Schleich FN, Manise M, Sele J, et al. 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