Stephen J. Fowler

Application of ’omics technologies to biomarker discovery in inflammatory lung diseases

Inflammatory lung diseases are highly complex in respect of pathogenesis and relationships between inflammation, clinical disease and response to treatment. Sophisticated large-scale analytical methods to quantify gene expression (transcriptomics), proteins (proteomics), lipids (lipidomics) and metabolites (metabolomics) in the lungs, blood and urine are now available to identify biomarkers that define disease in terms of combined clinical, physiological and patho-biological abnormalities. The aspiration is that these approaches will improve diagnosis, i.e. define pathological phenotypes, and facilitate the monitoring of disease and therapy, and also, unravel underlying molecular pathways. Biomarker studies can either select predefined biomarker(s) measured by specific methods or apply an “unbiased” approach involving detection platforms that are indiscriminate in focus. This article reviews the technologies presently available to study biomarkers of lung disease within the ’omics field. The contributions of the individual ’omics analytical platforms to the field of respiratory diseases are summarised, with the goal of providing background on their respective abilities to contribute to systems medicine-based studies of lung disease. Summary of the application of ’omics-based analytical platforms for biomarker discovery in inflammatory lung diseases http://ow.ly/mjGGc

Clinical and inflammatory characteristics of the European U-BIOPRED adult severe asthma cohort

U-BIOPRED is a European Union consortium of 20 academic institutions, 11 pharmaceutical companies and six patient organisations with the objective of improving the understanding of asthma disease mechanisms using a systems biology approach. This cross-sectional assessment of adults with severe asthma, mild/moderate asthma and healthy controls from 11 European countries consisted of analyses of patient-reported outcomes, lung function, blood and airway inflammatory measurements. Patients with severe asthma (nonsmokers, n=311; smokers/ex-smokers, n=110) had more symptoms and exacerbations compared to patients with mild/moderate disease (n=88) (2.5 exacerbations versus 0.4 in the preceding 12 months; p<0.001), with worse quality of life, and higher levels of anxiety and depression. They also had a higher incidence of nasal polyps and gastro-oesophageal reflux with lower lung function. Sputum eosinophil count was higher in severe asthma compared to mild/moderate asthma (median count 2.99% versus 1.05%; p=0.004) despite treatment with higher doses of inhaled and/or oral corticosteroids. Consistent with other severe asthma cohorts, U-BIOPRED is characterised by poor symptom control, increased comorbidity and airway inflammation, despite high levels of treatment. It is well suited to identify asthma phenotypes using the array of “omic” datasets that are at the core of this systems medicine approach. Severe asthma results in more airway inflammation, worse symptoms and lower lung function, despite increased therapy http://ow.ly/QznR3

Nontuberculous mycobacteria in bronchiectasis: prevalence and patient characteristics

The aim of the current study was to investigate the prevalence and clinical associations of nontuberculous mycobacteria (NTM) in a well-characterised cohort of patients with adult-onset bronchiectasis. The sputum of all patients attending a tertiary referral bronchiectasis clinic between April 2002 and August 2003 was examined for mycobacteria as part of an extensive diagnostic work-up. NTM-positive patients subsequently had further sputa examined. A modified bronchiectasis scoring system was applied to all high-resolution computed tomography (HRCT) scans from NTM-positive patients, and a matched cohort without NTM. Out of 98 patients attending the clinic, 10 had NTM in their sputum on first culture; of those, eight provided multiple positive cultures. Three patients were treated for NTM infection. A higher proportion of NTM-positive than -negative patients were subsequently diagnosed with cystic fibrosis (two out of nine versus two out of 75). On HRCT scoring, more patients in the NTM-positive group had peripheral mucus plugging than in the NTM-negative group. In the current prospective study of a large cohort of patients with bronchiectasis, 10% cultured positive for nontuberculous mycobacteria in a random clinic sputum sample. Few clinical parameters were helpful in discriminating between groups, except for a higher prevalence of previously undiagnosed cystic fibrosis and of peripheral mucus plugging on high-resolution computed tomography in the nontuberculous mycobacteria group.

Non-invasive metabolomic analysis of breath using differential mobility spectrometry in patients with chronic obstructive pulmonary disease and healthy smokers

The rapid, accurate and non-invasive diagnosis of respiratory disease represents a challenge to clinicians, and the development of new treatments can be confounded by insufficient knowledge of lung disease phenotypes. Exhaled breath contains a complex mixture of volatile organic compounds (VOCs), some of which could potentially represent biomarkers for lung diseases. We have developed an adaptive sampling methodology for collecting concentrated samples of exhaled air from participants with impaired respiratory function, against which we employed two-stage thermal desorption gas chromatography-differential mobility spectrometry (GC-DMS) analysis, and showed that it was possible to discriminate between participants with and without chronic obstructive pulmonary disease (COPD). A 2.5 dm(3) volume of end tidal breath was collected onto adsorbent traps (Tenax TA/Carbotrap), from participants with severe COPD and healthy volunteers. Samples were thermally desorbed and analysed by GC-DMS, and the chromatograms analysed by univariate and multivariate analyses. Kruskal-Wallis ANOVA indicated several discriminatory (p < 0.01) signals, with good classification performance (receiver operator characteristic area up to 0.82). Partial least squares discriminant analysis using the full DMS chromatograms also gave excellent discrimination between groups (alpha = 19% and beta = 12.4%).

Non-invasive phenotyping using exhaled volatile organic compounds in asthma

Background Breath volatile organic compounds (VOCs) may be useful for asthma diagnosis and phenotyping, identifying patients who could benefit from personalised therapeutic strategies. The authors aimed to identify specific patterns of breath VOCs in patients with asthma and in clinically relevant disease phenotypes. Methods Breath samples were analysed by gas chromatography–mass spectrometry. The Asthma Control Questionnaire was completed, together with lung function and induced sputum cell counts. Breath data were reduced to principal components, and these principal components were used in multiple logistic regression to identify discriminatory models for diagnosis, sputum inflammatory cell profile and asthma control. Results The authors recruited 35 patients with asthma and 23 matched controls. A model derived from 15 VOCs classified patients with asthma with an accuracy of 86%, and positive and negative predictive values of 0.85 and 0.89, respectively. Models also classified patients with asthma based on the following phenotypes: sputum (obtained in 18 patients with asthma) eosinophilia ≥2% area under the receiver operating characteristics (AUROC) curve 0.98, neutrophilia ≥40% AUROC 0.90 and uncontrolled asthma (Asthma Control Questionnaire ≥1) AUROC 0.96. Conclusions Detection of characteristic breath VOC profiles could classify patients with asthma versus controls, and clinically relevant disease phenotypes based on sputum inflammatory profile and asthma control. Prospective validation of these models may lead to clinical application of non-invasive breath profiling in asthma.

Effects of mediator antagonism on mannitol and adenosine monophosphate challenges

Background Airway hyper‐responsiveness (AHR) to indirect stimuli is a useful non‐invasive surrogate inflammatory marker in the evaluation of asthma, while histamine and cysteinyl leukotrienes are important inflammatory mediators.

Dose response of inhaled corticosteroids on bronchial hyperresponsiveness: a meta-analysis.

BACKGROUND There is a relatively steep dose-response curve for effects of inhaled corticosteroids on conventional airway markers of asthmatic disease control. OBJECTIVE We sought to determine whether a dose-response effect exists for bronchial hyperresponsiveness. METHODS A meta-analysis of placebo-controlled trials in asthmatic patients was performed using a computerized systematic review of databases. Doubling dose/dilution protection of inhaled corticosteroid was compared with placebo. Studies which used direct (methacholine and histamine) and indirect (adenosine monophosphate) bronchial challenge stimuli were eligible for inclusion. RESULTS Twenty-five studies fulfilled eligibility criteria (963 patients). Values for doubling dose/dilution protection categorized by low/medium dose (< 1,000 microg) and high dose (> or = 1,000 microg) of inhaled corticosteroid amounted to a 1.25 (95% confidence interval 1.08 to 1.42) and 2.16 (95% confidence interval 1.88 to 2.44) shift, respectively. CONCLUSIONS High doses of inhaled corticosteroids conferred greater improvements in bronchial hyperresponsiveness than low doses.

The burden of severe asthma in childhood and adolescence: results from the paediatric U-BIOPRED cohorts

U-BIOPRED aims to characterise paediatric and adult severe asthma using conventional and innovative systems biology approaches. A total of 99 school-age children with severe asthma and 81 preschoolers with severe wheeze were compared with 49 school-age children with mild/moderate asthma and 53 preschoolers with mild/moderate wheeze in a cross-sectional study. Despite high-dose treatment, the severe cohorts had more severe exacerbations compared with the mild/moderate ones (annual medians: school-aged 3.0 versus 1.1, preschool 3.9 versus 1.8; p<0.001). Exhaled tobacco exposure was common in the severe wheeze cohort. Almost all participants in each cohort were atopic and had a normal body mass index. Asthma-related quality of life, as assessed by the Paediatric Asthma Quality of Life Questionnaire (PAQLQ) and the Paediatric Asthma Caregivers Quality of Life Questionnaire (PACQLQ), was worse in the severe cohorts (mean±se school-age PAQLQ: 4.77±0.15 versus 5.80±0.19; preschool PACQLQ: 4.27±0.18 versus 6.04±0.18; both p≤0.001); however, mild/moderate cohorts also had significant morbidity. Impaired quality of life was associated with poor control and airway obstruction. Otherwise, the severe and mild/moderate cohorts were clinically very similar. Children with severe preschool wheeze or severe asthma are usually atopic and have impaired quality of life that is associated with poor control and airflow limitation: a very different phenotype from adult severe asthma. In-depth phenotyping of these children, integrating clinical data with high-dimensional biomarkers, may help to improve and tailor their clinical management. Children with severe preschool wheeze or severe asthma are usually atopic and have impaired quality of life http://ow.ly/RrrGE

Taking your breath away: metabolomics breathes life in to personalized medicine

Breath-based metabolomics (breathomics) is an exciting developing area of biotechnology that centers on the capture, identification, and quantification of volatile organic compound (VOC) patterns in human breath and their utilization as tools in the diagnosis of a broad spectrum of medical problems. With the age of personalized medicines demanding rapid bespoke diagnosis and treatment, this area of molecular diagnostics is beginning to see an upsurge in biotechnological advancement. Here, we discuss recent improvements and directions in the development of breath VOC analysis and diagnosis platforms that offer the potential for disease biomarker discovery and disease prognosis.

A European Respiratory Society technical standard: exhaled biomarkers in lung disease

Breath tests cover the fraction of nitric oxide in expired gas (FENO), volatile organic compounds (VOCs), variables in exhaled breath condensate (EBC) and other measurements. For EBC and for FENO, official recommendations for standardised procedures are more than 10 years old and there is none for exhaled VOCs and particles. The aim of this document is to provide technical standards and recommendations for sample collection and analytic approaches and to highlight future research priorities in the field. For EBC and FENO, new developments and advances in technology have been evaluated in the current document. This report is not intended to provide clinical guidance on disease diagnosis and management. Clinicians and researchers with expertise in exhaled biomarkers were invited to participate. Published studies regarding methodology of breath tests were selected, discussed and evaluated in a consensus-based manner by the Task Force members. Recommendations for standardisation of sampling, analysing and reporting of data and suggestions for research to cover gaps in the evidence have been created and summarised. Application of breath biomarker measurement in a standardised manner will provide comparable results, thereby facilitating the potential use of these biomarkers in clinical practice. ERS technical standard: exhaled biomarkers in lung disease http://ow.ly/mAjr309DBOP