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Granell R, Haider S, Deliu M, Ullah A, Mahmoud O, Fontanella S, Lowe L, Simpson A, Dodd JW, Arshad SH, Murray CS, Roberts G, Hughes A, Park C, Holloway JW, Custovic A. Lung function trajectories from school age to adulthood and their relationship with markers of cardiovascular disease risk. Thorax 2024; 79:770-777. [PMID: 38697843 PMCID: PMC11287578 DOI: 10.1136/thorax-2023-220485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 04/14/2024] [Indexed: 05/05/2024]
Abstract
RATIONALE Lung function in early adulthood is associated with subsequent adverse health outcomes. OBJECTIVES To ascertain whether stable and reproducible lung function trajectories can be derived in different populations and investigate their association with objective measures of cardiovascular structure and function. METHODS Using latent profile modelling, we studied three population-based birth cohorts with repeat spirometry data from childhood into early adulthood to identify trajectories of forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC). We used multinomial logistic regression models to investigate early-life predictors of the derived trajectories. We then ascertained the extent of the association between the derived FEV1/FVC trajectories and blood pressure and echocardiographic markers of increased cardiovascular risk and stroke in ~3200 participants at age 24 years in one of our cohorts. RESULTS We identified four FEV1/FVC trajectories with strikingly similar latent profiles across cohorts (pooled N=6377): above average (49.5%); average (38.3%); below average (10.6%); and persistently low (1.7%). Male sex, wheeze, asthma diagnosis/medication and allergic sensitisation were associated with trajectories with diminished lung function in all cohorts. We found evidence of an increase in cardiovascular risk markers ascertained by echocardiography (including left ventricular mass indexed to height and carotid intima-media thickness) with decreasing FEV1/FVC (with p values for the mean crude effects per-trajectory ranging from 0.10 to p<0.001). In this analysis, we considered trajectories as a pseudo-continuous variable; we confirmed the assumption of linearity in all the regression models. CONCLUSIONS Childhood lung function trajectories may serve as predictors in the development of not only future lung disease, but also the cardiovascular disease and multimorbidity in adulthood.
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Affiliation(s)
- Raquel Granell
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sadia Haider
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Matea Deliu
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Anhar Ullah
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Osama Mahmoud
- Mathematical Sciences, University of Essex, Colchester, UK
- Applied Statistics, Helwan University Faculty of Commerce, Cairo, Egypt
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Lesley Lowe
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - James William Dodd
- Academic Respiratory Unit, North Bristol NHS Trust, Westbury on Trym, UK
- MRC Integrative Epidemiology Unit, Bristol, UK
| | | | - Clare S Murray
- Respiratory Group, University of Manchester, School of Translational Medicine, Manchester, UK
| | - Graham Roberts
- Human Development and Health Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK
- Respiratory Biomedical Research Unit, Southampton University Hospitals Trust, Southampton, UK
| | - Alun Hughes
- MRC Unit for Lifelong Health and Ageing at UCL, Department of Population Science & Experimental Medicine, Institute of Cardiovascular Science, UCL, London, UK
| | - Chloe Park
- MRC Unit for Lifelong Health and Ageing at UCL, Department of Population Science & Experimental Medicine, Institute of Cardiovascular Science, UCL, London, UK
| | - John W Holloway
- Human Development and Health Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, UK
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Ullah A, Granell R, Haider S, Lowe L, Fontanella S, Arshad H, Murray CS, Turner S, Holloway JW, Simpson A, Roberts G, Custovic A. Obstructive and restrictive spirometry from school age to adulthood: three birth cohort studies. EClinicalMedicine 2024; 67:102355. [PMID: 38169936 PMCID: PMC10758747 DOI: 10.1016/j.eclinm.2023.102355] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 01/05/2024] Open
Abstract
Background Spirometric obstruction and restriction are two patterns of impaired lung function which are predictive of poor health. We investigated the development of these phenotypes and their transitions through childhood to early adulthood. Methods In this study, we analysed pooled data from three UK population-based birth cohorts established between 1989 and 1995. We applied descriptive statistics, regression modelling and data-driven modelling to data from three population-based birth cohorts with at least three spirometry measures from childhood to adulthood (mid-school: 8-10 years, n = 8404; adolescence: 15-18, n = 5764; and early adulthood: 20-26, n = 4680). Participants were assigned to normal, restrictive, and obstructive spirometry based on adjusted regression residuals. We considered two transitions: from 8-10 to 15-18 and from 15-18 to 20-26 years. Findings Obstructive phenotype was observed in ∼10%, and restrictive in ∼9%. A substantial proportion of children with impaired lung function in school age (between one third in obstructive and a half in restricted phenotype) improved and achieved normal and stable lung function to early adulthood. Of those with normal lung function in school-age, <5% declined to adulthood. Underweight restrictive and obese obstructive participants were less likely to transit to normal. Maternal smoking during pregnancy and current asthma diagnosis increased the risk of persistent obstruction and worsening. Significant associate of worsening in restrictive phenotypes was lower BMI at the first lung function assessment. Data-driven methodologies identified similar risk factors for obstructive and restrictive clusters. Interpretation The worsening and improvement in obstructive and restrictive spirometry were observed at all ages. Maintaining optimal weight during childhood and reducing maternal smoking during pregnancy may reduce spirometry obstruction and restriction and improve lung function. Funding MRC Grant MR/S025340/1.
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Affiliation(s)
- Anhar Ullah
- National Heart and Lung Institute, Imperial College London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
| | - Raquel Granell
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, UK
| | - Sadia Haider
- National Heart and Lung Institute, Imperial College London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
| | - Lesley Lowe
- Faculty of Biology, Medicine and Health, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Centre, UK
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
| | - Hasan Arshad
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Clare S. Murray
- Faculty of Biology, Medicine and Health, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Centre, UK
| | - Steve Turner
- Royal Aberdeen Children's Hospital NHS Grampian Aberdeen, AB25 2ZG, UK
- Child Health, University of Aberdeen, Aberdeen, UK
| | - John W. Holloway
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, UK
| | - Angela Simpson
- Faculty of Biology, Medicine and Health, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Centre, UK
| | - Graham Roberts
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
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Haider S, Granell R, Curtin JA, Holloway JW, Fontanella S, Hasan Arshad S, Murray CS, Cullinan P, Turner S, Roberts G, Simpson A, Custovic A. Identification of eczema clusters and their association with filaggrin and atopic comorbidities: analysis of five birth cohorts. Br J Dermatol 2023; 190:45-54. [PMID: 37935633 PMCID: PMC10733627 DOI: 10.1093/bjd/ljad326] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/23/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Longitudinal modelling of the presence/absence of current eczema through childhood has identified similar phenotypes, but their characteristics often differ between studies. OBJECTIVES To demonstrate that a more comprehensive description of longitudinal pattern of symptoms may better describe trajectories than binary information on eczema presence. METHODS We derived six multidimensional variables of eczema spells from birth to 18 years of age (including duration, temporal sequencing and the extent of persistence/recurrence). Spells were defined as consecutive observations of eczema separated by no eczema across 5 epochs in five birth cohorts: infancy (first year); early childhood (age 2-3 years); preschool/early school age (4-5 years); middle childhood (8-10 years); adolescence (14-18 years). We applied Partitioning Around Medoids clustering on these variables to derive clusters of the temporal patterns of eczema. We then investigated the stability of the clusters, within-cluster homogeneity and associated risk factors, including FLG mutations. RESULTS Analysis of 7464 participants with complete data identified five clusters: (i) no eczema (51.0%); (ii) early transient eczema (21.6%); (iii) late-onset eczema (LOE; 8.1%); (iv) intermittent eczema (INT; 7.5%); and (v) persistent eczema (PE; 11.8%). There was very-high agreement between the assignment of individual children into clusters when using complete or imputed (n = 15 848) data (adjusted Rand index = 0.99; i.e. the clusters were very stable). Within-individual symptom patterns across clusters confirmed within-cluster homogeneity, with consistent patterns of symptoms among participants within each cluster and no overlap between the clusters. Clusters were characterized by differences in associations with risk factors (e.g. parental eczema was associated with all clusters apart from LOE; sensitization to inhalant allergens was associated with all clusters, with the highest risk in the PE cluster). All clusters apart from LOE were associated with FLG mutations. Of note, the strongest association was for PE [relative risk ratio (RRR) 2.70, 95% confidence interval (CI) 2.24-3.26; P < 0.001] followed by INT (RRR 2.29, 95% CI 1.82-2.88; P < 0.001). CONCLUSIONS Clustering of multidimensional variables identified stable clusters with different genetic architectures. Using multidimensional variables may capture eczema development and derive stable and internally homogeneous clusters. However, deriving homogeneous symptom clusters does not necessarily mean that these are underpinned by completely unique mechanisms.
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Affiliation(s)
- Sadia Haider
- National Heart and Lung Institute, Imperial College London, UK
- NIHR Imperial Biomedical Research Centre (BRC), London, UK
| | - Raquel Granell
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - John A Curtin
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, UK
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, UK
- NIHR Imperial Biomedical Research Centre (BRC), London, UK
| | - Syed Hasan Arshad
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Newport, Isle of Wight, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Clare S Murray
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester, UK
| | - Paul Cullinan
- National Heart and Lung Institute, Imperial College London, UK
| | - Stephen Turner
- Royal Aberdeen Children’s Hospital, NHS Grampian, Aberdeen, UK
- Child Health, University of Aberdeen, Aberdeen, UK
| | - Graham Roberts
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Newport, Isle of Wight, UK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, UK
- NIHR Imperial Biomedical Research Centre (BRC), London, UK
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Custovic D, Fontanella S, Custovic A. Understanding progression from pre-school wheezing to school-age asthma: Can modern data approaches help? Pediatr Allergy Immunol 2023; 34:e14062. [PMID: 38146116 DOI: 10.1111/pai.14062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023]
Abstract
Preschool wheezing and childhood asthma create a heavy disease burden which is only exacerbated by the complexity of the conditions. Preschool wheezing exhibits both "curricular" and "aetiological" heterogeneity: that is, heterogeneity across patients both in the time-course of its development and in its underpinning pathological mechanisms. Since these are not fully understood, but clinical presentations across patients may nonetheless be similar, current diagnostic labels are imprecise-not mapping cleanly onto underlying disease mechanisms-and prognoses uncertain. These uncertainties also make a identifying new targets for therapeutic intervention difficult. In the past few decades, carefully designed birth cohort studies have collected "big data" on a large scale, incorporating not only a wealth of longitudinal clinical data, but also detailed information from modalities as varied as imaging, multiomics, and blood biomarkers. The profusion of big data has seen the proliferation of what we term "modern data approaches" (MDAs)-grouping together machine learning, artificial intelligence, and data science-to make sense and make use of this data. In this review, we survey applications of MDAs (with an emphasis on machine learning) in childhood wheeze and asthma, highlighting the extent of their successes in providing tools for prognosis, unpicking the curricular heterogeneity of these conditions, clarifying the limitations of current diagnostic criteria, and indicating directions of research for uncovering the etiology of the diseases underlying these conditions. Specifically, we focus on the trajectories of childhood wheeze phenotypes. Further, we provide an explainer of the nature and potential use of MDAs and emphasize the scope of what we can hope to achieve with them.
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Affiliation(s)
- Darije Custovic
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, UK
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Bush A. Going Down, Dooby Doo Down, Down: Identifying Rapid Spirometry Decline. Am J Respir Crit Care Med 2023; 208:1014-1015. [PMID: 37552692 PMCID: PMC10867937 DOI: 10.1164/rccm.202307-1212ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023] Open
Affiliation(s)
- Andrew Bush
- National Heart and Lung Institute Imperial College London, United Kingdom and Imperial Centre for Paediatrics and Child Health Royal Brompton Hospital London, England
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Reyna ME, Bedard MA, Subbarao P. Lung Function as a Biomarker of Health: An Old Concept Rediscovered. Am J Respir Crit Care Med 2023; 208:117-119. [PMID: 37311247 PMCID: PMC10395500 DOI: 10.1164/rccm.202305-0911ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/15/2023] Open
Affiliation(s)
- Myrtha E Reyna
- Translational Medicine Department The Hospital for Sick Children Toronto, Ontario, Canada
- Dalla Lana School of Public Health University of Toronto Toronto, Ontario, Canada
| | - Marc-Antoine Bedard
- Translational Medicine Department The Hospital for Sick Children Toronto, Ontario, Canada
- Laval University Hospital Center Laval University Quebec City, Quebec, Canada
| | - Padmaja Subbarao
- Translational Medicine Department The Hospital for Sick Children Toronto, Ontario, Canada
- Dalla Lana School of Public Health and Department of Physiology University of Toronto Toronto, Ontario, Canada
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7
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Granell R, Curtin JA, Haider S, Kitaba NT, Mathie SA, Gregory LG, Yates LL, Tutino M, Hankinson J, Perretti M, Vonk JM, Arshad HS, Cullinan P, Fontanella S, Roberts GC, Koppelman GH, Simpson A, Turner SW, Murray CS, Lloyd CM, Holloway JW, Custovic A. A meta-analysis of genome-wide association studies of childhood wheezing phenotypes identifies ANXA1 as a susceptibility locus for persistent wheezing. eLife 2023; 12:e84315. [PMID: 37227431 PMCID: PMC10292845 DOI: 10.7554/elife.84315] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/22/2023] [Indexed: 05/26/2023] Open
Abstract
Background Many genes associated with asthma explain only a fraction of its heritability. Most genome-wide association studies (GWASs) used a broad definition of 'doctor-diagnosed asthma', thereby diluting genetic signals by not considering asthma heterogeneity. The objective of our study was to identify genetic associates of childhood wheezing phenotypes. Methods We conducted a novel multivariate GWAS meta-analysis of wheezing phenotypes jointly derived using unbiased analysis of data collected from birth to 18 years in 9568 individuals from five UK birth cohorts. Results Forty-four independent SNPs were associated with early-onset persistent, 25 with pre-school remitting, 33 with mid-childhood remitting, and 32 with late-onset wheeze. We identified a novel locus on chr9q21.13 (close to annexin 1 [ANXA1], p<6.7 × 10-9), associated exclusively with early-onset persistent wheeze. We identified rs75260654 as the most likely causative single nucleotide polymorphism (SNP) using Promoter Capture Hi-C loops, and then showed that the risk allele (T) confers a reduction in ANXA1 expression. Finally, in a murine model of house dust mite (HDM)-induced allergic airway disease, we demonstrated that anxa1 protein expression increased and anxa1 mRNA was significantly induced in lung tissue following HDM exposure. Using anxa1-/- deficient mice, we showed that loss of anxa1 results in heightened airway hyperreactivity and Th2 inflammation upon allergen challenge. Conclusions Targeting this pathway in persistent disease may represent an exciting therapeutic prospect. Funding UK Medical Research Council Programme Grant MR/S025340/1 and the Wellcome Trust Strategic Award (108818/15/Z) provided most of the funding for this study.
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Affiliation(s)
- Raquel Granell
- MRC Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of BristolBristolUnited Kingdom
| | - John A Curtin
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUnited Kingdom
| | - Sadia Haider
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - Negusse Tadesse Kitaba
- Human Development and Health, Faculty of Medicine, University of SouthamptonSouthamptonUnited Kingdom
| | - Sara A Mathie
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - Lisa G Gregory
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - Laura L Yates
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - Mauro Tutino
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUnited Kingdom
| | - Jenny Hankinson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUnited Kingdom
| | - Mauro Perretti
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of LondonLondonUnited Kingdom
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen\GroningenNetherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC)GroningenNetherlands
| | - Hasan S Arshad
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation TrustSouthamptonUnited Kingdom
- David Hide Asthma and Allergy Research CentreIsle of WightUnited Kingdom
- Clinical and Experimental Sciences, Faculty of Medicine, University of SouthamptonSouthamptonUnited Kingdom
| | - Paul Cullinan
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - Graham C Roberts
- Human Development and Health, Faculty of Medicine, University of SouthamptonSouthamptonUnited Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation TrustSouthamptonUnited Kingdom
- David Hide Asthma and Allergy Research CentreIsle of WightUnited Kingdom
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC)GroningenNetherlands
- Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children’s HospitalGroningenNetherlands
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUnited Kingdom
| | - Steve W Turner
- Child Health, University of AberdeenAberdeenUnited Kingdom
| | - Clare S Murray
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUnited Kingdom
| | - Clare M Lloyd
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of SouthamptonSouthamptonUnited Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation TrustSouthamptonUnited Kingdom
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
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Haider S, Fontanella S, Ullah A, Turner S, Simpson A, Roberts G, Murray CS, Holloway JW, Curtin JA, Cullinan P, Arshad SH, Hurault G, Granell R, Custovic A. Evolution of Eczema, Wheeze, and Rhinitis from Infancy to Early Adulthood: Four Birth Cohort Studies. Am J Respir Crit Care Med 2022; 206:950-960. [PMID: 35679320 PMCID: PMC9802000 DOI: 10.1164/rccm.202110-2418oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/09/2022] [Indexed: 01/07/2023] Open
Abstract
Rationale: The relationship between eczema, wheeze or asthma, and rhinitis is complex, and epidemiology and mechanisms of their comorbidities is unclear. Objectives: To investigate within-individual patterns of morbidity of eczema, wheeze, and rhinitis from birth to adolescence/early adulthood. Methods: We investigated onset, progression, and resolution of eczema, wheeze, and rhinitis using descriptive statistics, sequence mining, and latent Markov modeling in four population-based birth cohorts. We used logistic regression to ascertain if early-life eczema or wheeze, or genetic factors (filaggrin [FLG] mutations and 17q21 variants), increase the risk of multimorbidity. Measurements and Main Results: Single conditions, although the most prevalent, were observed significantly less frequently than by chance. There was considerable variation in the timing of onset/remission/persistence/intermittence. Multimorbidity of eczema+wheeze+rhinitis was rare but significantly overrepresented (three to six times more often than by chance). Although infantile eczema was associated with subsequent multimorbidity, most children with eczema (75.4%) did not progress to any multimorbidity pattern. FLG mutations and rs7216389 were not associated with persistence of eczema/wheeze as single conditions, but both increased the risk of multimorbidity (FLG by 2- to 3-fold, rs7216389 risk variant by 1.4- to 1.7-fold). Latent Markov modeling revealed five latent states (no disease/low risk, mainly eczema, mainly wheeze, mainly rhinitis, multimorbidity). The most likely transition to multimorbidity was from eczema state (0.21). However, although this was one of the highest transition probabilities, only one-fifth of those with eczema transitioned to multimorbidity. Conclusions: Atopic diseases fit a multimorbidity framework, with no evidence for sequential atopic march progression. The highest transition to multimorbidity was from eczema, but most children with eczema (more than three-quarters) had no comorbidities.
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Affiliation(s)
| | | | | | - Stephen Turner
- Royal Aberdeen Children’s Hospital National Health Service Grampian Aberdeen, Aberdeen, United Kingdom
- Child Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Angela Simpson
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | - Graham Roberts
- Human Development and Health and
- National Institute for Health and Care Research Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
- David Hide Asthma and Allergy Research Centre, Isle of Wight, United Kingdom; and
| | - Clare S. Murray
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | - John W. Holloway
- Human Development and Health and
- National Institute for Health and Care Research Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - John A. Curtin
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | | | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- National Institute for Health and Care Research Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
- David Hide Asthma and Allergy Research Centre, Isle of Wight, United Kingdom; and
| | - Guillem Hurault
- Faculty of Engineering, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Raquel Granell
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
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Haider S, Granell R, Curtin J, Fontanella S, Cucco A, Turner S, Simpson A, Roberts G, Murray CS, Holloway JW, Devereux G, Cullinan P, Arshad SH, Custovic A. Modeling Wheezing Spells Identifies Phenotypes with Different Outcomes and Genetic Associates. Am J Respir Crit Care Med 2022; 205:883-893. [PMID: 35050846 PMCID: PMC9838626 DOI: 10.1164/rccm.202108-1821oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Rationale: Longitudinal modeling of current wheezing identified similar phenotypes, but their characteristics often differ between studies. Objectives: We propose that a more comprehensive description of wheeze may better describe trajectories than binary information on the presence/absence of wheezing. Methods: We derived six multidimensional variables of wheezing spells from birth to adolescence (including duration, temporal sequencing, and the extent of persistence/recurrence). We applied partition-around-medoids clustering on these variables to derive phenotypes in five birth cohorts. We investigated within- and between-phenotype differences compared with binary latent class analysis models and ascertained associations of these phenotypes with asthma and lung function and with polymorphisms in asthma loci 17q12-21 and CDHR3 (cadherin-related family member 3). Measurements and Main Results: Analysis among 7,719 participants with complete data identified five spell-based wheeze phenotypes with a high degree of certainty: never (54.1%), early-transient (ETW) (23.7%), late-onset (LOW) (6.9%), persistent (PEW) (8.3%), and a novel phenotype, intermittent wheeze (INT) (6.9%). FEV1/FVC was lower in PEW and INT compared with ETW and LOW and declined from age 8 years to adulthood in INT. 17q12-21 and CDHR3 polymorphisms were associated with higher odds of PEW and INT, but not ETW or LOW. Latent class analysis- and spell-based phenotypes appeared similar, but within-phenotype individual trajectories and phenotype allocation differed substantially. The spell-based approach was much more robust in dealing with missing data, and the derived clusters were more stable and internally homogeneous. Conclusions: Modeling of spell variables identified a novel intermittent wheeze phenotype associated with lung function decline to early adulthood. Using multidimensional spell variables may better capture wheeze development and provide a more robust input for phenotype derivation.
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Affiliation(s)
- Sadia Haider
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Raquel Granell
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - John Curtin
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Alex Cucco
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Stephen Turner
- Royal Aberdeen Children’s Hospital National Health Service Grampian, Aberdeen, United Kingdom;,Child Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Graham Roberts
- Human Development and Health and,National Institute for Health Research Southampton Biomedical Research Centre, University Hospitals Southampton National Health Service Foundation Trust, Southampton, United Kingdom;,David Hide Asthma and Allergy Research Centre, Isle of Wight, United Kingdom; and
| | - Clare S. Murray
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - John W. Holloway
- Human Development and Health and,National Institute for Health Research Southampton Biomedical Research Centre, University Hospitals Southampton National Health Service Foundation Trust, Southampton, United Kingdom
| | - Graham Devereux
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Paul Cullinan
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom;,National Institute for Health Research Southampton Biomedical Research Centre, University Hospitals Southampton National Health Service Foundation Trust, Southampton, United Kingdom;,David Hide Asthma and Allergy Research Centre, Isle of Wight, United Kingdom; and
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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10
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Custovic A, Siddiqui S, Saglani S. Considering biomarkers in asthma disease severity. J Allergy Clin Immunol 2021; 149:480-487. [PMID: 34942235 DOI: 10.1016/j.jaci.2021.11.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 10/19/2022]
Abstract
Amongst patients with asthma, reliance on the type/dose of prescribed medication and symptom control does not adequately capture those at risk of adverse outcomes, and we need biomarkers for risk and treatment stratification which are consistently accurate, readily quantifiable and reproducible. The majority of patients with severe asthma, regardless of age, have predominant type-2 (T2) inflammation mediated disease, making airway/blood eosinophils, FeNO, periostin and/or allergic sensitization potentially important biomarkers for severe disease. In both adult and pediatric asthma, there is scope to improve prediction of severe attacks by using a composite T2 biomarkers of blood eosinophils and FeNO. Technological advances in component-resolved diagnostics (CRD) microarray technologies coupled with the development of interpretation software offer a possibility to use CRD as biomarkers of asthma severity amongst sensitized asthmatics. Genetic predisposition and polygenic risk scores of relevant traits (e.g., lung function, host immune responses, biomarkers of exposure from the indoor and outdoor environment, infection and microbial dysbiosis) may also contribute to prediction algorithms. We challenge the idea that asthma can be accurately defined in an individual patient by a discrete and static "endotype" (e.g., T2-high asthma). As we traverse the new era of molecular endotyping in asthma, we need to understand how relevant mechanisms impact patient outcomes, and in parallel develop new tools and approaches to stratify therapies and define individual patient trajectories.
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Affiliation(s)
- Adnan Custovic
- National Heart and Lung Institute, Imperial College London, UK.
| | - Salman Siddiqui
- Department of Respiratory Sciences, University of Leicester and NIHR Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester UK
| | - Sejal Saglani
- National Heart and Lung Institute, Imperial College London, UK
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11
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Bush A. Impact of early life exposures on respiratory disease. Paediatr Respir Rev 2021; 40:24-32. [PMID: 34144911 DOI: 10.1016/j.prrv.2021.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/20/2021] [Indexed: 12/21/2022]
Abstract
The antecedents of asthma and chronic obstructive pulmonary disease (COPD) lie before school age. Adverse effects are transgenerational, antenatal and in the preschool years. Antenatal adverse effects impair spirometry by causing low birth weight, altered lung structure and immune function, and sensitizing the foetus to later insults. The key stages of normal lung health are lung function at birth, lung growth to a plateau age 20-25 years, and the phase of decline thereafter; contrary to perceived wisdom, accelerated decline is not related to smoking. There are different trajectories of lung function. Lung function usually tracks from preschool to late middle age. Asthma is driven by antenatal and early life influences. The airflow obstruction, emphysema and multi-morbidity of COPD all start early. Failure to reach a normal plateau and accelerated decline in lung function are risk factors for COPD. Airway disease cannot be prevented in adult life; prevention must start early.
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Affiliation(s)
- Andrew Bush
- Paediatrics and Paediatric Respirology, Imperial College, UK; Imperial Centre for Paediatrics and Child Health, UK; Consultant Paediatric Chest Physician, Royal Brompton Harefield NHS Foundation Trust, UK.
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12
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Haider S, Simpson A, Custovic A. Genetics of Asthma and Allergic Diseases. Handb Exp Pharmacol 2021; 268:313-329. [PMID: 34085121 DOI: 10.1007/164_2021_484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Asthma genes have been identified through a range of approaches, from candidate gene association studies and family-based genome-wide linkage analyses to genome-wide association studies (GWAS). The first GWAS of asthma, reported in 2007, identified multiple markers on chromosome 17q21 as associates of the childhood-onset asthma. This remains the best replicated asthma locus to date. However, notwithstanding undeniable successes, genetic studies have produced relatively heterogeneous results with limited replication, and despite considerable promise, genetics of asthma and allergy has, so far, had limited impact on patient care, our understanding of disease mechanisms, and development of novel therapeutic targets. The paucity of precise replication in genetic studies of asthma is partly explained by the existence of numerous gene-environment interactions. Another important issue which is often overlooked is that of time of the assessment of the primary outcome(s) and the relevant environmental exposures. Most large GWASs use the broadest possible definition of asthma to increase the sample size, but the unwanted consequence of this is increased phenotypic heterogeneity, which dilutes effect sizes. One way of addressing this is to precisely define disease subtypes (e.g. by applying novel mathematical approaches to rich phenotypic data) and use these latent subtypes in genetic studies.
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Affiliation(s)
- Sadia Haider
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, UK.
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13
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Ödling M, Wang G, Andersson N, Hallberg J, Janson C, Bergström A, Melén E, Kull I. Characterization of Asthma Trajectories from Infancy to Young Adulthood. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2021; 9:2368-2376.e3. [PMID: 33607340 DOI: 10.1016/j.jaip.2021.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Development of asthma is complicated by the multidimensional nature of the disease. OBJECTIVE To identify and characterize trajectories of asthma from infancy to young adulthood, and their associations with lung function and inflammatory and respiratory markers in adolescence and young adulthood. METHODS A latent class analysis was performed in a population-based cohort (N = 4089). Parental and self-reported symptoms of asthma were used to investigate asthma development. We characterized background factors, allergic comorbidity, and IgE sensitization and investigated associations with asthma markers. RESULTS A 4-class solution of asthma trajectories was identified: never/infrequent (n = 3291 [80.4%]), early-onset transient (n = 307 [7.5%]), adolescent-onset (n = 261 [6.4%]), and persistent asthma (n = 230 [5.6%]). Uncontrolled asthma was equally prevalent in the adolescent-onset and persistent asthma trajectory groups, at both age 16 (41.7% vs 42.4%; P = .90) and 24 years (53.7% vs 52.4%; P = .81). The persistent asthma trajectory group had a higher proportion of eosinophil counts greater than or equal to 0.3 (109 cells/L) at age 24 years compared with the adolescent-onset trajectory group (31.0% vs 18.5%; P < .01). CONCLUSIONS The adolescent-onset and persistent asthma trajectory groups had equal burdens of asthma control in adolescence and young adulthood. However, the persistent asthma trajectory group showed more signs of type 2 inflammation than the adolescent-onset trajectory group. This unbiased approach highlights the need of identifying patients with adolescent asthma to optimize care, because they suffer the same lack of asthma control as those with persistent asthma.
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Affiliation(s)
- Maria Ödling
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
| | - Gang Wang
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Sichuan, China; Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Niklas Andersson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Hallberg
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Stockholm, Sweden
| | - Christer Janson
- Department of Medical Sciences: Respiratory, Allergy and Sleep Research, Uppsala University, Uppsala, Sweden
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Stockholm, Sweden
| | - Inger Kull
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Stockholm, Sweden
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14
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Custovic A, Custovic D, Kljaić Bukvić B, Fontanella S, Haider S. Atopic phenotypes and their implication in the atopic march. Expert Rev Clin Immunol 2020; 16:873-881. [PMID: 32856959 DOI: 10.1080/1744666x.2020.1816825] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Eczema, allergic rhinitis, and asthma are traditionally considered atopic (or allergic) diseases. They are complex, multifactorial, and are caused by a variety of different mechanisms, which result in multiple heterogeneous clinical phenotypes. Atopic march is usually interpreted as the sequential development of symptoms from eczema in infancy, to asthma, and then allergic rhinitis. Areas covered: The authors reviewed the evidence on the multimorbidity of eczema, asthma, and rhinitis, and the implication of results of data-driven analyses on the concept framework of atopic march. A literature search was conducted in the PubMed and Web of Science for peer-reviewed articles published until July 2020. Application of Bayesian machine learning framework to rich phenotypic data from birth cohorts demonstrated that the postulated linear progression of symptoms (atopic march) does not capture the heterogeneity of allergic phenotypes. Expert opinion: Eczema, wheeze, and rhinitis co-exist more often than would be expected by chance, but their relationship can be best understood in a multimorbidity framework, rather than through atopic march sequence. The observation of their co-occurrence does not imply any specific relationship between them, and certainly not a progressive or causal one. It is unlikely that a sngle mechanism such as allergic sensitization underpins different multimorbidity manifestations.
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Affiliation(s)
- Adnan Custovic
- National Heart and Lung Institute, Imperial College London , London, UK
| | - Darije Custovic
- Department of Brain Sciences, Imperial College London , London, UK
| | - Blazenka Kljaić Bukvić
- Department of Pediatrics, General Hospital Dr Josip Benčević , Slavonski Brod, Croatia.,Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek , Osijek, Croatia.,Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek , Osijek, Croatia
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London , London, UK
| | - Sadia Haider
- National Heart and Lung Institute, Imperial College London , London, UK
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15
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Deliu M, Fontanella S, Haider S, Sperrin M, Geifman N, Murray C, Simpson A, Custovic A. Longitudinal trajectories of severe wheeze exacerbations from infancy to school age and their association with early-life risk factors and late asthma outcomes. Clin Exp Allergy 2020; 50:315-324. [PMID: 31876035 PMCID: PMC7065181 DOI: 10.1111/cea.13553] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Exacerbation-prone asthma subtype has been reported in studies using data-driven methodologies. However, patterns of severe exacerbations have not been studied. OBJECTIVE To investigate longitudinal trajectories of severe wheeze exacerbations from infancy to school age. METHODS We applied longitudinal k-means clustering to derive exacerbation trajectories among 887 participants from a population-based birth cohort with severe wheeze exacerbations confirmed in healthcare records. We examined early-life risk factors of the derived trajectories, and their asthma-related outcomes and lung function in adolescence. RESULTS 498/887 children (56%) had physician-confirmed wheeze by age 8 years, of whom 160 had at least one severe exacerbation. A two-cluster model provided the optimal solution for severe exacerbation trajectories among these 160 children: "Infrequent exacerbations (IE)" (n = 150, 93.7%) and "Early-onset frequent exacerbations (FE)" (n = 10, 6.3%). Shorter duration of breastfeeding was the strongest early-life risk factor for FE (weeks, median [IQR]: FE, 0 [0-1.75] vs. IE, 6 [0-20], P < .001). Specific airway resistance (sRaw ) was significantly higher in FE compared with IE trajectory throughout childhood. We then compared children in the two exacerbation trajectories with those who have never wheezed (NW, n = 389) or have wheezed but had no severe exacerbations (WNE, n = 338). At age 8 years, FEV1 /FVC was significantly lower and FeNO significantly higher among FE children compared with all other groups. By adolescence (age 16), subjects in FE trajectory were significantly more likely to have current asthma (67% FE vs. 30% IE vs. 13% WNE, P < .001) and use inhaled corticosteroids (77% FE vs. 15% IE vs. 18% WNE, P < .001). Lung function was significantly diminished in the FE trajectory (FEV1 /FVC, mean [95%CI]: 89.9% [89.3-90.5] vs. 88.1% [87.3-88.8] vs. 85.1% [83.4-86.7] vs. 74.7% [61.5-87.8], NW, WNE, IE, FE respectively, P < .001). CONCLUSION We have identified two distinct trajectories of severe exacerbations during childhood with different early-life risk factors and asthma-related outcomes in adolescence.
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Affiliation(s)
- Matea Deliu
- Division of Informatics, Imaging, and Data Science, Faculty of Medicine, Biology, and Health, University of Manchester, Manchester, UK
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College of Science, Technology, and Medicine, London, UK
| | - Sadia Haider
- National Heart and Lung Institute, Imperial College of Science, Technology, and Medicine, London, UK
| | - Matthew Sperrin
- Division of Informatics, Imaging, and Data Science, Faculty of Medicine, Biology, and Health, University of Manchester, Manchester, UK
| | - Nophar Geifman
- Division of Informatics, Imaging, and Data Science, Faculty of Medicine, Biology, and Health, University of Manchester, Manchester, UK
| | - Clare Murray
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Angela Simpson
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College of Science, Technology, and Medicine, London, UK
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16
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Saglani S, Custovic A. Childhood Asthma: Advances Using Machine Learning and Mechanistic Studies. Am J Respir Crit Care Med 2020; 199:414-422. [PMID: 30571146 DOI: 10.1164/rccm.201810-1956ci] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A paradigm shift brought by the recognition that childhood asthma is an aggregated diagnosis that comprises several different endotypes underpinned by different pathophysiology, coupled with advances in understanding potentially important causal mechanisms, offers a real opportunity for a step change to reduce the burden of the disease on individual children, families, and society. Data-driven methodologies facilitate the discovery of "hidden" structures within "big healthcare data" to help generate new hypotheses. These findings can be translated into clinical practice by linking discovered "phenotypes" to specific mechanisms and clinical presentations. Epidemiological studies have provided important clues about mechanistic avenues that should be pursued to identify interventions to prevent the development or alter the natural history of asthma-related diseases. Findings from cohort studies followed by mechanistic studies in humans and in neonatal mouse models provided evidence that environments such as traditional farming may offer protection by modulating innate immune responses and that impaired innate immunity may increase susceptibility. The key question of which component of these exposures can be translated into interventions requires confirmation. Increasing mechanistic evidence is demonstrating that shaping the microbiome in early life may modulate immune function to confer protection. Iterative dialogue and continuous interaction between experts with different but complementary skill sets, including data scientists who generate information about the hidden structures within "big data" assets, and medical professionals, epidemiologists, basic scientists, and geneticists who provide critical clinical and mechanistic insights about the mechanisms underpinning the architecture of the heterogeneity, are keys to delivering mechanism-based stratified treatments and prevention.
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Affiliation(s)
| | - Adnan Custovic
- 2 Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
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17
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Khan FZ, Soiland-Reyes S, Sinnott RO, Lonie A, Goble C, Crusoe MR. Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv. Gigascience 2019; 8:giz095. [PMID: 31675414 PMCID: PMC6824458 DOI: 10.1093/gigascience/giz095] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/23/2019] [Accepted: 07/17/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable automation, scaling, adaptation, and provenance support. However, there are still several challenges associated with the effective sharing, publication, and reproducibility of such workflows due to the incomplete capture of provenance and lack of interoperability between different technical (software) platforms. RESULTS Based on best-practice recommendations identified from the literature on workflow design, sharing, and publishing, we define a hierarchical provenance framework to achieve uniformity in provenance and support comprehensive and fully re-executable workflows equipped with domain-specific information. To realize this framework, we present CWLProv, a standard-based format to represent any workflow-based computational analysis to produce workflow output artefacts that satisfy the various levels of provenance. We use open source community-driven standards, interoperable workflow definitions in Common Workflow Language (CWL), structured provenance representation using the W3C PROV model, and resource aggregation and sharing as workflow-centric research objects generated along with the final outputs of a given workflow enactment. We demonstrate the utility of this approach through a practical implementation of CWLProv and evaluation using real-life genomic workflows developed by independent groups. CONCLUSIONS The underlying principles of the standards utilized by CWLProv enable semantically rich and executable research objects that capture computational workflows with retrospective provenance such that any platform supporting CWL will be able to understand the analysis, reuse the methods for partial reruns, or reproduce the analysis to validate the published findings.
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Affiliation(s)
- Farah Zaib Khan
- The University of Melbourne, School of Computing and Information System, Doug Mcdonnell Building, Parkville, Australia, 3052
- Common Workflow Language Project
| | | | - Richard O Sinnott
- The University of Melbourne, School of Computing and Information System, Doug Mcdonnell Building, Parkville, Australia, 3052
| | - Andrew Lonie
- The University of Melbourne, School of Computing and Information System, Doug Mcdonnell Building, Parkville, Australia, 3052
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18
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Simpson A, Brough HA, Haider S, Belgrave D, Murray CS, Custovic A. Early-life inhalant allergen exposure, filaggrin genotype, and the development of sensitization from infancy to adolescence. J Allergy Clin Immunol 2019; 145:993-1001. [PMID: 31629803 PMCID: PMC7057264 DOI: 10.1016/j.jaci.2019.08.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 07/18/2019] [Accepted: 08/21/2019] [Indexed: 12/11/2022]
Abstract
Background We hypothesized that filaggrin (FLG) loss-of-function mutations modify the effect of allergen exposure on the development of allergic sensitization. Objective We sought to determine whether early-life exposure to inhalant allergens increases the risk of specific sensitization and whether FLG mutations modulate these odds. Methods In a population-based birth cohort we measured mite, cat, and dog allergen levels in dust samples collected from homes within the first year of life. Sensitization was assessed at 6 time points between infancy and age 16 years. Genotyping was performed for 6 FLG mutations. Results In the longitudinal multivariable model (age 1-16 years), we observed a significant interaction between FLG and Fel d 1 exposure on cat sensitization, with the effect of exposure being significantly greater among children with FLG mutations compared with those without (odds ratio, 1.36; 95% CI, 1.02-1.80; P = .035). The increase in risk of mite sensitization with increasing Der p 1 exposure was consistently greater among children with FLG mutations, but the interaction did not reach statistical significance. Different associations were observed for dogs: there was a significant interaction between FLG and dog ownership, but the risk of sensitization to any allergen was significantly lower among children with FLG mutations who were exposed to a dog in infancy (odds ratio, 0.16; 95% CI, 0.03-0.86; P = .03). Conclusions FLG loss-of-function mutations modify the relationship between allergen exposure and sensitization, but effects differ at different ages and between different allergens.
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Affiliation(s)
- Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester and University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom
| | - Helen A Brough
- Children's Allergy Service, Evelina London, Guys and St Thomas' NHS Trust, London, United Kingdom; Paediatric Allergy Group, Department of Women and Children's Heath, School of Life Course Sciences, London, United Kingdom; Paediatric Allergy Group, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - Sadia Haider
- Section of Paediatrics, Imperial College London, United Kingdom; National Heart and Lung Institute, Imperial College London, United Kingdom
| | | | - Clare S Murray
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester and University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom
| | - Adnan Custovic
- Section of Paediatrics, Imperial College London, United Kingdom; National Heart and Lung Institute, Imperial College London, United Kingdom.
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19
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Ford E, Boyd A, Bowles JK, Havard A, Aldridge RW, Curcin V, Greiver M, Harron K, Katikireddi V, Rodgers SE, Sperrin M. Our data, our society, our health: A vision for inclusive and transparent health data science in the United Kingdom and beyond. Learn Health Syst 2019; 3:e10191. [PMID: 31317072 PMCID: PMC6628981 DOI: 10.1002/lrh2.10191] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/08/2019] [Accepted: 03/06/2019] [Indexed: 01/28/2023] Open
Abstract
The last 6 years have seen sustained investment in health data science in the United Kingdom and beyond, which should result in a data science community that is inclusive of all stakeholders, working together to use data to benefit society through the improvement of public health and well-being. However, opportunities made possible through the innovative use of data are still not being fully realised, resulting in research inefficiencies and avoidable health harms. In this paper, we identify the most important barriers to achieving higher productivity in health data science. We then draw on previous research, domain expertise, and theory to outline how to go about overcoming these barriers, applying our core values of inclusivity and transparency. We believe a step change can be achieved through meaningful stakeholder involvement at every stage of research planning, design, and execution and team-based data science, as well as harnessing novel and secure data technologies. Applying these values to health data science will safeguard a social licence for health data research and ensure transparent and secure data usage for public benefit.
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Affiliation(s)
- Elizabeth Ford
- Department of Primary Care and Public HealthBrighton and Sussex Medical SchoolBrightonUK
| | - Andy Boyd
- ALSPAC, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | | | - Alys Havard
- Centre for Big Data Research in HealthUniversity of New South WalesSydneyAustralia
| | | | - Vasa Curcin
- School of Population and Environmental Health Sciences, Faculty of Life Sciences and MedicineKing's College LondonUK
| | - Michelle Greiver
- Department of Family and Community MedicineUniversity of Toronto, North York General HospitalTorontoCanada
| | - Katie Harron
- Great Ormond Street Institute of Child HealthUCLLondonUK
| | - Vittal Katikireddi
- MRC/CSO Social and Public Health Sciences UnitUniversity of GlasgowGlasgowUK
| | - Sarah E. Rodgers
- Health Data Research UKSwansea UniversitySwanseaUK
- Public Health and PolicyUniversity of LiverpoolLiverpoolUK
| | - Matthew Sperrin
- School of Health Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
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Nakamura T, Haider S, Colicino S, Murray CS, Holloway J, Simpson A, Cullinan P, Custovic A. Different definitions of atopic dermatitis: impact on prevalence estimates and associated risk factors. Br J Dermatol 2019; 181:1272-1279. [PMID: 30822368 PMCID: PMC6916614 DOI: 10.1111/bjd.17853] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2019] [Indexed: 12/14/2022]
Abstract
Background There is no objective test that can unequivocally confirm the diagnosis of atopic dermatitis (AD), and no uniform clinical definition. Objectives To investigate to what extent operational definitions of AD cause fluctuation in the prevalence estimates and the associated risk factors. Methods We first reviewed the operational definitions of AD used in the literature. We then tested the impact of the choice of the most common definitions of ‘cases’ and ‘controls’ on AD prevalence estimates and associated risk factors (including filaggrin mutations) among children aged 5 years in two population‐based birth cohorts: the Manchester Asthma and Allergy Study (MAAS) and Asthma in Ashford. Model performance was measured by the percentage of children within an area of clinical indecision (defined as having a posterior probability of AD between 25% and 60%). Results We identified 59 different definitions of AD across 45 reviewed studies. Of those, we chose four common ‘case’ definitions and two definitions of ‘controls’. The prevalence estimates using different case definitions ranged between 22% and 33% in MAAS, and between 12% and 22% in Ashford. The area of clinical indecision ranged from 32% to 44% in MAAS and from 9% to 29% in Ashford. Depending on the case definition used, the associations with filaggrin mutations varied, with odds ratios (95% confidence intervals) ranging from 1·8 (1·1–2·9) to 2·2 (1·3–3·7) in MAAS and 1·7 (0·8–3·7) to 2·3 (1·2–4·5) in Ashford. Associations with filaggrin mutations also differed when using the same ‘case’ definition but different definitions of ‘controls’. Conclusions Use of different definitions of AD results in substantial differences in prevalence estimates, the performance of prediction models and association with risk factors. What's already known about this topic? There is no objective test that can unequivocally confirm the diagnosis of atopic dermatitis (AD) and no uniform clinical definition. This results in different definitions utilized in AD studies, raising concerns on the generalizability of the results and comparability across different studies.
What does this study add? This study has shown that different definitions of ‘cases’ and ‘controls’ have major impacts upon prevalence estimates and associations with risk factors, including genetics, in two population‐based birth cohorts. These findings suggest the importance of developing a consensus on AD definitions of both ‘controls’ and ‘cases’ to minimize biases in studies.
https://www.bjdonline.com/article/different-definitions-of-atopic-dermatitis-impact-on-prevalence-estimates-and-associated-risk-factors/ Linked Comment: https://doi.org/10.1111/bjd.18303. https://doi.org/10.1111/bjd.18571 available online
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Affiliation(s)
- T Nakamura
- Department of Paediatrics, Imperial College London, London, U.K
| | - S Haider
- Department of Paediatrics, Imperial College London, London, U.K
| | - S Colicino
- National Heart and Lung Institute, Imperial College London, London, U.K
| | - C S Murray
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, U.K
| | - J Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, U.K
| | - A Simpson
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, U.K
| | - P Cullinan
- National Heart and Lung Institute, Imperial College London, London, U.K
| | - A Custovic
- Department of Paediatrics, Imperial College London, London, U.K
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21
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Sonntag HJ, Filippi S, Pipis S, Custovic A. Blood Biomarkers of Sensitization and Asthma. Front Pediatr 2019; 7:251. [PMID: 31275911 PMCID: PMC6593482 DOI: 10.3389/fped.2019.00251] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/03/2019] [Indexed: 12/18/2022] Open
Abstract
Biomarkers are essential to determine different phenotypes of childhood asthma, and for the prediction of response to treatments. In young preschool children with asthma, aeroallergen sensitization, and blood eosinophil count of 300/μL or greater may identify those who can benefit from the daily use of inhaled corticosteroids (ICS). We propose that every preschool child who is considered for ICS treatment should have these two features measured as a minimum before a decision is made on the commencement of long-term preventive treatment. In practice, IgE-mediated sensitization should be considered as a quantifiable variable, i.e., we should use the titer of sIgE antibodies or the size of skin prick test response. A number of other blood biomarkers may prove useful (e.g., allergen-specific IgG/IgE antibody ratios amongst sensitized individuals, component-resolved diagnostics which measures sIgE response to a large number of allergenic molecules, assessment of immune responses to viruses, level of serum CC16, etc.), but it remains unclear whether these can be translated into clinically useful tests. Going forward, a more integrated approach which takes into account multiple domains of asthma, from the pattern of symptoms and blood biomarkers to genetic risk and lung function measures, is needed if we are to move toward a stratified approach to asthma management.
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Affiliation(s)
- Hans-Joachim Sonntag
- Respiratory Division, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Sarah Filippi
- Department of Mathematics, Imperial College London, London, United Kingdom
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Spyros Pipis
- Medical School, University of Nicosia, Nicosia, Cyprus
- Department of Paediatrics, Aretaeio Hospital, Nicosia, Cyprus
| | - Adnan Custovic
- Respiratory Division, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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22
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Gern JE, Jackson DJ, Lemanske RF, Seroogy CM, Tachinardi U, Craven M, Hwang SY, Hamilton CM, Huggins W, O’Connor GT, Gold DR, Miller R, Kattan M, Johnson CC, Ownby D, Zoratti EM, Wood RA, Visness CM, Martinez F, Wright A, Lynch S, Ober C, Khurana Hershey GK, Ryan P, Hartert T, Bacharier LB. The Children's Respiratory and Environmental Workgroup (CREW) birth cohort consortium: design, methods, and study population. Respir Res 2019; 20:115. [PMID: 31182091 PMCID: PMC6558735 DOI: 10.1186/s12931-019-1088-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/03/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single birth cohort studies have been the basis for many discoveries about early life risk factors for childhood asthma but are limited in scope by sample size and characteristics of the local environment and population. The Children's Respiratory and Environmental Workgroup (CREW) was established to integrate multiple established asthma birth cohorts and to investigate asthma phenotypes and associated causal pathways (endotypes), focusing on how they are influenced by interactions between genetics, lifestyle, and environmental exposures during the prenatal period and early childhood. METHODS AND RESULTS CREW is funded by the NIH Environmental influences on Child Health Outcomes (ECHO) program, and consists of 12 individual cohorts and three additional scientific centers. The CREW study population is diverse in terms of race, ethnicity, geographical distribution, and year of recruitment. We hypothesize that there are phenotypes in childhood asthma that differ based on clinical characteristics and underlying molecular mechanisms. Furthermore, we propose that asthma endotypes and their defining biomarkers can be identified based on personal and early life environmental risk factors. CREW has three phases: 1) to pool and harmonize existing data from each cohort, 2) to collect new data using standardized procedures, and 3) to enroll new families during the prenatal period to supplement and enrich extant data and enable unified systems approaches for identifying asthma phenotypes and endotypes. CONCLUSIONS The overall goal of CREW program is to develop a better understanding of how early life environmental exposures and host factors interact to promote the development of specific asthma endotypes.
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Affiliation(s)
- James E. Gern
- University of Wisconsin School of Medicine and Public Health, Madison, WI 53706 USA
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Clinical Science Center-K4/918, 600 Highland Ave, Madison, WI 53792-9988 USA
| | - Daniel J. Jackson
- University of Wisconsin School of Medicine and Public Health, Madison, WI 53706 USA
| | - Robert F. Lemanske
- University of Wisconsin School of Medicine and Public Health, Madison, WI 53706 USA
| | - Christine M. Seroogy
- University of Wisconsin School of Medicine and Public Health, Madison, WI 53706 USA
| | - Umberto Tachinardi
- University of Wisconsin School of Medicine and Public Health, Madison, WI 53706 USA
| | - Mark Craven
- University of Wisconsin School of Medicine and Public Health, Madison, WI 53706 USA
| | - Stephen Y. Hwang
- RTI International, East Cornwallis Road, Post Office Box 12194, Raleigh, Research Triangle Park, NC 27709-2194 USA
| | - Carol M. Hamilton
- RTI International, East Cornwallis Road, Post Office Box 12194, Raleigh, Research Triangle Park, NC 27709-2194 USA
| | - Wayne Huggins
- RTI International, East Cornwallis Road, Post Office Box 12194, Raleigh, Research Triangle Park, NC 27709-2194 USA
| | - George T. O’Connor
- Boston University School of Medicine, 72 E Concord St, Boston, MA 02118 USA
| | - Diane R. Gold
- Channing Laboratory, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Rachel Miller
- Columbia University, Vagelos College of Physicians and Surgeons, New York, NY 10032 USA
| | - Meyer Kattan
- Columbia University, Vagelos College of Physicians and Surgeons, New York, NY 10032 USA
| | | | | | | | - Robert A. Wood
- Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | | | | | | | - Susan Lynch
- University of California, San Francisco, CA 94143 USA
| | - Carole Ober
- University of Chicago, Chicago, IL 60637 USA
| | | | - Patrick Ryan
- University of Cincinnati, Cincinnati, OH 45220 USA
| | - Tina Hartert
- Vanderbilt University School of Medicine, Nashville, TN 37232 USA
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23
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Oksel C, Granell R, Mahmoud O, Custovic A, Henderson AJ. Causes of variability in latent phenotypes of childhood wheeze. J Allergy Clin Immunol 2019; 143:1783-1790.e11. [PMID: 30528616 PMCID: PMC6505513 DOI: 10.1016/j.jaci.2018.10.059] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/29/2018] [Accepted: 10/12/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND Latent class analysis (LCA) has been used extensively to identify (latent) phenotypes of childhood wheezing. However, the number and trajectory of discovered phenotypes differed substantially between studies. OBJECTIVE We sought to investigate sources of variability affecting the classification of phenotypes, identify key time points for data collection to understand wheeze heterogeneity, and ascertain the association of childhood wheeze phenotypes with asthma and lung function in adulthood. METHODS We used LCA to derive wheeze phenotypes among 3167 participants in the ALSPAC cohort who had complete information on current wheeze recorded at 14 time points from birth to age 16½ years. We examined the effects of sample size and data collection age and intervals on the results and identified time points. We examined the associations of derived phenotypes with asthma and lung function at age 23 to 24 years. RESULTS A relatively large sample size (>2000) underestimated the number of phenotypes under some conditions (eg, number of time points <11). Increasing the number of data points resulted in an increase in the optimal number of phenotypes, but an identical number of randomly selected follow-up points led to different solutions. A variable selection algorithm identified 8 informative time points (months 18, 42, 57, 81, 91, 140, 157, and 166). The proportion of asthmatic patients at age 23 to 24 years differed between phenotypes, whereas lung function was lower among persistent wheezers. CONCLUSIONS Sample size, frequency, and timing of data collection have a major influence on the number and type of wheeze phenotypes identified by using LCA in longitudinal data.
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Affiliation(s)
- Ceyda Oksel
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Raquel Granell
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Osama Mahmoud
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Adnan Custovic
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom.
| | - A John Henderson
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
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24
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Abstract
Antenatal and preschool factors are key in determining the progression to pre-school wheeze and eosinophilic school age asthma. The conventional view of eosinophilic asthma is that airway inflammation is the fundamental underlying abnormality, and airway inflammation and hyper-responsiveness are secondary; in fact, these three are parallel processes. Very early structural changes, independent of inflammation and infection, are associated with early airway hyper-responsiveness and later adverse respiratory outcomes. There is a bidirectional relationship between structural airway wall changes and airway inflammation, with airway contraction per se leading to the release of growth factors, and inflammatory pathways promoting airway remodeling. Early viral infection (and increasingly being appreciated, bacterial infection) is important in wheeze outcomes. There is evidence of abnormal immune function including cytokine release before the onset of viral infections. However, viral infections may also have prolonged effects on the host immune system, and the evidence for beneficial and adverse effects of viral infection is conflicting. In older children and adults, asthmatic epithelial cells show impaired interferon responses to viral infection, but only in the presence of uncontrolled type 2 inflammation, implying these are secondary phenomena. There are also compelling data relating the innate immune system to later asthma and atopy, and animal studies suggest that the effects of a high endotoxin, microbiologically diverse environment may be modulated via the epithelial alarmin IL-33. Whereas, previously only viral infection was thought to be important, early bacterial colonization of the upper airway is coming to the fore, associated with a mixed pattern of TH1/TH2/TH17 cytokine secretion, and adverse long term outcomes. Bacterial colonization is probably a marker of a subtle immune deficiency, rather than directly causal. The airway and gut microbiome critically impacts the development of Type 2 inflammatory responses. However, Type 2 inflammatory cytokines, which are critical both to progression from pre-school wheeze to eosinophilic asthma, and sustaining the eosinophilic asthmatic state, are not implicated in the very early development of the disease. Taken together, the evidence is that the earliest cytokine and chemokine signals will come from the study of bronchial epithelial cell function and their interactions with viruses and the microbiome.
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Affiliation(s)
- Andrew Bush
- Departments of Paediatrics and Paediatric Respiratory Medicine, Royal Brompton Harefield NHS Foundation Trust and Imperial College, London, United Kingdom
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25
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Dharmage SC, Perret JL, Custovic A. Epidemiology of Asthma in Children and Adults. Front Pediatr 2019; 7:246. [PMID: 31275909 PMCID: PMC6591438 DOI: 10.3389/fped.2019.00246] [Citation(s) in RCA: 555] [Impact Index Per Article: 111.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/29/2019] [Indexed: 11/23/2022] Open
Abstract
Asthma is a globally significant non-communicable disease with major public health consequences for both children and adults, including high morbidity, and mortality in severe cases. We have summarized the evidence on asthma trends, environmental determinants, and long-term impacts while comparing these epidemiological features across childhood asthma and adult asthma. While asthma incidence and prevalence are higher in children, morbidity, and mortality are higher in adults. Childhood asthma is more common in boys while adult asthma is more common in women, and the reversal of this sex difference in prevalence occurs around puberty suggesting sex hormones may play a role in the etiology of asthma. The global epidemic of asthma that has been observed in both children and adults is still continuing, especially in low to middle income countries, although it has subsided in some developed countries. As a heterogeneous disease, distinct asthma phenotypes, and endotypes need to be adequately characterized to develop more accurate and meaningful definitions for use in research and clinical settings. This may be facilitated by new clustering techniques such as latent class analysis, and computational phenotyping methods are being developed to retrieve information from electronic health records using natural language processing (NLP) algorithms to assist in the early diagnosis of asthma. While some important environmental determinants that trigger asthma are well-established, more work is needed to define the role of environmental exposures in the development of asthma in both children and adults. There is increasing evidence that investigation into possible gene-by-environment and environment-by-environment interactions may help to better uncover the determinants of asthma. Therefore, there is an urgent need to further investigate the interrelationship between environmental and genetic determinants to identify high risk groups and key modifiable exposures. For children, asthma may impair airway development and reduce maximally attained lung function, and these lung function deficits may persist into adulthood without additional progressive loss. Adult asthma may accelerate lung function decline and increase the risk of fixed airflow obstruction, with the effect of early onset asthma being greater than late onset asthma. Therefore, in managing asthma, our focus going forward should be firmly on improving not only short-term symptoms, but also the long-term respiratory and other health outcomes.
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Affiliation(s)
- Shyamali C Dharmage
- Allergy and Lung Health Unit, School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Jennifer L Perret
- Allergy and Lung Health Unit, School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia.,Institute for Breathing and Sleep, Melbourne, VIC, Australia
| | - Adnan Custovic
- Department of Paediatrics, Imperial College London, London, United Kingdom
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26
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Prosperi M, Min JS, Bian J, Modave F. Big data hurdles in precision medicine and precision public health. BMC Med Inform Decis Mak 2018; 18:139. [PMID: 30594159 PMCID: PMC6311005 DOI: 10.1186/s12911-018-0719-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/04/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Nowadays, trendy research in biomedical sciences juxtaposes the term 'precision' to medicine and public health with companion words like big data, data science, and deep learning. Technological advancements permit the collection and merging of large heterogeneous datasets from different sources, from genome sequences to social media posts or from electronic health records to wearables. Additionally, complex algorithms supported by high-performance computing allow one to transform these large datasets into knowledge. Despite such progress, many barriers still exist against achieving precision medicine and precision public health interventions for the benefit of the individual and the population. MAIN BODY The present work focuses on analyzing both the technical and societal hurdles related to the development of prediction models of health risks, diagnoses and outcomes from integrated biomedical databases. Methodological challenges that need to be addressed include improving semantics of study designs: medical record data are inherently biased, and even the most advanced deep learning's denoising autoencoders cannot overcome the bias if not handled a priori by design. Societal challenges to face include evaluation of ethically actionable risk factors at the individual and population level; for instance, usage of gender, race, or ethnicity as risk modifiers, not as biological variables, could be replaced by modifiable environmental proxies such as lifestyle and dietary habits, household income, or access to educational resources. CONCLUSIONS Data science for precision medicine and public health warrants an informatics-oriented formalization of the study design and interoperability throughout all levels of the knowledge inference process, from the research semantics, to model development, and ultimately to implementation.
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Affiliation(s)
- Mattia Prosperi
- Department of Epidemiology, College of Medicine & College of Public Health and Health Professions, University of Florida, Gainesville, FL, 32610, USA.
| | - Jae S Min
- Department of Epidemiology, College of Medicine & College of Public Health and Health Professions, University of Florida, Gainesville, FL, 32610, USA
| | - Jiang Bian
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - François Modave
- Center for Health Outcomes and Informatics Research, Loyola University Chicago, Maywood, IL, 60153, USA
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27
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Pembrey L, Barreto ML, Douwes J, Cooper P, Henderson J, Mpairwe H, Ardura-Garcia C, Chico M, Brooks C, Cruz AA, Elliott AM, Figueiredo CA, Langan SM, Nassanga B, Ring S, Rodrigues L, Pearce N. Understanding asthma phenotypes: the World Asthma Phenotypes (WASP) international collaboration. ERJ Open Res 2018; 4:00013-2018. [PMID: 30151371 PMCID: PMC6104297 DOI: 10.1183/23120541.00013-2018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/28/2018] [Indexed: 12/12/2022] Open
Abstract
The World Asthma Phenotypes (WASP) study started in 2016 and has been conducted in five centres, in the UK, New Zealand, Brazil, Ecuador and Uganda. The objectives of this study are to combine detailed biomarker and clinical information in order to 1) better understand and characterise asthma phenotypes in high-income countries (HICs) and low and middle-income countries (LMICs), and in high and low prevalence centres; 2) compare phenotype characteristics, including clinical severity; 3) assess the risk factors for each phenotype; and 4) assess how the distribution of phenotypes differs between high prevalence and low prevalence centres. Here we present the rationale and protocol for the WASP study to enable other centres around the world to carry out similar analyses using a standardised protocol. Large collaborative and integrative studies like this are essential to further our understanding of asthma phenotypes. The findings of this study will help elucidate the aetiological mechanisms of asthma and might potentially identify new causes and guide the development of new treatments, thereby enabling better management and prevention of asthma in both HICs and LMICs.
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Affiliation(s)
- Lucy Pembrey
- London School of Hygiene and Tropical Medicine, London, UK
| | - Mauricio L Barreto
- Institute of Collective Health, Federal University of Bahia, Salvador, Brazil.,Center for Data and Knowledge Integration for Health (CIDACS), Fiocruz, Salvador, Brazil
| | - Jeroen Douwes
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Philip Cooper
- St George's University of London, London, UK.,Universidad Internacional del Ecuador, Quito, Ecuador.,Fundacion Ecuatoriana Para Investigacion en Salud, Quito, Ecuador
| | - John Henderson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Harriet Mpairwe
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | - Martha Chico
- Fundacion Ecuatoriana Para Investigacion en Salud, Quito, Ecuador
| | - Collin Brooks
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Alvaro A Cruz
- The Programme for Control of Asthma and Allergic Rhinitis (ProAR), Federal University of Bahia, Salvador, Brazil.,Institute for Health Sciences, Federal University of Bahia, Salvador, Brazil
| | - Alison M Elliott
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Camila A Figueiredo
- Institute of Collective Health, Federal University of Bahia, Salvador, Brazil
| | | | - Beatrice Nassanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Susan Ring
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Neil Pearce
- London School of Hygiene and Tropical Medicine, London, UK.,Centre for Public Health Research, Massey University, Wellington, New Zealand
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28
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Farzan N, Vijverberg SJ, Kabesch M, Sterk PJ, Maitland-van der Zee AH. The use of pharmacogenomics, epigenomics, and transcriptomics to improve childhood asthma management: Where do we stand? Pediatr Pulmonol 2018; 53:836-845. [PMID: 29493882 DOI: 10.1002/ppul.23976] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/01/2018] [Indexed: 01/11/2023]
Abstract
Asthma is a complex multifactorial disease and it is the most common chronic disease in children. There is a high variability in response to asthma treatment, even in patients with good adherence to maintenance treatment, and a correct inhalation technique. Distinct underlying disease mechanisms in childhood asthma might be the reason of this heterogeneity. A deeper knowledge of the underlying molecular mechanisms of asthma has led to the recent development of advanced and mechanism-based treatments such as biologicals. However, biologicals are recommended only for patients with specific asthma phenotypes who remain uncontrolled despite high dosages of conventional asthma treatment. One of the main unmet needs in their application is lack of clinically available biomarkers to individualize pediatric asthma management and guide treatment. Pharmacogenomics, epigenomics, and transcriptomics are three omics fields that are rapidly advancing and can provide tools to identify novel asthma mechanisms and biomarkers to guide treatment. Pharmacogenomics focuses on variants in the DNA, epigenomics studies heritable changes that do not involve changes in the DNA sequence but lead to alteration of gene expression, and transcriptomics investigates gene expression by studying the complete set of mRNA transcripts in a cell or a population of cells. Advances in high-throughput technologies and statistical tools together with well-phenotyped patient inclusion and collaborations between different centers will expand our knowledge of underlying molecular mechanisms involved in disease onset and progress. Furthermore, it could help to select and stratify appropriate therapeutic strategies for subgroups of patients and hopefully bring precision medicine to daily practice.
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Affiliation(s)
- Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
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29
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Belgrave DCM, Granell R, Turner SW, Curtin JA, Buchan IE, Le Souëf PN, Simpson A, Henderson AJ, Custovic A. Lung function trajectories from pre-school age to adulthood and their associations with early life factors: a retrospective analysis of three population-based birth cohort studies. THE LANCET RESPIRATORY MEDICINE 2018; 6:526-534. [PMID: 29628377 DOI: 10.1016/s2213-2600(18)30099-7] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Maximal lung function in early adulthood is an important determinant of mortality and COPD. We investigated whether distinct trajectories of lung function are present during childhood and whether these extend to adulthood and infancy. METHODS To ascertain trajectories of FEV1, we studied two population-based birth cohorts (MAAS and ALSPAC) with repeat spirometry from childhood into early adulthood (1046 participants from 5-16 years and 1390 participants from 8-24 years). We used a third cohort (PIAF) with repeat lung function measures in infancy (V'maxFRC) and childhood (FEV1; 196 participants from 1 month to 18 years of age) to investigate whether these childhood trajectories extend from early life. We identified trajectories using latent profile modelling. We created an allele score to investigate genetic associations of trajectories, and constructed a multivariable model to identify their early-life predictors. FINDINGS We identified four childhood FEV1 trajectories: persistently high, normal, below average, and persistently low. The persistently low trajectory (129 [5%] of 2436 participants) was associated with persistent wheezing and asthma throughout follow-up. In genetic analysis, compared with the normal trajectory, the pooled relative risk ratio per allele was 0·96 (95% CI 0·92-1·01; p=0·13) for persistently high, 1·01 (0·99-1·02; p=0·49) for below average, and 1·05 (0·98-1·13; p=0·13) for persistently low. Most children in the low V'maxFRC trajectory in infancy did not progress to the low FEV1 trajectory in childhood. Early-life factors associated with the persistently low trajectory included recurrent wheeze with severe wheezing exacerbations, early allergic sensitisation, and tobacco smoke exposure. INTERPRETATION Reduction of childhood smoke exposure and minimisation of the risk of early-life sensitisation and wheezing exacerbations might reduce the risk of diminished lung function in early adulthood. FUNDING None.
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Affiliation(s)
| | - Raquel Granell
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - John A Curtin
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Manchester Academic Health Science Centre, Manchester, UK
| | - Iain E Buchan
- Health Informatics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Peter N Le Souëf
- School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Manchester Academic Health Science Centre, Manchester, UK
| | - A John Henderson
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Adnan Custovic
- Section of Paediatrics, Department of Medicine, Imperial College London, London, UK
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30
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Pavord ID, Beasley R, Agusti A, Anderson GP, Bel E, Brusselle G, Cullinan P, Custovic A, Ducharme FM, Fahy JV, Frey U, Gibson P, Heaney LG, Holt PG, Humbert M, Lloyd CM, Marks G, Martinez FD, Sly PD, von Mutius E, Wenzel S, Zar HJ, Bush A. After asthma: redefining airways diseases. Lancet 2018; 391:350-400. [PMID: 28911920 DOI: 10.1016/s0140-6736(17)30879-6] [Citation(s) in RCA: 671] [Impact Index Per Article: 111.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 02/26/2017] [Accepted: 03/07/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Ian D Pavord
- Respiratory Medicine Unit, Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre, University of Oxford, UK.
| | - Richard Beasley
- Medical Research Institute of New Zealand, Wellington, New Zealand
| | - Alvar Agusti
- Respiratory Institute, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain; CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Gary P Anderson
- Lung Health Research Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Elisabeth Bel
- Department of Respiratory Medicine, Academic Medical Center, University of Amsterdam, Netherlands
| | - Guy Brusselle
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium; Departments of Epidemiology and Respiratory Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - Paul Cullinan
- National Heart and Lung Institute, Imperial College, London, UK
| | | | - Francine M Ducharme
- Departments of Paediatrics and Social and Preventive Medicine, University of Montreal, Montreal, QC, Canada
| | - John V Fahy
- Cardiovascular Research Institute, and Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Urs Frey
- University Children's Hospital Basel, University of Basel, Basel, Switzerland
| | - Peter Gibson
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Hunter Medical Research Institute, Newcastle, NSW, Australia; Priority Research Centre for Asthma and Respiratory Disease, The University of Newcastle, Newcastle, NSW, Australia
| | - Liam G Heaney
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Patrick G Holt
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Marc Humbert
- L'Université Paris-Sud, Faculté de Médecine, Université Paris-Saclay, Paris, France; Service de Pneumologie, Hôpital Bicêtre, Paris, France; INSERM UMR-S 999, Hôpital Marie Lannelongue, Paris, France
| | - Clare M Lloyd
- National Heart and Lung Institute, Imperial College, London, UK
| | - Guy Marks
- Department of Respiratory Medicine, South Western Sydney Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Fernando D Martinez
- Asthma and Airway Disease Research Center, The University of Arizona, Tuscon, AZ, USA
| | - Peter D Sly
- Department of Children's Health and Environment, Children's Health Queensland, Brisbane, QLD, Australia; Centre for Children's Health Research, Brisbane, QLD, Australia
| | - Erika von Mutius
- Dr. von Haunersches Kinderspital, Ludwig Maximilians Universität, Munich, Germany
| | - Sally Wenzel
- University of Pittsburgh Asthma Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross Children's Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Andy Bush
- Department of Paediatrics, Imperial College, London, UK; Department of Paediatric Respiratory Medicine, Imperial College, London, UK
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31
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Oksel C, Haider S, Fontanella S, Frainay C, Custovic A. Classification of Pediatric Asthma: From Phenotype Discovery to Clinical Practice. Front Pediatr 2018; 6:258. [PMID: 30298124 PMCID: PMC6160736 DOI: 10.3389/fped.2018.00258] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/29/2018] [Indexed: 12/24/2022] Open
Abstract
Advances in big data analytics have created an opportunity for a step change in unraveling mechanisms underlying the development of complex diseases such as asthma, providing valuable insights that drive better diagnostic decision-making in clinical practice, and opening up paths to individualized treatment plans. However, translating findings from data-driven analyses into meaningful insights and actionable solutions requires approaches and tools which move beyond mining and patterning longitudinal data. The purpose of this review is to summarize recent advances in phenotyping of asthma, to discuss key hurdles currently hampering the translation of phenotypic variation into mechanistic insights and clinical setting, and to suggest potential solutions that may address these limitations and accelerate moving discoveries into practice. In order to advance the field of phenotypic discovery, greater focus should be placed on investigating the extent of within-phenotype variation. We advocate a more cautious modeling approach by "supervising" the findings to delineate more precisely the characteristics of the individual trajectories assigned to each phenotype. Furthermore, it is important to employ different methods within a study to compare the stability of derived phenotypes, and to assess the immutability of individual assignments to phenotypes. If we are to make a step change toward precision (stratified or personalized) medicine and capitalize on the available big data assets, we have to develop genuine cross-disciplinary collaborations, wherein data scientists who turn data into information using algorithms and machine learning, team up with medical professionals who provide deep insights on specific subjects from a clinical perspective.
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Affiliation(s)
- Ceyda Oksel
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Sadia Haider
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Sara Fontanella
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Clement Frainay
- Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, United Kingdom.,INRA, UMR1331, Toxalim, Research Centre in Food Toxicology, Toulouse, France
| | - Adnan Custovic
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
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32
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Deliu M, Yavuz TS, Sperrin M, Belgrave D, Sahiner UM, Sackesen C, Kalayci O, Custovic A. Features of asthma which provide meaningful insights for understanding the disease heterogeneity. Clin Exp Allergy 2018; 48:39-47. [PMID: 28833810 PMCID: PMC5763358 DOI: 10.1111/cea.13014] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 07/31/2017] [Accepted: 08/15/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Data-driven methods such as hierarchical clustering (HC) and principal component analysis (PCA) have been used to identify asthma subtypes, with inconsistent results. OBJECTIVE To develop a framework for the discovery of stable and clinically meaningful asthma subtypes. METHODS We performed HC in a rich data set from 613 asthmatic children, using 45 clinical variables (Model 1), and after PCA dimensionality reduction (Model 2). Clinical experts then identified a set of asthma features/domains which informed clusters in the two analyses. In Model 3, we reclustered the data using these features to ascertain whether this improved the discovery process. RESULTS Cluster stability was poor in Models 1 and 2. Clinical experts highlighted four asthma features/domains which differentiated the clusters in two models: age of onset, allergic sensitization, severity, and recent exacerbations. In Model 3 (HC using these four features), cluster stability improved substantially. The cluster assignment changed, providing more clinically interpretable results. In a 5-cluster model, we labelled the clusters as: "Difficult asthma" (n = 132); "Early-onset mild atopic" (n = 210); "Early-onset mild non-atopic: (n = 153); "Late-onset" (n = 105); and "Exacerbation-prone asthma" (n = 13). Multinomial regression demonstrated that lung function was significantly diminished among children with "Difficult asthma"; blood eosinophilia was a significant feature of "Difficult," "Early-onset mild atopic," and "Late-onset asthma." Children with moderate-to-severe asthma were present in each cluster. CONCLUSIONS AND CLINICAL RELEVANCE An integrative approach of blending the data with clinical expert domain knowledge identified four features, which may be informative for ascertaining asthma endotypes. These findings suggest that variables which are key determinants of asthma presence, severity, or control may not be the most informative for determining asthma subtypes. Our results indicate that exacerbation-prone asthma may be a separate asthma endotype and that severe asthma is not a single entity, but an extreme end of the spectrum of several different asthma endotypes.
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Affiliation(s)
- M. Deliu
- Division of Informatics, Imaging and Data SciencesFaculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - T. S. Yavuz
- Department of Pediatric AllergyGulhane School of MedicineAnkaraTurkey
- Department of Paediatric AllergyChildren's HospitalUniversity of BonnBonnGermany
| | - M. Sperrin
- Division of Informatics, Imaging and Data SciencesFaculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - D. Belgrave
- Department of MedicineSection of PaediatricsImperial College LondonLondonUK
| | - U. M. Sahiner
- Pediatric Allergy and Asthma UnitHacettepe University School of MedicineAnkaraTurkey
| | - C. Sackesen
- School of MedicinePediatric Allergy UnitKoc UniversityIstanbulTurkey
- Pediatric Allergy and Asthma UnitHacettepe University School of MedicineAnkaraTurkey
| | - O. Kalayci
- Pediatric Allergy and Asthma UnitHacettepe University School of MedicineAnkaraTurkey
| | - A. Custovic
- Department of MedicineSection of PaediatricsImperial College LondonLondonUK
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33
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Gill D, Sheehan NA, Wielscher M, Shrine N, Amaral AFS, Thompson JR, Granell R, Leynaert B, Real FG, Hall IP, Tobin MD, Auvinen J, Ring SM, Jarvelin MR, Wain LV, Henderson J, Jarvis D, Minelli C. Age at menarche and lung function: a Mendelian randomization study. Eur J Epidemiol 2017; 32:701-710. [PMID: 28624884 PMCID: PMC5591357 DOI: 10.1007/s10654-017-0272-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 06/07/2017] [Indexed: 12/18/2022]
Abstract
A trend towards earlier menarche in women has been associated with childhood factors (e.g. obesity) and hypothesised environmental exposures (e.g. endocrine disruptors present in household products). Observational evidence has shown detrimental effects of early menarche on various health outcomes including adult lung function, but these might represent spurious associations due to confounding. To address this we used Mendelian randomization where genetic variants are used as proxies for age at menarche, since genetic associations are not affected by classical confounding. We estimated the effects of age at menarche on forced vital capacity (FVC), a proxy for restrictive lung impairment, and ratio of forced expiratory volume in one second to FVC (FEV1/FVC), a measure of airway obstruction, in both adulthood and adolescence. We derived SNP-age at menarche association estimates for 122 variants from a published genome-wide meta-analysis (N = 182,416), with SNP-lung function estimates obtained by meta-analysing three studies of adult women (N = 46,944) and two of adolescent girls (N = 3025). We investigated the impact of departures from the assumption of no pleiotropy through sensitivity analyses. In adult women, in line with previous evidence, we found an effect on restrictive lung impairment with a 24.8 mL increase in FVC per year increase in age at menarche (95% CI 1.8-47.9; p = 0.035); evidence was stronger after excluding potential pleiotropic variants (43.6 mL; 17.2-69.9; p = 0.001). In adolescent girls we found an opposite effect (-56.5 mL; -108.3 to -4.7; p = 0.033), suggesting that the detrimental effect in adulthood may be preceded by a short-term post-pubertal benefit. Our secondary analyses showing results in the same direction in men and boys, in whom age at menarche SNPs have also shown association with sexual development, suggest a role for pubertal timing in general rather than menarche specifically. We found no effect on airway obstruction (FEV1/FVC).
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Affiliation(s)
- Dipender Gill
- Department of Clinical Pharmacology and Therapeutics, Imperial College London, Hammersmith Hospital, London, UK
- St. Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Nuala A Sheehan
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Andre F S Amaral
- Population Health and Occupational Disease, NHLI, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, SW3 6LR, London, UK
- MRC-PHE Centre for Environment and Health, London, UK
| | - John R Thompson
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Raquel Granell
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Bénédicte Leynaert
- UMR 1152, Pathophysiology and Epidemiology of Respiratory Diseases, Epidemiology Team, Inserm, Paris, France
- UMR 1152, Univ Paris Diderot - Paris 7, Paris, France
| | - Francisco Gómez Real
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ian P Hall
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Juha Auvinen
- Institute of Health Sciences, University of Oulu, Oulu, Finland
| | - Susan M Ring
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, London, UK
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Center for Life Course Epidemiology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - John Henderson
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Deborah Jarvis
- Population Health and Occupational Disease, NHLI, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, SW3 6LR, London, UK
- MRC-PHE Centre for Environment and Health, London, UK
| | - Cosetta Minelli
- Population Health and Occupational Disease, NHLI, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, SW3 6LR, London, UK.
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34
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Farzan N, Vijverberg SJ, Andiappan AK, Arianto L, Berce V, Blanca-López N, Bisgaard H, Bønnelykke K, Burchard EG, Campo P, Canino G, Carleton B, Celedón JC, Chew FT, Chiang WC, Cloutier MM, Daley D, Den Dekker HT, Dijk FN, Duijts L, Flores C, Forno E, Hawcutt DB, Hernandez-Pacheco N, de Jongste JC, Kabesch M, Koppelman GH, Manolopoulos VG, Melén E, Mukhopadhyay S, Nilsson S, Palmer CN, Pino-Yanes M, Pirmohamed M, Potočnik U, Raaijmakers JA, Repnik K, Schieck M, Sio YY, Smyth RL, Szalai C, Tantisira KG, Turner S, van der Schee MP, Verhamme KM, Maitland-van der Zee AH. Rationale and design of the multiethnic Pharmacogenomics in Childhood Asthma consortium. Pharmacogenomics 2017. [PMID: 28639505 DOI: 10.2217/pgs-2017-0035] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
AIM International collaboration is needed to enable large-scale pharmacogenomics studies in childhood asthma. Here, we describe the design of the Pharmacogenomics in Childhood Asthma (PiCA) consortium. MATERIALS & METHODS Investigators of each study participating in PiCA provided data on the study characteristics by answering an online questionnaire. RESULTS A total of 21 studies, including 14,227 children/young persons (58% male), from 12 different countries are currently enrolled in the PiCA consortium. Fifty six percent of the patients are Caucasians. In total, 7619 were inhaled corticosteroid users. Among patients from 13 studies with available data on asthma exacerbations, a third reported exacerbations despite inhaled corticosteroid use. In the future pharmacogenomics studies within the consortium, the pharmacogenomics analyses will be performed separately in each center and the results will be meta-analyzed. CONCLUSION PiCA is a valuable platform to perform pharmacogenetics studies within a multiethnic pediatric asthma population.
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Affiliation(s)
- Niloufar Farzan
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anand K Andiappan
- Singapore Immunology Network, Agency for Science, Technology & Research, Singapore 138648, Singapore
| | - Lambang Arianto
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Vojko Berce
- Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia.,Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | | | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Esteban G Burchard
- Departments of Medicine, Bioengineering & Therapeutic Sciences University of California, San Francisco, CA 94110, USA
| | - Paloma Campo
- Allergy Unit, IBIMA, Regional University Hospital of Malaga, Malaga, Spain
| | - Glorisa Canino
- Behavioral Sciences institute, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Bruce Carleton
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Juan C Celedón
- Division of Pulmonary Medicine, Allergy, & Immunology, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore
| | - Wen Chin Chiang
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore
| | - Michelle M Cloutier
- Asthma Center, Connecticut Children's Medical Center, University of Connecticut Health Center, CT 06106, USA
| | - Denis Daley
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Herman T Den Dekker
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - F Nicole Dijk
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands.,Groningen Research Institute for Asthma & COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Carlos Flores
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Erick Forno
- Division of Pulmonary Medicine, Allergy, & Immunology, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Daniel B Hawcutt
- Alder Hey Children's Hospital, Liverpool, UK.,Department of Women's & Children's Health, University of Liverpool, Liverpool, UK
| | - Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Johan C de Jongste
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Michael Kabesch
- Department of Pediatric Pneumology & Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands.,Groningen Research Institute for Asthma & COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vangelis G Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre of Occupational & Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Somnath Mukhopadhyay
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK.,Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital & Medical School University of Dundee, Dundee, UK
| | - Sara Nilsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre of Occupational & Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Colin N Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital & Medical School University of Dundee, Dundee, UK
| | - Maria Pino-Yanes
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Munir Pirmohamed
- Department of Molecular & Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Uros Potočnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Faculty for Chemistry & Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Jan A Raaijmakers
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Katja Repnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Faculty for Chemistry & Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Maximilian Schieck
- Department of Pediatric Pneumology & Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany.,Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Yang Yie Sio
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore
| | - Rosalind L Smyth
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Csaba Szalai
- Department of Genetics, Cell & Immuno-biology, Semmelweis University, Budapest, Hungary.,Central Laboratory, Heim Pal Children Hospital, Budapest, Hungary
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's hospital & Harvard Medical School, Boston, MA 02115, USA.,Division of Pulmonary & Critical Care Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
| | - Marc P van der Schee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Katia M Verhamme
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
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35
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Reliably estimating prevalences of atopic children: an epidemiological study in an extensive and representative primary care database. NPJ Prim Care Respir Med 2017; 27:23. [PMID: 28408759 PMCID: PMC5435092 DOI: 10.1038/s41533-017-0025-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 02/25/2017] [Accepted: 02/28/2017] [Indexed: 12/02/2022] Open
Abstract
Electronic health records stored in primary care databases might be a valuable source to study the epidemiology of atopic disorders and their impact on health-care systems and costs. However, the prevalence of atopic disorders in such databases varies considerably and needs to be addressed. For this study, all children aged 0–18 years listed in a representative primary care database in the period 2002–2014, with sufficient data quality, were selected. The effects of four different strategies on the prevalences of atopic disorders were examined: (1) the first strategy examined the diagnosis as recorded in the electronic health records, whereas the (2) second used additional requirements (i.e., the patient had at least two relevant consultations and at least two relevant prescriptions). Strategies (3) and (4) assumed the atopic disorders to be chronic based on strategy 1 and 2, respectively. When interested in cases with a higher probability of a clinically relevant disorder, strategy 2 yields a realistic estimation of the prevalence of atopic disorders derived from primary care data. Using this strategy, of the 478,076 included children, 28,946 (6.1%) had eczema, 29,182 (6.1%) had asthma, and 28,064 (5.9%) had allergic rhinitis; only 1251 (0.3%) children had all three atopic disorders. Prevalence rates are highly dependent on the clinical atopic definitions used. The strategy using cases with a higher probability of clinically relevant cases, yields realistic prevalences to establish the impact of atopic disorders on health-care systems. However, studies are needed to solve the problem of identifying atopic disorders that are missed or misclassified. The prevalence of atopic disorders in children can be more reliably calculated by incorporating clinical information with diagnosis data. Researchers in the Netherlands, led by David Pols from the Erasmus University Medical Center Rotterdam, examined the electronic health records of more than 660,000 children, aged 0 to 18, from a Dutch primary care database to determine the number of cases of atopic eczema, asthma, and allergic rhinitis. They looked for diagnosed children who also had at least two relevant clinical consultations and at least two relevant prescriptions. This strategy helps correct for the problem of overestimation, because it doesnot assume that a child, once diagnosed, will have an atopic disorder for life. However, other methods are still needed to identify cases that are missed or misclassified in the health database.
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36
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Mechanisms of the Development of Allergy (MeDALL): Introducing novel concepts in allergy phenotypes. J Allergy Clin Immunol 2017; 139:388-399. [DOI: 10.1016/j.jaci.2016.12.940] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/04/2016] [Accepted: 12/16/2016] [Indexed: 11/19/2022]
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37
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Belgrave D, Henderson J, Simpson A, Buchan I, Bishop C, Custovic A. Disaggregating asthma: Big investigation versus big data. J Allergy Clin Immunol 2017; 139:400-407. [PMID: 27871876 PMCID: PMC5292995 DOI: 10.1016/j.jaci.2016.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 12/21/2022]
Abstract
We are facing a major challenge in bridging the gap between identifying subtypes of asthma to understand causal mechanisms and translating this knowledge into personalized prevention and management strategies. In recent years, "big data" has been sold as a panacea for generating hypotheses and driving new frontiers of health care; the idea that the data must and will speak for themselves is fast becoming a new dogma. One of the dangers of ready accessibility of health care data and computational tools for data analysis is that the process of data mining can become uncoupled from the scientific process of clinical interpretation, understanding the provenance of the data, and external validation. Although advances in computational methods can be valuable for using unexpected structure in data to generate hypotheses, there remains a need for testing hypotheses and interpreting results with scientific rigor. We argue for combining data- and hypothesis-driven methods in a careful synergy, and the importance of carefully characterized birth and patient cohorts with genetic, phenotypic, biological, and molecular data in this process cannot be overemphasized. The main challenge on the road ahead is to harness bigger health care data in ways that produce meaningful clinical interpretation and to translate this into better diagnoses and properly personalized prevention and treatment plans. There is a pressing need for cross-disciplinary research with an integrative approach to data science, whereby basic scientists, clinicians, data analysts, and epidemiologists work together to understand the heterogeneity of asthma.
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Affiliation(s)
| | - John Henderson
- School of Social and Community Medicine, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Iain Buchan
- Health Informatics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | | | - Adnan Custovic
- Department of Paediatrics, Imperial College, London, United Kingdom.
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Del Giacco SR, Bakirtas A, Bel E, Custovic A, Diamant Z, Hamelmann E, Heffler E, Kalayci Ö, Saglani S, Sergejeva S, Seys S, Simpson A, Bjermer L. Allergy in severe asthma. Allergy 2017; 72:207-220. [PMID: 27775836 DOI: 10.1111/all.13072] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2016] [Indexed: 12/20/2022]
Abstract
It is well recognized that atopic sensitization is an important risk factor for asthma, both in adults and in children. However, the role of allergy in severe asthma is still under debate. The term 'Severe Asthma' encompasses a highly heterogeneous group of patients who require treatment on steps 4-5 of GINA guidelines to prevent their asthma from becoming 'uncontrolled', or whose disease remains 'uncontrolled' despite this therapy. Epidemiological studies on emergency room visits and hospital admissions for asthma suggest the important role of allergy in asthma exacerbations. In addition, allergic asthma in childhood is often associated with severe asthma in adulthood. A strong association exists between asthma exacerbations and respiratory viral infections, and interaction between viruses and allergy further increases the risk of asthma exacerbations. Furthermore, fungal allergy has been shown to play an important role in severe asthma. Other contributing factors include smoking, pollution and work-related exposures. The 'Allergy and Asthma Severity' EAACI Task Force examined the current evidence and produced this position document on the role of allergy in severe asthma.
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Affiliation(s)
- S. R. Del Giacco
- Department of Medical Sciences and Public Health; University of Cagliari; Cagliari Italy
| | - A. Bakirtas
- Department of Pediatric Allergy and Asthma; School of Medicine; Gazi University; Ankara Turkey
| | - E. Bel
- Department of Respiratory Medicine; Academic Medical Centre; University of Amsterdam; Amsterdam The Netherlands
| | - A. Custovic
- Department of Paediatrics; Imperial College London; London UK
| | - Z. Diamant
- Department of General Practice and Department of Clinical Pharmacy & Pharmacology; University Medical Centre Groningen; University of Groningen; Groningen The Netherlands
- Department of Respiratory Medicine and Allergology; Lund University; Lund Sweden
| | - E. Hamelmann
- Klinik für Kinder and Jugendmedizin Kinderzentrum; Bethel Evangelisches Krankenhaus; Allergy Center; Ruhr University Bochum; Bielefeld Germany
| | - E. Heffler
- Respiratory Medicine and Allergology - Department of Experimental and Clinical Medicine; University of Catania; Catania Italy
| | - Ö. Kalayci
- School of Medicine; Hacettepe University; Ankara Turkey
| | - S. Saglani
- National Heart & Lung Institute; Imperial College London; London UK
| | - S. Sergejeva
- Institute of Technology; University of Tartu; Tartu Estonia
| | - S. Seys
- Department of Microbiology and Immunology; Laboratory of Clinical Immunology; KU Leuven Belgium
| | - A. Simpson
- Centre Lead for Respiratory Medicine and Allergy; University Hospital of South Manchester; Education and Research Centre; University of Manchester; Manchester UK
| | - L. Bjermer
- Department of Respiratory Medicine and Allergology; Lund University; Lund Sweden
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Agache I, Rogozea L. Asthma Biomarkers: Do They Bring Precision Medicine Closer to the Clinic? ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2017; 9:466-476. [PMID: 28913985 PMCID: PMC5603474 DOI: 10.4168/aair.2017.9.6.466] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/03/2017] [Accepted: 03/13/2017] [Indexed: 12/11/2022]
Abstract
Measurement of biomarkers has been incorporated within clinical research of asthma to characterize the population and to associate the disease with environmental and therapeutic effects. Regrettably, at present, there are no specific biomarkers, none is validated or qualified, and endotype-driven choices overlap. Biomarkers have not yet reached clinical practice and are not included in current asthma guidelines. Last but not least, the choice of the outcome upholding the value of the biomarkers is extremely difficult, since it has to reflect the mechanistic intervention while being relevant to both the disease and the particular person. On the verge of a new age of asthma healthcare standard, we must embrace and adapt to the key drivers of change. Disease endotypes, biomarkers, and precision medicine represent an emerging model of patient care building on large-scale biologic databases, omics and diverse cellular assays, health information technology, and computational tools for analyzing sizable sets of data. A profound transformation of clinical and research pattern from population to individual risk and from investigator-imposed subjective disease clustering (hypothesis driven) to unbiased, data-driven models is facilitated by the endotype/biomarker-driven approach.
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Affiliation(s)
- Ioana Agache
- Faculty of Medicine, Department of Allergy and Clinical Immunology, Transylvania University of Brasov, Brasov, Romania.
| | - Liliana Rogozea
- Faculty of Medicine, Department of Allergy and Clinical Immunology, Transylvania University of Brasov, Brasov, Romania
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40
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Belgrave D, Custovic A. The importance of being earnest in epidemiology. Acta Paediatr 2016; 105:1384-1386. [PMID: 27870201 DOI: 10.1111/apa.13614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 09/30/2016] [Indexed: 11/28/2022]
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Deliu M, Belgrave D, Sperrin M, Buchan I, Custovic A. Asthma phenotypes in childhood. Expert Rev Clin Immunol 2016; 13:705-713. [PMID: 27817211 DOI: 10.1080/1744666x.2017.1257940] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Asthma is no longer thought of as a single disease, but rather a collection of varying symptoms expressing different disease patterns. One of the ongoing challenges is understanding the underlying pathophysiological mechanisms that may be responsible for the varying responses to treatment. Areas Covered: This review provides an overview of our current understanding of the asthma phenotype concept in childhood and describes key findings from both conventional and data-driven methods. Expert Commentary: With the vast amounts of data generated from cohorts, there is hope that we can elucidate distinct pathophysiological mechanisms, or endotypes. In return, this would lead to better patient stratification and disease management, thereby providing true personalised medicine.
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Affiliation(s)
- Matea Deliu
- a Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health , University of Manchester , Manchester , UK
| | - Danielle Belgrave
- b Department of Paediatrics , Imperial College of Science, Technology & Medicine , London , UK
| | - Matthew Sperrin
- a Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health , University of Manchester , Manchester , UK
| | - Iain Buchan
- a Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health , University of Manchester , Manchester , UK
| | - Adnan Custovic
- b Department of Paediatrics , Imperial College of Science, Technology & Medicine , London , UK
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Kouzouna A, Gilchrist FJ, Ball V, Kyriacou T, Henderson J, Pandyan AD, Lenney W. A systematic review of early life factors which adversely affect subsequent lung function. Paediatr Respir Rev 2016; 20:67-75. [PMID: 27197758 DOI: 10.1016/j.prrv.2016.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 03/08/2016] [Indexed: 01/15/2023]
Abstract
It has been known for many years that multiple early life factors can adversely affect lung function and future respiratory health. This is the first systematic review to attempt to analyse all these factors simultaneously. We adhered to strict a priori criteria for inclusion and exclusion of studies. The initial search yielded 29,351 citations of which 208 articles were reviewed in full and 25 were included in the review. This included 6 birth cohorts and 19 longitudinal population studies. The 25 studies reported the effect of 74 childhood factors (on their own or in combinations with other factors) on subsequent lung function reported as percent predicted forced expiration in one second (FEV1). The childhood factors that were associated with a significant reduction in future FEV1 could be grouped as: early infection, bronchial hyper-reactivity (BHR) / airway lability, a diagnosis of asthma, wheeze, family history of atopy or asthma, respiratory symptoms and prematurity / low birth weight. A complete mathematical model will only be possible if the raw data from all previous studies is made available. This highlights the need for increased cooperation between researchers and the need for international consensus about the outcome measures for future longitudinal studies.
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Affiliation(s)
- A Kouzouna
- Institute of Science and Technology in Medicine, Keele University, Staffordshire, ST5 5BG, UK; School of Health Rehabilitation, Keele University, Staffordshire, ST5 5BG, UK
| | - F J Gilchrist
- Institute of Science and Technology in Medicine, Keele University, Staffordshire, ST5 5BG, UK; Royal Stoke University Hospital, Stoke on Trent, Newcastle Road, ST4 6QG
| | - V Ball
- School of Health Rehabilitation, Keele University, Staffordshire, ST5 5BG, UK
| | - T Kyriacou
- School of Computing, Keele University, Staffordshire, ST5 5BG, UK
| | - J Henderson
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK
| | - A D Pandyan
- Institute of Science and Technology in Medicine, Keele University, Staffordshire, ST5 5BG, UK; School of Health Rehabilitation, Keele University, Staffordshire, ST5 5BG, UK
| | - W Lenney
- Institute of Science and Technology in Medicine, Keele University, Staffordshire, ST5 5BG, UK; Royal Stoke University Hospital, Stoke on Trent, Newcastle Road, ST4 6QG.
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Deliu M, Sperrin M, Belgrave D, Custovic A. Identification of Asthma Subtypes Using Clustering Methodologies. Pulm Ther 2016; 2:19-41. [PMID: 27512723 PMCID: PMC4959136 DOI: 10.1007/s41030-016-0017-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Indexed: 02/07/2023] Open
Abstract
Asthma is a heterogeneous disease comprising a number of subtypes which may be caused by different pathophysiologic mechanisms (sometimes referred to as endotypes) but may share similar observed characteristics (phenotypes). The use of unsupervised clustering in adult and paediatric populations has identified subtypes of asthma based on observable characteristics such as symptoms, lung function, atopy, eosinophilia, obesity, and age of onset. Here we describe different clustering methods and demonstrate their contributions to our understanding of the spectrum of asthma syndrome. Precise identification of asthma subtypes and their pathophysiological mechanisms may lead to stratification of patients, thus enabling more precise therapeutic and prevention approaches.
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Affiliation(s)
- Matea Deliu
- />Centre for Health Informatics, Institute of Population Health, University of Manchester, Manchester, UK
| | - Matthew Sperrin
- />Centre for Health Informatics, Institute of Population Health, University of Manchester, Manchester, UK
| | | | - Adnan Custovic
- />Department of Paediatrics, Imperial College London, London, UK
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Abstract
Asthma is not a single disease, but an umbrella term for a number of distinct diseases, each of which are caused by a distinct underlying pathophysiological mechanism. These discrete disease entities are often labelled as 'asthma endotypes'. The discovery of different asthma subtypes has moved from subjective approaches in which putative phenotypes are assigned by experts to data-driven ones which incorporate machine learning. This review focuses on the methodological developments of one such machine learning technique-latent class analysis-and how it has contributed to distinguishing asthma and wheezing subtypes in childhood. It also gives a clinical perspective, presenting the findings of studies from the past 5 years that used this approach. The identification of true asthma endotypes may be a crucial step towards understanding their distinct pathophysiological mechanisms, which could ultimately lead to more precise prevention strategies, identification of novel therapeutic targets and the development of effective personalized therapies.
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Affiliation(s)
- Rebecca Howard
- />Centre for Health Informatics, Institute of Population Health, University of Manchester, Manchester, UK
| | - Magnus Rattray
- />Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Mattia Prosperi
- />Centre for Health Informatics, Institute of Population Health, University of Manchester, Manchester, UK
- />University of Florida, Gainesville, FL USA
| | - Adnan Custovic
- />Centre for Respiratory Medicine and Allergy, Institute of Inflammation and Repair, University of Manchester and University Hospital of South Manchester, Manchester, M23 9LT UK
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