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van Breugel M, Fehrmann RSN, Bügel M, Rezwan FI, Holloway JW, Nawijn MC, Fontanella S, Custovic A, Koppelman GH. Current state and prospects of artificial intelligence in allergy. Allergy 2023; 78:2623-2643. [PMID: 37584170 DOI: 10.1111/all.15849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/08/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
The field of medicine is witnessing an exponential growth of interest in artificial intelligence (AI), which enables new research questions and the analysis of larger and new types of data. Nevertheless, applications that go beyond proof of concepts and deliver clinical value remain rare, especially in the field of allergy. This narrative review provides a fundamental understanding of the core concepts of AI and critically discusses its limitations and open challenges, such as data availability and bias, along with potential directions to surmount them. We provide a conceptual framework to structure AI applications within this field and discuss forefront case examples. Most of these applications of AI and machine learning in allergy concern supervised learning and unsupervised clustering, with a strong emphasis on diagnosis and subtyping. A perspective is shared on guidelines for good AI practice to guide readers in applying it effectively and safely, along with prospects of field advancement and initiatives to increase clinical impact. We anticipate that AI can further deepen our knowledge of disease mechanisms and contribute to precision medicine in allergy.
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Affiliation(s)
- Merlijn van Breugel
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- MIcompany, Amsterdam, the Netherlands
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Computer Science, Aberystwyth University, Aberystwyth, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health and Care Research Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, UK
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, London, UK
- National Institute for Health and Care Research Imperial Biomedical Research Centre (BRC), London, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, UK
- National Institute for Health and Care Research Imperial Biomedical Research Centre (BRC), London, UK
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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2
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Kilanowski A, Thiering E, Wang G, Kumar A, Kress S, Flexeder C, Bauer CP, Berdel D, von Berg A, Bergström A, Gappa M, Heinrich J, Herberth G, Koletzko S, Kull I, Melén E, Schikowski T, Peters A, Standl M. Allergic disease trajectories up to adolescence: Characteristics, early-life, and genetic determinants. Allergy 2023; 78:836-850. [PMID: 36069615 DOI: 10.1111/all.15511] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/27/2022] [Accepted: 08/13/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Allergic diseases often develop jointly during early childhood but differ in timing of onset, remission, and progression. Their disease course over time is often difficult to predict and determinants are not well understood. OBJECTIVES We aimed to identify trajectories of allergic diseases up to adolescence and to investigate their association with early-life and genetic determinants and clinical characteristics. METHODS Longitudinal k-means clustering was used to derive trajectories of allergic diseases (asthma, atopic dermatitis, and rhinitis) in two German birth cohorts (GINIplus/LISA). Associations with early-life determinants, polygenic risk scores, food and aeroallergen sensitization, and lung function were estimated by multinomial models. The results were replicated in the independent Swedish BAMSE cohort. RESULTS Seven allergic disease trajectories were identified: "Intermittently allergic," "rhinitis," "early-resolving dermatitis," "mid-persisting dermatitis," "multimorbid," "persisting dermatitis plus rhinitis," and "early-transient asthma." Family history of allergies was more prevalent in all allergic disease trajectories compared the non-allergic controls with stronger effect sizes for clusters comprising more than one allergic disease (e.g., RRR = 5.0, 95% CI = [3.1-8.0] in the multimorbid versus 1.8 [1.4-2.4] in the mild intermittently allergic cluster). Specific polygenic risk scores for single allergic diseases were significantly associated with their relevant trajectories. The derived trajectories and their association with genetic effects and clinical characteristics showed similar results in BAMSE. CONCLUSION Seven robust allergic clusters were identified and showed associations with early life and genetic factors as well as clinical characteristics.
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Affiliation(s)
- Anna Kilanowski
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology, Pettenkofer School of Public Health, LMU Munich, Munich, Germany.,Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Munich, Germany
| | - Elisabeth Thiering
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Munich, Germany
| | - Gang Wang
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Ashish Kumar
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Sara Kress
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany.,Medical Research School Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Claudia Flexeder
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Lung Research (DZL), Munich, Germany.,Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Carl-Peter Bauer
- Department of Pediatrics, Technical University of Munich, Munich, Germany
| | - Dietrich Berdel
- Research Institute, Department of Pediatrics, Marien-Hospital Wesel, Wesel, Germany
| | - Andrea von Berg
- Research Institute, Department of Pediatrics, Marien-Hospital Wesel, Wesel, Germany
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm, Sweden
| | - Monika Gappa
- Evangelisches Krankenhaus Düsseldorf, Children's Hospital, Düsseldorf, Germany
| | - Joachim Heinrich
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany.,Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Sibylle Koletzko
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Department of Pediatrics, Gastroenterology and Nutrition, School of Medicine Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland
| | - Inger Kull
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Sachs Children's and Youth Hospital, Stockholm, Sweden
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Tamara Schikowski
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Epidemiology, Ludwig-Maximilians University, Munich, Germany
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Lung Research (DZL), Munich, Germany
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3
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Custovic A, Fontanella S, Haider S. Reply to Beck et al. and to Owora. Am J Respir Crit Care Med 2023; 207:634-636. [PMID: 36480959 PMCID: PMC10870903 DOI: 10.1164/rccm.202211-2130le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Adnan Custovic
- National Heart and Lung InstituteImperial College London, United Kingdom
| | - Sara Fontanella
- National Heart and Lung InstituteImperial College London, United Kingdom
| | - Sadia Haider
- National Heart and Lung InstituteImperial College London, United Kingdom
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Kilanowski A, Merid SK, Abrishamcar S, Feil D, Thiering E, Waldenberger M, Melén E, Peters A, Standl M, Hüls A. DNA methylation and aeroallergen sensitization: The chicken or the egg? Clin Epigenetics 2022; 14:114. [PMID: 36114581 PMCID: PMC9482323 DOI: 10.1186/s13148-022-01332-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation (DNAm) is considered a plausible pathway through which genetic and environmental factors may influence the development of allergies. However, causality has yet to be determined as it is unknown whether DNAm is rather a cause or consequence of allergic sensitization. Here, we investigated the direction of the observed associations between well-known environmental and genetic determinants of allergy, DNAm, and aeroallergen sensitization using a combination of high-dimensional and causal mediation analyses.
Methods Using prospectively collected data from the German LISA birth cohort from two time windows (6–10 years: N = 234; 10–15 years: N = 167), we tested whether DNAm is a cause or a consequence of aeroallergen sensitization (specific immunoglobulin E > 0.35kU/l) by conducting mediation analyses for both effect directions using maternal smoking during pregnancy, family history of allergies, and a polygenic risk score (PRS) for any allergic disease as exposure variables. We evaluated individual CpG sites (EPIC BeadChip) and allergy-related methylation risk scores (MRS) as potential mediators in the mediation analyses. We applied three high-dimensional mediation approaches (HIMA, DACT, gHMA) and validated results using causal mediation analyses. A replication of results was attempted in the Swedish BAMSE cohort.
Results Using high-dimensional methods, we identified five CpGs as mediators of prenatal exposures to sensitization with significant (adjusted p < 0.05) indirect effects in the causal mediation analysis (maternal smoking: two CpGs, family history: one, PRS: two). None of these CpGs could be replicated in BAMSE. The effect of family history on allergy-related MRS was significantly mediated by aeroallergen sensitization (proportions mediated: 33.7–49.6%), suggesting changes in DNAm occurred post-sensitization. Conclusion The results indicate that DNAm may be a cause or consequence of aeroallergen sensitization depending on genomic location. Allergy-related MRS, identified as a potential cause of sensitization, can be considered as a cross-sectional biomarker of disease. Differential DNAm in individual CpGs, identified as mediators of the development of sensitization, could be used as clinical predictors of disease development. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01332-5.
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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: 18] [Impact Index Per Article: 9.0] [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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6
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Kotsapas C, Nicolaou N, Haider S, Kerry G, Turner PJ, Murray CS, Simpson A, Custovic A. Early-life predictors and risk factors of peanut allergy, and its association with asthma in later-life: Population-based birth cohort study. Clin Exp Allergy 2022; 52:646-657. [PMID: 35108754 PMCID: PMC9303430 DOI: 10.1111/cea.14103] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Understanding risk factors for peanut allergy (PA) is essential to develop effective preventive measures. OBJECTIVE To ascertain associates and predictors of PA, and the relationship between PA and asthma severity. METHODS In a population-based birth cohort, we investigated the association between objectively confirmed PA with early-life environmental exposures, filaggrin (FLG)-loss-of-function mutations and other atopic disease. We then examined the association of PA with longitudinal trajectories of sensitisation, wheeze and allergic comorbidities, which were previously derived using machine learning. Finally, we ascertained the relationship between PA and asthma severity. RESULTS PA was confirmed in 30/959 participants with evaluable data. In the multivariate analysis, eczema in infancy (OR=4.4, 95% CI 1.5-13.2, p=0.007), egg sensitisation at age 3 years (OR=9.7, 95% CI 3.3-29.9, p<0.001) and early-life cat ownership (OR=3.0, 95% CI 1.1-8.4, p=0.04) were independent associates of PA. In the stratified analysis among 700 participants with genetic information, in children with early-life eczema there was no difference in FLG mutations between children with and without PA (3/18 [16.7%] vs. 42/220 [19.1%], p=1.00). In contrast, among children without eczema, those with PA were almost 8-times more likely to have FLG mutations (2/6 [33.3%] vs. 27/456 [5.9%], p=0.049). We observed associations between PA and multiple allergic sensitisation profiles derived using machine learning, with ~60-fold increase in risk amongst individuals assigned to multiple early sensitisation. PA was significantly associated with persistent wheeze (but not other wheeze phenotypes), and with trajectories of atopic disease characterised by co-morbid persistent eczema and wheeze (but not with transient phenotypes). Children with PA were more likely to have asthma, but among asthmatics we found no evidence of an association between PA and asthma severity. CONCLUSIONS Peanut allergy is associated with multiple IgE-sensitisation and early-onset persistent eczema and wheeze. FLG loss-of-function mutations were associated with peanut allergy in children without eczema.
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Affiliation(s)
| | - Nicolaos Nicolaou
- University of Nicosia Medical School, Cyprus.,Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, and Manchester Academic Health Science Centre and NIHR Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Sadia Haider
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Gina Kerry
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, and Manchester Academic Health Science Centre and NIHR Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Paul J Turner
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Clare S Murray
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, and Manchester Academic Health Science Centre and NIHR Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, and Manchester Academic Health Science Centre and NIHR Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, UK
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7
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Laubhahn K, Böck A, Zeber K, Unterschemmann S, Kunze S, Schedel M, Schaub B. 17q12-21 risk-variants influence cord blood immune regulation and multitrigger-wheeze. Pediatr Allergy Immunol 2022; 33:e13721. [PMID: 34919286 DOI: 10.1111/pai.13721] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Childhood wheeze represents a first symptom of asthma. Early identification of children at risk for wheeze related to 17q12-21 variants and their underlying immunological mechanisms remain unknown. We aimed to assess the influence of 17q12-21 variants and mRNA expression at birth on the development of wheeze. METHODS Children were classified as multitrigger/viral/no wheeze until six years of age. The PAULINA/PAULCHEN birth cohorts were genotyped (n = 216; GSA-chip). mRNA expression of 17q21 and innate/adaptive genes was measured (qRT-PCR) in cord blood mononuclear cells. Expression quantitative trait loci (eQTL) and mediation analyses were performed. Genetic variation of 17q12-21 asthma-single nucleotide polymorphisms (SNPs) was summarized as the first principal component (PC1) and used to classify single SNP effects on gene expression as (locus)-dependent/independent eQTL SNPs. RESULTS Core region risk variants (IKZF3, ZPBP2, GSDMB, ORMDL3) were associated with multitrigger wheeze (OR: 3.05-5.43) and were locus-dependent eQTL SNPs with higher GSDMA, TLR2, TLR5, and lower TGFB1 expression. Increased risk of multitrigger wheeze with rs9303277 was in part mediated by TLR2 expression. Risk variants distal to the core region were mainly locus-independent eQTL SNPs with decreased CD209, CD86, TRAF6, RORA, and IL-9 expression. Distinct immune signatures in cord blood were associated either with multitrigger wheeze (increased innate genes, e.g., TLR2, IPS1, LY75) or viral wheeze (decreased NF-κB genes, e.g., TNFAIP3 and TNIP2). CONCLUSION Locus-dependent eQTL SNPs (core region) associated with increased inflammatory genes (primarily TLR2) at birth and subsequent multitrigger wheeze indicate that early priming and imbalance may be crucial for asthma pathophysiology. Locus-independent eQTL SNPs (mainly distal region, rs1007654) may be involved in the initiation of dendritic cell activation/maturation (TRAF6) and interaction with T cells (CD209, CD86). Identifying potential mechanistic pathways at birth may point to critical key points during early immune development predisposing to asthma.
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Affiliation(s)
- Kristina Laubhahn
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research - DZL, LMU Munich, Munich, Germany
| | - Andreas Böck
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Member of the CHildhood Allergy and tolerance consortium (CHAMP), LMU Munich, Munich, Germany
| | - Kathrin Zeber
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Member of the CHildhood Allergy and tolerance consortium (CHAMP), LMU Munich, Munich, Germany
| | - Sandra Unterschemmann
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michaela Schedel
- Department of Pulmonary Medicine, University Medical Center Essen-Ruhrlandklinik, Essen, Germany.,Department of Pulmonary Medicine, University Medicine Essen-University Hospital, Essen, Germany
| | - Bianca Schaub
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research - DZL, LMU Munich, Munich, Germany.,Member of the CHildhood Allergy and tolerance consortium (CHAMP), LMU Munich, Munich, Germany
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8
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Kothalawala DM, Kadalayil L, Curtin JA, Murray CS, Simpson A, Custovic A, Tapper WJ, Arshad SH, Rezwan FI, Holloway JW. Integration of Genomic Risk Scores to Improve the Prediction of Childhood Asthma Diagnosis. J Pers Med 2022; 12:75. [PMID: 35055391 PMCID: PMC8777841 DOI: 10.3390/jpm12010075] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/18/2021] [Accepted: 12/31/2021] [Indexed: 01/24/2023] Open
Abstract
Genome-wide and epigenome-wide association studies have identified genetic variants and differentially methylated nucleotides associated with childhood asthma. Incorporation of such genomic data may improve performance of childhood asthma prediction models which use phenotypic and environmental data. Using genome-wide genotype and methylation data at birth from the Isle of Wight Birth Cohort (n = 1456), a polygenic risk score (PRS), and newborn (nMRS) and childhood (cMRS) methylation risk scores, were developed to predict childhood asthma diagnosis. Each risk score was integrated with two previously published childhood asthma prediction models (CAPE and CAPP) and were validated in the Manchester Asthma and Allergy Study. Individually, the genomic risk scores demonstrated modest-to-moderate discriminative performance (area under the receiver operating characteristic curve, AUC: PRS = 0.64, nMRS = 0.55, cMRS = 0.54), and their integration only marginally improved the performance of the CAPE (AUC: 0.75 vs. 0.71) and CAPP models (AUC: 0.84 vs. 0.82). The limited predictive performance of each genomic risk score individually and their inability to substantially improve upon the performance of the CAPE and CAPP models suggests that genetic and epigenetic predictors of the broad phenotype of asthma are unlikely to have clinical utility. Hence, further studies predicting specific asthma endotypes are warranted.
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Affiliation(s)
- Dilini M. Kothalawala
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - John A. Curtin
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, Manchester University Hospital NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; (J.A.C.); (C.S.M.); (A.S.)
| | - Clare S. Murray
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, Manchester University Hospital NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; (J.A.C.); (C.S.M.); (A.S.)
| | - Angela Simpson
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, Manchester University Hospital NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; (J.A.C.); (C.S.M.); (A.S.)
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College of Science, Technology, and Medicine, London SW3 6LY, UK;
| | - William J. Tapper
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
| | - S. Hasan Arshad
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- The David Hide Asthma and Allergy Research Centre, St. Mary’s Hospital, Isle of Wight PO30 5TG, UK
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, UK
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
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9
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Haahtela T, Alenius H, Lehtimäki J, Sinkkonen A, Fyhrquist N, Hyöty H, Ruokolainen L, Mäkelä MJ. Immunological resilience and biodiversity for prevention of allergic diseases and asthma. Allergy 2021; 76:3613-3626. [PMID: 33959980 DOI: 10.1111/all.14895] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 02/07/2023]
Abstract
Increase of allergic conditions has occurred at the same pace with the Great Acceleration, which stands for the rapid growth rate of human activities upon earth from 1950s. Changes of environment and lifestyle along with escalating urbanization are acknowledged as the main underlying causes. Secondary (tertiary) prevention for better disease control has advanced considerably with innovations for oral immunotherapy and effective treatment of inflammation with corticosteroids, calcineurin inhibitors, and biological medications. Patients are less disabled than before. However, primary prevention has remained a dilemma. Factors predicting allergy and asthma risk have proven complex: Risk factors increase the risk, while protective factors counteract them. Interaction of human body with environmental biodiversity with micro-organisms and biogenic compounds as well as the central role of epigenetic adaptation in immune homeostasis have given new insight. Allergic diseases are good indicators of the twisted relation to environment. In various non-communicable diseases, the protective mode of the immune system indicates low-grade inflammation without apparent cause. Giving microbes, pro- and prebiotics, has shown some promise in prevention and treatment. The real-world public health programme in Finland (2008-2018) emphasized nature relatedness and protective factors for immunological resilience, instead of avoidance. The nationwide action mitigated the allergy burden, but in the lack of controls, primary preventive effect remains to be proven. The first results of controlled biodiversity interventions are promising. In the fast urbanizing world, new approaches are called for allergy prevention, which also has a major cost saving potential.
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Affiliation(s)
- Tari Haahtela
- Skin and Allergy Hospital Helsinki University HospitalUniversity of Helsinki Helsinki Finland
| | - Harri Alenius
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Department of Bacteriology and Immunology Medicum University of Helsinki Helsinki Finland
| | | | - Aki Sinkkonen
- Natural Resources Institute Finland, Horticulture Technologies Turku Finland
| | - Nanna Fyhrquist
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Department of Bacteriology and Immunology Medicum University of Helsinki Helsinki Finland
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology Tampere University Tampere Finland
- Fimlab Laboratories Pirkanmaa Hospital District Tampere Finland
| | - Lasse Ruokolainen
- Lasse Ruokolainen Department of Biosciences University of Helsinki Helsinki Finland
| | - Mika J. Mäkelä
- Skin and Allergy Hospital Helsinki University HospitalUniversity of Helsinki Helsinki Finland
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10
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Gabryszewski SJ, Hill DA. One march, many paths: Insights into allergic march trajectories. Ann Allergy Asthma Immunol 2021; 127:293-300. [PMID: 33971364 PMCID: PMC8418995 DOI: 10.1016/j.anai.2021.04.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The classical allergic march model posits that atopy begins in infancy with atopic dermatitis and progresses to asthma and allergic rhinitis in a subset of individuals. The growing prevalence and severity of allergic diseases have prompted renewed interest in refining this model. This review outlines epidemiologic evidence for the existence of allergic march trajectories (distinct paths of atopy development in individuals); reviews the roles that genetics, environment, and disease endotypes play in determining trajectory outcomes; and discusses the clinical utility of the trajectory model. DATA SOURCES PubMed search of English-language articles and reviews without date limits pertaining to the epidemiology, genetics, and immunologic mechanisms of allergic march trajectories and disease endotypes. STUDY SELECTIONS Studies and reviews were selected based on their high quality and direct relevance to the review topic. RESULTS Recent work in the field has revealed that immunoglobulin E-mediated food allergy and eosinophilic esophagitis are components of the allergic march. Furthermore, the field is acknowledging that variability exists in the number and sequence of allergic manifestations that individuals develop. These allergic march pathways, or trajectories, are influenced by genetic, environmental, and psychosocial factors that are incompletely understood. CONCLUSION Continued elucidation of the landscape and origins of allergic march trajectories will inform efforts to personalize allergic disease prevention, diagnosis, and treatment.
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Affiliation(s)
- Stanislaw J Gabryszewski
- Division of Allergy and Immunology and Center for Pediatric Eosinophilic Disorders, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - David A Hill
- Division of Allergy and Immunology and Center for Pediatric Eosinophilic Disorders, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Institute for Immunology and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania.
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11
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Clinical relevance of inherited genetic differences in human tryptases: Hereditary alpha-tryptasemia and beyond. Ann Allergy Asthma Immunol 2021; 127:638-647. [PMID: 34400315 DOI: 10.1016/j.anai.2021.08.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To describe our current understanding of hereditary α-tryptasemia (HαT), how HαT fits into the evolutionary context of tryptases and contemporary framework of mast cell-associated disorders, and to discuss the future clinical and therapeutic landscape for symptomatic individuals with HαT. DATA SOURCES Primary peer-reviewed literature. STUDY SELECTIONS Basic, clinical, and translational studies describing tryptase gene composition, generation, secretion, and elevation and the associated clinical impacts of HαT and treatment of such individuals were reviewed. RESULTS HαT is a common autosomal dominant genetic trait caused by increased TPSAB1 copy number encoding α-tryptase. Approximately 1 in 20 White individuals have HαT, making it by far the most common cause for elevated basal serum tryptase levels. Although many individuals with HαT may not manifest associated symptoms, the prevalence of HαT is increased in patients with clonal and nonclonal mast cell-associated disorders wherein it is linked to more prevalent and/or severe anaphylaxis and increased mast cell mediator-associated symptoms. Increased generation of mature α/β-tryptase heterotetramers, and their unique physiochemical properties, may be responsible for some of these clinical findings. CONCLUSION HαT is a common modifier of mast cell-associated disorders and reactions. Nevertheless, whether HαT may be an independent cause of clinical phenotypes with which it has been associated remains unproven. Correct identification of HαT is critical to accurate interpretation of serum tryptase levels in the clinical evaluation of patients. Beyond HαT, we foresee tryptase genotyping as an important parameter in the standard workup of patients with mast cell-associated disorders and development of therapeutic modalities targeting these patients and associated clinical phenotypes.
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12
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Seité S, Taieb C, Pham-Thi N, Barbaud A. Allergy Prevalence in France and Skin Impact - Epidemiological Survey of a Representative Sample of French Adults. Clin Cosmet Investig Dermatol 2021; 14:901-907. [PMID: 34285536 PMCID: PMC8286784 DOI: 10.2147/ccid.s307345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/02/2021] [Indexed: 12/29/2022]
Abstract
Background Increased allergy frequency may have a significant impact on the skin, one of the largest targeted organs for allergic and immunological responses. Methods An online survey of 2036 adults as a representative sample of the French general population was conducted to evaluate the prevalence of self-reported allergies, the populations who report allergies and the skin conditions related to allergies. Results In general, 20.2% of French adults (average age 45 ± 15.8 years) reported allergies. These allergies were respiratory allergies (55.3%), skin allergies (48.8%) and food allergies (27.9%), and 78.9% indicated that their reported allergies were diagnosed by a doctor. In addition, 53.2% of individuals reporting an allergy also indicated that they experienced associated skin reactions. In comparison to those who did not report an allergy, these individuals were 1.5 to 4 times more likely to have a skin disease and 3 times more likely to have sensitive skin or skin reactions when using skincare products. Conclusion It is estimated that over 10 million French adults have allergies. These data will help increase awareness among the allergic population and healthcare professionals about the burden associated with allergies and the need for management to reduce their health impact.
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Affiliation(s)
- Sophie Seité
- La Roche-Posay Dermatological Laboratories, Levallois-Perret, France
| | - Charles Taieb
- European Market Maintenance Assessment, Fontenay-sous-Bois, France
| | - Nhân Pham-Thi
- Ecole Polytechnique, Economics, Palaiseau, France.,Institut Pasteur Paris, Allergology, Paris, France
| | - Annick Barbaud
- Dermatology and Allergy Department, Tenon Hospital, Medicine Sorbonne University, Paris, France.,Assistance Publique-Hôpitaux de Paris, Paris, France
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13
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Polygenic prediction of atopic dermatitis improves with atopic training and filaggrin factors. J Allergy Clin Immunol 2021; 149:145-155. [PMID: 34111454 PMCID: PMC8973457 DOI: 10.1016/j.jaci.2021.05.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 04/26/2021] [Accepted: 05/20/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND While numerous genetic loci associated with atopic dermatitis (AD) have been discovered, to date, work leveraging the combined burden of AD risk variants across the genome to predict disease risk has been limited. OBJECTIVES This study aims to determine whether polygenic risk scores (PRSs) relying on genetic determinants for AD provide useful predictions for disease occurrence and severity. It also explicitly tests the value of including genome-wide association studies of related allergic phenotypes and known FLG loss-of-function (LOF) variants. METHODS AD PRSs were constructed for 1619 European American individuals from the Atopic Dermatitis Research Network using an AD training dataset and an atopic training dataset including AD, childhood onset asthma, and general allergy. Additionally, whole genome sequencing data were used to explore genetic scoring specific to FLG LOF mutations. RESULTS Genetic scores derived from the AD-only genome-wide association studies were predictive of AD cases (PRSAD: odds ratio [OR], 1.70; 95% CI, 1.49-1.93). Accuracy was first improved when PRSs were built off the larger atopy genome-wide association studies (PRSAD+: OR, 2.16; 95% CI, 1.89-2.47) and further improved when including FLG LOF mutations (PRSAD++: OR, 3.23; 95% CI, 2.57-4.07). Importantly, while all 3 PRSs correlated with AD severity, the best prediction was from PRSAD++, which distinguished individuals with severe AD from control subjects with OR of 3.86 (95% CI, 2.77-5.36). CONCLUSIONS This study demonstrates how PRSs for AD that include genetic determinants across atopic phenotypes and FLG LOF variants may be a promising tool for identifying individuals at high risk for developing disease and specifically severe disease.
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14
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Fontanella S, Cucco A, Custovic A. Machine learning in asthma research: moving toward a more integrated approach. Expert Rev Respir Med 2021; 15:609-621. [PMID: 33618597 DOI: 10.1080/17476348.2021.1894133] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Big data are reshaping the future of medicine. The growing availability and increasing complexity of data have favored the adoption of modern analytical and computational methodologies in every area of medicine. Over the past decades, asthma research has been characterized by a shift in the way studies are conducted and data are analyzed. Motivated by the assumptions that 'data will speak for themselves', hypothesis-driven approaches have been replaced by data-driven hypotheses-generating methods to explore hidden patterns and underlying mechanisms. However, even with all the advancement in technologies and the new important insight that we gained to understand and characterize asthma heterogeneity, very few research findings have been translated into clinically actionable solutions.Areas covered: To investigate some of the fundamental analytical approaches adopted in the current literature and appraise their impact and usefulness in medicine, we conducted a bibliometric analysis of big data analytics in asthma research in the past 50 years.Expert opinion: No single data source or methodology can uncover the complexity of human health and disease. To fully capitalize on the potential of 'big data', we will have to embrace the collaborative science and encourage the creation of integrated cross-disciplinary teams brought together around technological advances.
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Affiliation(s)
- Sara Fontanella
- National Heart and Lung Institute, Imperial College London, UK
| | - Alex Cucco
- National Heart and Lung Institute, Imperial College London, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, UK
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15
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Hübenthal M, Löscher BS, Erdmann J, Franke A, Gola D, König IR, Emmert H. Current Developments of Clinical Sequencing and the Clinical Utility of Polygenic Risk Scores in Inflammatory Diseases. Front Immunol 2021; 11:577677. [PMID: 33633722 PMCID: PMC7901950 DOI: 10.3389/fimmu.2020.577677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/10/2020] [Indexed: 12/03/2022] Open
Abstract
In this mini-review, we highlight selected research by the Deutsche Forschungsgemeinschaft (DFG) Cluster of Excellence “Precision Medicine in Chronic Inflammation” focusing on clinical sequencing and the clinical utility of polygenic risk scores as well as its implication on precision medicine in the field of the inflammatory diseases inflammatory bowel disease, atopic dermatitis and coronary artery disease. Additionally, we highlight current developments and discuss challenges to be faced in the future. Exemplary, we point to residual challenges in detecting disease-relevant variants resulting from difficulties in the interpretation of candidate variants and their potential interactions. While polygenic risk scores represent promising tools for the stratification of patient groups, currently, polygenic risk scores are not accurate enough for clinical setting. Precision medicine, incorporating additional data from genomics, transcriptomics and proteomics experiments, may enable the identification of distinct disease pathogeneses. In the future, data-intensive biomedical innovation will hopefully lead to improved patient stratification for personalized medicine.
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Affiliation(s)
- Matthias Hübenthal
- Department of Dermatology, Quincke Research Center, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Britt-Sabina Löscher
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Damian Gola
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
| | - Inke R König
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
| | - Hila Emmert
- Department of Dermatology, Quincke Research Center, University Hospital Schleswig-Holstein, Kiel, Germany
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Zhang HJ, Dong XL, Zhang YF, Fang YF, Zhang HY. [Effect of maternal immune level at different pregnancy stages on cow's milk protein allergy in infants]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:1221-1225. [PMID: 33172559 PMCID: PMC7666383 DOI: 10.7499/j.issn.1008-8830.2006070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To study the association between maternal Th1/Th2 immune level at different pregnancy stages and cow's milk protein allergy (CMPA) in infants. METHODS The healthy women with a singleton pregnancy, as well as their offspring, who attended Yidu Central Hospital of Weifang and Qingzhou Traditional Chinese Medicine Hospital from July 2016 to December 2018 were enrolled. The maternal levels of interleukin-2 (IL-2), interferon gamma (IFN-γ), interleukin-4 (IL-4), and interleukin-10 (IL-10) at the second and third trimesters of pregnancy were measured. A CMPA questionnaire survey was conducted within one year after birth. Food avoidance and cow's milk oral challenge tests were performed in infants suspected of CMPA. The 48 infants who met the diagnostic criteria for CMPA were included in the observation group, and the remaining 977 normal infants were included in the control group. A univariate analysis was performed on the infants with CMPA. A Poisson regression analysis was used to determine the association between maternal Th1/Th2 immune factors at different pregnancy stages and CMPA. RESULTS The detection rate of CMPA was 4.68%. The clinical manifestations included the symptoms of the digestive system, skin, and respiratory system and other symptoms. The univariate analysis showed that compared with the control group, the observation group had significantly higher incidence rates of maternal food allergy and maternal history of allergic diseases (P<0.05) and a significantly lower breastfeeding rate (P<0.05). The observation group had significantly lower maternal levels of IL-2 (second and third trimesters) and IFN-γ (third trimester) than the control group (P<0.05). Maternal low IFN-γ at the third trimester and maternal low IL-2 at the second and third trimesters were significantly associated with CMPA in infants (P<0.05). After correction of the factors of breastfeeding, maternal food allergy, and maternal history of allergic diseases, it was found that maternal low IL-2 and IFN-γ at the third trimester were still significantly associated with CMPA in infants (P<0.05). CONCLUSIONS The maternal decrease in Th1 level at the third trimester of pregnancy may lead to the change in fetal immunity and thus increase the risk of CMPA in offspring.
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Affiliation(s)
- Hai-Jun Zhang
- Department of Pediatrics, Yidu Central Hospital of Weifang, Weifang, Shandong 262500, China.
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17
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Zhang HJ, Dong XL, Zhang YF, Fang YF, Zhang HY. [Effect of maternal immune level at different pregnancy stages on cow's milk protein allergy in infants]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:1221-1225. [PMID: 33172559 PMCID: PMC7666383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/27/2020] [Indexed: 11/13/2023]
Abstract
OBJECTIVE To study the association between maternal Th1/Th2 immune level at different pregnancy stages and cow's milk protein allergy (CMPA) in infants. METHODS The healthy women with a singleton pregnancy, as well as their offspring, who attended Yidu Central Hospital of Weifang and Qingzhou Traditional Chinese Medicine Hospital from July 2016 to December 2018 were enrolled. The maternal levels of interleukin-2 (IL-2), interferon gamma (IFN-γ), interleukin-4 (IL-4), and interleukin-10 (IL-10) at the second and third trimesters of pregnancy were measured. A CMPA questionnaire survey was conducted within one year after birth. Food avoidance and cow's milk oral challenge tests were performed in infants suspected of CMPA. The 48 infants who met the diagnostic criteria for CMPA were included in the observation group, and the remaining 977 normal infants were included in the control group. A univariate analysis was performed on the infants with CMPA. A Poisson regression analysis was used to determine the association between maternal Th1/Th2 immune factors at different pregnancy stages and CMPA. RESULTS The detection rate of CMPA was 4.68%. The clinical manifestations included the symptoms of the digestive system, skin, and respiratory system and other symptoms. The univariate analysis showed that compared with the control group, the observation group had significantly higher incidence rates of maternal food allergy and maternal history of allergic diseases (P<0.05) and a significantly lower breastfeeding rate (P<0.05). The observation group had significantly lower maternal levels of IL-2 (second and third trimesters) and IFN-γ (third trimester) than the control group (P<0.05). Maternal low IFN-γ at the third trimester and maternal low IL-2 at the second and third trimesters were significantly associated with CMPA in infants (P<0.05). After correction of the factors of breastfeeding, maternal food allergy, and maternal history of allergic diseases, it was found that maternal low IL-2 and IFN-γ at the third trimester were still significantly associated with CMPA in infants (P<0.05). CONCLUSIONS The maternal decrease in Th1 level at the third trimester of pregnancy may lead to the change in fetal immunity and thus increase the risk of CMPA in offspring.
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Affiliation(s)
- Hai-Jun Zhang
- Department of Pediatrics, Yidu Central Hospital of Weifang, Weifang, Shandong 262500, China.
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Laulajainen‐Hongisto A, Lyly A, Hanif T, Dhaygude K, Kankainen M, Renkonen R, Donner K, Mattila P, Jartti T, Bousquet J, Kauppi P, Toppila‐Salmi S. Genomics of asthma, allergy and chronic rhinosinusitis: novel concepts and relevance in airway mucosa. Clin Transl Allergy 2020; 10:45. [PMID: 33133517 PMCID: PMC7592594 DOI: 10.1186/s13601-020-00347-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/25/2020] [Indexed: 12/14/2022] Open
Abstract
Genome wide association studies (GWASs) have revealed several airway disease-associated risk loci. Their role in the onset of asthma, allergic rhinitis (AR) or chronic rhinosinusitis (CRS), however, is not yet fully understood. The aim of this review is to evaluate the airway relevance of loci and genes identified in GWAS studies. GWASs were searched from databases, and a list of loci associating significantly (p < 10-8) with asthma, AR and CRS was created. This yielded a total of 267 significantly asthma/AR-associated loci from 31 GWASs. No significant CRS -associated loci were found in this search. A total of 170 protein coding genes were connected to these loci. Of these, 76/170 (44%) showed bronchial epithelial protein expression in stained microscopic figures of Human Protein Atlas (HPA), and 61/170 (36%) had a literature report of having airway epithelial function. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses were performed, and 19 functional protein categories were found as significantly (p < 0.05) enriched among these genes. These were related to cytokine production, cell activation and adaptive immune response, and all were strongly connected in network analysis. We also identified 15 protein pathways that were significantly (p < 0.05) enriched in these genes, related to T-helper cell differentiation, virus infection, JAK-STAT signaling pathway, and asthma. A third of GWAS-level risk loci genes of asthma or AR seemed to have airway epithelial functions according to our database and literature searches. In addition, many of the risk loci genes were immunity related. Some risk loci genes also related to metabolism, neuro-musculoskeletal or other functions. Functions overlapped and formed a strong network in our pathway analyses and are worth future studies of biomarker and therapeutics.
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Affiliation(s)
- Anu Laulajainen‐Hongisto
- Department of Otorhinolaryngology–Head and Neck SurgeryUniversity of Helsinki and Helsinki University HospitalP.O.Box 263Kasarmikatu 11‐1300029 HUSHelsinkiFinland
- Laboratory of Cellular and Molecular ImmunologyInstitute of Microbiology of the Czech Academy of SciencesPragueCzech Republic
| | - Annina Lyly
- Department of Otorhinolaryngology–Head and Neck SurgeryUniversity of Helsinki and Helsinki University HospitalP.O.Box 263Kasarmikatu 11‐1300029 HUSHelsinkiFinland
- Skin and Allergy HospitalUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | | | | | - Matti Kankainen
- HUS Diagnostic CenterHelsinki University HospitalHelsinkiFinland
- Hematology Research Unit HelsinkiDepartment of HematologyHelsinki University Hospital Comprehensive Cancer CenterHelsinkiFinland
- Translational Immunology Research Program and Department of Clinical ChemistryUniversity of HelsinkiHelsinkiFinland
| | - Risto Renkonen
- Haartman InstituteUniversity of HelsinkiHelsinkiFinland
- HUS Diagnostic CenterHelsinki University HospitalHelsinkiFinland
| | - Kati Donner
- Hematology Research Unit HelsinkiDepartment of HematologyHelsinki University Hospital Comprehensive Cancer CenterHelsinkiFinland
| | - Pirkko Mattila
- Haartman InstituteUniversity of HelsinkiHelsinkiFinland
- Hematology Research Unit HelsinkiDepartment of HematologyHelsinki University Hospital Comprehensive Cancer CenterHelsinkiFinland
| | - Tuomas Jartti
- Department of Pediatrics and Adolescent MedicineTurku University Hospital and University of TurkuTurkuFinland
| | - Jean Bousquet
- Université MontpellierMontpellierFrance
- MACVIA‐FranceMontpellierFrance
- Corporate Member of Freie Universität BerlinHumboldt‐Universität Zu BerlinBerlin Institute of HealthComprehensive Allergy CenterDepartment of Dermatology and AllergyCharité–Universitätsmedizin BerlinBerlinGermany
| | - Paula Kauppi
- Skin and Allergy HospitalUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Sanna Toppila‐Salmi
- Skin and Allergy HospitalUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Haartman InstituteUniversity of HelsinkiHelsinkiFinland
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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: 26] [Impact Index Per Article: 6.5] [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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Abstract
PURPOSE OF REVIEW Allergic diseases are prototypic examples for gene × environment-wide interactions. This review considers the current evidence for genetic and epigenetic mechanisms in allergic diseases and highlights barriers and facilitators for the implementation of these novel tools both for research and clinical practice. RECENT FINDINGS The value of whole-genome sequencing studies and the use of polygenic risk score analysis in homogeneous well characterized populations are currently being tested. Epigenetic mechanisms are known to play a crucial role in the pathogenesis of allergic disorders, especially through mediating the effects of the environmental factors, well recognized risk modifiers. There is emerging evidence for the immune-modulatory role of probiotics through epigenetic changes. Direct or indirect targeting of epigenetic mechanisms affect expression of the genes favouring the development of allergic diseases and can improve tissue biology. The ability to specifically edit the epigenome, especially using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology, holds the promise of enhancing understanding of how epigenetic modifications function and enabling manipulation of cell phenotype for research or therapeutic purposes. SUMMARY Additional research in the role of genetic and epigenetic mechanisms in relation to allergic diseases' endotypes is needed. An international project characterizing the human epigenome in relation to allergic diseases is warranted.
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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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Clark H, Granell R, Curtin JA, Belgrave D, Simpson A, Murray C, Henderson AJ, Custovic A, Paternoster L. Differential associations of allergic disease genetic variants with developmental profiles of eczema, wheeze and rhinitis. Clin Exp Allergy 2019; 49:1475-1486. [PMID: 31441980 PMCID: PMC6899469 DOI: 10.1111/cea.13485] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/11/2019] [Accepted: 08/01/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Allergic diseases (eczema, wheeze and rhinitis) in children often present as heterogeneous phenotypes. Understanding genetic associations of specific patterns of symptoms might facilitate understanding of the underlying biological mechanisms. OBJECTIVE To examine associations between allergic disease-related variants identified in a recent genome-wide association study and latent classes of allergic diseases (LCADs) in two population-based birth cohorts. METHODS Eight previously defined LCADs between birth and 11 years: "No disease," "Atopic march," "Persistent eczema and wheeze," "Persistent eczema with later-onset rhinitis," "Persistent wheeze with later-onset rhinitis," "Transient wheeze," "Eczema only" and "Rhinitis only" were used as the study outcome. Weighted multinomial logistic regression was used to estimate associations between 135 SNPs (and a polygenic risk score, PRS) and LCADs among 6345 individuals from The Avon Longitudinal Study of Parents and Children (ALSPAC). Heterogeneity across LCADs was assessed before and after Bonferroni correction. Results were replicated in Manchester Asthma and Allergy Study (MAAS) (n = 896) and pooled in a meta-analysis. RESULTS We found strong evidence for differential genetic associations across the LCADs; pooled PRS heterogeneity P-value = 3.3 × 10-14 , excluding "no disease" class. The associations between the PRS and LCADs in MAAS were remarkably similar to ALSPAC. Two SNPs (a protein-truncating variant in FLG and a SNP within an intron of GSDMB) had evidence for differential association (pooled P-values ≤ 0.006). The FLG locus was differentially associated across LCADs that included eczema, with stronger associations for LCADs with comorbid wheeze and rhinitis. The GSDMB locus in contrast was equally associated across LCADs that included wheeze. CONCLUSIONS AND CLINICAL RELEVANCE We have shown complex, but distinct patterns of genetic associations with LCADs, suggesting that heterogeneous mechanisms underlie individual disease trajectories. Establishing the combination of allergic diseases with which each genetic variant is associated may inform therapeutic development and/or predictive modelling.
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Affiliation(s)
- Hannah Clark
- MRC Integrative Epidemiology Unit (IEU)Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - Raquel Granell
- MRC Integrative Epidemiology Unit (IEU)Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - John A. Curtin
- Division of Infection, Immunity and Respiratory MedicineSchool of Biological SciencesThe University of ManchesterManchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUK
| | - Danielle Belgrave
- Section of PaediatricsDepartment of MedicineImperial College LondonLondonUK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory MedicineSchool of Biological SciencesThe University of ManchesterManchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUK
| | - Clare Murray
- Division of Infection, Immunity and Respiratory MedicineSchool of Biological SciencesThe University of ManchesterManchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUK
| | - A. John Henderson
- MRC Integrative Epidemiology Unit (IEU)Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - Adnan Custovic
- Section of PaediatricsDepartment of MedicineImperial College LondonLondonUK
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit (IEU)Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
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