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Hoda U, Pavlidis S, Bansal AT, Takahashi K, Hu S, Ng Kee Kwong F, Rossios C, Sun K, Bhavsar P, Loza M, Baribaud F, Chanez P, Fowler SJ, Horvath I, Montuschi P, Singer F, Musial J, Dahlen B, Krug N, Sandstrom T, Shaw DE, Lutter R, Fleming LJ, Howarth PH, Caruso M, Sousa AR, Corfield J, Auffray C, De Meulder B, Lefaudeux D, Dahlen SE, Djukanovic R, Sterk PJ, Guo Y, Adcock IM, Chung KF. Clinical and transcriptomic features of persistent exacerbation-prone severe asthma in U-BIOPRED cohort. Clin Transl Med 2022; 12:e816. [PMID: 35474304 PMCID: PMC9043117 DOI: 10.1002/ctm2.816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 01/28/2023] Open
Abstract
Background Exacerbation‐prone asthma is a feature of severe disease. However, the basis for its persistency remains unclear. Objectives To determine the clinical and transcriptomic features of frequent exacerbators (FEs) and persistent FEs (PFEs) in the U‐BIOPRED cohort. Methods We compared features of FE (≥2 exacerbations in past year) to infrequent exacerbators (IE, <2 exacerbations) and of PFE with repeat ≥2 exacerbations during the following year to persistent IE (PIE). Transcriptomic data in blood, bronchial and nasal epithelial brushings, bronchial biopsies and sputum cells were analysed by gene set variation analysis for 103 gene signatures. Results Of 317 patients, 62.4% had FE, of whom 63.6% had PFE, while 37.6% had IE, of whom 61.3% had PIE. Using multivariate analysis, FE was associated with short‐acting beta‐agonist use, sinusitis and daily oral corticosteroid use, while PFE was associated with eczema, short‐acting beta‐agonist use and asthma control index. CEA cell adhesion molecule 5 (CEACAM5) was the only differentially expressed transcript in bronchial biopsies between PE and IE. There were no differentially expressed genes in the other four compartments. There were higher expression scores for type 2, T‐helper type‐17 and type 1 pathway signatures together with those associated with viral infections in bronchial biopsies from FE compared to IE, while there were higher expression scores of type 2, type 1 and steroid insensitivity pathway signatures in bronchial biopsies of PFE compared to PIE. Conclusion The FE group and its PFE subgroup are associated with poor asthma control while expressing higher type 1 and type 2 activation pathways compared to IE and PIE, respectively.
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Affiliation(s)
- Uruj Hoda
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Stelios Pavlidis
- Department of Computing & Data Science Institute, Imperial College London
| | | | - Kentaro Takahashi
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK.,Research Centre for Allergy and Clinical Immunology, Asahi General Hospital, Asahi, Japan
| | | | - Francois Ng Kee Kwong
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Christos Rossios
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | | | - Pankaj Bhavsar
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Matthew Loza
- Janssen Research and Development, High Wycombe, Buckinghamshire, UK
| | | | - Pascal Chanez
- Assistance Publique des Hôpitaux de Marseille, Clinique des Bronches, Allergies et Sommeil, Aix Marseille Université, Marseille, France
| | - Stephen J Fowler
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, School of Biological Sciences, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, and NIHR Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Ildiko Horvath
- Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | | | - Florian Singer
- Department of Respiratory Medicine, University Children's Hospital Zurich and Childhood Research Center, Zurich, and Department of Paediatrics, Inselspital, University of Bern, Switzerland
| | - Jacek Musial
- Department of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Barbro Dahlen
- Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Norbert Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Thomas Sandstrom
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | | | - Rene Lutter
- Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Louise J Fleming
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Peter H Howarth
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, UK
| | - Massimo Caruso
- Department of Biochemical and Biotechnological Medicine, University of Catania, Catania, Italy
| | - Ana R Sousa
- Respiratory Therapeutic Unit, GSK, Stockley Park, UK
| | - Julie Corfield
- AstraZeneca R&D, Molndal, Sweden, and Areteva R&D, Nottingham, UK
| | - Charles Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Lyon, France
| | - Bertrand De Meulder
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Lyon, France
| | - Diane Lefaudeux
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Lyon, France
| | - Sven-Erik Dahlen
- Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Ratko Djukanovic
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, UK
| | - Peter J Sterk
- Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
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2
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Kuo CHS, Pavlidis S, Zhu J, Loza M, Baribaud F, Rowe A, Pandis I, Gibeon D, Hoda U, Sousa A, Wilson SJ, Howarth P, Shaw D, Fowler S, Dahlen B, Chanez P, Krug N, Sandstrom T, Fleming L, Corfield J, Auffray C, Djukanovic R, Sterk PJ, Guo Y, Adcock IM, Chung KF. Contribution of airway eosinophils in airway wall remodeling in asthma: Role of MMP-10 and MET. Allergy 2019; 74:1102-1112. [PMID: 30667542 DOI: 10.1111/all.13727] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/02/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Eosinophils play an important role in the pathophysiology of asthma being implicated in airway epithelial damage and airway wall remodeling. We determined the genes associated with airway remodeling and eosinophilic inflammation in patients with asthma. METHODS We analyzed the transcriptomic data from bronchial biopsies of 81 patients with moderate-to-severe asthma of the U-BIOPRED cohort. Expression profiling was performed using Affymetrix arrays on total RNA. Transcription binding site analysis used the PRIMA algorithm. Localization of proteins was by immunohistochemistry. RESULTS Using stringent false discovery rate analysis, MMP-10 and MET were significantly overexpressed in biopsies with high mucosal eosinophils (HE) compared to low mucosal eosinophil (LE) numbers. Immunohistochemical analysis confirmed increased expression of MMP-10 and MET in bronchial epithelial cells and in subepithelial inflammatory and resident cells in asthmatic biopsies. Using less-stringent conditions (raw P-value < 0.05, log2 fold change > 0.5), we defined a 73-gene set characteristic of the HE compared to the LE group. Thirty-three of 73 genes drove the pathway annotation that included extracellular matrix (ECM) organization, mast cell activation, CC-chemokine receptor binding, circulating immunoglobulin complex, serine protease inhibitors, and microtubule bundle formation pathways. Genes including MET and MMP10 involved in ECM organization correlated positively with submucosal thickness. Transcription factor binding site analysis identified two transcription factors, ETS-1 and SOX family proteins, that showed positive correlation with MMP10 and MET expression. CONCLUSION Pathways of airway remodeling and cellular inflammation are associated with submucosal eosinophilia. MET and MMP-10 likely play an important role in these processes.
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Affiliation(s)
- Chih-Hsi S. Kuo
- Airways Disease; National Heart & Lung Institute; Imperial College; London UK
- Biomedical Research Unit; Royal Brompton & Harefield NHS Trust; London UK
- Department of Computing & Data Science Institute; Imperial College; London UK
| | - Stelios Pavlidis
- Department of Computing & Data Science Institute; Imperial College; London UK
- Janssen Research and Development; High Wycombe UK
| | - Jie Zhu
- Airways Disease; National Heart & Lung Institute; Imperial College; London UK
| | - Matthew Loza
- Janssen Research and Development; High Wycombe UK
| | | | - Anthony Rowe
- Janssen Research and Development; High Wycombe UK
| | - Ioannis Pandis
- Airways Disease; National Heart & Lung Institute; Imperial College; London UK
- Biomedical Research Unit; Royal Brompton & Harefield NHS Trust; London UK
| | - David Gibeon
- Airways Disease; National Heart & Lung Institute; Imperial College; London UK
- Biomedical Research Unit; Royal Brompton & Harefield NHS Trust; London UK
| | - Uruj Hoda
- Department of Computing & Data Science Institute; Imperial College; London UK
| | - Ana Sousa
- Respiratory Therapeutic Unit; GlaxoSmithKline; Stockley Park UK
| | - Susan J. Wilson
- Faculty of Medicine; Southampton University; Southampton UK
- NIHR Southampton Respiratory Biomedical Research Unit; University Hospital Southampton; Southampton UK
| | - Peter Howarth
- Faculty of Medicine; Southampton University; Southampton UK
- NIHR Southampton Respiratory Biomedical Research Unit; University Hospital Southampton; Southampton UK
| | - Dominick Shaw
- Respiratory Research Unit; University of Nottingham; Nottingham UK
| | - Stephen Fowler
- Centre for Respiratory Medicine and Allergy; The University of Manchester; Manchester UK
| | - Barbro Dahlen
- The Centre for Allergy Research; The Institute of Environmental Medicine; Karolinska Institute; Stockholm Sweden
| | - Pascal Chanez
- Laboratoire d'immunologie; Département des Maladies Respiratoires; Aix Marseille Université Marseille; Marseille France
| | - Norbert Krug
- Immunology, Allergology and Clinical Inhalation; Fraunhofer Institute for Toxicology and Experimental Medicine; Hannover Germany
| | - Thomas Sandstrom
- Department of Medicine, Respiratory and Allergy unit; University Hospital; Umeå Sweden
| | - Louise Fleming
- Department of Computing & Data Science Institute; Imperial College; London UK
| | - Julie Corfield
- AstraZeneca R & D; Molndal Sweden
- Areteva R & D; Nottingham UK
| | - Charles Auffray
- European Institute for Systems Biology and Medicine; CNRS-ENS-UCBL; Université de Lyon; Lyon France
| | - Ratko Djukanovic
- Faculty of Medicine; Southampton University; Southampton UK
- NIHR Southampton Respiratory Biomedical Research Unit; University Hospital Southampton; Southampton UK
| | - Peter J. Sterk
- Faculty of Medicine; University of Amsterdam; Amsterdam The Netherland
| | - Yike Guo
- Department of Computing & Data Science Institute; Imperial College; London UK
| | - Ian M. Adcock
- Airways Disease; National Heart & Lung Institute; Imperial College; London UK
- Biomedical Research Unit; Royal Brompton & Harefield NHS Trust; London UK
| | - Kian Fan Chung
- Airways Disease; National Heart & Lung Institute; Imperial College; London UK
- Biomedical Research Unit; Royal Brompton & Harefield NHS Trust; London UK
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3
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Pavlidis S, Takahashi K, Ng Kee Kwong F, Xie J, Hoda U, Sun K, Elyasigomari V, Agapow P, Loza M, Baribaud F, Chanez P, Fowler SJ, Shaw DE, Fleming LJ, Howarth PH, Sousa AR, Corfield J, Auffray C, De Meulder B, Knowles R, Sterk PJ, Guo Y, Adcock IM, Djukanovic R, Fan Chung K. "T2-high" in severe asthma related to blood eosinophil, exhaled nitric oxide and serum periostin. Eur Respir J 2019; 53:13993003.00938-2018. [PMID: 30578390 DOI: 10.1183/13993003.00938-2018] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/26/2018] [Indexed: 11/05/2022]
Abstract
Type-2 (T2) immune responses in airway epithelial cells (AECs) classifies mild-moderate asthma into a T2-high phenotype. We examined whether currently available clinical biomarkers can predict AEC-defined T2-high phenotype within the U-BIOPRED cohort.The transcriptomic profile of AECs obtained from brushings of 103 patients with asthma and 44 healthy controls was obtained and gene set variation analysis used to determine the relative expression score of T2 asthma using a signature from interleukin (IL)-13-exposed AECs.37% of asthmatics (45% nonsmoking severe asthma, n=49; 33% of smoking or ex-smoking severe asthma, n=18; and 28% mild-moderate asthma, n=36) were T2-high using AEC gene expression. They were more symptomatic with higher exhaled nitric oxide fraction (F eNO) and blood and sputum eosinophils, but not serum IgE or periostin. Sputum eosinophilia correlated best with the T2-high signature. F eNO (≥30 ppb) and blood eosinophils (≥300 cells·µL-1) gave a moderate prediction of T2-high asthma. Sputum IL-4, IL-5 and IL-13 protein levels did not correlate with gene expression.T2-high severe asthma can be predicted to some extent from raised levels of F eNO, blood and sputum eosinophil counts, but serum IgE or serum periostin were poor predictors. Better bedside biomarkers are needed to detect T2-high.
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Affiliation(s)
- Stelios Pavlidis
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK.,Dept of Computing and Data Science Institute, Imperial College London, London, UK
| | - Kentaro Takahashi
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK.,Research Centre for Allergy and Clinical Immunology, Asahi General Hospital, Asahi, Japan
| | - Francois Ng Kee Kwong
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Jiaxing Xie
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Uruj Hoda
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Kai Sun
- Dept of Computing and Data Science Institute, Imperial College London, London, UK
| | - Vahid Elyasigomari
- Dept of Computing and Data Science Institute, Imperial College London, London, UK
| | - Paul Agapow
- Dept of Computing and Data Science Institute, Imperial College London, London, UK
| | - Matthew Loza
- Janssen Research and Development, High Wycombe, UK
| | | | - Pascal Chanez
- Assistance Publique des Hôpitaux de Marseille - Clinique des bronches, allergies et sommeil, Aix Marseille Université, Marseille, France
| | - Steve J Fowler
- Centre for Respiratory Medicine and Allergy, Institute of Inflammation and Repair, University of Manchester and University Hospital of South Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Dominic E Shaw
- Respiratory Research Unit, University of Nottingham, Nottingham, UK
| | - Louise J Fleming
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Peter H Howarth
- NIHR Southampton Respiratory Biomedical Research Unit, Clinical and Experimental Sciences and Human Development and Health, Southampton, UK
| | - Ana R Sousa
- Respiratory Therapeutic Unit, GSK, Stockley Park, UK
| | - Julie Corfield
- AstraZeneca R&D, Molndal, Sweden.,Areteva R&D, Nottingham, UK
| | - Charles Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Lyon, France
| | - Bertrand De Meulder
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Lyon, France
| | | | - Peter J Sterk
- Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Yike Guo
- Dept of Computing and Data Science Institute, Imperial College London, London, UK
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK.,Dept of Computing and Data Science Institute, Imperial College London, London, UK
| | - Ratko Djukanovic
- NIHR Southampton Respiratory Biomedical Research Unit, Clinical and Experimental Sciences and Human Development and Health, Southampton, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK.,Dept of Computing and Data Science Institute, Imperial College London, London, UK
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4
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Takahashi K, Pavlidis S, Ng Kee Kwong F, Hoda U, Rossios C, Sun K, Loza M, Baribaud F, Chanez P, Fowler SJ, Horvath I, Montuschi P, Singer F, Musial J, Dahlen B, Dahlen SE, Krug N, Sandstrom T, Shaw DE, Lutter R, Bakke P, Fleming LJ, Howarth PH, Caruso M, Sousa AR, Corfield J, Auffray C, De Meulder B, Lefaudeux D, Djukanovic R, Sterk PJ, Guo Y, Adcock IM, Chung KF. Sputum proteomics and airway cell transcripts of current and ex-smokers with severe asthma in U-BIOPRED: an exploratory analysis. Eur Respir J 2018; 51:13993003.02173-2017. [PMID: 29650557 DOI: 10.1183/13993003.02173-2017] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/22/2018] [Indexed: 12/14/2022]
Abstract
Severe asthma patients with a significant smoking history have airflow obstruction with reported neutrophilia. We hypothesise that multi-omic analysis will enable the definition of smoking and ex-smoking severe asthma molecular phenotypes.The U-BIOPRED cohort of severe asthma patients, containing current-smokers (CSA), ex-smokers (ESA), nonsmokers and healthy nonsmokers was examined. Blood and sputum cell counts, fractional exhaled nitric oxide and spirometry were obtained. Exploratory proteomic analysis of sputum supernatants and transcriptomic analysis of bronchial brushings, biopsies and sputum cells was performed.Colony-stimulating factor (CSF)2 protein levels were increased in CSA sputum supernatants, with azurocidin 1, neutrophil elastase and CXCL8 upregulated in ESA. Phagocytosis and innate immune pathways were associated with neutrophilic inflammation in ESA. Gene set variation analysis of bronchial epithelial cell transcriptome from CSA showed enrichment of xenobiotic metabolism, oxidative stress and endoplasmic reticulum stress compared to other groups. CXCL5 and matrix metallopeptidase 12 genes were upregulated in ESA and the epithelial protective genes, mucin 2 and cystatin SN, were downregulated.Despite little difference in clinical characteristics, CSA were distinguishable from ESA subjects at the sputum proteomic level, with CSA patients having increased CSF2 expression and ESA patients showing sustained loss of epithelial barrier processes.
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Affiliation(s)
- Kentaro Takahashi
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK.,Research Centre for Allergy and Clinical Immunology, Asahi General Hospital, Matsudo, Japan
| | - Stelios Pavlidis
- Dept of Computing and Data Science Institute, Imperial College London, London, UK
| | - Francois Ng Kee Kwong
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Uruj Hoda
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Christos Rossios
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Kai Sun
- Dept of Computing and Data Science Institute, Imperial College London, London, UK
| | - Matthew Loza
- Janssen Research and Development, High Wycombe, UK
| | | | - Pascal Chanez
- Assistance Publique des Hôpitaux de Marseille, Clinique des Bronches, Allergies et Sommeil, Aix Marseille Université, Marseille, France
| | - Steve J Fowler
- Centre for Respiratory Medicine and Allergy, Institute of Inflammation and Repair, University of Manchester and University Hospital of South Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | | | | | - Florian Singer
- Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jacek Musial
- Dept of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Barbro Dahlen
- Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Sven-Eric Dahlen
- Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Norbert Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Thomas Sandstrom
- Dept of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Dominic E Shaw
- Respiratory Research Unit, University of Nottingham, Nottingham, UK
| | - Rene Lutter
- Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Per Bakke
- Dept of Clinical Science, University of Bergen, Bergen, Norway
| | - Louise J Fleming
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Peter H Howarth
- NIHR Southampton Respiratory Biomedical Research Unit, Clinical and Experimental Sciences and Human Development and Health, Southampton, UK
| | - Massimo Caruso
- Dept Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Ana R Sousa
- Respiratory Therapeutic Unit, GSK, Stockley Park, UK
| | - Julie Corfield
- AstraZeneca R&D, Molndal, Sweden.,Areteva R&D, Nottingham, UK
| | - Charles Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Lyon, France
| | - Bertrand De Meulder
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Lyon, France
| | - Diane Lefaudeux
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Lyon, France
| | - Ratko Djukanovic
- NIHR Southampton Respiratory Biomedical Research Unit, Clinical and Experimental Sciences and Human Development and Health, Southampton, UK
| | - Peter J Sterk
- Dept of Clinical Science, University of Bergen, Bergen, Norway
| | - Yike Guo
- Dept of Computing and Data Science Institute, Imperial College London, London, UK
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK.,Dept of Computing and Data Science Institute, Imperial College London, London, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, and Biomedical Research Unit, Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, UK.,Dept of Computing and Data Science Institute, Imperial College London, London, UK
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5
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Kuo CHS, Pavlidis S, Loza M, Baribaud F, Rowe A, Pandis I, Hoda U, Rossios C, Sousa A, Wilson SJ, Howarth P, Dahlen B, Dahlen SE, Chanez P, Shaw D, Krug N, Sandstrӧm T, De Meulder B, Lefaudeux D, Fowler S, Fleming L, Corfield J, Auffray C, Sterk PJ, Djukanovic R, Guo Y, Adcock IM, Chung KF. A Transcriptome-driven Analysis of Epithelial Brushings and Bronchial Biopsies to Define Asthma Phenotypes in U-BIOPRED. Am J Respir Crit Care Med 2017; 195:443-455. [PMID: 27580351 DOI: 10.1164/rccm.201512-2452oc] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
RATIONALE Asthma is a heterogeneous disease driven by diverse immunologic and inflammatory mechanisms. OBJECTIVES Using transcriptomic profiling of airway tissues, we sought to define the molecular phenotypes of severe asthma. METHODS The transcriptome derived from bronchial biopsies and epithelial brushings of 107 subjects with moderate to severe asthma were annotated by gene set variation analysis using 42 gene signatures relevant to asthma, inflammation, and immune function. Topological data analysis of clinical and histologic data was performed to derive clusters, and the nearest shrunken centroid algorithm was used for signature refinement. MEASUREMENTS AND MAIN RESULTS Nine gene set variation analysis signatures expressed in bronchial biopsies and airway epithelial brushings distinguished two distinct asthma subtypes associated with high expression of T-helper cell type 2 cytokines and lack of corticosteroid response (group 1 and group 3). Group 1 had the highest submucosal eosinophils, as well as high fractional exhaled nitric oxide levels, exacerbation rates, and oral corticosteroid use, whereas group 3 patients showed the highest levels of sputum eosinophils and had a high body mass index. In contrast, group 2 and group 4 patients had an 86% and 64% probability, respectively, of having noneosinophilic inflammation. Using machine learning tools, we describe an inference scheme using the currently available inflammatory biomarkers sputum eosinophilia and fractional exhaled nitric oxide levels, along with oral corticosteroid use, that could predict the subtypes of gene expression within bronchial biopsies and epithelial cells with good sensitivity and specificity. CONCLUSIONS This analysis demonstrates the usefulness of a transcriptomics-driven approach to phenotyping that segments patients who may benefit the most from specific agents that target T-helper cell type 2-mediated inflammation and/or corticosteroid insensitivity.
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Affiliation(s)
- Chih-Hsi Scott Kuo
- 1 Department of Computing.,2 Data Science Institute, and.,3 Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Stelios Pavlidis
- 1 Department of Computing.,2 Data Science Institute, and.,4 Janssen Research and Development, High Wycombe, United Kingdom
| | - Matthew Loza
- 4 Janssen Research and Development, High Wycombe, United Kingdom
| | - Fred Baribaud
- 4 Janssen Research and Development, High Wycombe, United Kingdom
| | - Anthony Rowe
- 4 Janssen Research and Development, High Wycombe, United Kingdom
| | - Ioannis Pandis
- 1 Department of Computing.,2 Data Science Institute, and
| | - Uruj Hoda
- 3 Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom.,5 Biomedical Research Unit, Royal Brompton & Harefield National Health Service Trust, London, United Kingdom
| | - Christos Rossios
- 3 Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Ana Sousa
- 6 Respiratory Therapeutic Unit, GlaxoSmithKline, Stockley Park, United Kingdom
| | - Susan J Wilson
- 7 Faculty of Medicine, Southampton University, Southampton, United Kingdom
| | - Peter Howarth
- 7 Faculty of Medicine, Southampton University, Southampton, United Kingdom
| | - Barbro Dahlen
- 8 Centre for Allergy Research, Karolinska Institute, Stockholm, Sweden
| | - Sven-Erik Dahlen
- 8 Centre for Allergy Research, Karolinska Institute, Stockholm, Sweden
| | | | - Dominick Shaw
- 10 Centre for Respiratory Research, University of Nottingham, Nottingham, United Kingdom
| | - Norbert Krug
- 11 Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany
| | - Thomas Sandstrӧm
- 12 Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Bertrand De Meulder
- 13 European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, University of Lyon, Lyon, France
| | - Diane Lefaudeux
- 13 European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, University of Lyon, Lyon, France
| | - Stephen Fowler
- 14 Centre for Respiratory Medicine and Allergy, University of Manchester, Manchester, United Kingdom
| | - Louise Fleming
- 3 Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom.,5 Biomedical Research Unit, Royal Brompton & Harefield National Health Service Trust, London, United Kingdom
| | - Julie Corfield
- 15 AstraZeneca R&D, Molndal, Sweden.,16 Areteva R&D, Nottingham, United Kingdom; and
| | - Charles Auffray
- 13 European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, University of Lyon, Lyon, France
| | - Peter J Sterk
- 17 Faculty of Medicine, University of Amsterdam, Amsterdam, the Netherlands
| | - Ratko Djukanovic
- 7 Faculty of Medicine, Southampton University, Southampton, United Kingdom
| | - Yike Guo
- 1 Department of Computing.,2 Data Science Institute, and
| | - Ian M Adcock
- 3 Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom.,5 Biomedical Research Unit, Royal Brompton & Harefield National Health Service Trust, London, United Kingdom
| | - Kian Fan Chung
- 3 Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom.,5 Biomedical Research Unit, Royal Brompton & Harefield National Health Service Trust, London, United Kingdom
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Lefaudeux D, De Meulder B, Loza MJ, Peffer N, Rowe A, Baribaud F, Bansal AT, Lutter R, Sousa AR, Corfield J, Pandis I, Bakke PS, Caruso M, Chanez P, Dahlén SE, Fleming LJ, Fowler SJ, Horvath I, Krug N, Montuschi P, Sanak M, Sandstrom T, Shaw DE, Singer F, Sterk PJ, Roberts G, Adcock IM, Djukanovic R, Auffray C, Chung KF, Adriaens N, Ahmed H, Aliprantis A, Alving K, Badorek P, Balgoma D, Barber C, Bautmans A, Behndig AF, Bel E, Beleta J, Berglind A, Berton A, Bigler J, Bisgaard H, Bochenek G, Boedigheimer MJ, Bøonnelykke K, Brandsma J, Braun A, Brinkman P, Burg D, Campagna D, Carayannopoulos L, Carvalho da Purfição Rocha JP, Chaiboonchoe A, Chaleckis R, Coleman C, Compton C, D'Amico A, Dahlén B, De Alba J, de Boer P, De Lepeleire I, Dekker T, Delin I, Dennison P, Dijkhuis A, Draper A, Edwards J, Emma R, Ericsson M, Erpenbeck V, Erzen D, Faulenbach C, Fichtner K, Fitch N, Flood B, Frey U, Gahlemann M, Galffy G, Gallart H, Garret T, Geiser T, Gent J, Gerhardsson de Verdier M, Gibeon D, Gomez C, Gove K, Gozzard N, Guo YK, Hashimoto S, Haughney J, Hedlin G, Hekking PP, Henriksson E, Hewitt L, Higgenbottam T, Hoda U, Hohlfeld J, Holweg C, Howarth P, Hu R, Hu S, Hu X, Hudson V, James AJ, Kamphuis J, Kennington EJ, Kerry D, Klüglich M, Knobel H, Knowles R, Knox A, Kolmert J, Konradsen J, Kots M, Krueger L, Kuo S, Kupczyk M, Lambrecht B, Lantz AS, Larsson L, Lazarinis N, Lone-Satif S, Marouzet L, Martin J, Masefield S, Mathon C, Matthews JG, Mazein A, Meah S, Maiser A, Menzies-Gow A, Metcalf L, Middelveld R, Mikus M, Miralpeix M, Monk P, Mores N, Murray CS, Musial J, Myles D, Naz S, Nething K, Nicholas B, Nihlen U, Nilsson P, Nordlund B, Östling J, Pacino A, Pahus L, Palkonnen S, Pavlidis S, Pennazza G, Petrén A, Pink S, Postle A, Powel P, Rahman-Amin M, Rao N, Ravanetti L, Ray E, Reinke S, Reynolds L, Riemann K, Riley J, Robberechts M, Roberts A, Rossios C, Russell K, Rutgers M, Santini G, Sentoninco M, Schoelch C, Schofield JP, Seibold W, Sigmund R, Sjödin M, Skipp PJ, Smids B, Smith C, Smith J, Smith KM, Söderman P, Sogbesan A, Staykova D, Strandberg K, Sun K, Supple D, Szentkereszty M, Tamasi L, Tariq K, Thörngren JO, Thornton B, Thorsen J, Valente S, van Aalderenm W, van de Pol M, van Drunen K, van Geest M, Versnel J, Vestbo J, Vink A, Vissing N, von Garnier C, Wagerner A, Wagers S, Wald F, Walker S, Ward J, Weiszhart Z, Wetzel K, Wheelock CE, Wiegman C, Williams S, Wilson SJ, Woosdcock A, Yang X, Yeyashingham E, Yu W, Zetterquist W, Zwinderman K. U-BIOPRED clinical adult asthma clusters linked to a subset of sputum omics. J Allergy Clin Immunol 2017; 139:1797-1807. [DOI: 10.1016/j.jaci.2016.08.048] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 07/23/2016] [Accepted: 08/08/2016] [Indexed: 01/20/2023]
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Rossios C, Pavlidis S, Hoda U, Kuo CH, Wiegman C, Russell K, Sun K, Loza MJ, Baribaud F, Durham AL, Ojo O, Lutter R, Rowe A, Bansal A, Auffray C, Sousa A, Corfield J, Djukanovic R, Guo Y, Sterk PJ, Chung KF, Adcock IM. Sputum transcriptomics reveal upregulation of IL-1 receptor family members in patients with severe asthma. J Allergy Clin Immunol 2017; 141:560-570. [PMID: 28528200 DOI: 10.1016/j.jaci.2017.02.045] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 01/21/2017] [Accepted: 02/01/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND Sputum analysis in asthmatic patients is used to define airway inflammatory processes and might guide therapy. OBJECTIVE We sought to determine differential gene and protein expression in sputum samples from patients with severe asthma (SA) compared with nonsmoking patients with mild/moderate asthma. METHODS Induced sputum was obtained from nonsmoking patients with SA, smokers/ex-smokers with severe asthma, nonsmoking patients with mild/moderate asthma (MMAs), and healthy nonsmoking control subjects. Differential cell counts, microarray analysis of cell pellets, and SOMAscan analysis of sputum analytes were performed. CRID3 was used to inhibit the inflammasome in a mouse model of SA. RESULTS Eosinophilic and mixed neutrophilic/eosinophilic inflammation were more prevalent in patients with SA compared with MMAs. Forty-two genes probes were upregulated (>2-fold) in nonsmoking patients with severe asthma compared with MMAs, including IL-1 receptor (IL-1R) family and nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain containing 3 (NRLP3) inflammasome members (false discovery rate < 0.05). The inflammasome proteins nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1 (NLRP1), NLRP3, and nucleotide-binding oligomerization domain (NOD)-like receptor C4 (NLRC4) were associated with neutrophilic asthma and with sputum IL-1β protein levels, whereas eosinophilic asthma was associated with an IL-13-induced TH2 signature and IL-1 receptor-like 1 (IL1RL1) mRNA expression. These differences were sputum specific because no activation of NLRP3 or enrichment of IL-1R family genes in bronchial brushings or biopsy specimens in patients with SA was observed. Expression of NLRP3 and of the IL-1R family genes was validated in the Airway Disease Endotyping for Personalized Therapeutics cohort. Inflammasome inhibition using CRID3 prevented airway hyperresponsiveness and airway inflammation (both neutrophilia and eosinophilia) in a mouse model of severe allergic asthma. CONCLUSION IL1RL1 gene expression is associated with eosinophilic SA, whereas NLRP3 inflammasome expression is highest in patients with neutrophilic SA. TH2-driven eosinophilic inflammation and neutrophil-associated inflammasome activation might represent interacting pathways in patients with SA.
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Affiliation(s)
- Christos Rossios
- Airways Disease, National Heart & Lung Institute, Imperial College London, and the Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom
| | - Stelios Pavlidis
- Department of Computing & Data Science Institute, Imperial College London, London, United Kingdom; Janssen Research and Development, High Wycombe, United Kingdom
| | - Uruj Hoda
- Airways Disease, National Heart & Lung Institute, Imperial College London, and the Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom
| | - Chih-Hsi Kuo
- Department of Computing & Data Science Institute, Imperial College London, London, United Kingdom
| | - Coen Wiegman
- Airways Disease, National Heart & Lung Institute, Imperial College London, and the Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom
| | - Kirsty Russell
- Airways Disease, National Heart & Lung Institute, Imperial College London, and the Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom
| | - Kai Sun
- Department of Computing & Data Science Institute, Imperial College London, London, United Kingdom
| | - Matthew J Loza
- Janssen Research and Development, High Wycombe, United Kingdom
| | | | - Andrew L Durham
- Airways Disease, National Heart & Lung Institute, Imperial College London, and the Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom
| | - Oluwaseun Ojo
- Airways Disease, National Heart & Lung Institute, Imperial College London, and the Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom
| | - Rene Lutter
- Faculty of Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - Anthony Rowe
- Janssen Research and Development, High Wycombe, United Kingdom
| | - Aruna Bansal
- Acclarogen, St John's Innovation Centre, Cambridge, United Kingdom
| | - Charles Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, Université de Lyon, Lyon, France
| | - Ana Sousa
- Respiratory Therapeutic Unit, GSK, Stockley Park, United Kingdom
| | - Julie Corfield
- AstraZeneca R&D, Molndal, Sweden, and Areteva R&D, Nottingham, United Kingdom
| | - Ratko Djukanovic
- Faculty of Medicine, Southampton University, and the NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton, United Kingdom
| | - Yike Guo
- Department of Computing & Data Science Institute, Imperial College London, London, United Kingdom
| | - Peter J Sterk
- Faculty of Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - Kian Fan Chung
- Airways Disease, National Heart & Lung Institute, Imperial College London, and the Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom
| | - Ian M Adcock
- Airways Disease, National Heart & Lung Institute, Imperial College London, and the Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia.
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Hoda U, Dockree E, Succony L, Byers E, Win T. 63 Use of a feedback questionnaire to improve effectiveness of MDT. Lung Cancer 2011. [DOI: 10.1016/s0169-5002(11)70063-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Succony L, Dockree E, Blake A, Hoda U, Win T. 64 Patient choice in lung cancer at the East and North Hertfordshire NHS Trust. Lung Cancer 2011. [DOI: 10.1016/s0169-5002(11)70064-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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