1
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Faiz A, Mahbub RM, Boedijono FS, Tomassen MI, Kooistra W, Timens W, Nawijn M, Hansbro PM, Johansen MD, Pouwels SD, Heijink IH, Massip F, de Biase MS, Schwarz RF, Adcock IM, Chung KF, van der Does A, Hiemstra PS, Goulaouic H, Xing H, Abdulai R, de Rinaldis E, Cunoosamy D, Harel S, Lederer D, Nivens MC, Wark PA, Kerstjens HAM, Hylkema MN, Brandsma CA, van den Berge M. IL-33 Expression Is Lower in Current Smokers at both Transcriptomic and Protein Levels. Am J Respir Crit Care Med 2023; 208:1075-1087. [PMID: 37708400 PMCID: PMC10867944 DOI: 10.1164/rccm.202210-1881oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/09/2022] [Accepted: 09/14/2023] [Indexed: 09/16/2023] Open
Abstract
Rationale: IL-33 is a proinflammatory cytokine thought to play a role in the pathogenesis of asthma and chronic obstructive pulmonary disease (COPD). A recent clinical trial using an anti-IL-33 antibody showed a reduction in exacerbation and improved lung function in ex-smokers but not current smokers with COPD. Objectives: This study aimed to understand the effects of smoking status on IL-33. Methods: We investigated the association of smoking status with the level of gene expression of IL-33 in the airways in eight independent transcriptomic studies of lung airways. Additionally, we performed Western blot analysis and immunohistochemistry for IL-33 in lung tissue to assess protein levels. Measurements and Main Results: Across the bulk RNA-sequencing datasets, IL-33 gene expression and its signaling pathway were significantly lower in current versus former or never-smokers and increased upon smoking cessation (P < 0.05). Single-cell sequencing showed that IL-33 is predominantly expressed in resting basal epithelial cells and decreases during the differentiation process triggered by smoke exposure. We also found a higher transitioning of this cellular subpopulation into a more differentiated cell type during chronic smoking, potentially driving the reduction of IL-33. Protein analysis demonstrated lower IL-33 levels in lung tissue from current versus former smokers with COPD and a lower proportion of IL-33-positive basal cells in current versus ex-smoking controls. Conclusions: We provide strong evidence that cigarette smoke leads to an overall reduction in IL-33 expression in transcriptomic and protein level, and this may be due to the decrease in resting basal cells. Together, these findings may explain the clinical observation that a recent antibody-based anti-IL-33 treatment is more effective in former than current smokers with COPD.
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Affiliation(s)
- Alen Faiz
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Rashad M. Mahbub
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Fia Sabrina Boedijono
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
| | - Milan I. Tomassen
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Wierd Kooistra
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn Nawijn
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Philip M. Hansbro
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
| | - Simon D. Pouwels
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Irene H. Heijink
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Florian Massip
- Centre for Computational Biology, Mines ParisTech, Paris Sciences et Lettres Research University, Paris, France
- Cancer and Genome: Bioinformatics, Biostatistics and Epidemiology of Complex Systems Institut Curie, Paris, France
- Institut Nationale de la Santé et de la Recherche Médicale U900, Paris, France
| | - Maria Stella de Biase
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Computational Cancer Biology, Center for Integrated Oncology, Cancer Research Center Cologne Essen, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Ian M. Adcock
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Kian F. Chung
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Anne van der Does
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Pieter S. Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | | | | | - Sivan Harel
- Regeneron Pharmaceuticals, Tarrytown, New York
| | | | | | - Peter A. Wark
- Centre for Asthma & Respiratory Disease, The University of Newcastle, Newcastle, New South Wales, Australia; and
- Hunter Medical Research Institute, Vaccines, Infection, Viruses & Asthma Newcastle, New South Wales, Australia
| | - Huib A. M. Kerstjens
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Machteld N. Hylkema
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- Groningen Research Institute for Asthma and COPD
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - the Cambridge Lung Cancer Early Detection Programme
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
- Department of Pathology & Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
- Centre for Computational Biology, Mines ParisTech, Paris Sciences et Lettres Research University, Paris, France
- Cancer and Genome: Bioinformatics, Biostatistics and Epidemiology of Complex Systems Institut Curie, Paris, France
- Institut Nationale de la Santé et de la Recherche Médicale U900, Paris, France
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Computational Cancer Biology, Center for Integrated Oncology, Cancer Research Center Cologne Essen, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
- Sanofi, Chilly-Mazarin, France
- Sanofi, Cambridge, Massachusetts
- Regeneron Pharmaceuticals, Tarrytown, New York
- Centre for Asthma & Respiratory Disease, The University of Newcastle, Newcastle, New South Wales, Australia; and
- Hunter Medical Research Institute, Vaccines, Infection, Viruses & Asthma Newcastle, New South Wales, Australia
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2
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Kermani N, Versi A, Gay A, Vlasma J, Jayalatha AKS, Koppelman GH, Nawijn M, Faiz A, van den Berge M, Adcock IM, Chung KF. Gene signatures in U-BIOPRED severe asthma for molecular phenotyping and precision medicine: time for clinical use. Expert Rev Respir Med 2023; 17:965-971. [PMID: 37997709 DOI: 10.1080/17476348.2023.2278606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
INTRODUCTION The use and generation of gene signatures have been established as a method to define molecular endotypes in complex diseases such as severe asthma. Bioinformatic approaches have now been applied to large omics datasets to define the various co-existing inflammatory and cellular functional pathways driving or characterizing a particular molecular endotype. AREAS COVERED Molecular phenotypes and endotypes of Type 2 inflammatory pathways and also of non-Type 2 inflammatory pathways, such as IL-6 trans-signaling, IL-17 activation, and IL-22 activation, have been defined in the Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes dataset. There has also been the identification of the role of mast cell activation and of macrophage dysfunction in various phenotypes of severe asthma. EXPERT OPINION Phenotyping on the basis of clinical treatable traits is not sufficient for understanding of mechanisms driving the disease in severe asthma. It is time to consider whether certain patients with severe asthma, such as those non-responsive to current therapies, including Type 2 biologics, would be better served using an approach of molecular endotyping using gene signatures for management purposes rather than the current sole reliance on blood eosinophil counts or exhaled nitric oxide measurements.
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Affiliation(s)
- Nazanin Kermani
- National Heart & Lung Institute & Data Science Institute, Imperial College London, London, UK
| | - Ali Versi
- National Heart & Lung Institute & Data Science Institute, Imperial College London, London, UK
| | - Aurore Gay
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Centre Groningen, Groningen, The Netherlands
| | - Jelmer Vlasma
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Gerard H Koppelman
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Centre Groningen, Groningen, The Netherlands
- Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, Groningen, the Netherlands
| | - Martijn Nawijn
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Centre Groningen, Groningen, The Netherlands
| | - Alen Faiz
- School of Life Sciences, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, Australia
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Centre Groningen, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ian M Adcock
- National Heart & Lung Institute & Data Science Institute, Imperial College London, London, UK
| | - Kian Fan Chung
- National Heart & Lung Institute & Data Science Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospital, London, UK
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3
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Porsbjerg C, Maitland-van der Zee AH, Brusselle G, Canonica GW, Agusti A, Faner R, Vogelmeier CF, Nawijn M, van den Berge M, Rusconi F, Pilette C, Ramiconi V, Coleman C, Chaudhuri R, Chung KF, Wedzicha J, Saglani S, Van der Schee MP, Heaney L, Bourdin A, Roberts G, Djukanovic R, Kuna P, Kupczyk M, Axmann J, Staudinger H, Clarke GW, Dahlen SE, Brightling C. 3TR: a pan-European cross-disease research consortium aimed at improving personalised biological treatment of asthma and COPD. Eur Respir J 2021; 58:58/4/2102168. [PMID: 34675035 DOI: 10.1183/13993003.02168-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/20/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Celeste Porsbjerg
- Dept of Respiratory Medicine, Bispebjerg University Hospital, Copenhagen, Denmark .,Copenhagen Center for Translational Research, Bispebjerg Hospital, Copenhagen, Denmark
| | - Anke H Maitland-van der Zee
- Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Dept of Pediatric Pulmonology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Guy Brusselle
- Dept of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Giorgio Walter Canonica
- Personalized Medicine, Asthma and Allergy Humanitas Clinical and Research Center IRCCS, Rozzano, Italy.,Dept of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Alvar Agusti
- Hospital Clinic, University of Barcelona, Barcelona, Spain.,IDIBAPS, CIBERES, Barcelona, Spain
| | - Rosa Faner
- Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Claus F Vogelmeier
- Dept of Medicine, Pulmonary and Critical Care Medicine, University of Marburg (UMR), Marburg, Germany.,Member of the German Center for Lung Research (DZL), Marburg, Germany
| | - Martijn Nawijn
- Dept of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands
| | - Maarten van den Berge
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Franca Rusconi
- Unit of Epidemiology, Meyer Children's University Hospital, Florence, Italy
| | - Charles Pilette
- Dept of pneumology, Cliniques universitaires Saint-Luc and Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Valeria Ramiconi
- European Federation of Allergy and Airways Diseases Patients' Associations (EFA), Brussels, Belgium
| | | | - Rekha Chaudhuri
- Division of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jadwiga Wedzicha
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Sejla Saglani
- National Heart and Lung Institute, Imperial College London, London, UK.,Dept of Paediatric Respiratory Medicine, Royal Brompton Hospital, London, UK
| | | | - Liam Heaney
- Wellcome-Wolfson Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, UK
| | - Arnaud Bourdin
- Dept of Respiratory Diseases, Univ Montpellier, CHU Montpellier, Montpellier, France.,PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Graham Roberts
- Faculty of Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,The David Hide Asthma and Allergy Research Centre, St Mary's Hospital, Isle of Wight, UK
| | - Ratko Djukanovic
- Clinical and Experimental Science, Faculty of Medicine and NIHR Southampton Biomedical Research centre, Southampton, UK
| | - Piotr Kuna
- Dept of Internal Medicine, Asthma and Allergy, Medical University of Lodz, Lodz, Poland
| | - Maceij Kupczyk
- Dept of Internal Medicine, Asthma and Allergy, Medical University of Lodz, Lodz, Poland
| | - Judith Axmann
- Immunology, Infectious Diseases and Ophthalmology Discovery and Translational Area, Roche Pharma Research & Early Development, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Heribert Staudinger
- Clinical Strategy Lead, Immunology and Inflammation Therapeutic Area, Sanofi Genzyme, Bridgewater, NJ, USA
| | - Graham W Clarke
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sven Erik Dahlen
- The Center for Allergy Research and the Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Dept of Respiratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Chris Brightling
- Dept of Respiratory Sciences, University of Leicester, Leicester, UK
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4
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Ditz B, Boekhoudt JG, Aliee H, Theis FJ, Nawijn M, Brandsma CA, Hiemstra PS, Timens W, Tew GW, Grimbaldeston MA, Neighbors M, Guryev V, van den Berge M, Faiz A. Comparison of genome-wide gene expression profiling by RNA Sequencing versus microarray in bronchial biopsies of COPD patients before and after inhaled corticosteroid treatment: does it provide new insights? ERJ Open Res 2021; 7:00104-2021. [PMID: 34164552 PMCID: PMC8215328 DOI: 10.1183/23120541.00104-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/02/2021] [Indexed: 11/05/2022] Open
Abstract
More DEGs are detected by RNA-Seq than microarrays in COPD lung biopsies and are associated with immunological pathways. Performing bulk tissue cell-type deconvolution in microarray lung samples, using the SVR method, reflects RNA-Seq results. https://bit.ly/2N8sY3s.
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Affiliation(s)
- Benedikt Ditz
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands
- Co-first authors
| | - Jeunard G. Boekhoudt
- University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands
- Dept of Pathology and Medical Biology, section Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Co-first authors
| | - Hananeh Aliee
- Institute of Computational Biology, Helmholtz Centre, Munich, Germany
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Centre, Munich, Germany
- Dept of Mathematics, Technical University of Munich, Munich, Germany
| | - Martijn Nawijn
- University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands
- Dept of Pathology and Medical Biology, section Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands
- Dept of Pathology and Medical Biology, section Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pieter S. Hiemstra
- Dept of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands
- Dept of Pathology and Medical Biology, section Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gaik W. Tew
- OMNI Biomarker Development, Genentech Inc, San Francisco, CA, USA
| | | | | | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands
- Co-senior authors
| | - Alen Faiz
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands
- Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
- Co-senior authors
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5
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 DOI: 10.1101/121202] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 05/28/2023] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Ewan Birney
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Ian Dunham
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Wolfgang Enard
- Department of Biology II, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Andrew Farmer
- Takara Bio United States, Inc., Mountain View, United States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, United States
- Massachusetts General Hospital Cancer Center, Boston, United States
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of Medicine, Stanford University School of Medicine, Stanford, United States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Genetics, Stanford University, Stanford, United States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, United States
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, United States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of Bioengineering, Stanford University, Stanford, United States
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Rahul Satija
- Department of Biology, New York University, New York, United States
- New York Genome Center, New York University, New York, United States
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alex Shalek
- Broad Institute of MIT and Harvard, Cambridge, United States
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer Center, University of Texas, Houston, United States
| | - Jay W Shin
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Oliver Stegle
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Fabian J Theis
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of Proteomics, KTH Royal Institute of Technology, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical Institute, Chevy Chase, United States
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, United States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
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6
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 PMCID: PMC5762154 DOI: 10.7554/elife.27041] [Citation(s) in RCA: 1156] [Impact Index Per Article: 165.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 12/12/2022] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
| | - Eric S Lander
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Ido Amit
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
| | - Ewan Birney
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
| | - Ian Dunham
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
| | - Wolfgang Enard
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
| | - Andrew Farmer
- Takara Bio United States, Inc.Mountain ViewUnited States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
| | - Berthold Göttgens
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and HarvardCambridgeUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Muzlifah Haniffa
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Emma Lundberg
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Miriam Merad
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
| | - Garry Nolan
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
| | - Dana Pe'er
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
| | - Rahul Satija
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
| | - Ton N Schumacher
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Alex Shalek
- Broad Institute of MIT and HarvardCambridgeUnited States
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Jay W Shin
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Oliver Stegle
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | - Fabian J Theis
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Barbara Wold
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Ramnik Xavier
- Broad Institute of MIT and HarvardCambridgeUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Human Cell Atlas Meeting Participants
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
- Takara Bio United States, Inc.Mountain ViewUnited States
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Massachusetts General Hospital Cancer CenterBostonUnited States
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Allen Institute for Brain ScienceSeattleUnited States
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
- National Institute of Biomedical GenomicsKalyaniIndia
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
- Hubrecht Institute and University Medical Center UtrechtUtrechtThe Netherlands
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
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7
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Vermeulen C, Vonk J, Postma D, Xu CJ, ten Hacken N, Timens W, Heijink I, Nawijn M, van Oosterhout A, Affleck K, Koppelman G, van den Berge M. Gene expression in bronchial biopsies from subjects with persistent asthma and asthma in remission. Genes Environ 2017. [DOI: 10.1183/1393003.congress-2017.pa1822] [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: 11/05/2022] Open
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8
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Bousquet J, Anto JM, Akdis M, Auffray C, Keil T, Momas I, Postma D, Valenta R, Wickman M, Cambon‐Thomsen A, Haahtela T, Lambrecht BN, Lodrup Carlsen KC, Koppelman GH, Sunyer J, Zuberbier T, Annesi‐Maesano I, Arno A, Bindslev‐Jensen C, De Carlo G, Forastiere F, Heinrich J, Kowalski ML, Maier D, Melén E, Palkonen S, Smit HA, Standl M, Wright J, Asarnoj A, Benet M, Ballardini N, Garcia‐Aymerich J, Gehring U, Guerra S, Hohman C, Kull I, Lupinek C, Pinart M, Skrindo I, Westman M, Smagghe D, Akdis C, Albang R, Anastasova V, Anderson N, Bachert C, Ballereau S, Ballester F, Basagana X, Bedbrook A, Bergstrom A, Berg A, Brunekreef B, Burte E, Carlsen KH, Chatzi L, Coquet JM, Curin M, Demoly P, Eller E, Fantini MP, Gerhard B, Hammad H, Hertzen L, Hovland V, Jacquemin B, Just J, Keller T, Kerkhof M, Kiss R, Kogevinas M, Koletzko S, Lau S, Lehmann I, Lemonnier N, McEachan R, Mäkelä M, Mestres J, Minina E, Mowinckel P, Nadif R, Nawijn M, Oddie S, Pellet J, Pin I, Porta D, Rancière F, Rial‐Sebbag A, Saeys Y, Schuijs MJ, Siroux V, Tischer CG, Torrent M, Varraso R, De Vocht J, Wenger K, Wieser S, Xu C. Paving the way of systems biology and precision medicine in allergic diseases: the MeDALL success story: Mechanisms of the Development of ALLergy; EU FP7-CP-IP; Project No: 261357; 2010-2015. Allergy 2016; 71:1513-1525. [PMID: 26970340 PMCID: PMC5248602 DOI: 10.1111/all.12880] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [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] [Accepted: 03/06/2016] [Indexed: 01/06/2023]
Abstract
MeDALL (Mechanisms of the Development of ALLergy; EU FP7-CP-IP; Project No: 261357; 2010-2015) has proposed an innovative approach to develop early indicators for the prediction, diagnosis, prevention and targets for therapy. MeDALL has linked epidemiological, clinical and basic research using a stepwise, large-scale and integrative approach: MeDALL data of precisely phenotyped children followed in 14 birth cohorts spread across Europe were combined with systems biology (omics, IgE measurement using microarrays) and environmental data. Multimorbidity in the same child is more common than expected by chance alone, suggesting that these diseases share causal mechanisms irrespective of IgE sensitization. IgE sensitization should be considered differently in monosensitized and polysensitized individuals. Allergic multimorbidities and IgE polysensitization are often associated with the persistence or severity of allergic diseases. Environmental exposures are relevant for the development of allergy-related diseases. To complement the population-based studies in children, MeDALL included mechanistic experimental animal studies and in vitro studies in humans. The integration of multimorbidities and polysensitization has resulted in a new classification framework of allergic diseases that could help to improve the understanding of genetic and epigenetic mechanisms of allergy as well as to better manage allergic diseases. Ethics and gender were considered. MeDALL has deployed translational activities within the EU agenda.
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Affiliation(s)
- J. Bousquet
- University Hospital Montpellier France
- MACVIA‐LR Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc‐Roussillon European Innovation Partnership on Active and Healthy Ageing Reference Site France
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - J. M. Anto
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - M. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - C. Auffray
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - T. Keil
- Institute of Social Medicine, Epidemiology and Health Economics Charité–Universitätsmedizin Berlin Berlin Germany
- Institute for Clinical Epidemiology and Biometry University of Wuerzburg Wuerzburg Germany
| | - I. Momas
- Department of Public Health and Health Products Paris Descartes University‐Sorbonne Paris Cité Paris France
- Paris Municipal Department of Social Action, Childhood, and Health Paris France
| | - D.S. Postma
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - R. Valenta
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - M. Wickman
- Sachs’ Children and Youth Hospital, Södersjukhuset Stockholm and Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - A. Cambon‐Thomsen
- UMR Inserm U1027 and Université de Toulouse III Paul Sabatier Toulouse France
| | - T. Haahtela
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | - B. N. Lambrecht
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - K. C. Lodrup Carlsen
- Department of Paediatrics Faculty of Medicine Institute of Clinical Medicine Oslo University Hospital University of Oslo Oslo Norway
| | - G. H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - J. Sunyer
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - T. Zuberbier
- Secretary General of the Global Allergy and Asthma European Network (GALEN) Allergy‐Centre‐Charité at the Department of Dermatology Charité–Universitätsmedizin Berlin Berlin Germany
| | | | - A. Arno
- Onmedic Networks Barcelona Spain
| | - C. Bindslev‐Jensen
- Department of Dermatology and Allergy Centre Odense University Hospital Odense Denmark
| | - G. De Carlo
- EFA European Federation of Allergy and Airways Diseases Patients’ Associations Brussels Belgium
| | - F. Forastiere
- Department of Epidemiology Regional Health Service Lazio Region Rome Italy
| | - J. Heinrich
- Institute of Epidemiology I German Research Centre for Environmental Health Helmholtz Zentrum München Neuherberg Germany
| | - M. L. Kowalski
- Department of Immunology, Rheumatology and Allergy Medical University of Lodz Lodz Poland
| | - D. Maier
- Biomax Informatics AG Munich Germany
| | - E. Melén
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
- Stockholm County Council Centre for Occupational and Environmental Medicine Stockholm Sweden
| | - S. Palkonen
- EFA European Federation of Allergy and Airways Diseases Patients’ Associations Brussels Belgium
| | - H. A. Smit
- Julius Center of Health Sciences and Primary Care University Medical Center Utrecht University of Utrecht Utrecht the Netherlands
| | - M. Standl
- Institute of Epidemiology I German Research Centre for Environmental Health Helmholtz Zentrum München Neuherberg Germany
| | - J. Wright
- Bradford Institute for Health Research Bradford Royal Infirmary Bradford UK
| | - A. Asarnoj
- Clinical Immunology and Allergy Unit Department of Medicine Solna Karolinska Institutet Stockholm Sweden
- Astrid Lindgren Children's Hospital Department of Pediatric Pulmonology and Allergy Karolinska University Hospital Stockholm Sweden
| | - M. Benet
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - N. Ballardini
- Sachs’ Children and Youth Hospital, Södersjukhuset Stockholm and Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- St John's Institute of Dermatology King's College London London UK
| | - J. Garcia‐Aymerich
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - U. Gehring
- Institute for Risk Assessment Sciences Utrecht University Utrecht the Netherlands
| | - S. Guerra
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - C. Hohman
- Institute of Social Medicine, Epidemiology and Health Economics Charité–Universitätsmedizin Berlin Germany
| | - I. Kull
- Sachs’ Children and Youth Hospital, Södersjukhuset Stockholm and Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Department of Clinical Science and Education, Södersjukhuset Karolinska InstitutetStockholm Sweden
| | - C. Lupinek
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - M. Pinart
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - I. Skrindo
- Department of Paediatrics Faculty of Medicine Institute of Clinical Medicine Oslo University Hospital University of Oslo Oslo Norway
| | - M. Westman
- Department of Clinical Science, Intervention and Technology Karolinska Institutet Stockholm Sweden
- Department of ENT Diseases Karolinska University Hospital Stockholm Sweden
| | | | - C. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - R. Albang
- Biomax Informatics AG Munich Germany
| | - V. Anastasova
- UMR Inserm U1027 and Université de Toulouse III Paul Sabatier Toulouse France
| | - N. Anderson
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - C. Bachert
- ENT Department Ghent University Hospital Gent Belgium
| | - S. Ballereau
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - F. Ballester
- Environment and Health Area Centre for Public Health Research (CSISP) CIBERESP Department of Nursing University of Valencia Valencia Spain
| | - X. Basagana
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - A. Bedbrook
- MACVIA‐LR Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc‐Roussillon European Innovation Partnership on Active and Healthy Ageing Reference Site France
| | - A. Bergstrom
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - A. Berg
- Research Institute Department of Pediatrics Marien‐Hospital Wesel Germany
| | - B. Brunekreef
- Julius Center of Health Sciences and Primary Care University Medical Center Utrecht University of Utrecht Utrecht the Netherlands
| | - E. Burte
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - K. H. Carlsen
- Department of Paediatrics Oslo University Hospital University of Oslo Oslo Norway
| | - L. Chatzi
- Department of Social Medicine Faculty of Medicine University of Crete Heraklion Crete Greece
| | - J. M. Coquet
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - M. Curin
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - P. Demoly
- Department of Respiratory Diseases Montpellier University Hospital France
| | - E. Eller
- Department of Dermatology and Allergy Centre Odense University Hospital Odense Denmark
| | - M. P. Fantini
- Department of Medicine and Public Health Alma Mater Studiorum–University of Bologna Bologna Italy
| | | | - H. Hammad
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - L. Hertzen
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | - V. Hovland
- Department of Paediatrics Oslo University Hospital University of Oslo Oslo Norway
| | - B. Jacquemin
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - J. Just
- Allergology Department Centre de l'Asthme et des Allergies Hôpital d'Enfants Armand‐Trousseau (APHP) Sorbonne Universités Institut Pierre Louis d'Epidémiologie et de Santé Publique Paris France
| | - T. Keller
- Institute of Social Medicine, Epidemiology and Health Economics Charité–Universitätsmedizin Berlin Germany
| | - M. Kerkhof
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - R. Kiss
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - M. Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - S. Koletzko
- Division of Paediatric Gastroenterology and Hepatology Ludwig Maximilians University of Munich Munich Germany
| | - S. Lau
- Department for Pediatric Pneumology and Immunology Charité Medical University Berlin Germany
| | - I. Lehmann
- Department of Environmental Immunology/Core Facility Studies Helmholtz Centre for Environmental Research, UFZ Leipzig Germany
| | - N. Lemonnier
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - R. McEachan
- Bradford Institute for Health Research Bradford Royal Infirmary Bradford UK
| | - M. Mäkelä
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | - J. Mestres
- Chemotargets SL and Chemogenomics Laboratory GRIB Unit IMIM‐Hospital del Mar and University Pompeu Fabra Barcelona Catalonia Spain
| | - E. Minina
- Biomax Informatics AG Munich Germany
| | - P. Mowinckel
- Department of Paediatrics Oslo University Hospital University of Oslo Oslo Norway
| | - R. Nadif
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - M. Nawijn
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - S. Oddie
- Bradford Institute for Health Research Bradford Royal Infirmary Bradford UK
| | - J. Pellet
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - I. Pin
- Département de Pédiatrie CHU de Grenoble Grenoble Cedex 9 France
| | - D. Porta
- Department of Epidemiology Regional Health Service Lazio Region Rome Italy
| | - F. Rancière
- Department of Public Health and Health Products Paris Descartes University‐Sorbonne Paris Cité Paris France
| | - A. Rial‐Sebbag
- UMR Inserm U1027 and Université de Toulouse III Paul Sabatier Toulouse France
| | - Y. Saeys
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - M. J. Schuijs
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | | | - C. G. Tischer
- Institute of Epidemiology I German Research Centre for Environmental Health Helmholtz Zentrum München Neuherberg Germany
| | - M. Torrent
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- ib‐salut Area de Salut de Menorca Spain
| | - R. Varraso
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - J. De Vocht
- EFA European Federation of Allergy and Airways Diseases Patients’ Associations Brussels Belgium
| | - K. Wenger
- Biomax Informatics AG Munich Germany
| | - S. Wieser
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - C. Xu
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
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9
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Bousquet J, Anto JM, Wickman M, Keil T, Valenta R, Haahtela T, Lodrup Carlsen K, van Hage M, Akdis C, Bachert C, Akdis M, Auffray C, Annesi-Maesano I, Bindslev-Jensen C, Cambon-Thomsen A, Carlsen KH, Chatzi L, Forastiere F, Garcia-Aymerich J, Gehrig U, Guerra S, Heinrich J, Koppelman GH, Kowalski ML, Lambrecht B, Lupinek C, Maier D, Melén E, Momas I, Palkonen S, Pinart M, Postma D, Siroux V, Smit HA, Sunyer J, Wright J, Zuberbier T, Arshad SH, Nadif R, Thijs C, Andersson N, Asarnoj A, Ballardini N, Ballereau S, Bedbrook A, Benet M, Bergstrom A, Brunekreef B, Burte E, Calderon M, De Carlo G, Demoly P, Eller E, Fantini MP, Hammad H, Hohman C, Just J, Kerkhof M, Kogevinas M, Kull I, Lau S, Lemonnier N, Mommers M, Nawijn M, Neubauer A, Oddie S, Pellet J, Pin I, Porta D, Saes Y, Skrindo I, Tischer CG, Torrent M, von Hertzen L. Are allergic multimorbidities and IgE polysensitization associated with the persistence or re-occurrence of foetal type 2 signalling? The MeDALL hypothesis. Allergy 2015; 70:1062-78. [PMID: 25913421 DOI: 10.1111/all.12637] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2015] [Indexed: 12/22/2022]
Abstract
Allergic diseases [asthma, rhinitis and atopic dermatitis (AD)] are complex. They are associated with allergen-specific IgE and nonallergic mechanisms that may coexist in the same patient. In addition, these diseases tend to cluster and patients present concomitant or consecutive diseases (multimorbidity). IgE sensitization should be considered as a quantitative trait. Important clinical and immunological differences exist between mono- and polysensitized subjects. Multimorbidities of allergic diseases share common causal mechanisms that are only partly IgE-mediated. Persistence of allergic diseases over time is associated with multimorbidity and/or IgE polysensitization. The importance of the family history of allergy may decrease with age. This review puts forward the hypothesis that allergic multimorbidities and IgE polysensitization are associated and related to the persistence or re-occurrence of foetal type 2 signalling. Asthma, rhinitis and AD are manifestations of a common systemic immune imbalance (mesodermal origin) with specific patterns of remodelling (ectodermal or endodermal origin). This study proposes a new classification of IgE-mediated allergic diseases that allows the definition of novel phenotypes to (i) better understand genetic and epigenetic mechanisms, (ii) better stratify allergic preschool children for prognosis and (iii) propose novel strategies of treatment and prevention.
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Affiliation(s)
- J. Bousquet
- University Hospital; Montpellier France
- MACVIA-LR; Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc-Roussillon; European Innovation Partnership on Active and Healthy Ageing Reference Site; Paris France
- INSERM; VIMA: Ageing and Chronic Diseases Epidemiological and Public Health Approaches, U1168; Paris France
- UVSQ; UMR-S 1168; Université Versailles St-Quentin-en-Yvelines; Versailles France
| | - J. M. Anto
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- Hospital del Mar Research Institute (IMIM); Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP); Barcelona Spain
- Department of Experimental and Health Sciences; University of Pompeu Fabra (UPF); Barcelona Spain
| | - M. Wickman
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - T. Keil
- Institute of Social Medicine, Epidemiology and Health Economics; Charité - Universitätsmedizin Berlin; Berlin Germany
- Institute for Clinical Epidemiology and Biometry; University of Wuerzburg; Wuerzburg Germany
| | - R. Valenta
- Division of Immunopathology; Department of Pathophysiology and Allergy Research; Center for Pathophysiology, Infectiology and Immunology; Medical University of Vienna; Vienna Austria
| | - T. Haahtela
- Skin and Allergy Hospital; Helsinki University Hospital; Helsinki Finland
| | - K. Lodrup Carlsen
- Department of Paediatrics; Oslo University Hospital; Oslo Norway
- Faculty of Medicine; Institute of Clinical Medicine; University of Oslo; Oslo Norway
| | - M. van Hage
- Clinical Immunology and Allergy Unit; Department of Medicine Solna; Karolinska Institutet and University Hospital; Stockholm Sweden
| | - C. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF); University of Zurich; Davos Switzerland
| | - C. Bachert
- ENT Department; Ghent University Hospital; Gent Belgium
| | - M. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF); University of Zurich; Davos Switzerland
| | - C. Auffray
- European Institute for Systems Biology and Medicine; Lyon France
| | - I. Annesi-Maesano
- EPAR U707 INSERM; Paris France
- EPAR UMR-S UPMC; Paris VI; Paris France
| | - C. Bindslev-Jensen
- Department of Dermatology and Allergy Centre; Odense University Hospital; Odense Denmark
| | - A. Cambon-Thomsen
- UMR Inserm U1027; Université de Toulouse III Paul Sabatier; Toulouse France
| | - K. H. Carlsen
- Department of Paediatrics; Oslo University Hospital; Oslo Norway
- University of Oslo; Oslo Norway
| | - L. Chatzi
- Department of Social Medicine; Faculty of Medicine; University of Crete; Heraklion Crete Greece
| | - F. Forastiere
- Department of Epidemiology; Regional Health Service Lazio Region; Rome Italy
| | - J. Garcia-Aymerich
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- Hospital del Mar Research Institute (IMIM); Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP); Barcelona Spain
- Department of Experimental and Health Sciences; University of Pompeu Fabra (UPF); Barcelona Spain
| | - U. Gehrig
- Julius Center of Health Sciences and Primary Care; University Medical Center Utrecht; University of Utrecht; Utrecht the Netherlands
| | - S. Guerra
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
| | - J. Heinrich
- Institute of Epidemiology; German Research Centre for Environmental Health; Helmholtz Zentrum München; Neuherberg Germany
| | - G. H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology; GRIAC Research Institute; University Medical Center Groningen; Beatrix Children's Hospital; University of Groningen; Groningen the Netherlands
| | - M. L. Kowalski
- Department of Immunology, Rheumatology and Allergy; Medical University of Lodz; Lodz Poland
| | - B. Lambrecht
- VIB Inflammation Research Center; Ghent University; Ghent Belgium
| | - C. Lupinek
- Division of Immunopathology; Department of Pathophysiology and Allergy Research; Center for Pathophysiology, Infectiology and Immunology; Medical University of Vienna; Vienna Austria
| | | | - E. Melén
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - I. Momas
- Department of Public Health and Biostatistics, EA 4064; Paris Descartes University; Paris France
- Paris Municipal Department of Social Action, Childhood, and Health; Paris France
| | - S. Palkonen
- EFA European Federation of Allergy and Airways Diseases Patients' Associations; Brussels Belgium
| | - M. Pinart
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
| | - D. Postma
- Department of Respiratory Medicine; GRIAC Research Institute; University Medical Center Groningen; Beatrix Children's Hospital; University of Groningen; Groningen the Netherlands
| | | | - H. A. Smit
- Julius Center of Health Sciences and Primary Care; University Medical Center Utrecht; University of Utrecht; Utrecht the Netherlands
| | - J. Sunyer
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- Hospital del Mar Research Institute (IMIM); Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP); Barcelona Spain
- Department of Experimental and Health Sciences; University of Pompeu Fabra (UPF); Barcelona Spain
| | - J. Wright
- Bradford Institute for Health Research; Bradford Royal Infirmary; Bradford UK
| | - T. Zuberbier
- Allergy-Centre-Charité at the Department of Dermatology; Charité - Universitätsmedizin Berlin; Berlin Germany
- Secretary General of the Global Allergy and Asthma European Network (GA2LEN); Berlin Germany
| | - S. H. Arshad
- David Hide Asthma and Allergy Research Centre; Isle of Wight UK
| | - R. Nadif
- INSERM; VIMA: Ageing and Chronic Diseases Epidemiological and Public Health Approaches, U1168; Paris France
- UVSQ; UMR-S 1168; Université Versailles St-Quentin-en-Yvelines; Versailles France
| | - C. Thijs
- Department of Epidemiology; CAPHRI School of Public Health and Primary Care; Maastricht University; Maastricht the Netherlands
| | - N. Andersson
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - A. Asarnoj
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - N. Ballardini
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - S. Ballereau
- European Institute for Systems Biology and Medicine; Lyon France
| | - A. Bedbrook
- MACVIA-LR; Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc-Roussillon; European Innovation Partnership on Active and Healthy Ageing Reference Site; Paris France
| | - M. Benet
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
| | - A. Bergstrom
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - B. Brunekreef
- Julius Center of Health Sciences and Primary Care; University Medical Center Utrecht; University of Utrecht; Utrecht the Netherlands
| | - E. Burte
- INSERM; VIMA: Ageing and Chronic Diseases Epidemiological and Public Health Approaches, U1168; Paris France
- UVSQ; UMR-S 1168; Université Versailles St-Quentin-en-Yvelines; Versailles France
| | - M. Calderon
- National Heart and Lung Institute; Imperial College London; Royal Brompton Hospital NHS; London UK
| | - G. De Carlo
- EFA European Federation of Allergy and Airways Diseases Patients' Associations; Brussels Belgium
| | - P. Demoly
- Department of Respiratory Diseases; Montpellier University Hospital; Montpellier France
| | - E. Eller
- Department of Dermatology and Allergy Centre; Odense University Hospital; Odense Denmark
| | - M. P. Fantini
- Department of Medicine and Public Health; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - H. Hammad
- VIB Inflammation Research Center; Ghent University; Ghent Belgium
| | - C. Hohman
- Institute of Social Medicine, Epidemiology and Health Economics; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - J. Just
- Allergology Department; Centre de l'Asthme et des Allergies; Hôpital d'Enfants Armand-Trousseau (APHP); Paris France
- Institut Pierre Louis d'Epidémiologie et de Santé Publique; Equipe EPAR; Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136; Paris France
| | - M. Kerkhof
- Department of Respiratory Medicine; GRIAC Research Institute; University Medical Center Groningen; Beatrix Children's Hospital; University of Groningen; Groningen the Netherlands
| | - M. Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- Hospital del Mar Research Institute (IMIM); Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP); Barcelona Spain
- Department of Experimental and Health Sciences; University of Pompeu Fabra (UPF); Barcelona Spain
| | - I. Kull
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - S. Lau
- Department for Pediatric Pneumology and Immunology; Charité Medical University; Berlin Germany
| | - N. Lemonnier
- European Institute for Systems Biology and Medicine; Lyon France
| | - M. Mommers
- Department of Epidemiology; CAPHRI School of Public Health and Primary Care; Maastricht University; Maastricht the Netherlands
| | - M. Nawijn
- Department of Pediatric Pulmonology and Pediatric Allergology; GRIAC Research Institute; University Medical Center Groningen; Beatrix Children's Hospital; University of Groningen; Groningen the Netherlands
| | | | - S. Oddie
- Bradford Institute for Health Research; Bradford Royal Infirmary; Bradford UK
| | - J. Pellet
- European Institute for Systems Biology and Medicine; Lyon France
| | - I. Pin
- Département de pédiatrie; CHU de Grenoble; Grenoble Cedex 9 France
| | - D. Porta
- Department of Epidemiology; Regional Health Service Lazio Region; Rome Italy
| | - Y. Saes
- VIB Inflammation Research Center; Ghent University; Ghent Belgium
| | - I. Skrindo
- Department of Paediatrics; Oslo University Hospital; Oslo Norway
- Faculty of Medicine; Institute of Clinical Medicine; University of Oslo; Oslo Norway
| | - C. G. Tischer
- Institute of Epidemiology; German Research Centre for Environmental Health; Helmholtz Zentrum München; Neuherberg Germany
| | - M. Torrent
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- Area de Salut de Menorca, ib-salut; Illes Balears Spain
| | - L. von Hertzen
- Skin and Allergy Hospital; Helsinki University Hospital; Helsinki Finland
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10
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Bidad K, Nawijn M, van Oosterhout AJM, van der Heide S, Oude Elberink JNG. Basophil activation test in the diagnosis and monitoring of mastocytosis patients with wasp venom allergy. Cytometry B Clin Cytom 2014:n/a-n/a. [PMID: 25088565 DOI: 10.1002/cytob.21181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 07/30/2014] [Indexed: 11/08/2022]
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11
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Post S, Nawijn M, van Oosterhout A, Heijink I. House dust mite-induced ATP release plays a role in the innate immunological response and barrier dysfunction of airway epithelium. Pneumologie 2012. [DOI: 10.1055/s-0032-1329799] [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: 10/27/2022]
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12
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Krimpenfort P, Ijpenberg A, Song JY, van der Valk M, Nawijn M, Zevenhoven J, Berns A. p15Ink4b is a critical tumour suppressor in the absence of p16Ink4a. Nature 2007; 448:943-6. [PMID: 17713536 DOI: 10.1038/nature06084] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 07/09/2007] [Indexed: 01/09/2023]
Abstract
The CDKN2b-CDKN2a locus on chromosome 9p21 in human (chromosome 4 in mouse) is frequently lost in cancer. The locus encodes three cell cycle inhibitory proteins: p15INK4b encoded by CDKN2b, p16INK4a encoded by CDKN2a and p14ARF (p19Arf in mice) encoded by an alternative reading frame of CDKN2a (ref. 1). Whereas the tumour suppressor functions for p16INK4a and p14ARF have been firmly established, the role of p15INK4b remains ambiguous. However, many 9p21 deletions also remove CDKN2b, so we hypothesized a synergistic effect of the combined deficiency for p15INK4b, p14ARF and p16INK4a. Here we report that mice deficient for all three open reading frames (Cdkn2ab-/-) are more tumour-prone and develop a wider spectrum of tumours than Cdkn2a mutant mice, with a preponderance of skin tumours and soft tissue sarcomas (for example, mesothelioma) frequently composed of mixed cell types and often showing biphasic differentiation. Cdkn2ab-/- mouse embryonic fibroblasts (MEFs) are substantially more sensitive to oncogenic transformation than Cdkn2a mutant MEFs. Under conditions of stress, p15Ink4b protein levels are significantly elevated in MEFs deficient for p16Ink4a. Our data indicate that p15Ink4b can fulfil a critical backup function for p16Ink4a and provide an explanation for the frequent loss of the complete CDKN2b-CDKN2a locus in human tumours.
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Affiliation(s)
- Paul Krimpenfort
- Division of Molecular Genetics and Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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13
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van Amerongen R, Nawijn M, Franca-Koh J, Zevenhoven J, van der Gulden H, Jonkers J, Berns A. Frat is dispensable for canonical Wnt signaling in mammals. Genes Dev 2005; 19:425-30. [PMID: 15681612 PMCID: PMC548942 DOI: 10.1101/gad.326705] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Wnt-signal transduction through beta-catenin is thought to require the inhibition of GSK3 by Frat/GBP. To investigate the role of Frat in mammalian development, we have generated mice with targeted mutations in all three murine Frat homologs. We show that Frat is normally expressed at sites of active Wnt signaling. Surprisingly, Frat-deficient mice do not display gross abnormalities. Moreover, canonical Wnt signaling in primary cells is unaffected by the loss of Frat. These studies show that Frat is not an essential component of the canonical Wnt pathway in higher organisms, despite the strict requirement of Frat/GBP for maternal Wnt signaling in Xenopus.
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Affiliation(s)
- Renée van Amerongen
- Division of Molecular Genetics, Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
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14
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Mikkers H, Nawijn M, Allen J, Brouwers C, Verhoeven E, Jonkers J, Berns A. Mice deficient for all PIM kinases display reduced body size and impaired responses to hematopoietic growth factors. Mol Cell Biol 2004; 24:6104-15. [PMID: 15199164 PMCID: PMC480904 DOI: 10.1128/mcb.24.13.6104-6115.2004] [Citation(s) in RCA: 255] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Pim family of proto-oncogenes encodes a distinct class of serine/threonine kinases consisting of PIM1, PIM2, and PIM3. Although the Pim genes are evolutionarily highly conserved, the contribution of PIM proteins to mammalian development is unclear. PIM1-deficient mice were previously described but showed only minor phenotypic aberrations. To assess the role of PIM proteins in mammalian physiology, compound Pim knockout mice were generated. Mice lacking expression of Pim1, Pim2, and Pim3 are viable and fertile. However, PIM-deficient mice show a profound reduction in body size at birth and throughout postnatal life. In addition, the in vitro response of distinct hematopoietic cell populations to growth factors is severely impaired. In particular, PIM proteins are required for the efficient proliferation of peripheral T lymphocytes mediated by synergistic T-cell receptor and interleukin-2 signaling. These results indicate that members of the PIM family of proteins are important but dispensable factors for growth factor signaling.
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Affiliation(s)
- Harald Mikkers
- Division of Molecular Genetics and Centre of Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
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