1
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Visser N, Herreman LCM, Vandooren J, Pereira RVS, Opdenakker G, Spelbrink REJ, Wilbrink MH, Bremer E, Gosens R, Nawijn MC, van der Ende-Metselaar HH, Smit JM, Laus MC, Laman JD. Novel high-yield potato protease inhibitor panels block a wide array of proteases involved in viral infection and crucial tissue damage. J Mol Med (Berl) 2024; 102:521-536. [PMID: 38381158 DOI: 10.1007/s00109-024-02423-x] [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: 01/17/2024] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Viruses critically rely on various proteases to ensure host cell entry and replication. In response to viral infection, the host will induce acute tissue inflammation pulled by granulocytes. Upon hyperactivation, neutrophil granulocytes may cause undue tissue damage through proteolytic degradation of the extracellular matrix. Here, we assess the potential of protease inhibitors (PI) derived from potatoes in inhibiting viral infection and reducing tissue damage. The original full spectrum of potato PI was developed into five fractions by means of chromatography and hydrolysis. Individual fractions showed varying inhibitory efficacy towards a panel of proteases including trypsin, chymotrypsin, ACE2, elastase, and cathepsins B and L. The fractions did not interfere with SARS-CoV-2 infection of Vero E6 cells in vitro. Importantly, two of the fractions fully inhibited elastin-degrading activity of complete primary human neutrophil degranulate. These data warrant further development of potato PI fractions for biomedical purposes, including tissue damage crucial to SARS-CoV-2 pathogenesis. KEY MESSAGES: Protease inhibitor fractions from potato differentially inhibit a series of human proteases involved in viral replication and in tissue damage by overshoot inflammation. Protease inhibition of cell surface receptors such as ACE2 does not prevent virus infection of Vero cells in vitro. Protease inhibitors derived from potato can fully inhibit elastin-degrading primary human neutrophil proteases. Protease inhibitor fractions can be produced at high scale (hundreds of thousands of kilograms, i.e., tons) allowing economically feasible application in lower and higher income countries.
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Affiliation(s)
- Nienke Visser
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | | | - Jennifer Vandooren
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Louvain, Belgium
| | - Rafaela Vaz Sousa Pereira
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Louvain, Belgium
| | - Ghislain Opdenakker
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Louvain, Belgium
| | | | | | - Edwin Bremer
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC) Research Institute, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD (GRIAC) Research Institute, University of Groningen, 9713 GZ, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
| | - Heidi H van der Ende-Metselaar
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Jolanda M Smit
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Marc C Laus
- Avebe Innovation Center Groningen, 9747 AW, Groningen, The Netherlands
| | - Jon D Laman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands.
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2
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Voskamp AL, de Jong NW, Jochems SP, Ozir-Fazalalikhan A, van Hengel ORJ, van der Vlugt LEPM, Stam KA, van den Berge M, Nawijn MC, Braunstahl GJ, Möller GM, van Wijk RG, Smits HH. Early expansion of allergen-responsive LAP + B regulatory cells in allergic rhinitis but not in allergic asthma subjects during allergen immunotherapy. Allergy 2024; 79:1060-1064. [PMID: 38169044 DOI: 10.1111/all.15973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 11/19/2023] [Accepted: 11/26/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Astrid L Voskamp
- Department of Parasitology, Leiden University Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Nicolette W de Jong
- Department of Internal Medicine, Section Allergology and Clinical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Simon P Jochems
- Department of Parasitology, Leiden University Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Arifa Ozir-Fazalalikhan
- Department of Parasitology, Leiden University Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Oscar R J van Hengel
- Department of Parasitology, Leiden University Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Luciën E P M van der Vlugt
- Department of Parasitology, Leiden University Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Koen Alexander Stam
- Department of Parasitology, Leiden University Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Gert-Jan Braunstahl
- Department of Pulmonology, Franciscus Gasthuis and Vlietland, Rotterdam, The Netherlands
- Department of Pulmonology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gertrude M Möller
- Netherlands Center of Clinical Occupational Medicine, The Netherlands
| | - Roy Gerth van Wijk
- Department of Internal Medicine, Section Allergology and Clinical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hermelijn H Smits
- Department of Parasitology, Leiden University Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
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3
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Jiménez-Gracia L, Marchese D, Nieto JC, Caratù G, Melón-Ardanaz E, Gudiño V, Roth S, Wise K, Ryan NK, Jensen KB, Hernando-Momblona X, Bernardes JP, Tran F, Sievers LK, Schreiber S, van den Berge M, Kole T, van der Velde PL, Nawijn MC, Rosenstiel P, Batlle E, Butler LM, Parish IA, Plummer J, Gut I, Salas A, Heyn H, Martelotto LG. FixNCut: single-cell genomics through reversible tissue fixation and dissociation. Genome Biol 2024; 25:81. [PMID: 38553769 PMCID: PMC10979608 DOI: 10.1186/s13059-024-03219-5] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.
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Affiliation(s)
- Laura Jiménez-Gracia
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Domenica Marchese
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Juan C Nieto
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Elisa Melón-Ardanaz
- Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Victoria Gudiño
- Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Sara Roth
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
- Monash University Department of Surgery, Alfred Hospital, Melbourne, VIC, Australia
| | - Kellie Wise
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Australian Genomics Research Facility, Adelaide, South Australia, Australia
| | - Natalie K Ryan
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Kirk B Jensen
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Australian Genomics Research Facility, Adelaide, South Australia, Australia
| | - Xavier Hernando-Momblona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Joana P Bernardes
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Laura Katharina Sievers
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Tessa Kole
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Petra L van der Velde
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Lisa M Butler
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Jasmine Plummer
- St Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain.
- Universitat de Barcelona (UB), Barcelona, Spain.
- Omniscope, Barcelona, Spain.
| | - Luciano G Martelotto
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia.
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia.
- Omniscope, Barcelona, Spain.
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4
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Gay ACA, Banchero M, Carpaij O, Kole TM, Apperloo L, van Gosliga D, Fajar PA, Koppelman GH, Bont L, Hendriks RW, van den Berge M, Nawijn MC. Airway epithelial cell response to RSV is mostly impaired in goblet and multiciliated cells in asthma. Thorax 2024:thorax-2023-220230. [PMID: 38373824 DOI: 10.1136/thorax-2023-220230] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/27/2023] [Indexed: 02/21/2024]
Abstract
BACKGROUND In patients with asthma, respiratory syncytial virus (RSV) infections can cause disease exacerbation by infecting the epithelial layer of the airways, inducing subsequent immune response. The type I interferon antiviral response of epithelial cells upon RSV infection is found to be reduced in asthma in most-but not all-studies. Moreover, the molecular mechanisms causing the differences in the asthmatic bronchial epithelium in response to viral infection are poorly understood. METHODS Here, we investigated the transcriptional response to RSV infection of primary bronchial epithelial cells (pBECs) from patients with asthma (n=8) and healthy donors (n=8). The pBECs obtained from bronchial brushes were differentiated in air-liquid interface conditions and infected with RSV. After 3 days, cells were processed for single-cell RNA sequencing. RESULTS A strong antiviral response to RSV was observed for all cell types, for all samples (p<1e-48). Most (1045) differentially regulated genes following RSV infection were found in cells transitioning to secretory cells. Goblet cells from patients with asthma showed lower expression of genes involved in the interferon response (false discovery rate <0.05), including OASL, ICAM1 and TNFAIP3. In multiciliated cells, an impairment of the signalling pathways involved in the response to RSV in asthma was observed. CONCLUSION Our results highlight that the response to RSV infection of the bronchial epithelium in asthma and healthy airways was largely similar. However, in asthma, the response of goblet and multiciliated cells is impaired, highlighting the need for studying airway epithelial cells at high resolution in the context of asthma exacerbation.
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Affiliation(s)
- Aurore C A Gay
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin Banchero
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
| | - Orestes Carpaij
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tessa M Kole
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Leonie Apperloo
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
| | - Djoke van Gosliga
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Putri Ayu Fajar
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard H Koppelman
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Louis Bont
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
- Division of Infectious Diseases, Department of Pediatrics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Maarten van den Berge
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- GRIAC research institute, University Medical Center Groningen, Groningen, the Netherlands
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5
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Song S, van Dijk F, Vasse GF, Liu Q, Gosselink IF, Weltjens E, Remels AHV, de Jager MH, Bos S, Li C, Stoeger T, Rehberg M, Kutschke D, van Eck GWA, Wu X, Willems SH, Boom DHA, Kooter IM, Spierings D, Wardenaar R, Cole M, Nawijn MC, Salvati A, Gosens R, Melgert BN. Inhalable Textile Microplastic Fibers Impair Airway Epithelial Differentiation. Am J Respir Crit Care Med 2024; 209:427-443. [PMID: 37971785 DOI: 10.1164/rccm.202211-2099oc] [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: 11/14/2022] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
Rationale: Microplastics are a pressing global concern, and inhalation of microplastic fibers has been associated with interstitial and bronchial inflammation in flock workers. However, how microplastic fibers affect the lungs is unknown. Objectives: Our aim was to assess the effects of 12 × 31 μm nylon 6,6 (nylon) and 15 × 52 μm polyethylene terephthalate (polyester) textile microplastic fibers on lung epithelial growth and differentiation. Methods: We used human and murine alveolar and airway-type organoids as well as air-liquid interface cultures derived from primary lung epithelial progenitor cells and incubated these with either nylon or polyester fibers or nylon leachate. In addition, mice received one dose of nylon fibers or nylon leachate, and, 7 days later, organoid-forming capacity of isolated epithelial cells was investigated. Measurements and Main Results: We observed that nylon microfibers, more than polyester, inhibited developing airway organoids and not established ones. This effect was mediated by components leaching from nylon. Epithelial cells isolated from mice exposed to nylon fibers or leachate also formed fewer airway organoids, suggesting long-lasting effects of nylon components on epithelial cells. Part of these effects was recapitulated in human air-liquid interface cultures. Transcriptomic analysis revealed upregulation of Hoxa5 after exposure to nylon fibers. Inhibiting Hoxa5 during nylon exposure restored airway organoid formation, confirming Hoxa5's pivotal role in the effects of nylon. Conclusions: These results suggest that components leaching from nylon 6,6 may especially harm developing airways and/or airways undergoing repair, and we strongly encourage characterization in more detail of both the hazard of and the exposure to microplastic fibers.
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Affiliation(s)
- Shanshan Song
- Department of Molecular Pharmacology
- Groningen Research Institute for Asthma and COPD
| | - Fransien van Dijk
- Department of Molecular Pharmacology
- Groningen Research Institute for Asthma and COPD
| | - Gwenda F Vasse
- Department of Molecular Pharmacology
- Groningen Research Institute for Asthma and COPD
| | - Qiongliang Liu
- Comprehensive Pneumology Center, Institute of Lung Health and Immunity, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, German Center for Lung Research (DZL), Munich, Germany
| | - Irene F Gosselink
- Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Ellen Weltjens
- Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Alex H V Remels
- Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, the Netherlands
| | | | | | - Chenxi Li
- Comprehensive Pneumology Center, Institute of Lung Health and Immunity, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, German Center for Lung Research (DZL), Munich, Germany
| | - Tobias Stoeger
- Comprehensive Pneumology Center, Institute of Lung Health and Immunity, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, German Center for Lung Research (DZL), Munich, Germany
| | - Markus Rehberg
- Comprehensive Pneumology Center, Institute of Lung Health and Immunity, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, German Center for Lung Research (DZL), Munich, Germany
| | - David Kutschke
- Comprehensive Pneumology Center, Institute of Lung Health and Immunity, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, German Center for Lung Research (DZL), Munich, Germany
| | | | - Xinhui Wu
- Department of Molecular Pharmacology
- Groningen Research Institute for Asthma and COPD
| | | | - Devin H A Boom
- The Netherlands Organization for Applied Scientific Research (TNO), Utrecht, the Netherlands; and
| | - Ingeborg M Kooter
- Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, the Netherlands
- The Netherlands Organization for Applied Scientific Research (TNO), Utrecht, the Netherlands; and
| | | | - René Wardenaar
- European Research Institute for the Biology of Ageing, and
| | - Matthew Cole
- Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Anna Salvati
- Department of Nanomedicine & Drug Targeting, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, the Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology
- Groningen Research Institute for Asthma and COPD
| | - Barbro N Melgert
- Department of Molecular Pharmacology
- Groningen Research Institute for Asthma and COPD
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6
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Khalenkow D, Brandsma CA, Timens W, Choy DF, Grimbaldeston MA, Rosenberger CM, Slebos DJ, Kerstjens HAM, Faiz A, Koppelman GH, Nawijn MC, van den Berge M, Guryev V. Alternative Splicing Is a Major Factor Shaping Transcriptome Diversity in Mild and Severe COPD. Am J Respir Cell Mol Biol 2024. [PMID: 38315810 DOI: 10.1165/rcmb.2023-0296oc] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/05/2024] [Indexed: 02/07/2024] Open
Abstract
The role of alternative splicing in Chronic Obstructive Pulmonary Disease (COPD) is still largely unknown. We aimed to investigate the differences in alternatively splicing events between patients with mild-to-moderate and severe COPD compared to non-COPD controls and to identify splicing factors associated with aberrant alternative splicing in COPD. For this purpose, we performed genome-wide RNA-seq analysis of bronchial brushings from 23 mild-to-moderate, 121 severe COPD patients, and 23 non-COPD controls. We found a significant difference in the frequency of alternative splicing events in mild-to-moderate and severe COPD compared to non-COPD controls. There were from 2x to 8x (depending on event type) more differential alternative splicing events in the severe than in the mild-to-moderate stage. The samples from severe COPD patients showed less intron retention and more exon skipping. Interestingly, the transcript levels of the top 10 differentially expressed splicing factors were significantly correlated with the percentage of many alternatively spliced transcripts in severe COPD. The aberrant alternative splicing in severe COPD was predicted to increase the overall protein-coding capacity of gene products. In conclusion, we observed large and significant differences in alternative splicing between bronchial samples of COPD and control individuals, with more events observed in severe than in mild-to-moderate COPD. The changes in the expression of several splicing factors correlated with prevalence of alternative splicing in severe COPD. Alternative splicing can indirectly impact gene expression by changing the relative abundance of protein-coding isoforms potentially influencing pathophysiological changes. The presented results provide a better understanding of COPD-related alternative splicing changes.
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Affiliation(s)
- Dmitry Khalenkow
- University Medical Centre Groningen, 10173, Department of Pulmonology and Pediatric Allergy, Groningen, Netherlands
- ERIBA, 548577, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Corry-Anke Brandsma
- University Medical Centre Groningen, 10173, Department of Pathology and Medical Biology, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Wim Timens
- University Medical Centre Groningen, 10173, Department of Pathology and Medical Biology, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - David F Choy
- Genentech Inc, 7412, South San Francisco, California, United States
| | | | | | - Dirk-Jan Slebos
- University Medical Centre Groningen, 10173, Department of Pulmonary diseases, Groningen, Netherlands
| | - Huib A M Kerstjens
- University Medical Centre Groningen, 10173, Department of Pulmonology and Tuberculosis, Groningen, Netherlands
| | - Alen Faiz
- University of Technology Sydney, 1994, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, New South Wales, Australia
| | - Gerard H Koppelman
- University Medical Centre Groningen, 10173, Department of Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Martijn C Nawijn
- University Medical Centre Groningen, 10173, Lab allergology and pulmonary diseases, department of pathology and medical biology, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Maarten van den Berge
- University Medical Centre Groningen, 10173, Department of Pulmonary Diseases, Groningen, Netherlands
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Victor Guryev
- University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
- ERIBA, 548577, Groningen, Netherlands;
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7
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Wijsman PC, Goorsenberg AWM, Keijzer N, d'Hooghe JNS, Ten Hacken NHT, Shah PL, Weersink EJM, de Brito JM, de Souza Xavier Costa N, Mauad T, Nawijn MC, Vonk JM, Annema JT, Burgess JK, Bonta PI. Airway wall extracellular matrix changes induced by bronchial thermoplasty in severe asthma. J Allergy Clin Immunol 2024; 153:435-446.e4. [PMID: 37805024 DOI: 10.1016/j.jaci.2023.09.035] [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: 02/02/2023] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Airway remodeling is a prominent feature of asthma, which involves increased airway smooth muscle mass and altered extracellular matrix composition. Bronchial thermoplasty (BT), a bronchoscopic treatment for severe asthma, targets airway remodeling. OBJECTIVE We sought to investigate the effect of BT on extracellular matrix composition and its association with clinical outcomes. METHODS This is a substudy of the TASMA trial. Thirty patients with severe asthma were BT-treated, of whom 13 patients were treated for 6 months with standard therapy (control group) before BT. Demographic data, clinical data including pulmonary function, and bronchial biopsies were collected. Biopsies at BT-treated and nontreated locations were analyzed by histological and immunohistochemical staining. Associations between histology and clinical outcomes were explored. RESULTS Six months after treatment, it was found that the reticular basement membrane thickness was reduced from 7.28 μm to 5.74 μm (21% relative reduction) and the percentage area of tissue positive for collagen increased from 26.3% to 29.8% (13% relative increase). Collagen structure analysis revealed a reduction in the curvature frequency of fibers. The percentage area positive for fibulin-1 and fibronectin increased by 2.5% and 5.9%, respectively (relative increase of 124% and 15%). No changes were found for elastin. The changes in collagen and fibulin-1 negatively associated with changes in FEV1 reversibility. CONCLUSIONS Besides reduction of airway smooth muscle mass, BT has an impact on reticular basement membrane thickness and the extracellular matrix arrangement characterized by an increase in tissue area occupied by collagen with a less dense fiber organization. Both collagen and fibulin-1 are negatively associated with the change in FEV1 reversibility.
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Affiliation(s)
- Pieta C Wijsman
- Department of Pulmonary Medicine, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Annika W M Goorsenberg
- Department of Pulmonary Medicine, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Noa Keijzer
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Julia N S d'Hooghe
- Department of Pulmonary Medicine, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Nick H T Ten Hacken
- Department of Pulmonology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Pallav L Shah
- Department of Pulmonology, Royal Brompton Hospital, Chelsea & Westminster Hospital, London, United Kingdom; National Heart and Lung Institute, Imperial College, Chelsea & Westminster Hospital, London, United Kingdom; Department of Pulmonology, Chelsea & Westminster Hospital, London, United Kingdom
| | - Els J M Weersink
- Department of Pulmonary Medicine, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jôse Mara de Brito
- Departamento de Patologia, LIM-05 Laboratório de Patologia Ambiental, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Natalia de Souza Xavier Costa
- Departamento de Patologia, LIM-05 Laboratório de Patologia Ambiental, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Thais Mauad
- Departamento de Patologia, LIM-05 Laboratório de Patologia Ambiental, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jouke T Annema
- Department of Pulmonary Medicine, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Janette K Burgess
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Peter I Bonta
- Department of Pulmonary Medicine, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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8
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Saikumar Jayalatha AK, Jonker MR, Carpaij OA, van den Berge M, Affleck KX, Koppelman GH, Nawijn MC. Lack of a transcriptional response of primary bronchial epithelial cells from patients with asthma and controls to IL-33. Am J Physiol Lung Cell Mol Physiol 2024; 326:L65-L70. [PMID: 38050688 DOI: 10.1152/ajplung.00298.2023] [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: 09/20/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/06/2023] Open
Abstract
IL-33 and IL-1RL1 are well-replicated asthma genes that act in a single pathway toward type-2 immune responses. IL-33 is expressed by basal epithelial cells, and the release of IL-33 upon epithelial damage can activate innate lymphoid cells, T helper-2 cells, basophilic granulocytes, and mast cells through a receptor complex containing IL-1RL1. However, it is unknown how bronchial epithelial cells respond to IL-33, and whether this response is increased in the disease. We aimed to characterize the IL-33-driven transcriptomic changes in cultured primary bronchial epithelial cells from patients with asthma and healthy controls. Primary bronchial epithelial cells (PBECs) were obtained by bronchial brushing from six healthy control for air-liquid interface (ALI) cultures, whereas we selected eight healthy controls and seven patients with asthma for epithelial organoid cultures. We then stimulated the cultures for 24 h with recombinant IL-33 (rhIL33) at various concentrations with 1, 10, and 50 ng/mL for the ALI cultures and 20 ng/mL and 100 ng/mL for the organoid cultures, followed by RNA-sequencing and differential gene expression analysis. We did not detect any genome-wide significant differentially expressed genes after stimulation of PBECs with IL-33, irrespective of growth in three-dimensional (3-D) epithelial organoids or after differentiation in ALI cultures. These results were identical between PBECs obtained from patients with asthma or from healthy control subjects. We detected very low levels of IL-1RL1 gene expression in these airway epithelial cell cultures. We conclude that bronchial epithelial cells do not have a transcriptional response to IL-33, independent of their differentiation state. Hence, the airway epithelium acts as a source of IL-33 but does not seem to contribute to the response upon release of the alarmin after epithelial damage.NEW & NOTEWORTHY The IL-33/IL-1RL1 pathway stands as a formidable genetic predisposition for asthma, with ongoing clinical developments of various drugs designed to mitigate its influence in patients with asthma. The absence of a transcriptomic reaction to IL-33 within the bronchial epithelium holds significance in the pursuit of identifying biomarkers that can aid in pinpointing those individuals who would derive the greatest benefit from therapies targeting the IL-33 pathway.
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Affiliation(s)
- Akshaya Keerthi Saikumar Jayalatha
- Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marnix R Jonker
- Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Orestes A Carpaij
- Department of Pulmonary Diseases, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonary Diseases, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Karen X Affleck
- Immunology Research Unit, GlaxoSmithkline, Stevenage, United Kingdom
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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9
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El-Husseini ZW, Khalenkow D, Lan A, van der Molen T, Brightling C, Papi A, Rabe KF, Siddiqui S, Singh D, Kraft M, Beghe B, van den Berge M, van Gosliga D, Nawijn MC, Rose-John S, Koppelman GH, Gosens R. An epithelial gene signature of trans-IL-6 signaling defines a subgroup of type 2-low asthma. Respir Res 2023; 24:308. [PMID: 38062491 PMCID: PMC10704725 DOI: 10.1186/s12931-023-02617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Asthma is stratified into type 2-high and type 2-low inflammatory phenotypes. Limited success has been achieved in developing drugs that target type 2-low inflammation. Previous studies have linked IL-6 signaling to severe asthma. IL-6 cooperates with soluble-IL-6Rα to activate cell signaling in airway epithelium. OBJECTIVE We sought to study the role of sIL-6Rα amplified IL-6 signaling in airway epithelium and to develop an IL-6+ sIL-6Rα gene signature that may be used to select asthma patients who potentially respond to anti-IL-6 therapy. METHODS Human airway epithelial cells were stimulated with combinations of IL-6, sIL-6Rα, and inhibitors, sgp130 (Olamkicept), and anti-IL-6R (Tocilizumab), to assess effects on pathway activation, epithelial barrier integrity, and gene expression. A gene signature was generated to identify IL-6 high patients using bronchial biopsies and nasal brushes. RESULTS Soluble-IL-6Rα amplified the activation of the IL-6 pathway, shown by the increase of STAT3 phosphorylation and stronger gene induction in airway epithelial cells compared to IL-6 alone. Olamkicept and Tocilizumab inhibited the effect of IL-6 + sIL-6Rα on gene expression. We developed an IL-6 + sIL-6Rα gene signature and observed enrichment of this signature in bronchial biopsies but not nasal brushes from asthma patients compared to healthy controls. An IL-6 + sIL-6Rα gene signature score was associated with lower levels of sputum eosinophils in asthma. CONCLUSION sIL-6Rα amplifies IL-6 signaling in bronchial epithelial cells. Higher local airway IL-6 + sIL-6Rα signaling is observed in asthma patients with low sputum eosinophils.
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Affiliation(s)
- Zaid W El-Husseini
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Dmitry Khalenkow
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Andy Lan
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Thys van der Molen
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Chris Brightling
- Department of Infection, Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, UK
| | - Alberto Papi
- Department of Respiratory Medicine, University of Ferrara, Ferrara, Italy
| | - Klaus F Rabe
- Department of Medicine, Christian Albrechts University Kiel, Kiel and Lungen Clinic Grosshansdorf (Members of the German Center for Lung Research (DZL)), Grosshansdorf, Germany
| | - Salman Siddiqui
- National Heart and Lung Institute, Imperial College and Imperial NIHR Biomedical Research Centre, London, UK
| | - Dave Singh
- Medicines Evaluation Unit, Manchester University NHS Foundation Hospital Trust, University of Manchester, Manchester, UK
| | - Monica Kraft
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Bianca Beghe
- University of Modena and Reggio Emilia, AOU of Modena, Modena, Italy
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Djoke van Gosliga
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pathology and Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pathology and Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Reinoud Gosens
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands.
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10
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Berg M, Petoukhov I, van den Ende I, Meyer KB, Guryev V, Vonk JM, Carpaij O, Banchero M, Hendriks RW, van den Berge M, Nawijn MC. FastCAR: fast correction for ambient RNA to facilitate differential gene expression analysis in single-cell RNA-sequencing datasets. BMC Genomics 2023; 24:722. [PMID: 38030970 PMCID: PMC10687889 DOI: 10.1186/s12864-023-09822-3] [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: 05/14/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
Cell type-specific differential gene expression analyses based on single-cell transcriptome datasets are sensitive to the presence of cell-free mRNA in the droplets containing single cells. This so-called ambient RNA contamination may differ between samples obtained from patients and healthy controls. Current ambient RNA correction methods were not developed specifically for single-cell differential gene expression (sc-DGE) analyses and might therefore not sufficiently correct for ambient RNA-derived signals. Here, we show that ambient RNA levels are highly sample-specific. We found that without ambient RNA correction, sc-DGE analyses erroneously identify transcripts originating from ambient RNA as cell type-specific disease-associated genes. We therefore developed a computationally lean and intuitive correction method, Fast Correction for Ambient RNA (FastCAR), optimized for sc-DGE analysis of scRNA-Seq datasets generated by droplet-based methods including the 10XGenomics Chromium platform. FastCAR uses the profile of transcripts observed in libraries that likely represent empty droplets to determine the level of ambient RNA in each individual sample, and then corrects for these ambient RNA gene expression values. FastCAR can be applied as part of the data pre-processing and QC in sc-DGE workflows comparing scRNA-Seq data in a health versus disease experimental design. We compared FastCAR with two methods previously developed to remove ambient RNA, SoupX and CellBender. All three methods identified additional genes in sc-DGE analyses that were not identified in the absence of ambient RNA correction. However, we show that FastCAR performs better at correcting gene expression values attributed to ambient RNA, resulting in a lower frequency of false-positive observations. Moreover, the use of FastCAR in a sc-DGE workflow increases the cell-type specificity of sc-DGE analyses across disease conditions.
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Affiliation(s)
- Marijn Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands.
| | | | | | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Victor Guryev
- University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Orestes Carpaij
- University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martin Banchero
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands
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11
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Nizamoglu M, Koloko Ngassie ML, Meuleman RA, Banchero M, Borghuis T, Timens W, Nawijn MC, Melgert BN, Heijink IH, Brandsma CA, Burgess JK. Collagen type XIV is proportionally lower in the lung tissue of patients with IPF. Sci Rep 2023; 13:19393. [PMID: 37938243 PMCID: PMC10632429 DOI: 10.1038/s41598-023-46733-5] [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: 07/27/2023] [Accepted: 11/04/2023] [Indexed: 11/09/2023] Open
Abstract
Abnormal deposition of extracellular matrix (ECM) in lung tissue is a characteristic of idiopathic pulmonary fibrosis (IPF). Increased collagen deposition is also accompanied by altered collagen organization. Collagen type XIV, a fibril-associated collagen, supports collagen fibril organization. Its status in IPF has not been described at the protein level yet. In this study, we utilized publicly available datasets for single-cell RNA-sequencing for characterizing collagen type XIV expression at the gene level. For protein level comparison, we applied immunohistochemical staining for collagen type XIV on lung tissue sections from IPF patients and compared it to lung tissue sections from never smoking and ex-smoking donors. Analyzing the relative amounts of collagen type XIV at the whole tissue level, as well as in parenchyma, airway wall and bronchial epithelium, we found consistently lower proportions of collagen type XIV in all lung tissue compartments across IPF samples. Our study suggests proportionally lower collagen type XIV in IPF lung tissues may have implications for the assembly of the ECM fibers potentially contributing to progression of fibrosis.
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Affiliation(s)
- Mehmet Nizamoglu
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Maunick Lefin Koloko Ngassie
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rhode A Meuleman
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Martin Banchero
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Theo Borghuis
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Barbro N Melgert
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Irene H Heijink
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pulmonology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Janette K Burgess
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 [HPC EA11], 9713 GZ, Groningen, The Netherlands.
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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12
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Melén E, Lambrecht BN, Lloyd CM, Rothenberg ME, Kabashima K, Luciani F, Coquet JM, Ober C, Nawijn MC, Platts-Mills T, von Mutius E. A conversation on allergy: recognizing the past and looking to the future. Immunol Cell Biol 2023; 101:936-946. [PMID: 37688499 DOI: 10.1111/imcb.12688] [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: 07/20/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023]
Abstract
Allergy is an ever-evolving group of disorders, which includes asthma, atopic dermatitis, rhinitis and food allergies and that currently affects over 1 billion people worldwide. This group of disorders has exploded in incidence since around the start of the 20th century, implying that genetics is not solely responsible for its development but that environmental factors have an important role. Here, Fabio Luciani and Jonathan Coquet, in their role as editors at Immunology & Cell Biology, asked nine prominent researchers in the field of allergy to define the term 'allergy', discuss the role of genetics and the environment, nominate the most important discoveries of the past decade and describe the best strategies to combat allergy at the population level going forward.
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Affiliation(s)
- Erik Melén
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - Bart N Lambrecht
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Clare M Lloyd
- National Heart & Lung Institute, Faculty of Medicine, Imperial College, London, UK
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kenji Kabashima
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fabio Luciani
- UNSW Sydney, School of Medical Sciences, Kirby Institute, Sydney, NSW, Australia
| | - Jonathan M Coquet
- Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Martijn C Nawijn
- University of Groningen, University Medical Center Groningen, Department of Pathology & Medical Biology, GRIAC Research Institute, Groningen, The Netherlands
| | | | - Erika von Mutius
- Ludwig Maximilians University Munich, Institute of Asthma and Allergy Prevention at Helmholtz Centre Munich, Munich, Germany
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13
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van Breugel M, Fehrmann RSN, Bügel M, Rezwan FI, Holloway JW, Nawijn MC, Fontanella S, Custovic A, Koppelman GH. Current state and prospects of artificial intelligence in allergy. Allergy 2023; 78:2623-2643. [PMID: 37584170 DOI: 10.1111/all.15849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/08/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
The field of medicine is witnessing an exponential growth of interest in artificial intelligence (AI), which enables new research questions and the analysis of larger and new types of data. Nevertheless, applications that go beyond proof of concepts and deliver clinical value remain rare, especially in the field of allergy. This narrative review provides a fundamental understanding of the core concepts of AI and critically discusses its limitations and open challenges, such as data availability and bias, along with potential directions to surmount them. We provide a conceptual framework to structure AI applications within this field and discuss forefront case examples. Most of these applications of AI and machine learning in allergy concern supervised learning and unsupervised clustering, with a strong emphasis on diagnosis and subtyping. A perspective is shared on guidelines for good AI practice to guide readers in applying it effectively and safely, along with prospects of field advancement and initiatives to increase clinical impact. We anticipate that AI can further deepen our knowledge of disease mechanisms and contribute to precision medicine in allergy.
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Affiliation(s)
- Merlijn van Breugel
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- MIcompany, Amsterdam, the Netherlands
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Computer Science, Aberystwyth University, Aberystwyth, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health and Care Research Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, UK
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, London, UK
- National Institute for Health and Care Research Imperial Biomedical Research Centre (BRC), London, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, UK
- National Institute for Health and Care Research Imperial Biomedical Research Centre (BRC), London, UK
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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14
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Kapellos TS, Baßler K, Fujii W, Nalkurthi C, Schaar AC, Bonaguro L, Pecht T, Galvao I, Agrawal S, Saglam A, Dudkin E, Frishberg A, de Domenico E, Horne A, Donovan C, Kim RY, Gallego-Ortega D, Gillett TE, Ansari M, Schulte-Schrepping J, Offermann N, Antignano I, Sivri B, Lu W, Eapen MS, van Uelft M, Osei-Sarpong C, van den Berge M, Donker HC, Groen HJM, Sohal SS, Klein J, Schreiber T, Feißt A, Yildirim AÖ, Schiller HB, Nawijn MC, Becker M, Händler K, Beyer M, Capasso M, Ulas T, Hasenauer J, Pizarro C, Theis FJ, Hansbro PM, Skowasch D, Schultze JL. Systemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease. Cell Rep 2023; 42:112525. [PMID: 37243592 PMCID: PMC10320832 DOI: 10.1016/j.celrep.2023.112525] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 11/07/2022] [Revised: 03/18/2023] [Accepted: 05/01/2023] [Indexed: 05/29/2023] Open
Abstract
Systemic inflammation is established as part of late-stage severe lung disease, but molecular, functional, and phenotypic changes in peripheral immune cells in early disease stages remain ill defined. Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small-airway inflammation, emphysema, and severe breathing difficulties. Using single-cell analyses we demonstrate that blood neutrophils are already increased in early-stage COPD, and changes in molecular and functional neutrophil states correlate with lung function decline. Assessing neutrophils and their bone marrow precursors in a murine cigarette smoke exposure model identified similar molecular changes in blood neutrophils and precursor populations that also occur in the blood and lung. Our study shows that systemic molecular alterations in neutrophils and their precursors are part of early-stage COPD, a finding to be further explored for potential therapeutic targets and biomarkers for early diagnosis and patient stratification.
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Affiliation(s)
- Theodore S Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Wataru Fujii
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Christina Nalkurthi
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia
| | - Anna C Schaar
- Institute of Computational Biology (ICB), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Lorenzo Bonaguro
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany
| | - Tal Pecht
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Izabela Galvao
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia
| | - Shobhit Agrawal
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Adem Saglam
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany
| | - Erica Dudkin
- Computational Life Sciences, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Amit Frishberg
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Institute of Computational Biology (ICB), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Elena de Domenico
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany
| | - Arik Horne
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Chantal Donovan
- University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia; Immune Health, Hunter Medical Research Institute, New Lambton and The University of Newcastle, Newcastle, NSW 2305, Australia
| | - Richard Y Kim
- University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia; Immune Health, Hunter Medical Research Institute, New Lambton and The University of Newcastle, Newcastle, NSW 2305, Australia
| | - David Gallego-Ortega
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Garvan Institute of Medical Research, and St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Tessa E Gillett
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 AB Groningen, the Netherlands; GRIAC Research Institute, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Meshal Ansari
- Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Computational Biology (ICB), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jonas Schulte-Schrepping
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Nina Offermann
- Immunregulation, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Ignazio Antignano
- Immunregulation, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Burcu Sivri
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Wenying Lu
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, 7250 TAS, Australia
| | - Mathew S Eapen
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, 7250 TAS, Australia
| | - Martina van Uelft
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Collins Osei-Sarpong
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Maarten van den Berge
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 AB Groningen, the Netherlands; Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Hylke C Donker
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 AB Groningen, the Netherlands; Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Harry J M Groen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 AB Groningen, the Netherlands; Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Sukhwinder S Sohal
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, 7250 TAS, Australia
| | - Johanna Klein
- Department of Internal Medicine II, Pneumology, University Hospital Bonn, 53127 Bonn, Germany
| | - Tina Schreiber
- Department of Internal Medicine II, Pneumology, University Hospital Bonn, 53127 Bonn, Germany
| | - Andreas Feißt
- University Clinics for Radiology, University Hospital Bonn, 53127 Bonn, Germany
| | - Ali Önder Yildirim
- Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Herbert B Schiller
- Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 AB Groningen, the Netherlands; GRIAC Research Institute, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Matthias Becker
- Modular HPC and AI, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Kristian Händler
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany; Institute of Human Genetics, University of Lübeck, 23562 Lübeck, Germany
| | - Marc Beyer
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany; Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Melania Capasso
- Immunregulation, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Thomas Ulas
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany
| | - Jan Hasenauer
- Institute of Computational Biology (ICB), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München, 85748 Garching, Germany; Computational Life Sciences, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Carmen Pizarro
- Department of Internal Medicine II, Pneumology, University Hospital Bonn, 53127 Bonn, Germany
| | - Fabian J Theis
- Institute of Computational Biology (ICB), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia; University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia
| | - Dirk Skowasch
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, 7250 TAS, Australia
| | - Joachim L Schultze
- Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München, 85748 Garching, Germany.
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15
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Van Buren E, Radicioni G, Lester S, O’Neal WK, Dang H, Kasela S, Garudadri S, Curtis JL, Han MK, Krishnan JA, Wan ES, Silverman EK, Hastie A, Ortega VE, Lappalainen T, Nawijn MC, van den Berge M, Christenson SA, Li Y, Cho MH, Kesimer M, Kelada SNP. Genetic regulators of sputum mucin concentration and their associations with COPD phenotypes. PLoS Genet 2023; 19:e1010445. [PMID: 37352370 PMCID: PMC10325042 DOI: 10.1371/journal.pgen.1010445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 07/06/2023] [Accepted: 04/26/2023] [Indexed: 06/25/2023] Open
Abstract
Hyper-secretion and/or hyper-concentration of mucus is a defining feature of multiple obstructive lung diseases, including chronic obstructive pulmonary disease (COPD). Mucus itself is composed of a mixture of water, ions, salt and proteins, of which the gel-forming mucins, MUC5AC and MUC5B, are the most abundant. Recent studies have linked the concentrations of these proteins in sputum to COPD phenotypes, including chronic bronchitis (CB) and acute exacerbations (AE). We sought to determine whether common genetic variants influence sputum mucin concentrations and whether these variants are also associated with COPD phenotypes, specifically CB and AE. We performed a GWAS to identify quantitative trait loci for sputum mucin protein concentration (pQTL) in the Sub-Populations and InteRmediate Outcome Measures in COPD Study (SPIROMICS, n = 708 for total mucin, n = 215 for MUC5AC, MUC5B). Subsequently, we tested for associations of mucin pQTL with CB and AE using regression modeling (n = 822-1300). Replication analysis was conducted using data from COPDGene (n = 5740) and by examining results from the UK Biobank. We identified one genome-wide significant pQTL for MUC5AC (rs75401036) and two for MUC5B (rs140324259, rs10001928). The strongest association for MUC5B, with rs140324259 on chromosome 11, explained 14% of variation in sputum MUC5B. Despite being associated with lower MUC5B, the C allele of rs140324259 conferred increased risk of CB (odds ratio (OR) = 1.42; 95% confidence interval (CI): 1.10-1.80) as well as AE ascertained over three years of follow up (OR = 1.41; 95% CI: 1.02-1.94). Associations between rs140324259 and CB or AE did not replicate in COPDGene. However, in the UK Biobank, rs140324259 was associated with phenotypes that define CB, namely chronic mucus production and cough, again with the C allele conferring increased risk. We conclude that sputum MUC5AC and MUC5B concentrations are associated with common genetic variants, and the top locus for MUC5B may influence COPD phenotypes, in particular CB.
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Affiliation(s)
- Eric Van Buren
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Giorgia Radicioni
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sarah Lester
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Wanda K. O’Neal
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Silva Kasela
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Suresh Garudadri
- Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jeffrey L. Curtis
- Pulmonary & Critical Care Medicine Division, University of Michigan, Ann Arbor, Michigan, United States of America
- Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, Michigan, United States of America
| | - MeiLan K. Han
- Pulmonary & Critical Care Medicine Division, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jerry A. Krishnan
- Breathe Chicago Center, University of Illinois, Chicago, Illinois, United States of America
| | - Emily S. Wan
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- VA Boston Healthcare System, Jamaica Plain, Massachusetts, United States of America
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annette Hastie
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Victor E. Ortega
- Department of Internal Medicine, Division of Respiratory Medicine, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Tuuli Lappalainen
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, the Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mehmet Kesimer
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Samir N. P. Kelada
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
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16
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Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. An integrated cell atlas of the lung in health and disease. Nat Med 2023; 29:1563-1577. [PMID: 37291214 PMCID: PMC10287567 DOI: 10.1038/s41591-023-02327-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [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: 03/10/2022] [Accepted: 03/30/2023] [Indexed: 06/10/2023]
Abstract
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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Grants
- R01 HL153375 NHLBI NIH HHS
- R01 HL127349 NHLBI NIH HHS
- U54 HL165443 NHLBI NIH HHS
- P01 HL107202 NHLBI NIH HHS
- U01 HL148856 NHLBI NIH HHS
- R21 HL156124 NHLBI NIH HHS
- U54 AG075931 NIA NIH HHS
- Wellcome Trust
- R01 HL146557 NHLBI NIH HHS
- R01 HL123766 NHLBI NIH HHS
- U01 HL148861 NHLBI NIH HHS
- R01 HL141852 NHLBI NIH HHS
- R01 ES034350 NIEHS NIH HHS
- UL1 TR001863 NCATS NIH HHS
- R01 HL126176 NHLBI NIH HHS
- R21 HL161760 NHLBI NIH HHS
- R01 HL145372 NHLBI NIH HHS
- P01 AG049665 NIA NIH HHS
- K12 HD105271 NICHD NIH HHS
- U19 AI135964 NIAID NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 HL142568 NHLBI NIH HHS
- R01 HL153312 NHLBI NIH HHS
- U54 AG079754 NIA NIH HHS
- R56 HL157632 NHLBI NIH HHS
- R01 HL158139 NHLBI NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL153045 NHLBI NIH HHS
- U54 HL145608 NHLBI NIH HHS
- P50 AR060780 NIAMS NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL146519 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R01 HL068702 NHLBI NIH HHS
- U01 HL145567 NHLBI NIH HHS
- P01 HL132821 NHLBI NIH HHS
- MR/R015635/1 Medical Research Council
- R01 MD010443 NIMHD NIH HHS
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” NIH 1U54HL145608-01 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- ESPOD fellowship of EMBL-EBI and Sanger Institute
- 3IA Cote d’Azur PhD program
- The Ministry of Economic Affairs and Climate Policy by means of the PPP
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Joachim Herz Stiftung (Joachim Herz Foundation)
- P50 AR060780-06A1
- University College London, Birkbeck MRC Doctoral Training Programme
- Jikei University School of Medicine (Jikei University)
- 5R01HL14254903, 4UH3CA25513503
- R01HL127349, R01HL141852, U01HL145567 and CZI
- MRC Clinician Scientist Fellowship (MR/W00111X/1)
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” 2R01HL068702
- R01 HL135156, R01 MD010443, R01 HL128439, P01 HL132821, P01 HL107202, R01 HL117004, and DOD Grant W81WH-16-2-0018
- HL142568 and HL14507 from the NHLBI
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”, 2R01HL068702
- Wellcome (WT211276/Z/18/Z) Sanger core grant WT206194 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- R21HL156124, R56HL157632, and R21HL161760
- CZI, 5U01HL148856
- CZI, 5U01HL148856, R01 HL153045
- U.S. Department of Defense (United States Department of Defense)
- The National Institute of Health R01HL145372
- Fondation pour la Recherche Médicale (Foundation for Medical Research in France)
- Conseil Départemental des Alpes Maritimes
- Inserm Cross-cutting Scientific Program HuDeCA 2018, ANR SAHARRA (ANR-19-CE14–0027), ANR-19-P3IA-0002–3IA, the National Infrastructure France Génomique (ANR-10-INBS-09-03), PPIA 4D-OMICS (21-ESRE-0052), and the Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”.
- Wellcome Trust (Wellcome)
- Sanger core grant WT206194 Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- Doris Duke Charitable Foundation (DDCF)
- The National Institute of Health R01HL145372 Department of Defense W81XWH-19-1-0416
- The National Institute of Health R01HL146557 and R01HL153375 and funds from Chan Zuckerberg Initiative - Human Lung Cell Atlas-pilot award
- 1U54HL145608-01
- CZI Deep Visual Proteomics
- 1U54HL145608-01, U01HL148861-03
- 1) the Chan Zuckerberg Initiative, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”; 2) R01 HL153312; 3) U19 AI135964; 4) P01 AG049665
- Netherlands Lung Foundation project nos. 5.1.14.020 and 4.1.18.226, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”
- grant number 2019-002438 from the Chan Zuckerberg Foundation, by the Helmholtz Association’s Initiative and Networking Fund through Helmholtz AI [ZT-I-PF-5-01] and by the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Association “ForInter” (Interaction of human brain cells)
- 1 U01 HL14555-01, R01 HL123766-04
- NIH U54 AG075931, 5R01 HL146519
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Affiliation(s)
- Lisa Sikkema
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ciro Ramírez-Suástegui
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Daniel C Strobl
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tessa E Gillett
- Experimental Pulmonary and Inflammatory Research, Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Luke Zappia
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | | | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Laure-Emmanuelle Zaragosi
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Yuge Ji
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Meshal Ansari
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Marie-Jeanne Arguel
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Leonie Apperloo
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Martin Banchero
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Christophe Bécavin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Marijn Berg
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Antoine Collin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Aurore C A Gay
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Janine Gote-Schniering
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Baharak Hooshiar Kashani
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Kemal Inecik
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Theodore S Kapellos
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Tessa M Kole
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sylvie Leroy
- Pulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Christoph H Mayr
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | | | - Lance Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Chuan Xu
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Linh T Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Carlo De Donno
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Leander Dony
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry and International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- School of Life Sciences, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, Australia
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, US
| | | | - Lukas Heumos
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Ni Huang
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ignacio L Ibarra
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Preetish Kadur Lakshminarasimha Murthy
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Mohammad Lotfollahi
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carlos Talavera-López
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Klinikum der Lüdwig-Maximilians-Universität, Munich, Germany
| | - Kyle J Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kaylee B Worlock
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Tushar J Desai
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marko Z Nikolic
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Joseph E Powell
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Mauricio Rojas
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cellular and Tissue Genomics, Genentech, South San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Douglas P Shepherd
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Whitsett
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yan Xu
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Thu Elizabeth Duong
- Department of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christine S Falk
- Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany
| | | | - Jonathan A Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Dana Pe'er
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herbert B Schiller
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | - Joachim L Schultze
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen and University of Bonn, Bonn, Germany
| | - Sara A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Malte D Luecken
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.
| | - Fabian J Theis
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
- Department of Mathematics, Technical University of Munich, Garching, Germany.
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17
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Kapellos TS, Nawijn MC. Editorial: Molecular mechanisms regulating phenotypic heterogeneity in human inflammatory diseases. Front Immunol 2023; 14:1214255. [PMID: 37266418 PMCID: PMC10231677 DOI: 10.3389/fimmu.2023.1214255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023] Open
Affiliation(s)
- Theodore S. Kapellos
- Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Neuherberg, Germany
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- GRIAC Research Institute, University Medical Center Groningen, Groningen, Netherlands
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18
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Abstract
Segmental allergen challenge in allergic patients with asthma reveals a previously unknown role for monocytes in the T helper 2 (TH2)-dependent inflammatory response, whereas in allergic controls without asthma, allergen unresponsiveness seems to be maintained through epithelial-myeloid cell cross-talk that prevents TH2 cell activation (see related Research Article by Alladina et al.).
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Affiliation(s)
- Aurore C A Gay
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
- GRIAC Research Institute, University of Groningen, Groningen, Netherlands
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
- GRIAC Research Institute, University of Groningen, Groningen, Netherlands
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19
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Faiz A, Pavlidis S, Kuo CH, Rowe A, Hiemstra PS, Timens W, Berg M, Wisman M, Guo YK, Djukanović R, Sterk P, Meyer KB, Nawijn MC, Adcock I, Chung KF, van den Berge M. Th2 high and mast cell gene signatures are associated with corticosteroid sensitivity in COPD. Thorax 2023; 78:335-343. [PMID: 36598042 PMCID: PMC10086461 DOI: 10.1136/thorax-2021-217736] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 07/06/2021] [Accepted: 10/27/2022] [Indexed: 12/12/2022]
Abstract
RATIONALE Severe asthma and chronic obstructive pulmonary disease (COPD) share common pathophysiological traits such as relative corticosteroid insensitivity. We recently published three transcriptome-associated clusters (TACs) using hierarchical analysis of the sputum transcriptome in asthmatics from the Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED) cohort comprising one Th2-high inflammatory signature (TAC1) and two Th2-low signatures (TAC2 and TAC3). OBJECTIVE We examined whether gene expression signatures obtained in asthma can be used to identify the subgroup of patients with COPD with steroid sensitivity. METHODS Using gene set variation analysis, we examined the distribution and enrichment scores (ES) of the 3 TACs in the transcriptome of bronchial biopsies from 46 patients who participated in the Groningen Leiden Universities Corticosteroids in Obstructive Lung Disease COPD study that received 30 months of treatment with inhaled corticosteroids (ICS) with and without an added long-acting β-agonist (LABA). The identified signatures were then associated with longitudinal clinical variables after treatment. Differential gene expression and cellular convolution were used to define key regulated genes and cell types. MEASUREMENTS AND MAIN RESULTS Bronchial biopsies in patients with COPD at baseline showed a wide range of expression of the 3 TAC signatures. After ICS±LABA treatment, the ES of TAC1 was significantly reduced at 30 months, but those of TAC2 and TAC3 were unaffected. A corticosteroid-sensitive TAC1 signature was developed from the TAC1 ICS-responsive genes. This signature consisted of mast cell-specific genes identified by single-cell RNA-sequencing and positively correlated with bronchial biopsy mast cell numbers following ICS±LABA. Baseline levels of gene transcription correlated with the change in RV/TLC %predicted following 30-month ICS±LABA. CONCLUSION Sputum-derived transcriptomic signatures from an asthma cohort can be recapitulated in bronchial biopsies of patients with COPD and identified a signature of airway mast cells as a predictor of corticosteroid responsiveness.
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Affiliation(s)
- Alen Faiz
- Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Ultimo, New South Wales, Australia
- Pulmonary Diseases, UMCG, Groningen, The Netherlands
- GRAIC, University of Groningen, Groningen, The Netherlands
| | - Stelios Pavlidis
- Department of Computing and Data Science Institute, Imperial College London, London, UK
| | - Chih-Hsi Kuo
- Department of Computing and Data Science Institute, Imperial College London, London, UK
- Airways Disease, Respiratory Cell & Molecular Biology, Airways Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Anthony Rowe
- Discovery IT, Janssen Research and Development LLC, High Wycombe, UK
| | - Pieter S Hiemstra
- Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wim Timens
- GRAIC, University of Groningen, Groningen, The Netherlands
- Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Marijn Berg
- GRAIC, University of Groningen, Groningen, The Netherlands
- Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Marissa Wisman
- GRAIC, University of Groningen, Groningen, The Netherlands
- Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Yi-Ke Guo
- Department of Computing and Data Science Institute, Imperial College London, London, UK
| | - Ratko Djukanović
- Academic Unit of Clinical and Experimental Sciences, Southampton University Faculty of Medicine, Southampton, UK
| | - Peter Sterk
- Respiratory Medicine, Amsterdam UMC-Locatie AMC, Amsterdam, The Netherlands
| | - Kerstin B Meyer
- Gene expression genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Martijn C Nawijn
- GRAIC, University of Groningen, Groningen, The Netherlands
- Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Ian Adcock
- Department of Computing and Data Science Institute, Imperial College London, London, UK
- Airways Disease, Respiratory Cell & Molecular Biology, Airways Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Kian Fan Chung
- Department of Computing and Data Science Institute, Imperial College London, London, UK
- Airways Disease, Respiratory Cell & Molecular Biology, Airways Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Maarten van den Berge
- Pulmonary Diseases, UMCG, Groningen, The Netherlands
- GRAIC, University of Groningen, Groningen, The Netherlands
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20
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Kole TM, Pouwels SD, Bults R, Ketelaar ME, Guryev V, Koll L, Kerstjens HA, Nawijn MC, Faiz A, van den Berge M. Airway wall splice-QTL analysis reveals novel downstream mechanisms for known asthma-SNPs. ERJ Open Res 2023; 9:00413-2022. [PMID: 37020836 PMCID: PMC10068516 DOI: 10.1183/23120541.00413-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023] Open
Abstract
Studying the effects of asthma SNPs on alternative splicing can lead to new insights into asthma pathophysiology. More specifically, a 17q12 SNP is associated to alternative splicing of GSDMB. https://bit.ly/3W49oTs.
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21
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Kole TM, Vanden Berghe E, Kraft M, Vonk JM, Nawijn MC, Siddiqui S, Sun K, Fabbri LM, Rabe KF, Chung KF, Nicolini G, Papi A, Brightling C, Singh D, van der Molen T, Dahlén SE, Agusti A, Faner R, Wedzicha JA, Donaldson GC, Adcock IM, Lahousse L, Kerstjens HAM, van den Berge M. Predictors and associations of the persistent airflow limitation phenotype in asthma: a post-hoc analysis of the ATLANTIS study. Lancet Respir Med 2023; 11:55-64. [PMID: 35907424 DOI: 10.1016/s2213-2600(22)00185-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Persistent airflow limitation (PAL) occurs in a subset of patients with asthma. Previous studies on PAL in asthma have included relatively small populations, mostly restricted to severe asthma, or have no included longitudinal data. The aim of this post-hoc analysis was to investigate the determinants, clinical implications, and outcome of PAL in patients with asthma who were included in the ATLANTIS study. METHODS In this post-hoc analysis of the ATLANTIS study, we assessed the prevalence, clinical characteristics, and implications of PAL across the full range of asthma severity. The study population included patients aged 18-65 years who had been diagnosed with asthma at least 6 months before inclusion. We defined PAL as a post-bronchodilator FEV1/forced vital capacity (FVC) of less than the lower limit of normal at recruitment. Asthma severity was defined according to the Global Initiative for Asthma. We used Mann-Whitney U test, t test, or χ2 test to analyse differences in baseline characteristics between patients with and without PAL. Logistic regression was used for multivariable analysis of the associations between PAL and baseline data. Cox regression was used to analyse risk of exacerbation in relation to PAL, and a linear mixed-effects model was used to analyse change in FEV1 over time in patients with versus patients without PAL. Results were validated in the U-BIOPRED cohort. FINDINGS Between June 30, 2014 and March 3, 2017, 773 patients were enrolled in the ATLANTIS study of whom 760 (98%) had post-bronchodilator FEV1/FVC data available. Of the included patients with available data, mean age was 44 years (SD 13), 441 (58%) of 760 were women, 578 (76%) were never-smokers, and 248 (33%) had PAL. PAL was not only present in patients with severe asthma, but also in 21 (16%) of 133 patients with GINA step 1 and 24 (29%) of 83 patients with GINA step 2. PAL was independently associated with older age at baseline (46 years in PAL group vs 43 years in non-PAL group), longer duration of asthma (24 years vs 12 years), male sex (51% vs 38%), higher blood eosinophil counts (median 0·27 × 109 cells per L vs 0·20 × 109 cells per L), more small airway dysfunction, and more exacerbations during 1 year of follow-up. Associations between PAL, age, and eosinophilic inflammation were validated in the U-BIOPRED cohort, whereas associations with sex, duration of asthma, and risk of exacerbations were not validated. INTERPRETATION PAL is not only present in severe disease, but also in a considerable proportion of patients with milder disease. In patients with mild asthma, PAL is associated with eosinophilic inflammation and a higher risk of exacerbations. Our findings are important because they suggest that increasing treatment intensity should be considered in patients with milder asthma and PAL. FUNDING Chiesi Farmaceutici and Dutch Ministry of Economic Affairs and Climate Policy (by means of the public-private partnership programme).
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Affiliation(s)
- Tessa M Kole
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands; Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
| | - Elise Vanden Berghe
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands; Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands; Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Monica Kraft
- Department of Medicine and the Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Judith M Vonk
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands; Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands; Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Salman Siddiqui
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kai Sun
- Data Science Institute, Imperial College, London, UK
| | - Leonardo M Fabbri
- Department of Respiratory Medicine and Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Klaus F Rabe
- Department of Medicine, Christian Albrechts University of Kiel, Kiel, Germany; LungenClinic Grosshansdorf, Airway Research Center North in the German Center for Lung Research, Grosshansdorf, Germany
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Gabriele Nicolini
- Department of Global Clinical Development, Chiesi Farmaceutici, Parma, Italy
| | - Alberto Papi
- Department of Respiratory Medicine and Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Chris Brightling
- Institute for Lung Health, National Institute for Health Research Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Dave Singh
- Centre for Respiratory Medicine and Allergy, University of Manchester, Manchester University NHS Foundation Trust, Manchester, UK
| | - Thys van der Molen
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands; Department of General Practice and Elderly Care Medicine, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Sven-Erik Dahlén
- Institute of Environmental Medicine and Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Alvar Agusti
- Instituto de Investigaciones Biomédicas August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain; Respiratory Institute, Universitat de Barcelona, Barcelona, Spain
| | - Rosa Faner
- Instituto de Investigaciones Biomédicas August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | | | - Gavin C Donaldson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Huib A M Kerstjens
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands; Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands; Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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22
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Qi C, Berg M, Chu X, Timens W, Kole T, van den Berge M, Xu CJ, Koppelman GH, Nawijn MC, Li Y. Cell-type eQTL deconvolution of bronchial epithelium through integration of single-cell and bulk RNA-seq. Allergy 2022; 77:3663-3666. [PMID: 35708915 DOI: 10.1111/all.15410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 01/28/2023]
Affiliation(s)
- Cancan Qi
- Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Centre for Individualized Infection Medicine (CiiM), a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany
| | - Marijn Berg
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Xiaojing Chu
- Centre for Individualized Infection Medicine (CiiM), a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tessa Kole
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cheng-Jian Xu
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Centre for Individualized Infection Medicine (CiiM), a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany.,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands
| | - Martijn C Nawijn
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.,Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yang Li
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Centre for Individualized Infection Medicine (CiiM), a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany
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23
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Onnes MC, Alheraky A, Nawijn MC, Sluijter TE, Mulder AB, Arends S, Oude Elberink HNG. Detection of clonal mast cell disease in wasp venom allergic patients with normal tryptase. Clin Transl Allergy 2022; 12:e12174. [PMID: 36090584 PMCID: PMC9449818 DOI: 10.1002/clt2.12174] [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: 04/20/2022] [Revised: 05/19/2022] [Accepted: 06/19/2022] [Indexed: 11/06/2022] Open
Abstract
Background Clonal mast cell disease (CMD) is an underlying aggravating condition in wasp venom allergy (WVA) which requires a different treatment strategy. CMD is increasingly recognized in patients with normal basal serum tryptase (bsT). However, methods to identify at risk patients have not yet been assessed in large cohorts of WVA patients with normal bsT. Methods This retrospective study evaluated the reliability of the REMA score in detecting CMD in a cohort of grade IV WVA patients with normal bsT and assessed the added value of other clinical parameters, KIT D816V mutation analysis in peripheral blood (PB) and the diagnosis of hereditary alpha tryptasemia (HAT). All patients had a conclusive bone marrow evaluation that demonstrated or excluded underlying CMD. Results In total 35 CMD and 96 non‐CMD patients were included. REMA score had a sensitivity of 72% (95% CI 56%–88%) and specificity of 79% (95% CI 70%–87%) in this cohort. Loss of consciousness during systemic reaction and bsT between 6.3 and 11.4 ng/ml were additional parameters independently associated with CMD. Sensitivity of KIT in PB was relatively low, 56% (95% CI 36%–75%), but had added value as screening method in patients with a low REMA score due to 100% specificity. Conclusion The REMA score is a relatively reliable method to detect patients at risk of CMD among WVA patients with normal bsT. KIT mutation analysis in PB could serve as additional screening method in patients with low REMA scores.
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Affiliation(s)
- Merel C Onnes
- Department of Internal Medicine Division of Allergology University Medical Center Groningen University of Groningen Groningen The Netherlands.,Department of Pathology and Medical Biology University Medical Center Groningen University of Groningen Groningen The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC) Research Institute University Medical Center Groningen Groningen The Netherlands
| | - Abdulrazzaq Alheraky
- Department of Laboratory Medicine University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology University Medical Center Groningen University of Groningen Groningen The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC) Research Institute University Medical Center Groningen Groningen The Netherlands
| | - Tim E Sluijter
- Department of Internal Medicine Division of Allergology University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - André B Mulder
- Department of Laboratory Medicine University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Suzanne Arends
- Department of Rheumatology and Clinical Immunology University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Hanneke N G Oude Elberink
- Department of Internal Medicine Division of Allergology University Medical Center Groningen University of Groningen Groningen The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC) Research Institute University Medical Center Groningen Groningen The Netherlands
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24
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Hesse L, Oude Elberink J, van Oosterhout AJ, Nawijn MC. Allergen immunotherapy for allergic airway diseases: Use lessons from the past to design a brighter future. Pharmacol Ther 2022; 237:108115. [DOI: 10.1016/j.pharmthera.2022.108115] [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] [Received: 02/25/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 10/19/2022]
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25
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Luecken MD, Zaragozi LE, Madissoon E, Sikkema L, Firsova AB, De Domenico E, Kümmerle L, Saglam A, Berg M, Gay ACA, Schniering J, Mayr CH, Abalo XM, Larsson L, Sountoulidis A, Teichmann S, van Eunen K, Koppelman GH, Saeb-Parsy K, Leroy S, Powell P, Sarkans U, Timens W, Lundeberg J, van den Berge M, Nilsson M, Horváth P, Denning J, Papatheodorou I, Schultze J, Schiller HB, Barbry P, Petoukhov I, Misharin AV, Adcock I, von Papen M, Theis FJ, Samakovlis C, Meyer KB, Nawijn MC. The discovAIR project: a roadmap towards the Human Lung Cell Atlas. Eur Respir J 2022; 60:13993003.02057-2021. [PMID: 35086829 PMCID: PMC9386332 DOI: 10.1183/13993003.02057-2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/23/2021] [Indexed: 12/01/2022]
Abstract
The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell–cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions. The discovAIR project contributes to the Human Cell Atlas Lung Biological Network by establishing a first draft of the Human Lung Cell Atlas, advancing our insight into the cellular complexity and spatial organisation of the lung in health and diseasehttps://bit.ly/3zX4cad
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Affiliation(s)
- Malte D Luecken
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Laure-Emmanuelle Zaragozi
- Université Côte d'Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France.,These authors made an equal contribution to this manuscript
| | - Elo Madissoon
- Wellcome Sanger Institute, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.,These authors made an equal contribution to this manuscript
| | - Lisa Sikkema
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Alexandra B Firsova
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,These authors made an equal contribution to this manuscript
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,These authors made an equal contribution to this manuscript
| | - Louis Kümmerle
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,These authors made an equal contribution to this manuscript
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,These authors made an equal contribution to this manuscript
| | - Marijn Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,These authors made an equal contribution to this manuscript
| | - Aurore C A Gay
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,These authors made an equal contribution to this manuscript
| | - Janine Schniering
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.,These authors made an equal contribution to this manuscript
| | - Christoph H Mayr
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany.,These authors made an equal contribution to this manuscript
| | - Xesús M Abalo
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,These authors made an equal contribution to this manuscript
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,These authors made an equal contribution to this manuscript
| | - Alexandros Sountoulidis
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,These authors made an equal contribution to this manuscript
| | - Sarah Teichmann
- Wellcome Sanger Institute, Cambridge, UK.,Theory of Condensed Matter, Cavendish Laboratory, Cambridge, UK
| | - Karen van Eunen
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,UMCG Research BV, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard H Koppelman
- GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Sylvie Leroy
- Département de Pneumologie, Université Côte d'Azur and CHU Nice, FHU-OncoAge, Nice, France
| | | | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Maarten van den Berge
- GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands.,Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Peter Horváth
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, Hungary
| | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Joachim Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Herbert B Schiller
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Pascal Barbry
- Université Côte d'Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France
| | - Ilya Petoukhov
- A Beta World (former Principal at MIcompany), Amsterdam, the Netherlands
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Ian Adcock
- Airway Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | | | - Fabian J Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Institute of Computational Biology, Helmholtz Center Munich (HMGU), Neuherberg, Germany
| | - Christos Samakovlis
- Science for Life Laboratory, Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands .,GRIAC research institute at the University Medical Center Groningen, Groningen, the Netherlands
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26
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Dinesh Kumar N, ter Ellen BM, Bouma EM, Troost B, van de Pol DPI, van der Ende-Metselaar HH, van Gosliga D, Apperloo L, Carpaij OA, van den Berge M, Nawijn MC, Stienstra Y, Rodenhuis-Zybert IA, Smit JM. Moxidectin and Ivermectin Inhibit SARS-CoV-2 Replication in Vero E6 Cells but Not in Human Primary Bronchial Epithelial Cells. Antimicrob Agents Chemother 2022; 66:e0154321. [PMID: 34633839 PMCID: PMC8765325 DOI: 10.1128/aac.01543-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 08/04/2021] [Accepted: 10/08/2021] [Indexed: 11/20/2022] Open
Abstract
Antiviral therapies are urgently needed to treat and limit the development of severe COVID-19 disease. Ivermectin, a broad-spectrum anti-parasitic agent, has been shown to have anti-SARS-CoV-2 activity in Vero cells at a concentration of 5 μM. These limited in vitro results triggered the investigation of ivermectin as a treatment option to alleviate COVID-19 disease. However, in April 2021, the World Health Organization stated the following: "The current evidence on the use of ivermectin to treat COVID-19 patients is inconclusive." It is speculated that the in vivo concentration of ivermectin is too low to exert a strong antiviral effect. Here, we performed a head-to-head comparison of the antiviral activity of ivermectin and the structurally related, but metabolically more stable moxidectin in multiple in vitro models of SARS-CoV-2 infection, including physiologically relevant human respiratory epithelial cells. Both moxidectin and ivermectin exhibited antiviral activity in Vero E6 cells. Subsequent experiments revealed that these compounds predominantly act on the steps following virus cell entry. Surprisingly, however, in human-airway-derived cell models, both moxidectin and ivermectin failed to inhibit SARS-CoV-2 infection, even at concentrations of 10 μM. These disappointing results call for a word of caution in the interpretation of anti-SARS-CoV-2 activity of drugs solely based on their activity in Vero cells. Altogether, these findings suggest that even using a high-dose regimen of ivermectin, or switching to another drug in the same class, is unlikely to be useful for treatment of SARS-CoV-2 in humans.
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Affiliation(s)
- Nilima Dinesh Kumar
- Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bram M. ter Ellen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ellen M. Bouma
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Berit Troost
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Denise P. I. van de Pol
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Heidi H. van der Ende-Metselaar
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Djoke van Gosliga
- Department of Pediatrics, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, GRIAC Research Institute, Groningen, The Netherlands
| | - Leonie Apperloo
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, GRIAC Research Institute, Groningen, The Netherlands
| | - Orestes A. Carpaij
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, GRIAC Research Institute, Groningen, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, GRIAC Research Institute, Groningen, The Netherlands
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, GRIAC Research Institute, Groningen, The Netherlands
| | - Ymkje Stienstra
- Department of Internal Medicine/Infectious Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Izabela A. Rodenhuis-Zybert
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jolanda M. Smit
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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27
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Moreno P, Fexova S, George N, Manning JR, Miao Z, Mohammed S, Muñoz-Pomer A, Fullgrabe A, Bi Y, Bush N, Iqbal H, Kumbham U, Solovyev A, Zhao L, Prakash A, García-Seisdedos D, Kundu DJ, Wang S, Walzer M, Clarke L, Osumi-Sutherland D, Tello-Ruiz MK, Kumari S, Ware D, Eliasova J, Arends MJ, Nawijn MC, Meyer K, Burdett T, Marioni J, Teichmann S, Vizcaíno JA, Brazma A, Papatheodorou I. Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Res 2022; 50:D129-D140. [PMID: 34850121 PMCID: PMC8728300 DOI: 10.1093/nar/gkab1030] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/11/2021] [Accepted: 11/19/2021] [Indexed: 01/21/2023] Open
Abstract
The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or protein of interest is expressed. Expression Atlas brings together data from >4500 expression studies from >65 different species, across different conditions and tissues. It makes these data freely available in an easy to visualise form, after expert curation to accurately represent the intended experimental design, re-analysed via standardised pipelines that rely on open-source community developed tools. Each study's metadata are annotated using ontologies. The data are re-analyzed with the aim of reproducing the original conclusions of the underlying experiments. Expression Atlas is currently divided into Bulk Expression Atlas and Single Cell Expression Atlas. Expression Atlas contains data from differential studies (microarray and bulk RNA-Seq) and baseline studies (bulk RNA-Seq and proteomics), whereas Single Cell Expression Atlas is currently dedicated to Single Cell RNA-Sequencing (scRNA-Seq) studies. The resource has been in continuous development since 2009 and it is available at https://www.ebi.ac.uk/gxa.
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Affiliation(s)
- Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Silvie Fexova
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Jonathan R Manning
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Zhichiao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Suhaib Mohammed
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Alfonso Muñoz-Pomer
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Anja Fullgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Yalan Bi
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Natassja Bush
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Haider Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Upendra Kumbham
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Andrey Solovyev
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Lingyun Zhao
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Ananth Prakash
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - David García-Seisdedos
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Deepti J Kundu
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Shengbo Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Mathias Walzer
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - David Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | | | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- USDA ARS NEA, Plant Soil & Nutrition Laboratory Research Unit, Ithaca, NY 14853, USA
| | - Jana Eliasova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Mark J Arends
- Edinburgh Pathology, University of Edinburgh, Institute of Genetics & Cancer, Edinburgh, UK
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, GRIAC research institute, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Kerstin Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - John Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Sarah Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
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Kuchibhotla VNS, Starkey MR, Reid AT, Heijink IH, Nawijn MC, Hansbro PM, Knight DA. Inhibition of β-Catenin/CREB Binding Protein Signaling Attenuates House Dust Mite-Induced Goblet Cell Metaplasia in Mice. Front Physiol 2021; 12:690531. [PMID: 34385933 PMCID: PMC8353457 DOI: 10.3389/fphys.2021.690531] [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] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/05/2021] [Indexed: 11/26/2022] Open
Abstract
Excessive mucus production is a major feature of allergic asthma. Disruption of epithelial junctions by allergens such as house dust mite (HDM) results in the activation of β-catenin signaling, which has been reported to stimulate goblet cell differentiation. β-catenin interacts with various co-activators including CREB binding protein (CBP) and p300, thereby regulating the expression of genes involved in cell proliferation and differentiation, respectively. We specifically investigated the role of the β-catenin/CBP signaling pathway in goblet cell metaplasia in a HDM-induced allergic airway disease model in mice using ICG-001, a small molecule inhibitor that blocks the binding of CBP to β-catenin. Female 6- 8-week-old BALB/c mice were sensitized to HDM/saline on days 0, 1, and 2, followed by intranasal challenge with HDM/saline with or without subcutaneous ICG-001/vehicle treatment from days 14 to 17, and samples harvested 24 h after the last challenge/treatment. Differential inflammatory cells in bronchoalveolar lavage (BAL) fluid were enumerated. Alcian blue (AB)/Periodic acid–Schiff (PAS) staining was used to identify goblet cells/mucus production, and airway hyperresponsiveness (AHR) was assessed using invasive plethysmography. Exposure to HDM induced airway inflammation, goblet cell metaplasia and increased AHR, with increased airway resistance in response to the non-specific spasmogen methacholine. Inhibition of the β-catenin/CBP pathway using treatment with ICG-001 significantly attenuated the HDM-induced goblet cell metaplasia and infiltration of macrophages, but had no effect on eosinophils, neutrophils, lymphocytes or AHR. Increased β-catenin/CBP signaling may promote HDM-induced goblet cell metaplasia in mice.
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Affiliation(s)
- Virinchi N S Kuchibhotla
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.,School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,GRIAC Research Institute, University Medical Center Groningen, Groningen, Netherlands.,Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research, University of Groningen, Groningen, Netherlands
| | - Malcolm R Starkey
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Priority Research Centre GrowUpWell and Hunter Medical Research Institute, Faculty of Health and Medicine, The University of Newcastle, Newcastle, NSW, Australia.,Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Andrew T Reid
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.,School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | - Irene H Heijink
- GRIAC Research Institute, University Medical Center Groningen, Groningen, Netherlands.,Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research, University of Groningen, Groningen, Netherlands.,Department of Pulmonology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Martijn C Nawijn
- GRIAC Research Institute, University Medical Center Groningen, Groningen, Netherlands.,Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research, University of Groningen, Groningen, Netherlands
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.,School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Darryl A Knight
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.,School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Providence Health Care Research Institute, Vancouver, BC, Canada.,Department of Anesthesiology, Pharmacology and Therapeutics, The University of British Columbia, Vancouver, BC, Canada
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29
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Schupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe’er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung. Circulation 2021; 144:286-302. [PMID: 34030460 PMCID: PMC8300155 DOI: 10.1161/circulationaha.120.052318] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/21/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cellular diversity of the lung endothelium has not been systematically characterized in humans. We provide a reference atlas of human lung endothelial cells (ECs) to facilitate a better understanding of the phenotypic diversity and composition of cells comprising the lung endothelium. METHODS We reprocessed human control single-cell RNA sequencing (scRNAseq) data from 6 datasets. EC populations were characterized through iterative clustering with subsequent differential expression analysis. Marker genes were validated by fluorescent microscopy and in situ hybridization. scRNAseq of primary lung ECs cultured in vitro was performed. The signaling network between different lung cell types was studied. For cross-species analysis or disease relevance, we applied the same methods to scRNAseq data obtained from mouse lungs or from human lungs with pulmonary hypertension. RESULTS Six lung scRNAseq datasets were reanalyzed and annotated to identify >15 000 vascular EC cells from 73 individuals. Differential expression analysis of EC revealed signatures corresponding to endothelial lineage, including panendothelial, panvascular, and subpopulation-specific marker gene sets. Beyond the broad cellular categories of lymphatic, capillary, arterial, and venous ECs, we found previously indistinguishable subpopulations; among venous EC, we identified 2 previously indistinguishable populations: pulmonary-venous ECs (COL15A1neg) localized to the lung parenchyma and systemic-venous ECs (COL15A1pos) localized to the airways and the visceral pleura; among capillary ECs, we confirmed their subclassification into recently discovered aerocytes characterized by EDNRB, SOSTDC1, and TBX2 and general capillary EC. We confirmed that all 6 endothelial cell types, including the systemic-venous ECs and aerocytes, are present in mice and identified endothelial marker genes conserved in humans and mice. Ligand-receptor connectome analysis revealed important homeostatic crosstalk of EC with other lung resident cell types. scRNAseq of commercially available primary lung ECs demonstrated a loss of their native lung phenotype in culture. scRNAseq revealed that endothelial diversity is maintained in pulmonary hypertension. Our article is accompanied by an online data mining tool (www.LungEndothelialCellAtlas.com). CONCLUSIONS Our integrated analysis provides a comprehensive and well-crafted reference atlas of ECs in the normal lung and confirms and describes in detail previously unrecognized endothelial populations across a large number of humans and mice.
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Affiliation(s)
- Jonas C. Schupp
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Taylor S. Adams
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Carlos Cosme
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering (M.S.B.R., L.E.N.), Yale University, New Haven, CT
- Vascular Biology and Therapeutics (M.S.B.R., Y.Y., L.E.N.), Yale University, New Haven, CT
| | - Yifan Yuan
- Vascular Biology and Therapeutics (M.S.B.R., Y.Y., L.E.N.), Yale University, New Haven, CT
- Department of Anesthesiology (Y.Y., L.E.N.), Yale University, New Haven, CT
| | - Norihito Omote
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Sergio Poli
- Department of Medicine, Baylor College of Medicine, Houston, TX (S.P., I.O.R.)
- Division of Internal Medicine, Mount Sinai Medical Center, Miami Beach, FL (S.P.)
| | - Maurizio Chioccioli
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Kadi-Ann Rose
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Edward P. Manning
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
- VA Connecticut Healthcare System (E.P.M.), West Haven
| | - Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Giuseppe DeIuliis
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Farida Ahangari
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Nir Neumark
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Arun C. Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (A.C.H., J.A.K.)
| | - Austin J. Gutierrez
- Translational Genomics Research Institute, Phoenix, AZ (A.J.G., L.T.B., N.E.B.)
| | - Linh T. Bui
- Translational Genomics Research Institute, Phoenix, AZ (A.J.G., L.T.B., N.E.B.)
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, PA (R.L.)
| | - Richard W. Pierce
- Department of Pediatrics (R.W.P.), Yale University School of Medicine, New Haven, CT
| | - Kerstin B. Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (K.B.M., S.A.T.)
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology (M.C.N.), University Medical Center Groningen, University of Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (M.C.N.), University Medical Center Groningen, University of Groningen, The Netherlands
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (K.B.M., S.A.T.)
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, UK (S.A.T.)
| | | | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (A.C.H., J.A.K.)
- Department of Veterans Affairs Medical Center, Nashville, TN (J.A.K.)
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN (J.A.K.)
| | - Laura E. Niklason
- Department of Biomedical Engineering (M.S.B.R., L.E.N.), Yale University, New Haven, CT
- Vascular Biology and Therapeutics (M.S.B.R., Y.Y., L.E.N.), Yale University, New Haven, CT
- Department of Anesthesiology (Y.Y., L.E.N.), Yale University, New Haven, CT
| | - Dana Pe’er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (D.P.)
| | - Xiting Yan
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
| | - Robert J. Homer
- Department of Pathology (R.J.H.), Yale University School of Medicine, New Haven, CT
- Pathology and Laboratory Medicine Service (R.J.H.), West Haven
| | - Ivan O. Rosas
- Department of Medicine, Baylor College of Medicine, Houston, TX (S.P., I.O.R.)
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine (J.C.S., T.S.A., C.C., N.O., M.C., K.-A.R., E.P.M., M.S., G.D., F.A., N.N., X.Y., N.K.), Yale University School of Medicine, New Haven, CT
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30
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ter Ellen BM, Dinesh Kumar N, Bouma EM, Troost B, van de Pol DP, van der Ende-Metselaar HH, Apperloo L, van Gosliga D, van den Berge M, Nawijn MC, van der Voort PH, Moser J, Rodenhuis-Zybert IA, Smit JM. Resveratrol and Pterostilbene Inhibit SARS-CoV-2 Replication in Air-Liquid Interface Cultured Human Primary Bronchial Epithelial Cells. Viruses 2021; 13:v13071335. [PMID: 34372541 PMCID: PMC8309965 DOI: 10.3390/v13071335] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
The current COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has an enormous impact on human health and economy. In search for therapeutic options, researchers have proposed resveratrol, a food supplement with known antiviral, anti-inflammatory, and antioxidant properties as an advantageous antiviral therapy for SARS-CoV-2 infection. Here, we provide evidence that both resveratrol and its metabolically more stable structural analog, pterostilbene, exhibit potent antiviral properties against SARS-CoV-2 in vitro. First, we show that resveratrol and pterostilbene antiviral activity in African green monkey kidney cells. Both compounds actively inhibit virus replication within infected cells as reduced virus progeny production was observed when the compound was added at post-inoculation conditions. Without replenishment of the compound, antiviral activity was observed up to roughly five rounds of replication, demonstrating the long-lasting effect of these compounds. Second, as the upper respiratory tract represents the initial site of SARS-CoV-2 replication, we also assessed antiviral activity in air-liquid interface (ALI) cultured human primary bronchial epithelial cells, isolated from healthy volunteers. Resveratrol and pterostilbene showed a strong antiviral effect in these cells up to 48 h post-infection. Collectively, our data indicate that resveratrol and pterostilbene are promising antiviral compounds to inhibit SARS-CoV-2 infection. Because these results represent laboratory findings in cells, we advocate evaluation of these compounds in clinical trials before statements are made whether these drugs are advantageous for COVID-19 treatment.
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Affiliation(s)
- Bram M. ter Ellen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (B.M.t.E.); (N.D.K.); (E.M.B.); (B.T.); (D.P.I.v.d.P.); (H.H.v.d.E.-M.); (I.A.R.-Z.)
| | - Nilima Dinesh Kumar
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (B.M.t.E.); (N.D.K.); (E.M.B.); (B.T.); (D.P.I.v.d.P.); (H.H.v.d.E.-M.); (I.A.R.-Z.)
- Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Ellen M. Bouma
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (B.M.t.E.); (N.D.K.); (E.M.B.); (B.T.); (D.P.I.v.d.P.); (H.H.v.d.E.-M.); (I.A.R.-Z.)
| | - Berit Troost
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (B.M.t.E.); (N.D.K.); (E.M.B.); (B.T.); (D.P.I.v.d.P.); (H.H.v.d.E.-M.); (I.A.R.-Z.)
| | - Denise P.I. van de Pol
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (B.M.t.E.); (N.D.K.); (E.M.B.); (B.T.); (D.P.I.v.d.P.); (H.H.v.d.E.-M.); (I.A.R.-Z.)
| | - Heidi H. van der Ende-Metselaar
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (B.M.t.E.); (N.D.K.); (E.M.B.); (B.T.); (D.P.I.v.d.P.); (H.H.v.d.E.-M.); (I.A.R.-Z.)
| | - Leonie Apperloo
- Department of Pathology and Medical Biology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.A.); (M.C.N.)
| | - Djoke van Gosliga
- Department of Pediatrics, Beatrix Children’s Hospital, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands;
| | - Maarten van den Berge
- Department of Pulmonary Diseases, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands;
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.A.); (M.C.N.)
| | - Peter H.J. van der Voort
- Department of Critical Care, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.H.J.v.d.V.); (J.M.)
| | - Jill Moser
- Department of Critical Care, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.H.J.v.d.V.); (J.M.)
| | - Izabela A. Rodenhuis-Zybert
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (B.M.t.E.); (N.D.K.); (E.M.B.); (B.T.); (D.P.I.v.d.P.); (H.H.v.d.E.-M.); (I.A.R.-Z.)
| | - Jolanda M. Smit
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (B.M.t.E.); (N.D.K.); (E.M.B.); (B.T.); (D.P.I.v.d.P.); (H.H.v.d.E.-M.); (I.A.R.-Z.)
- Correspondence:
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31
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van de Wetering C, Elko E, Berg M, Schiffers CHJ, Stylianidis V, van den Berge M, Nawijn MC, Wouters EFM, Janssen-Heininger YMW, Reynaert NL. Glutathione S-transferases and their implications in the lung diseases asthma and chronic obstructive pulmonary disease: Early life susceptibility? Redox Biol 2021; 43:101995. [PMID: 33979767 PMCID: PMC8131726 DOI: 10.1016/j.redox.2021.101995] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 01/01/2023] Open
Abstract
Our lungs are exposed daily to airborne pollutants, particulate matter, pathogens as well as lung allergens and irritants. Exposure to these substances can lead to inflammatory responses and may induce endogenous oxidant production, which can cause chronic inflammation, tissue damage and remodeling. Notably, the development of asthma and Chronic Obstructive Pulmonary Disease (COPD) is linked to the aforementioned irritants. Some inhaled foreign chemical compounds are rapidly absorbed and processed by phase I and II enzyme systems critical in the detoxification of xenobiotics including the glutathione-conjugating enzymes Glutathione S-transferases (GSTs). GSTs, and in particular genetic variants of GSTs that alter their activities, have been found to be implicated in the susceptibility to and progression of these lung diseases. Beyond their roles in phase II metabolism, evidence suggests that GSTs are also important mediators of normal lung growth. Therefore, the contribution of GSTs to the development of lung diseases in adults may already start in utero, and continues through infancy, childhood, and adult life. GSTs are also known to scavenge oxidants and affect signaling pathways by protein-protein interaction. Moreover, GSTs regulate reversible oxidative post-translational modifications of proteins, known as protein S-glutathionylation. Therefore, GSTs display an array of functions that impact the pathogenesis of asthma and COPD. In this review we will provide an overview of the specific functions of each class of mammalian cytosolic GSTs. This is followed by a comprehensive analysis of their expression profiles in the lung in healthy subjects, as well as alterations that have been described in (epithelial cells of) asthmatics and COPD patients. Particular emphasis is placed on the emerging evidence of the regulatory properties of GSTs beyond detoxification and their contribution to (un)healthy lungs throughout life. By providing a more thorough understanding, tailored therapeutic strategies can be designed to affect specific functions of particular GSTs.
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Affiliation(s)
- Cheryl van de Wetering
- Department of Respiratory Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands; Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA
| | - Evan Elko
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA
| | - Marijn Berg
- Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Caspar H J Schiffers
- Department of Respiratory Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands; Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA
| | - Vasili Stylianidis
- Department of Respiratory Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Maarten van den Berge
- Pulmonology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Martijn C Nawijn
- Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Emiel F M Wouters
- Department of Respiratory Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands; Ludwig Boltzmann Institute for Lung Health, Vienna, Austria
| | - Yvonne M W Janssen-Heininger
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA.
| | - Niki L Reynaert
- Department of Respiratory Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands.
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32
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Saikumar Jayalatha AK, Hesse L, Ketelaar ME, Koppelman GH, Nawijn MC. The central role of IL-33/IL-1RL1 pathway in asthma: From pathogenesis to intervention. Pharmacol Ther 2021; 225:107847. [PMID: 33819560 DOI: 10.1016/j.pharmthera.2021.107847] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
Interleukin-33 (IL-33), a member of the IL-1 family, and its cognate receptor, Interleukin-1 receptor like-1 (IL-1RL1 or ST2), are susceptibility genes for childhood asthma. In response to cellular damage, IL-33 is released from barrier tissues as an 'alarmin' to activate the innate immune response. IL-33 drives type 2 responses by inducing signalling through its receptor IL-1RL1 in several immune and structural cells, thereby leading to type 2 cytokine and chemokine production. IL-1RL1 gene transcript encodes different isoforms generated through alternative splicing. Its soluble isoform, IL-1RL1-a or sST2, acts as a decoy receptor by sequestering IL-33, thereby inhibiting IL1RL1-b/IL-33 signalling. IL-33 and its receptor IL-1RL1 are therefore considered as putative biomarkers or targets for pharmacological intervention in asthma. This review will provide an overview of the genetics and biology of the IL-33/IL-1RL1 pathway in the context of asthma pathogenesis. It will discuss the potential and complexities of targeting the cytokine or its receptor, how genetics or biomarkers may inform precision medicine for asthma targeting this pathway, and the possible positioning of therapeutics targeting IL-33 or its receptor in the expanding landscape of novel biologicals applied in asthma management.
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Affiliation(s)
- A K Saikumar Jayalatha
- University of Groningen, University Medical Centre Groningen, Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - L Hesse
- University of Groningen, University Medical Centre Groningen, Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - M E Ketelaar
- University of Groningen, University Medical Centre Groningen, Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Beatrix Children's Hospital, Department of Paediatric Pulmonology and Paediatric Allergology, Groningen, the Netherlands
| | - G H Koppelman
- University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Beatrix Children's Hospital, Department of Paediatric Pulmonology and Paediatric Allergology, Groningen, the Netherlands
| | - M C Nawijn
- University of Groningen, University Medical Centre Groningen, Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands.
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Dwyer DF, Ordovas-Montanes J, Allon SJ, Buchheit KM, Vukovic M, Derakhshan T, Feng C, Lai J, Hughes TK, Nyquist SK, Giannetti MP, Berger B, Bhattacharyya N, Roditi RE, Katz HR, Nawijn MC, Berg M, van den Berge M, Laidlaw TM, Shalek AK, Barrett NA, Boyce JA. Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation. Sci Immunol 2021; 6:6/56/eabb7221. [PMID: 33637594 DOI: 10.1126/sciimmunol.abb7221] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 01/28/2021] [Indexed: 12/31/2022]
Abstract
Mast cells (MCs) play a pathobiologic role in type 2 (T2) allergic inflammatory diseases of the airway, including asthma and chronic rhinosinusitis with nasal polyposis (CRSwNP). Distinct MC subsets infiltrate the airway mucosa in T2 disease, including subepithelial MCs expressing the proteases tryptase and chymase (MCTC) and epithelial MCs expressing tryptase without chymase (MCT). However, mechanisms underlying MC expansion and the transcriptional programs underlying their heterogeneity are poorly understood. Here, we use flow cytometry and single-cell RNA-sequencing (scRNA-seq) to conduct a comprehensive analysis of human MC hyperplasia in CRSwNP, a T2 cytokine-mediated inflammatory disease. We link discrete cell surface phenotypes to the distinct transcriptomes of CRSwNP MCT and MCTC, which represent polarized ends of a transcriptional gradient of nasal polyp MCs. We find a subepithelial population of CD38highCD117high MCs that is markedly expanded during T2 inflammation. These CD38highCD117high MCs exhibit an intermediate phenotype relative to the expanded MCT and MCTC subsets. CD38highCD117high MCs are distinct from circulating MC progenitors and are enriched for proliferation, which is markedly increased in CRSwNP patients with aspirin-exacerbated respiratory disease, a severe disease subset characterized by increased MC burden and elevated MC activation. We observe that MCs expressing a polyp MCT-like effector program are also found within the lung during fibrotic diseases and asthma, and further identify marked differences between MCTC in nasal polyps and skin. These results indicate that MCs display distinct inflammation-associated effector programs and suggest that in situ MC proliferation is a major component of MC hyperplasia in human T2 inflammation.
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Affiliation(s)
- Daniel F Dwyer
- Jeff and Penny Vinik Immunology Center, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA.,Program in Immunology, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Samuel J Allon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Kathleen M Buchheit
- Jeff and Penny Vinik Immunology Center, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marko Vukovic
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Tahereh Derakhshan
- Jeff and Penny Vinik Immunology Center, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Chunli Feng
- Jeff and Penny Vinik Immunology Center, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Juying Lai
- Jeff and Penny Vinik Immunology Center, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Travis K Hughes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Sarah K Nyquist
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Program in Computational and Systems Biology, MIT, Cambridge, MA, USA
| | - Matthew P Giannetti
- Jeff and Penny Vinik Immunology Center, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Lab and Department of Mathematics, MIT, Cambridge, MA, USA
| | - Neil Bhattacharyya
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Rachel E Roditi
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Howard R Katz
- Jeff and Penny Vinik Immunology Center, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Pathology and Medical Biology, Laboratory of Experimental Immunology and Respiratory Research (EXPIRE), University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Marijn Berg
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Pathology and Medical Biology, Laboratory of Experimental Immunology and Respiratory Research (EXPIRE), University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Tanya M Laidlaw
- Jeff and Penny Vinik Immunology Center, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Nora A Barrett
- Jeff and Penny Vinik Immunology Center, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Program in Immunology, Harvard Medical School, Boston, MA, USA
| | - Joshua A Boyce
- Jeff and Penny Vinik Immunology Center, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Program in Immunology, Harvard Medical School, Boston, MA, USA
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Burgess JK, Jonker MR, Berg M, Ten Hacken NTH, Meyer KB, van den Berge M, Nawijn MC, Heijink IH. Periostin: contributor to abnormal airway epithelial function in asthma? Eur Respir J 2021; 57:13993003.01286-2020. [PMID: 32907887 DOI: 10.1183/13993003.01286-2020] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/17/2020] [Indexed: 11/05/2022]
Abstract
Periostin (POSTN) may serve as a biomarker for Type-2 mediated eosinophilic airway inflammation in asthma. We hypothesised that a Type-2 cytokine, interleukin (IL)-13, induces airway epithelial expression of POSTN, which in turn contributes to epithelial changes observed in asthma.We studied the effect of IL-13 on POSTN expression in BEAS-2B and air-liquid interface differentiated primary bronchial epithelial cells (PBECs). Additionally, the effects of recombinant human POSTN on epithelial-to-mesenchymal transition (EMT) markers and mucin genes were assessed. POSTN single cell gene expression and protein levels were analysed in bronchial biopsies and induced sputum from asthma patients and healthy controls.IL-13 increased POSTN expression in both cell types and this was accompanied by EMT-related features in BEAS-2B. In air-liquid interface differentiated PBECs, IL-13 increased POSTN basolateral and apical release. Apical administration of POSTN increased the expression of MMP-9, MUC5B and MUC5AC In bronchial biopsies, POSTN expression was mainly confined to basal epithelial cells, ionocytes, endothelial cells and fibroblasts, showing higher expression in basal epithelial cells from asthma patients versus those from controls. A higher level of POSTN protein expression in epithelial and subepithelial layers was confirmed in bronchial biopsies from asthma patients when compared to healthy controls. Although sputum POSTN levels were not higher in asthma, levels correlated with eosinophil numbers and with the coughing-up of mucus.POSTN expression is increased by IL-13 in bronchial epithelial cells and is higher in bronchial biopsies from asthma patients. This may have important consequences, as administration of POSTN increases epithelial expression of mucin genes, supporting the relationship of POSTN with Type-2 mediated asthma and mucus secretion.
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Affiliation(s)
- Janette K Burgess
- Dept of Pathology and Medical Biology, Experimental Pulmonology and Inflammation Research, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Marnix R Jonker
- Dept of Pathology and Medical Biology, Experimental Pulmonology and Inflammation Research, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Marijn Berg
- Dept of Pathology and Medical Biology, Experimental Pulmonology and Inflammation Research, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Nick T H Ten Hacken
- Dept of Pulmonology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Maarten van den Berge
- GRIAC Research Institute, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Dept of Pulmonology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- Dept of Pathology and Medical Biology, Experimental Pulmonology and Inflammation Research, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Irene H Heijink
- Dept of Pathology and Medical Biology, Experimental Pulmonology and Inflammation Research, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Dept of Pulmonology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
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35
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Ketelaar ME, Westerlaken-van Ginkel CD, Nawijn MC, Ej Dubois A, Koppelman GH. IL-1RL1a serum levels and IL1RL1 SNPs in the prediction of food allergy. Clin Exp Allergy 2021; 51:614-619. [PMID: 33278838 PMCID: PMC8048844 DOI: 10.1111/cea.13802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/09/2020] [Accepted: 11/28/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Maria E Ketelaar
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Centre Groningen, Groningen, The Netherlands.,Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), GRIAC, University Medical Centre Groningen, Groningen, The Netherlands
| | - C Doriene Westerlaken-van Ginkel
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Centre Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), GRIAC, University Medical Centre Groningen, Groningen, The Netherlands
| | - Antony Ej Dubois
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Centre Groningen, Groningen, The Netherlands
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Centre Groningen, Groningen, The Netherlands
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36
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Xu CJ, Gruzieva O, Qi C, Esplugues A, Gehring U, Bergström A, Mason D, Chatzi L, Porta D, Lodrup Carlsen KC, Baïz N, Madore AM, Alenius H, van Rijkom B, Jankipersadsing SA, van der Vlies P, Kull I, van Hage M, Bustamante M, Lertxundi A, Torrent M, Santorelli G, Fantini MP, Hovland V, Pesce G, Fyhrquist N, Laatikainen T, Nawijn MC, Li Y, Wijmenga C, Netea MG, Bousquet J, Anto JM, Laprise C, Haahtela T, Annesi-Maesano I, Carlsen KH, Gori D, Kogevinas M, Wright J, Söderhäll C, Vonk JM, Sunyer J, Melén E, Koppelman GH. Shared DNA methylation signatures in childhood allergy: The MeDALL study. J Allergy Clin Immunol 2020; 147:1031-1040. [PMID: 33338541 DOI: 10.1016/j.jaci.2020.11.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/14/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Differential DNA methylation associated with allergy might provide novel insights into the shared or unique etiology of asthma, rhinitis, and eczema. OBJECTIVE We sought to identify DNA methylation profiles associated with childhood allergy. METHODS Within the European Mechanisms of the Development of Allergy (MeDALL) consortium, we performed an epigenome-wide association study of whole blood DNA methylation by using a cross-sectional design. Allergy was defined as having symptoms from at least 1 allergic disease (asthma, rhinitis, or eczema) and positive serum-specific IgE to common aeroallergens. The discovery study included 219 case patients and 417 controls at age 4 years and 228 case patients and 593 controls at age 8 years from 3 birth cohorts, with replication analyses in 325 case patients and 1111 controls. We performed additional analyses on 21 replicated sites in 785 case patients and 2124 controls by allergic symptoms only from 8 cohorts, 3 of which were not previously included in analyses. RESULTS We identified 80 differentially methylated CpG sites that showed a 1% to 3% methylation difference in the discovery phase, of which 21 (including 5 novel CpG sites) passed genome-wide significance after meta-analysis. All 21 CpG sites were also significantly differentially methylated with allergic symptoms and shared between asthma, rhinitis, and eczema. The 21 CpG sites mapped to relevant genes, including ACOT7, LMAN3, and CLDN23. All 21 CpG sties were differently methylated in asthma in isolated eosinophils, and 10 were replicated in respiratory epithelium. CONCLUSION Reduced whole blood DNA methylation at 21 CpG sites was significantly associated with childhood allergy. The findings provide novel insights into the shared molecular mechanisms underlying asthma, rhinitis, and eczema.
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Affiliation(s)
- Cheng-Jian Xu
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Centre for Individualized Infection Medicine, CiiM, a joint venture between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Cancan Qi
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ana Esplugues
- Nursing Department, Faculty of Nursing and Chiropody, Universitat de València, València, Spain; FISABIO-Universitat Jaume I-Universitat de València Joint Research Unit of Epidemiology and Environmental Health, València, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Dan Mason
- Bradford Institute for Health Research, Bradford, United Kingdom
| | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles
| | - Daniela Porta
- Department of Epidemiology, Lazio Regional Health Service, Rome, Italy
| | - Karin C Lodrup Carlsen
- Division of Paediatric and Adolescent Medicine, The Faculty of Medicine, University of Oslo, Oslo, Norway; Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Nour Baïz
- Sorbonne University and INSERM, Epidemiology of Allergic and Respiratory Diseases (EPAR) Department, IPLESP, Medical School Saint Antoine, Paris, France
| | - Anne-Marie Madore
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec City, Canada
| | - Harri Alenius
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bianca van Rijkom
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Soesma A Jankipersadsing
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Pieter van der Vlies
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; HZPC Research BV, Metslawier, The Netherlands
| | - Inger Kull
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - Marianne van Hage
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Mariona Bustamante
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Institute of Global Health, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
| | - Aitana Lertxundi
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Preventive Medicine and Public Health Department, University of Basque Country (UPV/EHU), Leioa, Bizkaia, Spain; Health Research institute Biodonostia, Donostia-San Sebastian, Gipuzkoa, Spain
| | - Matias Torrent
- Health Research Institute of the Balearic Islands, Spain; ib-salut, Area de Salut de Menorca, Spain
| | | | - Maria Pia Fantini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Vegard Hovland
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Giancarlo Pesce
- Sorbonne University and INSERM, Epidemiology of Allergic and Respiratory Diseases (EPAR) Department, IPLESP, Medical School Saint Antoine, Paris, France
| | | | - Nanna Fyhrquist
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Human Microbiome Program, Medicum, University of Helsinki, Helsinki, Finland
| | - Tiina Laatikainen
- Finnish Institute for Health and Welfare, Helsinki, Finland; Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Martijn C Nawijn
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, Experimental Pulmonology and Inflammation Research, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yang Li
- Centre for Individualized Infection Medicine, CiiM, a joint venture between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands; Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Jean Bousquet
- University Hospital, Montpellier, France; Department of Dermatology, Charité, Berlin, Germany
| | - Josep M Anto
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Institute of Global Health, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec City, Canada; Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec City, Canada; Centre de santé et de services sociaux du Saguenay-Lac-Saint-Jean, Saguenay, Québec, Canada
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Isabella Annesi-Maesano
- Sorbonne University and INSERM, Epidemiology of Allergic and Respiratory Diseases (EPAR) Department, IPLESP, Medical School Saint Antoine, Paris, France
| | - Kai-Håkon Carlsen
- Division of Paediatric and Adolescent Medicine, The Faculty of Medicine, University of Oslo, Oslo, Norway; Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Davide Gori
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | | | - John Wright
- Bradford Institute for Health Research, Bradford, United Kingdom
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Judith M Vonk
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jordi Sunyer
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Institute of Global Health, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Erik Melén
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden; Sachs' Children's Hospital, Stockholm, Sweden
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Hesse L, van Ieperen N, Petersen AH, Elberink JNGO, van Oosterhout AJM, Nawijn MC. High dose vitamin D 3 empowers effects of subcutaneous immunotherapy in a grass pollen-driven mouse model of asthma. Sci Rep 2020; 10:20876. [PMID: 33257771 PMCID: PMC7705678 DOI: 10.1038/s41598-020-77947-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 08/31/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
Allergen-specific immunotherapy (AIT) has the potential to provide long-term protection against allergic diseases. However, efficacy of AIT is suboptimal, while application of high doses allergen has safety concerns. The use of adjuvants, like 1,25(OH)2VitD3 (VitD3), can improve efficacy of AIT. We have previously shown that low dose VitD3 can enhance suppression of airway inflammation, but not airway hyperresponsiveness in a grass pollen (GP)-subcutaneous immunotherapy (SCIT) mouse model of allergic asthma. We here aim to determine the optimal dose and formulation of VitD3 for the GP SCIT. GP-sensitized BALBc/ByJ mice received three SCIT injections of VitD3-GP (30, 100, and 300 ng or placebo). Separately, synthetic lipids, SAINT, was added to the VitD3-GP-SCIT formulation (300 nmol) and control groups. Subsequently, mice were challenged with intranasal GP, and airway hyperresponsiveness, GP-specific IgE, -IgG1, and -IgG2a, ear-swelling responses (ESR), eosinophils in broncho-alveolar lavage fluid and lung were measured. VitD3 supplementation of GP-SCIT dose-dependently induced significantly enhanced suppression of spIgE, inflammation and hyperresponsiveness, while neutralizing capacity was improved and ESR were reduced. Addition of VitD3 further decreased Th2 cytokine responses and innate cytokines to allergens in lung tissue by GP-SCIT. However, addition of synthetic lipids to the allergen/VitD3 mixes had no additional effect on VitD3-GP-SCIT. We find a clear, dose dependent effect of VitD3 on GP-SCIT-mediated suppression of allergic inflammation and airway hyperresponsiveness. In contrast, addition of synthetic lipids to the allergen/VitD3 mix had no therapeutic effect. These studies underscore the relevance of VitD3 as an adjuvant to improve clinical efficacy of SCIT treatment regimens.
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Affiliation(s)
- Laura Hesse
- Department of Pathology and Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), University Medical Center Groningen (UMCG), Groningen Research Institute of Asthma and COPD (GRIAC), University of Groningen, Internal Postcode EA52, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute of Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - N van Ieperen
- Department of Pathology and Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), University Medical Center Groningen (UMCG), Groningen Research Institute of Asthma and COPD (GRIAC), University of Groningen, Internal Postcode EA52, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute of Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Arjen H Petersen
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J N G Oude Elberink
- Division of Allergy, Department of Internal Medicine, University Medical Centre Groningen, Groningen, The Netherlands
| | - Antoon J M van Oosterhout
- Department of Pathology and Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), University Medical Center Groningen (UMCG), Groningen Research Institute of Asthma and COPD (GRIAC), University of Groningen, Internal Postcode EA52, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute of Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), University Medical Center Groningen (UMCG), Groningen Research Institute of Asthma and COPD (GRIAC), University of Groningen, Internal Postcode EA52, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
- Groningen Research Institute of Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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Boudewijn IM, Roffel MP, Vermeulen CJ, Nawijn MC, Kok K, Terpstra MM, Koppelman GH, Guryev V, van den Berge M. A Novel Role for Bronchial MicroRNAs and Long Noncoding RNAs in Asthma Remission. Am J Respir Crit Care Med 2020; 202:614-618. [PMID: 32339464 DOI: 10.1164/rccm.201908-1610le] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ilse M Boudewijn
- University Medical Center Groningen, University of GroningenGroningen, the Netherlands
| | - Mirjam P Roffel
- University Medical Center Groningen, University of GroningenGroningen, the Netherlands
| | - Cornelis J Vermeulen
- University Medical Center Groningen, University of GroningenGroningen, the Netherlands
| | - Martijn C Nawijn
- University Medical Center Groningen, University of GroningenGroningen, the Netherlands
| | - Klaas Kok
- University Medical Center Groningen, University of GroningenGroningen, the Netherlands
| | - M Martijn Terpstra
- University Medical Center Groningen, University of GroningenGroningen, the Netherlands
| | - Gerard H Koppelman
- University Medical Center Groningen, University of GroningenGroningen, the Netherlands
| | - Victor Guryev
- University Medical Center Groningen, University of GroningenGroningen, the Netherlands
| | - Maarten van den Berge
- University Medical Center Groningen, University of GroningenGroningen, the Netherlands
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Aliee H, Massip F, Qi C, de Biase MS, van Nijnatten J, Kersten ETG, Kermani NZ, Khuder B, Vonk JM, Vermeulen RCH, Neighbors M, Tew GW, Grimbaldeston M, Ten Hacken NHT, Hu S, Guo Y, Zhang X, Sun K, Hiemstra PS, Ponder BA, Mäkelä MJ, Malmström K, Rintoul RC, Reyfman PA, Theis FJ, Brandsma CA, Adcock IM, Timens W, Xu CJ, van den Berge M, Schwarz RF, Koppelman GH, Nawijn MC, Faiz A. Determinants of SARS-CoV-2 receptor gene expression in upper and lower airways. medRxiv 2020:2020.08.31.20169946. [PMID: 32909007 PMCID: PMC7480059 DOI: 10.1101/2020.08.31.20169946] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The recent outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has led to a worldwide pandemic. One week after initial symptoms develop, a subset of patients progresses to severe disease, with high mortality and limited treatment options. To design novel interventions aimed at preventing spread of the virus and reducing progression to severe disease, detailed knowledge of the cell types and regulating factors driving cellular entry is urgently needed. Here we assess the expression patterns in genes required for COVID-19 entry into cells and replication, and their regulation by genetic, epigenetic and environmental factors, throughout the respiratory tract using samples collected from the upper (nasal) and lower airways (bronchi). Matched samples from the upper and lower airways show a clear increased expression of these genes in the nose compared to the bronchi and parenchyma. Cellular deconvolution indicates a clear association of these genes with the proportion of secretory epithelial cells. Smoking status was found to increase the majority of COVID-19 related genes including ACE2 and TMPRSS2 but only in the lower airways, which was associated with a significant increase in the predicted proportion of goblet cells in bronchial samples of current smokers. Both acute and second hand smoke were found to increase ACE2 expression in the bronchus. Inhaled corticosteroids decrease ACE2 expression in the lower airways. No significant effect of genetics on ACE2 expression was observed, but a strong association of DNA- methylation with ACE2 and TMPRSS2- mRNA expression was identified in the bronchus.
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Affiliation(s)
- H Aliee
- Institute of Computational Biology, Helmholtz Centre, Munich, Germany
| | - F Massip
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - C Qi
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, the Netherlands
| | - M Stella de Biase
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - J van Nijnatten
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, Australia
| | - E T G Kersten
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, the Netherlands
| | - N Z Kermani
- Department of computing, Data Science Institute, Imperial College London, London, UK
| | - B Khuder
- Northwestern University Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, USA
| | - J M Vonk
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of epidemiology, Groningen, the Netherlands
| | - R C H Vermeulen
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Institute for Risk Assessment Science (IRAS), Division of Environmental Epidemiology (EEPI), Utrecht University, Utrecht, The Netherlands
| | - M Neighbors
- OMNI Biomarker Development, Genentech Inc. South San Francisco. CA, USA
| | - G W Tew
- Product Development Immunology, Infectious Disease & Opthalmology, Genentech Inc. South San Francisco. CA, USA
| | - M Grimbaldeston
- OMNI Biomarker Development, Genentech Inc. South San Francisco. CA, USA
| | - N H T Ten Hacken
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - S Hu
- Department of statistics, university of Oxford, Oxford, UK
| | - Y Guo
- Department of computing, Data Science Institute, Imperial College London, London, UK
| | - X Zhang
- Department of computing, Data Science Institute, Imperial College London, London, UK
| | - K Sun
- Department of computing, Data Science Institute, Imperial College London, London, UK
| | - P S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - B A Ponder
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, CB2 0XZ, UK
| | - M J Mäkelä
- Dept. of Allergy, University of Helsinki and Helsinki University Hospital, PO Box 160, FI-00029, Helsinki, Finland
| | - K Malmström
- Dept. of Allergy, University of Helsinki and Helsinki University Hospital, PO Box 160, FI-00029, Helsinki, Finland
| | - R C Rintoul
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, CB2 0XZ, UK
- Royal Papworth Hospital, Cambridge, Papworth Road, Cambridge Biomedical Campus, CB2 0AY, UK
| | - P A Reyfman
- Northwestern University Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, USA
| | - F J Theis
- Institute of Computational Biology, Helmholtz Centre, Munich, Germany
- Department of Mathematics, Technical University of Munich, Germany
| | - C A Brandsma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology
| | - I M Adcock
- National Heart and Lung Institute, London, UK
| | - W Timens
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology
| | - C J Xu
- Research group Bioinformatics and Computational Genomics, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - M van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - R F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - G H Koppelman
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, the Netherlands
| | - M C Nawijn
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- National Heart and Lung Institute, London, UK
| | - A Faiz
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, Australia
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40
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Carpaij OA, Goorsenberg AWM, d’Hooghe JNS, de Bruin DM, van den Elzen RM, Nawijn MC, Annema JT, van den Berge M, Bonta PI, Burgess JK. Optical Coherence Tomography Intensity Correlates with Extracellular Matrix Components in the Airway Wall. Am J Respir Crit Care Med 2020; 202:762-766. [DOI: 10.1164/rccm.201908-1512le] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Heijink IH, Kuchibhotla VNS, Roffel MP, Maes T, Knight DA, Sayers I, Nawijn MC. Epithelial cell dysfunction, a major driver of asthma development. Allergy 2020; 75:1902-1917. [PMID: 32460363 PMCID: PMC7496351 DOI: 10.1111/all.14421] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [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: 03/01/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Airway epithelial barrier dysfunction is frequently observed in asthma and may have important implications. The physical barrier function of the airway epithelium is tightly interwoven with its immunomodulatory actions, while abnormal epithelial repair responses may contribute to remodelling of the airway wall. We propose that abnormalities in the airway epithelial barrier play a crucial role in the sensitization to allergens and pathogenesis of asthma. Many of the identified susceptibility genes for asthma are expressed in the airway epithelium, supporting the notion that events at the airway epithelial surface are critical for the development of the disease. However, the exact mechanisms by which the expression of epithelial susceptibility genes translates into a functionally altered response to environmental risk factors of asthma are still unknown. Interactions between genetic factors and epigenetic regulatory mechanisms may be crucial for asthma susceptibility. Understanding these mechanisms may lead to identification of novel targets for asthma intervention by targeting the airway epithelium. Moreover, exciting new insights have come from recent studies using single‐cell RNA sequencing (scRNA‐Seq) to study the airway epithelium in asthma. This review focuses on the role of airway epithelial barrier function in the susceptibility to develop asthma and novel insights in the modulation of epithelial cell dysfunction in asthma.
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Affiliation(s)
- Irene H. Heijink
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Pulmonology University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Virinchi N. S. Kuchibhotla
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- School of Biomedical Sciences and Pharmacy University of Newcastle Callaghan NSW Australia
| | - Mirjam P. Roffel
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Respiratory Medicine Laboratory for Translational Research in Obstructive Pulmonary Diseases Ghent University Hospital Ghent University Ghent Belgium
| | - Tania Maes
- Department of Respiratory Medicine Laboratory for Translational Research in Obstructive Pulmonary Diseases Ghent University Hospital Ghent University Ghent Belgium
| | - Darryl A. Knight
- School of Biomedical Sciences and Pharmacy University of Newcastle Callaghan NSW Australia
- UBC Providence Health Care Research Institute Vancouver BC Canada
- Department of Anesthesiology, Pharmacology and Therapeutics University of British Columbia Vancouver BC Canada
| | - Ian Sayers
- Division of Respiratory Medicine National Institute for Health Research Nottingham Biomedical Research Centre University of Nottingham Biodiscovery Institute University of Nottingham Nottingham UK
| | - Martijn C. Nawijn
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
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42
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Kuchibhotla VNS, Jonker MR, Bruin HG, Noordhoek JA, Knight DA, Nawijn MC, Heijink IH. Inhibition of β-catenin/CBP signalling improves airway epithelial barrier function and suppresses CCL20 release. Allergy 2020; 75:1786-1789. [PMID: 32027380 PMCID: PMC7383853 DOI: 10.1111/all.14216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/11/2020] [Accepted: 01/30/2020] [Indexed: 12/01/2022]
Affiliation(s)
- Virinchi N. S. Kuchibhotla
- Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE) Department of Pathology & Medical Biology University Medical Center Groningen University of Groningen Groningen The Netherlands
- University Medical Center Groningen GRIAC Research Institute University of Groningen Groningen The Netherlands
| | - Marnix R. Jonker
- Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE) Department of Pathology & Medical Biology University Medical Center Groningen University of Groningen Groningen The Netherlands
- University Medical Center Groningen GRIAC Research Institute University of Groningen Groningen The Netherlands
| | - Harold G. Bruin
- Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE) Department of Pathology & Medical Biology University Medical Center Groningen University of Groningen Groningen The Netherlands
- University Medical Center Groningen GRIAC Research Institute University of Groningen Groningen The Netherlands
| | - Jacobien A. Noordhoek
- Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE) Department of Pathology & Medical Biology University Medical Center Groningen University of Groningen Groningen The Netherlands
- University Medical Center Groningen GRIAC Research Institute University of Groningen Groningen The Netherlands
- Department of Pulmonology University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Darryl A. Knight
- School of Biomedical Sciences and Pharmacy University of Newcastle Callaghan NSW Australia
- Priority Research Centre for Healthy Lungs Hunter Medical Research Institute New Lambton Heights NSW Australia
| | - Martijn C. Nawijn
- Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE) Department of Pathology & Medical Biology University Medical Center Groningen University of Groningen Groningen The Netherlands
- University Medical Center Groningen GRIAC Research Institute University of Groningen Groningen The Netherlands
| | - Irene H. Heijink
- Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE) Department of Pathology & Medical Biology University Medical Center Groningen University of Groningen Groningen The Netherlands
- University Medical Center Groningen GRIAC Research Institute University of Groningen Groningen The Netherlands
- Department of Pulmonology University Medical Center Groningen University of Groningen Groningen The Netherlands
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Abstract
Infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) leads to coronavirus disease 2019 (COVID-19), which poses an unprecedented worldwide health crisis, and has been declared a pandemic by the World Health Organization (WHO) on March 11, 2020. The angiotensin converting enzyme 2 (ACE2) has been suggested to be the key protein used by SARS-CoV-2 for host cell entry. In their recent work, Lindskog and colleagues (Hikmet et al, 2020) report that ACE2 is expressed at very low protein levels-if at all-in respiratory epithelial cells. Severe COVID-19, however, is characterized by acute respiratory distress syndrome and extensive damage to the alveoli in the lung parenchyma. Then, what is the role of the airway epithelium in the early stages of COVID-19, and which cells need to be studied to characterize the biological mechanisms responsible for the progression to severe disease after initial infection by the novel coronavirus?
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Affiliation(s)
- Martijn C Nawijn
- Department of Pathology and Medical BiologyUniversity Medical Center GroningenGRIAC Research InstituteUniversity of GroningenGroningenThe Netherlands
| | - Wim Timens
- Department of Pathology and Medical BiologyUniversity Medical Center GroningenGRIAC Research InstituteUniversity of GroningenGroningenThe Netherlands
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44
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Hesse L, Petersen AH, Oude Elberink JNG, van Oosterhout AJM, Nawijn MC. 1,25(OH) 2VitD3 supplementation enhances suppression of grass pollen-induced allergic asthma by subcutaneous and sublingual immunotherapy in a mouse model. Sci Rep 2020; 10:8960. [PMID: 32488022 PMCID: PMC7265339 DOI: 10.1038/s41598-020-65946-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/05/2020] [Indexed: 12/03/2022] Open
Abstract
Allergen specific immunotherapy (AIT) can provide long-term alleviation of symptoms for allergic disease but is hampered by suboptimal efficiency. We and others have previously shown that 1,25(OH)2-VitaminD3 (VitD3) can improve therapeutic efficacy of AIT. However, it is unknown whether VitD3 supplementation has similar effects in sublingual and subcutaneous immunotherapy. Therefore, we aimed to test VitD3 supplementation in both grass pollen (GP) subcutaneous-IT (SCIT) and sublingual-IT (SLIT) in a mouse model for allergic airway inflammation. To this end, GP-sensitized BALB/c mice received GP-SCIT or GP-SLIT with or without 10 ng VitD3, followed by intranasal GP challenges and measurement of airway hyperresponsiveness (AHR) and inflammation. VitD3 supplementation of GP-SCIT resulted in enhanced induction of GP-specific (sp)-IgG2a and suppression of spIgE after challenge. In addition, eosinophil numbers were reduced and levels of IL10 and Amphiregulin were increased in lung tissue. In GP-SLIT, VitD3 supplementation resulted in enhanced sp-IgG2a levels in serum, enhanced suppression of eosinophils and increased IL10 levels in lung tissue, as well as suppression of AHR to methacholine. These data show that VitD3 increases efficacy of both SCIT and SLIT, by enhancing induction of blocking antibodies and suppression of airway inflammation, underscoring the relevance of proficient VitD3 levels for successful AIT.
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Affiliation(s)
- Laura Hesse
- University of Groningen, University Medical Center Groningen, Department of Pathology & Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), Groningen, The Netherlands
- Groningen Research Institute of Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arjen H Petersen
- University of Groningen, University Medical Center Groningen, Department of Pathology & Medical Biology, Medical Biology section, Groningen, The Netherlands
| | - Joanne N G Oude Elberink
- University Medical Centre Groningen, Department of internal medicine, Division of Allergy, Groningen, The Netherlands
| | - Antoon J M van Oosterhout
- University of Groningen, University Medical Center Groningen, Department of Pathology & Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), Groningen, The Netherlands
| | - Martijn C Nawijn
- University of Groningen, University Medical Center Groningen, Department of Pathology & Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), Groningen, The Netherlands.
- Groningen Research Institute of Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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Ketelaar ME, Portelli MA, Dijk FN, Shrine N, Faiz A, Vermeulen CJ, Xu CJ, Hankinson J, Bhaker S, Henry AP, Billington CK, Shaw DE, Johnson SR, Benest AV, Pang V, Bates DO, Pogson ZEK, Fogarty A, McKeever TM, Singapuri A, Heaney LG, Mansur AH, Chaudhuri R, Thomson NC, Holloway JW, Lockett GA, Howarth PH, Niven R, Simpson A, Tobin MD, Hall IP, Wain LV, Blakey JD, Brightling CE, Obeidat M, Sin DD, Nickle DC, Bossé Y, Vonk JM, van den Berge M, Koppelman GH, Sayers I, Nawijn MC. Phenotypic and functional translation of IL33 genetics in asthma. J Allergy Clin Immunol 2020; 147:144-157. [PMID: 32442646 DOI: 10.1016/j.jaci.2020.04.051] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 03/22/2020] [Accepted: 04/14/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Asthma is a complex disease with multiple phenotypes that may differ in disease pathobiology and treatment response. IL33 single nucleotide polymorphisms (SNPs) have been reproducibly associated with asthma. IL33 levels are elevated in sputum and bronchial biopsies of patients with asthma. The functional consequences of IL33 asthma SNPs remain unknown. OBJECTIVE This study sought to determine whether IL33 SNPs associate with asthma-related phenotypes and with IL33 expression in lung or bronchial epithelium. This study investigated the effect of increased IL33 expression on human bronchial epithelial cell (HBEC) function. METHODS Association between IL33 SNPs (Chr9: 5,815,786-6,657,983) and asthma phenotypes (Lifelines/DAG [Dutch Asthma GWAS]/GASP [Genetics of Asthma Severity & Phenotypes] cohorts) and between SNPs and expression (lung tissue, bronchial brushes, HBECs) was done using regression modeling. Lentiviral overexpression was used to study IL33 effects on HBECs. RESULTS We found that 161 SNPs spanning the IL33 region associated with 1 or more asthma phenotypes after correction for multiple testing. We report a main independent signal tagged by rs992969 associating with blood eosinophil levels, asthma, and eosinophilic asthma. A second, independent signal tagged by rs4008366 presented modest association with eosinophilic asthma. Neither signal associated with FEV1, FEV1/forced vital capacity, atopy, and age of asthma onset. The 2 IL33 signals are expression quantitative loci in bronchial brushes and cultured HBECs, but not in lung tissue. IL33 overexpression in vitro resulted in reduced viability and reactive oxygen species-capturing of HBECs, without influencing epithelial cell count, metabolic activity, or barrier function. CONCLUSIONS We identify IL33 as an epithelial susceptibility gene for eosinophilia and asthma, provide mechanistic insight, and implicate targeting of the IL33 pathway specifically in eosinophilic asthma.
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Affiliation(s)
- Maria E Ketelaar
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Division of Respiratory Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.
| | - Michael A Portelli
- Division of Respiratory Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - F Nicole Dijk
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom; National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Leicester, United Kingdom
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cornelis J Vermeulen
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cheng J Xu
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; CiiM & TWINCORE, Helmholtz-Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Jenny Hankinson
- Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Sangita Bhaker
- Division of Respiratory Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Amanda P Henry
- Division of Respiratory Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Charlote K Billington
- Division of Respiratory Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Dominick E Shaw
- Division of Respiratory Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Simon R Johnson
- Division of Respiratory Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Andrew V Benest
- Division of Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, and COMPARE University of Birmingham and University of Nottingham, Nottingham, United Kingdom
| | - Vincent Pang
- Division of Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, and COMPARE University of Birmingham and University of Nottingham, Nottingham, United Kingdom
| | - David O Bates
- Division of Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, and COMPARE University of Birmingham and University of Nottingham, Nottingham, United Kingdom
| | - Z E K Pogson
- Department of Respiratory Medicine, Lincoln County Hospital, Lincoln, United Kingdom; Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
| | - Andrew Fogarty
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
| | - Tricia M McKeever
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
| | - Amisha Singapuri
- Institute for Lung Health, Department of Respiratory Sciences, Glenfield Hospital, University of Leicester, Leicester, United Kingdom
| | - Liam G Heaney
- Centre for Infection and Immunity, Queen's University of Belfast, Belfast, United Kingdom
| | - Adel H Mansur
- Respiratory Medicine, Birmingham Heartlands Hospital and University of Birmingham, Birmingham, United Kingdom
| | - Rekha Chaudhuri
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Neil C Thomson
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - John W Holloway
- Human Development and Health, Faculty of Medicine and National Institute of Health Biomedical Research Centre, University of Southampton, Southampton, United Kingdom; Clinical and Experimental Sciences, Faculty of Medicine and National Institute of Health Biomedical Research Centre, University of Southampton, Southampton, United Kingdom
| | - Gabrielle A Lockett
- Human Development and Health, Faculty of Medicine and National Institute of Health Biomedical Research Centre, University of Southampton, Southampton, United Kingdom; Clinical and Experimental Sciences, Faculty of Medicine and National Institute of Health Biomedical Research Centre, University of Southampton, Southampton, United Kingdom
| | - Peter H Howarth
- Human Development and Health, Faculty of Medicine and National Institute of Health Biomedical Research Centre, University of Southampton, Southampton, United Kingdom; Clinical and Experimental Sciences, Faculty of Medicine and National Institute of Health Biomedical Research Centre, University of Southampton, Southampton, United Kingdom
| | - Robert Niven
- Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Angela Simpson
- Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom; National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Leicester, United Kingdom
| | - Ian P Hall
- Division of Respiratory Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom; National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Leicester, United Kingdom
| | - John D Blakey
- Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Australia
| | - Christopher E Brightling
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Leicester, United Kingdom; Institute for Lung Health, Department of Respiratory Sciences, Glenfield Hospital, University of Leicester, Leicester, United Kingdom
| | - Ma'en Obeidat
- The Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Don D Sin
- The Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David C Nickle
- Department of Genetics and Pharmacogenomics, Merck Research Laboratories, Boston, Mass
| | - Yohan Bossé
- Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec City, Quebec, Canada
| | - Judith M Vonk
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Division of Respiratory Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Gerard H Koppelman
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ian Sayers
- Division of Respiratory Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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46
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Portelli MA, Dijk FN, Ketelaar ME, Shrine N, Hankinson J, Bhaker S, Grotenboer NS, Obeidat M, Henry AP, Billington CK, Shaw D, Johnson SR, Pogson ZE, Fogarty A, McKeever TM, Nickle DC, Bossé Y, van den Berge M, Faiz A, Brouwer S, Vonk JM, de Vos P, Brandsma CA, Vermeulen CJ, Singapuri A, Heaney LG, Mansur AH, Chaudhuri R, Thomson NC, Holloway JW, Lockett GA, Howarth PH, Niven R, Simpson A, Blakey JD, Tobin MD, Postma DS, Hall IP, Wain LV, Nawijn MC, Brightling CE, Koppelman GH, Sayers I. Phenotypic and functional translation of IL1RL1 locus polymorphisms in lung tissue and asthmatic airway epithelium. JCI Insight 2020; 5:132446. [PMID: 32324168 PMCID: PMC7205441 DOI: 10.1172/jci.insight.132446] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/12/2020] [Indexed: 12/22/2022] Open
Abstract
The IL1RL1 (ST2) gene locus is robustly associated with asthma; however, the contribution of single nucleotide polymorphisms (SNPs) in this locus to specific asthma subtypes and the functional mechanisms underlying these associations remain to be defined. We tested for association between IL1RL1 region SNPs and characteristics of asthma as defined by clinical and immunological measures and addressed functional effects of these genetic variants in lung tissue and airway epithelium. Utilizing 4 independent cohorts (Lifelines, Dutch Asthma GWAS [DAG], Genetics of Asthma Severity and Phenotypes [GASP], and Manchester Asthma and Allergy Study [MAAS]) and resequencing data, we identified 3 key signals associated with asthma features. Investigations in lung tissue and primary bronchial epithelial cells identified context-dependent relationships between the signals and IL1RL1 mRNA and soluble protein expression. This was also observed for asthma-associated IL1RL1 nonsynonymous coding TIR domain SNPs. Bronchial epithelial cell cultures from asthma patients, exposed to exacerbation-relevant stimulations, revealed modulatory effects for all 4 signals on IL1RL1 mRNA and/or protein expression, suggesting SNP-environment interactions. The IL1RL1 TIR signaling domain haplotype affected IL-33–driven NF-κB signaling, while not interfering with TLR signaling. In summary, we identify that IL1RL1 genetic signals potentially contribute to severe and eosinophilic phenotypes in asthma, as well as provide initial mechanistic insight, including genetic regulation of IL1RL1 isoform expression and receptor signaling.
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Affiliation(s)
- Michael A Portelli
- Division of Respiratory Medicine, NIHR, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - F Nicole Dijk
- Department of Pediatric Pulmonology and Pediatric Allergology, and
| | - Maria E Ketelaar
- Division of Respiratory Medicine, NIHR, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.,Department of Pediatric Pulmonology and Pediatric Allergology, and.,Department of Pathology and Medical Biology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, University of Groningen, Groningen, Netherlands
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Jenny Hankinson
- Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Sangita Bhaker
- Division of Respiratory Medicine, NIHR, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Néomi S Grotenboer
- Department of Pediatric Pulmonology and Pediatric Allergology, and.,Department of Pathology and Medical Biology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, University of Groningen, Groningen, Netherlands
| | - Ma'en Obeidat
- The University of British Columbia Center for Heart Lung Innovation, St. Paul's Hospital Vancouver, Vancouver, British Columbia, Canada
| | - Amanda P Henry
- Division of Respiratory Medicine, NIHR, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Charlotte K Billington
- Division of Respiratory Medicine, NIHR, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Dominick Shaw
- Division of Respiratory Medicine, NIHR, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Simon R Johnson
- Division of Respiratory Medicine, NIHR, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Zara Ek Pogson
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
| | - Andrew Fogarty
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
| | - Tricia M McKeever
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
| | - David C Nickle
- Departments of Genetics and Pharmacogenomics, Merck Research Laboratories, Boston, Massachusetts, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Department of Pulmonary Diseases, and
| | - Alen Faiz
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Department of Pulmonary Diseases, and
| | - Sharon Brouwer
- Department of Pathology and Medical Biology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, University of Groningen, Groningen, Netherlands
| | - Judith M Vonk
- Department of Epidemiology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, University of Groningen, Groningen, Netherlands
| | - Paul de Vos
- Department of Pathology and Medical Biology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, University of Groningen, Groningen, Netherlands
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, University of Groningen, Groningen, Netherlands
| | - Cornelis J Vermeulen
- Department of Pathology and Medical Biology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, University of Groningen, Groningen, Netherlands
| | - Amisha Singapuri
- Respiratory sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
| | - Liam G Heaney
- Centre for Experimental Medicine, Queens University of Belfast, Belfast, United Kingdom
| | - Adel H Mansur
- Department of Respiratory Medicine, Birmingham Heartlands Hospital and University of Birmingham, Birmingham, United Kingdom
| | - Rekha Chaudhuri
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Neil C Thomson
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - John W Holloway
- Department of Human Development and.,Department of Health & Clinical and Experimental Sciences, Faculty of Medicine and NIH Research (NIHR), Southampton Biomedical Research Centre, University of Southampton, Southampton, United Kingdom
| | - Gabrielle A Lockett
- Department of Human Development and.,Department of Health & Clinical and Experimental Sciences, Faculty of Medicine and NIH Research (NIHR), Southampton Biomedical Research Centre, University of Southampton, Southampton, United Kingdom
| | - Peter H Howarth
- Department of Human Development and.,Department of Health & Clinical and Experimental Sciences, Faculty of Medicine and NIH Research (NIHR), Southampton Biomedical Research Centre, University of Southampton, Southampton, United Kingdom
| | - Robert Niven
- Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Angela Simpson
- Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - John D Blakey
- Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Australia
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom.,NIHR, Leicester Respiratory Biomedical Research Centre, University of Leicester, Leicester, United Kingdom
| | - Dirkje S Postma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Department of Pulmonary Diseases, and
| | - Ian P Hall
- Division of Respiratory Medicine, NIHR, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom.,NIHR, Leicester Respiratory Biomedical Research Centre, University of Leicester, Leicester, United Kingdom
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, University of Groningen, Groningen, Netherlands
| | - Christopher E Brightling
- Respiratory sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom.,NIHR, Leicester Respiratory Biomedical Research Centre, University of Leicester, Leicester, United Kingdom
| | | | - Ian Sayers
- Division of Respiratory Medicine, NIHR, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
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47
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Koopmans T, Hesse L, Nawijn MC, Kumawat K, Menzen MH, Sophie T Bos I, Smits R, Bakker ERM, van den Berge M, Koppelman GH, Guryev V, Gosens R. Smooth-muscle-derived WNT5A augments allergen-induced airway remodelling and Th2 type inflammation. Sci Rep 2020; 10:6754. [PMID: 32317758 PMCID: PMC7174298 DOI: 10.1038/s41598-020-63741-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/06/2020] [Indexed: 12/21/2022] Open
Abstract
Asthma is a heterogeneous disease characterized by chronic inflammation and structural changes in the airways. The airway smooth muscle (ASM) is responsible for airway narrowing and an important source of inflammatory mediators. We and others have previously shown that WNT5A mRNA and protein expression is higher in the ASM of asthmatics compared to healthy controls. Here, we aimed to characterize the functional role of (smooth muscle-derived) WNT5A in asthma. We generated a tet-ON smooth-muscle-specific WNT5A transgenic mouse model, enabling in vivo characterization of smooth-muscle-derived WNT5A in response to ovalbumin. Smooth muscle specific WNT5A overexpression showed a clear trend towards enhanced actin (α-SMA) expression in the ASM in ovalbumin challenged animals, but had no effect on collagen content. WNT5A overexpression in ASM also significantly enhanced the production of the Th2-cytokines IL4 and IL5 in lung tissue after ovalbumin exposure. In line with this, WNT5A increased mucus production, and enhanced eosinophilic infiltration and serum IgE production in ovalbumin-treated animals. In addition, CD4+ T cells of asthma patients and healthy controls were stimulated with WNT5A and changes in gene transcription assessed by RNA-seq. WNT5A promoted expression of 234 genes in human CD4+ T cells, among which the Th2 cytokine IL31 was among the top 5 upregulated genes. IL31 was also upregulated in response to smooth muscle-specific WNT5A overexpression in the mouse. In conclusion, smooth-muscle derived WNT5A augments Th2 type inflammation and remodelling. Our findings imply a pro-inflammatory role for smooth muscle-derived WNT5A in asthma, resulting in increased airway wall inflammation and remodelling.
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Affiliation(s)
- Tim Koopmans
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Laura Hesse
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Experimental Pulmonology and Inflammation Research, Groningen, The Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Experimental Pulmonology and Inflammation Research, Groningen, The Netherlands
| | - Kuldeep Kumawat
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Mark H Menzen
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - I Sophie T Bos
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Ron Smits
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Groningen, The Netherlands
| | - Elvira R M Bakker
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Groningen, The Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
| | - Gerard H Koppelman
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children 's Hospital, Groningen, The Netherlands
| | - Victor Guryev
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands. .,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.
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48
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Dijk FN, Vijverberg SJ, Hernandez‐Pacheco N, Repnik K, Karimi L, Mitratza M, Farzan N, Nawijn MC, Burchard EG, Engelkes M, Verhamme KM, Potočnik U, Pino‐Yanes M, Postma DS, Maitland‐van der Zee A, Koppelman GH. IL1RL1 gene variations are associated with asthma exacerbations in children and adolescents using inhaled corticosteroids. Allergy 2020; 75:984-989. [PMID: 31755552 PMCID: PMC7176513 DOI: 10.1111/all.14125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- F. Nicole Dijk
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Susanne J. Vijverberg
- Department of Respiratory Medicine Amsterdam University Medical Centers University of Amsterdam Amsterdam The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
| | - Natalia Hernandez‐Pacheco
- Research Unit Hospital Universitario N.S. de Candelaria Universidad de La Laguna Santa Cruz de Tenerife Spain
- Genomics and Health Group Department of Biochemistry, Microbiology, Cell Biology and Genetics Universidad de La Laguna La Laguna, Tenerife Spain
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics Faculty of Medicine University of Maribor Maribor Slovenia
- Laboratory for Biochemistry Molecular Biology and Genomics Faculty for Chemistry and Chemical Engineering University of Maribor Maribor Slovenia
| | - Leila Karimi
- Department of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - Marianna Mitratza
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
| | - Niloufar Farzan
- Department of Respiratory Medicine Amsterdam University Medical Centers University of Amsterdam Amsterdam The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
| | - Martijn C. Nawijn
- Laboratory of Allergology and Pulmonary Diseases, Pathology and Medical Biology Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Esteban G. Burchard
- Department of Medicine University of California San Francisco CA USA
- Department of Bioengineering and Therapeutic Sciences University of California San Francisco CA USA
| | - Marjolein Engelkes
- Department of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - Katia M. Verhamme
- Department of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics Faculty of Medicine University of Maribor Maribor Slovenia
- Laboratory for Biochemistry Molecular Biology and Genomics Faculty for Chemistry and Chemical Engineering University of Maribor Maribor Slovenia
| | - Maria Pino‐Yanes
- Research Unit Hospital Universitario N.S. de Candelaria Universidad de La Laguna Santa Cruz de Tenerife Spain
- Genomics and Health Group Department of Biochemistry, Microbiology, Cell Biology and Genetics Universidad de La Laguna La Laguna, Tenerife Spain
- CIBER de Enfermedades Respiratorias Instituto de Salud Carlos III Madrid Spain
| | - Dirkje S. Postma
- Department of Pulmonary Diseases Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Anke‐Hilse Maitland‐van der Zee
- Department of Respiratory Medicine Amsterdam University Medical Centers University of Amsterdam Amsterdam The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
- Department of Pediatric Respiratory Medicine and Allergy Emma's Children Hospital Academic Medical Center (AMC) University of Amsterdam Amsterdam The Netherlands
| | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
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49
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van der Wijst MGP, de Vries DH, Groot HE, Trynka G, Hon CC, Bonder MJ, Stegle O, Nawijn MC, Idaghdour Y, van der Harst P, Ye CJ, Powell J, Theis FJ, Mahfouz A, Heinig M, Franke L. The single-cell eQTLGen consortium. eLife 2020; 9:e52155. [PMID: 32149610 PMCID: PMC7077978 DOI: 10.7554/elife.52155] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [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: 09/24/2019] [Accepted: 03/03/2020] [Indexed: 12/17/2022] Open
Abstract
In recent years, functional genomics approaches combining genetic information with bulk RNA-sequencing data have identified the downstream expression effects of disease-associated genetic risk factors through so-called expression quantitative trait locus (eQTL) analysis. Single-cell RNA-sequencing creates enormous opportunities for mapping eQTLs across different cell types and in dynamic processes, many of which are obscured when using bulk methods. Rapid increase in throughput and reduction in cost per cell now allow this technology to be applied to large-scale population genetics studies. To fully leverage these emerging data resources, we have founded the single-cell eQTLGen consortium (sc-eQTLGen), aimed at pinpointing the cellular contexts in which disease-causing genetic variants affect gene expression. Here, we outline the goals, approach and potential utility of the sc-eQTLGen consortium. We also provide a set of study design considerations for future single-cell eQTL studies.
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Affiliation(s)
- MGP van der Wijst
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - DH de Vries
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - HE Groot
- Department of Cardiology, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - G Trynka
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Open TargetsHinxtonUnited Kingdom
| | - CC Hon
- RIKEN Center for Integrative Medical SciencesYokahamaJapan
| | - MJ Bonder
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ)HeidelbergGermany
- Genome Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - O Stegle
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ)HeidelbergGermany
- Genome Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - MC Nawijn
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Y Idaghdour
- Program in Biology, Public Health Research Center, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - P van der Harst
- Department of Cardiology, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - CJ Ye
- Institute for Human Genetics, Bakar Computational Health Sciences Institute, Bakar ImmunoX Initiative, Department of Medicine, Department of Bioengineering and Therapeutic Sciences, Department of Epidemiology and Biostatistics, Chan Zuckerberg Biohub, University of California San FranciscoSan FranciscoUnited States
| | - J Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute, UNSW Cellular Genomics Futures Institute, University of New South WalesSydneyAustralia
| | - FJ Theis
- Institute of Computational Biology, Helmholtz Zentrum MünchenNeuherbergGermany
- Department of Mathematics, Technical University of MunichGarching bei MünchenGermany
| | - A Mahfouz
- Leiden Computational Biology Center, Leiden University Medical CenterLeidenNetherlands
- Delft Bioinformatics Lab, Delft University of TechnologyDelftNetherlands
| | - M Heinig
- Institute of Computational Biology, Helmholtz Zentrum MünchenNeuherbergGermany
- Department of Informatics, Technical University of MunichGarching bei MünchenGermany
| | - L Franke
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center GroningenGroningenNetherlands
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50
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Vermeulen CJ, Xu CJ, Vonk JM, Ten Hacken NHT, Timens W, Heijink IH, Nawijn MC, Boekhoudt J, van Oosterhout AJ, Affleck K, Weckmann M, Koppelman GH, van den Berge M. Differential DNA methylation in bronchial biopsies between persistent asthma and asthma in remission. Eur Respir J 2020; 55:13993003.01280-2019. [PMID: 31699840 DOI: 10.1183/13993003.01280-2019] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/18/2019] [Indexed: 11/05/2022]
Abstract
Approximately 40% of asthmatics experience remission of asthma symptoms. A better understanding of biological pathways leading to asthma remission may provide insight into new therapeutic targets for asthma. As an important mechanism of gene regulation, investigation of DNA methylation provides a promising approach. Our objective was to identify differences in epigenome wide DNA methylation levels in bronchial biopsies between subjects with asthma remission and subjects with persistent asthma or healthy controls.We analysed differential DNA methylation in bronchial biopsies from 26 subjects with persistent asthma, 39 remission subjects and 70 healthy controls, using the limma package. The comb-p tool was used to identify differentially methylated regions. DNA methylation of CpG-sites was associated to expression of nearby genes from the same biopsies to understand function.Four CpG-sites and 42 regions were differentially methylated between persistent asthma and remission. DNA methylation at two sites was correlated i n cis with gene expression at ACKR2 and DGKQ Between remission subjects and healthy controls 1163 CpG-sites and 328 regions were differentially methylated. DNA methylation was associated with expression of a set of genes expressed in ciliated epithelium.CpGs differentially methylated between remission and persistent asthma identify genetic loci associated with resolution of inflammation and airway responsiveness. Despite the absence of symptoms, remission subjects have a DNA methylation profile that is distinct from that of healthy controls, partly due to changes in cellular composition, with a higher gene expression signal related to ciliated epithelium in remission versus healthy controls.
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Affiliation(s)
- Cornelis J Vermeulen
- Dept of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands .,University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Cheng-Jian Xu
- University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,Dept of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, The Netherlands.,CiiM & TWINCORE, Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Judith M Vonk
- University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,Dept of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Nick H T Ten Hacken
- Dept of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Wim Timens
- University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,Dept of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Irene H Heijink
- Dept of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,Dept of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,Dept of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jeunard Boekhoudt
- Dept of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Karen Affleck
- Allergic Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, UK
| | - Markus Weckmann
- Dept of Pediatric Pneumology and Allergology, University Medical Center of Schlesswig-Holstein, Airway Research Centre North, Member of the German Centre of Lung Research, Lübeck, Germany
| | - Gerard H Koppelman
- University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,Dept of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, The Netherlands
| | - Maarten van den Berge
- Dept of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
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