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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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