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Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP. SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants. Stem Cell Reports 2023; 18:636-653. [PMID: 36827975 PMCID: PMC9948283 DOI: 10.1016/j.stemcr.2023.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/25/2023] Open
Abstract
Ancestral SARS coronavirus-2 (SARS-CoV-2) and variants of concern (VOC) caused a global pandemic with a spectrum of disease severity. The mechanistic explaining variations related to airway epithelium are relatively understudied. Here, we biobanked airway organoids (AO) by preserving stem cell function. We optimized viral infection with H1N1/PR8 and comprehensively characterized epithelial responses to SARS-CoV-2 infection in phenotypically stable AO from 20 different subjects. We discovered Tetraspanin-8 (TSPAN8) as a facilitator of SARS-CoV-2 infection. TSPAN8 facilitates SARS-CoV-2 infection rates independently of ACE2-Spike interaction. In head-to-head comparisons with Ancestral SARS-CoV-2, Delta and Omicron VOC displayed lower overall infection rates of AO but triggered changes in epithelial response. All variants shared highest tropism for ciliated and goblet cells. TSPAN8-blocking antibodies diminish SARS-CoV-2 infection and may spur novel avenues for COVID-19 therapy.
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Affiliation(s)
- Lisiena Hysenaj
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Samantha Little
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Kayla Kulhanek
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Melia Magnen
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kriti Bahl
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Oghenekevwe M Gbenedio
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Morgan Prinz
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Lauren Rodriguez
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher Andersen
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Arjun Arkal Rao
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alan Shen
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Leonard C Lupin-Jimenez
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Luke R Bonser
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nina K Serwas
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Mir M Khalid
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Taha Y Taha
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Renuka Kumar
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jack Z Li
- Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Vivianne W Ding
- Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shotaro Matsumoto
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mazharul Maishan
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bharath Sreekumar
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Camille Simoneau
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; German Cancer Consortium, Partner Site Freiburg and German Cancer Research Center, Heidelberg, Germany
| | - Michael G Tomlinson
- School of Biosciences, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands, UK
| | - Khajida Khan
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Max Planck Institute for Infection Biology, Berlin, Germany; Centre for the AIDS Program of Research, Durban, South Africa
| | - Mark R Looney
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David M Jablons
- Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles R Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Michael Matthay
- Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew Krummel
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David J Erle
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA
| | - Alexis J Combes
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA
| | - Johannes R Kratz
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
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Hysenaj L, Little S, Kulhanek K, Gbenedio OM, Rodriguez L, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Bahl K, Mick E, Li JZ, Ding VW, Matsumoto S, Maishan M, Simoneau C, Fragiadakis G, Jablons DM, Langelier CR, Matthay M, Ott M, Krummel M, Combes AJ, Sil A, Erle DJ, Kratz JR, Roose JP. SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.06.01.446640. [PMID: 34100012 PMCID: PMC8183007 DOI: 10.1101/2021.06.01.446640] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SARS coronavirus-2 (SARS-CoV-2) is causing a global pandemic with large variation in COVID-19 disease spectrum. SARS-CoV-2 infection requires host receptor ACE2 on lung epithelium, but epithelial underpinnings of variation are largely unknown. We capitalized on comprehensive organoid assays to report remarkable variation in SARS-CoV-2 infection rates of lung organoids from different subjects. Tropism is highest for TUBA- and MUC5AC-positive organoid cells, but levels of TUBA-, MUC5A-, or ACE2- positive cells do not predict infection rate. We identify surface molecule Tetraspanin 8 (TSPAN8) as novel mediator of SARS-CoV-2 infection, which is not downregulated by this specific virus. TSPAN8 levels, prior to infection, strongly correlate with infection rate and TSPAN8-blocking antibodies diminish SARS-CoV-2 infection. We propose TSPAN8 as novel functional biomarker and potential therapeutic target for COVID-19.
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Affiliation(s)
- Lisiena Hysenaj
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
| | - Samantha Little
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kayla Kulhanek
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
| | - Oghenekevwe M. Gbenedio
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
| | - Lauren Rodriguez
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, California 94143, USA
| | - Alan Shen
- UCSF CoLabs, University of California San Francisco, San Francisco, California 94143, USA
| | - Jean-Christophe Lone
- School of Life Science, University of Essex, Wivenhoe Park,Colchester C04 3SQ, United Kingdom
| | | | - Luke R. Bonser
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Nina K. Serwas
- Department of Pathology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kriti Bahl
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
| | - Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, California 94143, USA and Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, California 94143, USA
| | - Jack Z. Li
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, California 94143, USA
| | - Vivianne W. Ding
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, California 94143, USA
| | - Shotaro Matsumoto
- Gladstone Institute of Virology, Department of Medicine, University of California San Francisco, California 94143, USA
| | - Mazharul Maishan
- Gladstone Institute of Virology, Department of Medicine, University of California San Francisco, California 94143, USA
| | - Camille Simoneau
- Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Gabriela Fragiadakis
- UCSF CoLabs, University of California San Francisco, San Francisco, California 94143, USA
| | - David M. Jablons
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, California 94143, USA
| | - Charles R. Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, California 94143, USA and Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, California 94143, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Michael Matthay
- Gladstone Institute of Virology, Department of Medicine, University of California San Francisco, California 94143, USA
| | - Melanie Ott
- Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Matthew Krummel
- Department of Pathology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Alexis J. Combes
- UCSF CoLabs, University of California San Francisco, San Francisco, California 94143, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California 94143, USA
| | - David J. Erle
- UCSF CoLabs, University of California San Francisco, San Francisco, California 94143, USA
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Johannes R. Kratz
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, California 94143, USA
| | - Jeroen P. Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
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