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SARS-CoV-2 Infection of Lung Organoids Reveals Conserved Use of Tetraspanin-8 by Ancestral-, Delta-, and Omicron- Variants

75 Pages Posted: 7 Sep 2022 Publication Status: Review Complete

See all articles by Lisiena Hysenaj

Lisiena Hysenaj

University of California, San Francisco (UCSF) - Department of Anatomy

Samantha Little

University of California, San Francisco (UCSF) - Department of Anatomy

Kayla R. Kulhanek

University of California, San Francisco (UCSF) - Department of Anatomy

Melia Magnen

University of California, San Francisco (UCSF) - ImmunoX Initiative

Kriti Bahl

University of California, San Francisco (UCSF) - Department of Anatomy

Oghenekevwe Michelle Gbenedio

University of California, San Francisco (UCSF) - Department of Anatomy

Morgan Prinz

University of California, San Francisco (UCSF) - Department of Anatomy

Lauren Rodriguez

University of California, San Francisco (UCSF) - Department of Microbiology and Immunology

Christopher Andersen

University of California, San Francisco (UCSF) - UCSF CoLabs

Arjun Arkal Rao

University of California, San Francisco (UCSF) - UCSF CoLabs

Alan Shen

University of California, San Francisco (UCSF) - UCSF CoLabs

Jean Christophe Lone

University of Essex - School of Life Science

Leonard C. Lupin Jimenez

University of California, San Francisco (UCSF) - UCSF CoLabs

Luke Bonser

University of California, San Francisco (UCSF) - Lung Biology Center

Nina K. Serwas

University of California, San Francisco (UCSF) - Department of Pathology

Eran Mick

University of California, San Francisco (UCSF) - Division of Infectious Diseases

Mir M. Khalid

University of California, San Francisco (UCSF) - Gladstone Institutes

Taha Y. Taha

University of California, San Francisco (UCSF) - Gladstone Institutes

Renuka Kumar

University of California, San Francisco (UCSF) - Gladstone Institutes

Jack Z. Li

University of California, San Francisco (UCSF) - Department of Surgery

Vivianne W. Ding

University of California, San Francisco (UCSF) - Department of Surgery

Shotaro Matsumoto

University of California, San Francisco (UCSF) - Cardiovascular Research Institute

Mazharul Maishan

University of California, San Francisco (UCSF) - Cardiovascular Research Institute

Bharath Sreekumar

University of California, San Francisco (UCSF) - Gladstone Institutes

Camille Simoneau

University of California, San Francisco (UCSF) - Gladstone Institutes

Irina Nazarenko

University of Freiburg - Center for Complementary Medicine, Institute for Infection Prevention and Hospital Epidemiology, Medical Center

Michael Tomlinson

University of Birmingham - School of Biosciences

Khadija Khan

Africa Health Research Institute

Ann Von Gottberg

University of the Witwatersrand - Department of Clinical Microbiology and Infectious Diseases

Alex Sigal

Africa Health Research Institute

Mark R. Looney

University of California, San Francisco (UCSF) - ImmunoX Initiative

Gabriela K. Fragiadakis

University of California, San Francisco (UCSF) - UCSF CoLabs; University of California, San Francisco (UCSF)

David M. Jablons

Division of Pulmonary and Critical Care

Charles Langelier

University of California, San Francisco (UCSF) - Division of Infectious Diseases

Michael A. Matthay

Division of Pulmonary and Critical Care

Matthew F. Krummel

University of California, San Francisco (UCSF) - Department of Pathology; University of California, San Francisco (UCSF) - Department of Anatomy

David J. Erle

University of California, San Francisco (UCSF) - UCSF CoLabs

Alexis J. Combes

University of California, San Francisco (UCSF) - UCSF CoLabs

Anita Sil

University of California, San Francisco (UCSF) - Department of Microbiology and Immunology

Melanie Ott

University of California, San Francisco (UCSF) - Gladstone Institutes

Johannes R. Kratz

University of California, San Francisco (UCSF) - ImmunoX Initiative

Jeroen P. Roose

University of California, San Francisco (UCSF) - Department of Anatomy

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Abstract

Ancestral SARS coronavirus-2 (SARS-CoV-2) and variants of concern (VOC) caused a global pandemic with a spectrum of disease variation linked to immune dysfunction. The mechanistic underpinnings of variation related to lung epithelium are relatively understudied. Here, we biobanked lung organoids by preserving stem cell function. We optimized viral infection with H1N1 swine flu and next comprehensively characterized epithelial responses to SARS-CoV-2 infection in phenotypically stable lung organoids from twenty different subjects. We discovered Tetraspanin 8 (TSPAN8) as a novel mediator of SARS-CoV-2-infection. TSPAN8 facilitates SARS-CoV-2 infection rates but does not via enhanced ACE-2-mediated entry.  In head-to-head comparisons with Ancestral SARS-CoV-2, Delta- and Omicron- VOC displayed lower overall infection rates of organoids but triggered increased epithelial interferon responses. All variants shared highest tropism for ciliated- and goblet- cells. ACE2- and TSPAN8- expression are universal features of infected cells. TSPAN8-blocking antibodies diminish SARS-CoV-2 infection and may spur novel avenues for COVID-19 therapy.

Funding Information: Most of the work was supported by an Administrative COVID-19 Supplement 3P01AI091580- 09S1 (to JPR) on the parent NIH/NIAID P01-AI091580 (Weiss). Organoids were generated in the Roose Organoid D2B unit, started through a UCSF PBBR TMC (Technologies, methodologies, and Cores) grant in 2018 and a gift from the Pathology department and now, in part, funded through a Mark Foundation for Cancer Research Endeavor Program grant (all to JPR). KB is a Mark Foundation Momentum fellow. The UCSF CoLabs and BSL-3 Junior CoLab are in part supported by the Bakar ImmunoX Initiative. JRK is funded by the UCSF Bakar ImmunoX Initiative, the UCSF Helen Diller Family Cancer Center, and the American Association for Thoracic Surgery Foundation. DMJ is funded by a private endowment fund. Human Frontier Science 20 Program Fellowship LT000061/2018-L to NKS Additional funds gave a grant from the Innovative Genomics Institute and UCSF PBBR (M.O.). M.O. thanks the Rodenberry foundation, NIH grant R37AI083139, and the Gladstone Institutes for their support. We thank the Core Facility Signaling Factory of the University Freiburg for providing the plasmids and cloning service of the plasmids. DJE and LRB are supported by NIH grants U19 AI077439 and R35 HL145235. AS was supported by the Bill and Melinda Gates award INV-018944, National Institutes of Health award R01 AI138546 and South African Medical Research Council award 6084-CO-AP-2020.

Declaration of Interests: The authors have no potential conflicts of interest. A patent “INHIBITORS OF SARS-COV-2 INFECTION AND OTHER CORONA VIRUS INFECTIONS” SF-2021-201-2- PCT-0 has been filed.

Ethics Approval Statement: Human cancer patient samples, 2425LL, 2450UL, 2477UL, 2478UL, 2520LL, 2521UL, 2522UL, 2524UL, 2525UL, 2526UL,2527UL, 2531UL, 2547UL, 2551ML, were collected under UCSF study CC#00654 (IRB 11-06107) from patients undergoing thoracic surgery.

Donor lungs rejected for transplantation were received from organ procurement organization (Donor Network West) as previously described (Ross et al., 2019). Explicit approval for the use of donor lungs for research was sought from each donor’s family by Donor Network West as part of the standard organ donation process. Local institutional review board approval is not required because research on tissues from deceased organ donors is not considered human subject research, although institutional biosafety approval was obtained from University of California, San Francisco (UCSF) Institutional Review Board.

Blood samples were obtained after written informed consent from adults with PCR confirmed SARS-CoV-2 infection who were enrolled in a prospective cohort study approved by the Biomedical Research Ethics Committee at the University of KwaZulu– Natal (reference BREC/00001275/2020).

BA.1 and BA.1.1 isolate: The Omicron/BA.1 was isolated from a residual swab sample with SARS-CoV-2 isolation from the sample approved by the University of the Witwatersrand Human Research Ethics Committee (HREC) (ref. M210752) as described in Cele et al (Cele et al., 2022).

Keywords: Organoids, Biobank, Lung, Infection, Influenzas, SARS-CoV-2

Suggested Citation

Hysenaj, Lisiena and Little, Samantha and Kulhanek, Kayla R. and Magnen, Melia and Bahl, Kriti and Gbenedio, Oghenekevwe M. Gbenedio and Prinz, Morgan and Rodriguez, Lauren and Andersen, Christopher and Rao, Arjun Arkal and Shen, Alan and Lone, Jean Christophe and Lupin Jimenez, Leonard C. and Bonser, Luke and Serwas, Nina K. and Mick, Eran and Khalid, Mir M. and Taha, Taha Y. and Kumar, Renuka and Li, Jack Z. and Ding, Vivianne W. and Matsumoto, Shotaro and Maishan, Mazharul and Sreekumar, Bharath and Simoneau, Camille and Nazarenko, Irina and Tomlinson, Michael and Khan, Khadija and Von Gottberg, Ann and Sigal, Alex and Looney, Mark R. and Fragiadakis, Gabriela K. and Jablons, David M. and Langelier, Charles and Matthay, Michael A. and Krummel, Matthew F. and Erle, David J. and Combes, Alexis J. and Sil, Anita and Ott, Melanie and Kratz, Johannes R. and Roose, Jeroen P., SARS-CoV-2 Infection of Lung Organoids Reveals Conserved Use of Tetraspanin-8 by Ancestral-, Delta-, and Omicron- Variants. Available at SSRN: https://ssrn.com/abstract=4198511 or http://dx.doi.org/10.2139/ssrn.4198511
This version of the paper has not been formally peer reviewed.

Lisiena Hysenaj

University of California, San Francisco (UCSF) - Department of Anatomy ( email )

Samantha Little

University of California, San Francisco (UCSF) - Department of Anatomy ( email )

Kayla R. Kulhanek

University of California, San Francisco (UCSF) - Department of Anatomy ( email )

Melia Magnen

University of California, San Francisco (UCSF) - ImmunoX Initiative ( email )

San Francisco, CA
United States

Kriti Bahl

University of California, San Francisco (UCSF) - Department of Anatomy ( email )

Oghenekevwe M. Gbenedio Gbenedio

University of California, San Francisco (UCSF) - Department of Anatomy ( email )

Morgan Prinz

University of California, San Francisco (UCSF) - Department of Anatomy ( email )

Lauren Rodriguez

University of California, San Francisco (UCSF) - Department of Microbiology and Immunology ( email )

San Francisco, CA 94143
United States

Christopher Andersen

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

Arjun Arkal Rao

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

Alan Shen

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

Jean Christophe Lone

University of Essex - School of Life Science ( email )

Wivenhoe Park
Colchester, C04 3SQ
United Kingdom

Leonard C. Lupin Jimenez

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

Luke Bonser

University of California, San Francisco (UCSF) - Lung Biology Center ( email )

San Francisco, CA
United States

Nina K. Serwas

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Eran Mick

University of California, San Francisco (UCSF) - Division of Infectious Diseases ( email )

San Francisco, CA
United States

Mir M. Khalid

University of California, San Francisco (UCSF) - Gladstone Institutes ( email )

1650 OWENS STREET
San Francisco, CA 94158
United States

Taha Y. Taha

University of California, San Francisco (UCSF) - Gladstone Institutes ( email )

1650 OWENS STREET
San Francisco, CA 94158
United States

Renuka Kumar

University of California, San Francisco (UCSF) - Gladstone Institutes ( email )

1650 OWENS STREET
San Francisco, CA 94158
United States

Jack Z. Li

University of California, San Francisco (UCSF) - Department of Surgery ( email )

San Francisco, CA
United States

Vivianne W. Ding

University of California, San Francisco (UCSF) - Department of Surgery ( email )

San Francisco, CA
United States

Shotaro Matsumoto

University of California, San Francisco (UCSF) - Cardiovascular Research Institute ( email )

San Francisco, CA 94143
United States

Mazharul Maishan

University of California, San Francisco (UCSF) - Cardiovascular Research Institute ( email )

San Francisco, CA 94143
United States

Bharath Sreekumar

University of California, San Francisco (UCSF) - Gladstone Institutes ( email )

1650 OWENS STREET
San Francisco, CA 94158
United States

Camille Simoneau

University of California, San Francisco (UCSF) - Gladstone Institutes ( email )

1650 OWENS STREET
San Francisco, CA 94158
United States

Irina Nazarenko

University of Freiburg - Center for Complementary Medicine, Institute for Infection Prevention and Hospital Epidemiology, Medical Center ( email )

Breisacher Str. 115B
Freiburg, 79110

Michael Tomlinson

University of Birmingham - School of Biosciences ( email )

Birmingham
United Kingdom

Khadija Khan

Africa Health Research Institute ( email )

719 Umbilo Road
K-RITH Tower Building, level 3
Durban, KwaZulu-Natal 4001
South Africa

Ann Von Gottberg

University of the Witwatersrand - Department of Clinical Microbiology and Infectious Diseases ( email )

Alex Sigal

Africa Health Research Institute ( email )

Mark R. Looney

University of California, San Francisco (UCSF) - ImmunoX Initiative ( email )

San Francisco, CA
United States

Gabriela K. Fragiadakis

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

University of California, San Francisco (UCSF) ( email )

David M. Jablons

Division of Pulmonary and Critical Care ( email )

United States

Charles Langelier

University of California, San Francisco (UCSF) - Division of Infectious Diseases ( email )

San Francisco, CA
United States

Michael A. Matthay

Division of Pulmonary and Critical Care ( email )

San Francisco, CA 94143
United States

Matthew F. Krummel

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

University of California, San Francisco (UCSF) - Department of Anatomy ( email )

San Francisco, CA 94143
United States

David J. Erle

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

Alexis J. Combes

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

Anita Sil

University of California, San Francisco (UCSF) - Department of Microbiology and Immunology ( email )

San Francisco, CA 94143
United States

Melanie Ott

University of California, San Francisco (UCSF) - Gladstone Institutes ( email )

Johannes R. Kratz

University of California, San Francisco (UCSF) - ImmunoX Initiative ( email )

San Francisco, CA
United States

Jeroen P. Roose (Contact Author)

University of California, San Francisco (UCSF) - Department of Anatomy ( email )

San Francisco, CA 94143
United States

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