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
More...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
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