Opposing activities of IFITM proteins in SARS-CoV-2 infection

  1. Guoli Shi
  2. Adam D. Kenney
  3. Elena Kudryashova
  4. Lizhi Zhang
  5. Luanne Hall-Stoodley
  6. Richard T. Robinson
  7. Dmitri S. Kudryashov
  8. Alex A. Compton
  9. Jacob S. Yount

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Abstract

Interferon-induced transmembrane proteins (IFITMs) restrict infections by many viruses, but a subset of IFITMs enhance infections by specific coronaviruses through currently unknown mechanisms. Here we show that SARS-CoV-2 Spike-pseudotyped virus and genuine SARS-CoV-2 infections are generally restricted by expression of human IFITM1, IFITM2, and IFITM3, using both gain- and loss-of-function approaches. Mechanistically, restriction of SARS-CoV-2 occurred independently of IFITM3 S -palmitoylation sites, indicating a restrictive capacity that is distinct from reported inhibition of other viruses. In contrast, the IFITM3 amphipathic helix and its amphipathic properties were required for virus restriction. Mutation of residues within the human IFITM3 endocytosis-promoting YxxΦ motif converted human IFITM3 into an enhancer of SARS-CoV-2 infection, and cell-to-cell fusion assays confirmed the ability of endocytic mutants to enhance Spike-mediated fusion with the plasma membrane. Overexpression of TMPRSS2, which reportedly increases plasma membrane fusion versus endosome fusion of SARS-CoV-2, attenuated IFITM3 restriction and converted amphipathic helix mutants into strong enhancers of infection. In sum, these data uncover new pro- and anti-viral mechanisms of IFITM3, with clear distinctions drawn between enhancement of viral infection at the plasma membrane and amphipathicity-based mechanisms used for endosomal virus restriction. Indeed, the net effect of IFITM3 on SARS-CoV-2 infections may be a result of these opposing activities, suggesting that shifts in the balance of these activities could be coopted by viruses to escape this important first line innate defense mechanism.

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    SciScore for 10.1101/2020.08.11.246678: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIACUC: Biosafety: All work with live SARS-CoV-2 was performed at Biosafety Level 3 (BSL3) according to standard operating procedures approved by the Ohio State University BSL3 Operations Group and Institutional Biosafety Committee.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line AuthenticationAuthentication: The origin of our U2OS cells are unknown, but the identity and purity of the cells were verified by STR profiling.
    Contamination: Vero E6 cells were a kind gift from Dr. Mark Peeples (Nationwide Children’s Hospital) and were treated with Mycoplasma Removal Agent (MP Biomedical) for 1 month to ensure lack of contamination before virus propagation.

    Table 2: Resources

    Antibodies
    SentencesResources
    Primary antibody labeling was followed by labeling with anti-mouse-AlexaFluor-647 and anti-rabbit-AlexaFluor-555 secondary antibodies (Life Technologies).
    anti-mouse-AlexaFluor-647
    suggested: None
    anti-rabbit-AlexaFluor-555
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    HEK293T, Calu-3, and Caco-2 were purchased from ATCC.
    Calu-3
    suggested: KCLB Cat# 30055, RRID:CVCL_0609)
    Vero E6 cells were a kind gift from Dr. Mark Peeples (Nationwide Children’s Hospital) and were treated with Mycoplasma Removal Agent (MP Biomedical) for 1 month to ensure lack of contamination before virus propagation.
    Vero E6
    suggested: RRID:CVCL_XD71)
    HEK293T cells stably expressing GFP-tagged human ACE2 (Origene) were generated using the same methodology.
    HEK293T
    suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
    Type-I interferon (human recombinant interferon beta, NR-3085, BEI Resources) was added to Caco-2 cells at 48h post siRNA transfection at a concentration of 250 IU/mL.
    Caco-2
    suggested: None
    The viral stock titer was further confirmed by standard plaque assay with 0.3% agarose (Sigma) overlay and visualization with 0.25% Crystal Violet (Sigma) in Vero cells.
    Vero
    suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
    Cell fusion assay: Using Lipofectamine 3000 (Life Technologies), U2OS cells were co-transfected with pmCherry and either empty pCAGGS vector or SARS-CoV-2 Spike Glycoprotein (BEI Resources, deposited by Dr. Florian Krammer
    U2OS
    suggested: CLS Cat# 300364/p489_U-2_OS, RRID:CVCL_0042)
    Software and Algorithms
    SentencesResources
    Data analysis was performed using FlowJo software.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 18 and 19. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.08.11.246678 on bioRxiv