SARS-CoV-2 induces double-stranded RNA-mediated innate immune responses in respiratory epithelial derived cells and cardiomyocytes

  1. Yize Li
  2. David M Renner
  3. Courtney E Comar
  4. Jillian N Whelan
  5. Hanako M Reyes
  6. Fabian Leonardo Cardenas-Diaz
  7. Rachel Truitt
  8. Li Hui Tan
  9. Beihua Dong
  10. Konstantinos Dionysios Alysandratos
  11. Jessie Huang
  12. James N. Palmer
  13. Nithin D. Adappa
  14. Michael A. Kohanski
  15. Darrell N. Kotton
  16. Robert H Silverman
  17. Wenli Yang
  18. Edward Morrisey
  19. Noam A. Cohen
  20. Susan R Weiss

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Abstract

Coronaviruses are adept at evading host antiviral pathways induced by viral double-stranded RNA, including interferon (IFN) signaling, oligoadenylate synthetase–ribonuclease L (OAS-RNase L), and protein kinase R (PKR). While dysregulated or inadequate IFN responses have been associated with severe coronavirus infection, the extent to which the recently emerged SARS-CoV-2 activates or antagonizes these pathways is relatively unknown. We found that SARS-CoV-2 infects patient-derived nasal epithelial cells, present at the initial site of infection, induced pluripotent stem cell-derived alveolar type 2 cells (iAT2), the major cell type infected in the lung, and cardiomyocytes (iCM), consistent with cardiovascular consequences of COVID-19 disease. Robust activation of IFN or OAS-RNase L is not observed in these cell types, while PKR activation is evident in iAT2 and iCM. In SARS-CoV-2 infected Calu-3 and A549 ACE2 lung-derived cell lines, IFN induction remains relatively weak; however activation of OAS-RNase L and PKR is observed. This is in contrast to MERS-CoV, which effectively inhibits IFN signaling as well as OAS-RNase L and PKR pathways, but similar to mutant MERS-CoV lacking innate immune antagonists. Remarkably, both OAS-RNase L and PKR are activated in MAVS knockout A549 ACE2 cells, demonstrating that SARS-CoV-2 can induce these host antiviral pathways despite minimal IFN production. Moreover, increased replication and cytopathic effect in RNASEL knockout A549 ACE2 cells implicates OAS-RNase L in restricting SARS-CoV-2. Finally, while SARS-CoV-2 fails to antagonize these host defense pathways, which contrasts with other coronaviruses, the IFN signaling response is generally weak. These host-virus interactions may contribute to the unique pathogenesis of SARS-CoV-2.

Significance

SARS-CoV-2 emergence in late 2019 led to the COVID-19 pandemic that has had devastating effects on human health and the economy. Early innate immune responses are essential for protection against virus invasion. While inadequate innate immune responses are associated with severe COVID-19 diseases, understanding of the interaction of SARS-CoV-2 with host antiviral pathways is minimal. We have characterized the innate immune response to SARS-CoV-2 infections in relevant respiratory tract derived cells and cardiomyocytes and found that SARS-CoV-2 activates two antiviral pathways, oligoadenylate synthetase–ribonuclease L (OAS-RNase L), and protein kinase R (PKR), while inducing minimal levels of interferon. This in contrast to MERS-CoV which inhibits all three pathways. Activation of these pathways may contribute to the distinctive pathogenesis of SARS-CoV-2.

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  1. ScreenIT

    SciScore for 10.1101/2020.09.24.312553: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Viruses: SARS-CoV-2 (USA-WA1/2020 strain) was obtained from BEI and propagated in Vero-E6 cells.
    Vero-E6
    suggested: None
    Recombinant MERS-CoV and MERS-CoV-ΔNS4ab were described previously (10) and were propagated in Vero-CCL81 cells.
    Vero-CCL81
    suggested: None
    Cell lines: African green monkey kidney Vero cells (E6) or (CCL81) (obtained from ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco catalog no. 11965), supplemented with 10% fetal bovine serum (FBS), 100 U/ml of penicillin, 100 μg/ml streptomycin, 50 μg/ml gentamicin, 1mM sodium pyruvate, and 10mM HEPES.
    Vero
    suggested: ATCC Cat# CCL-81, RRID:CVCL_0059)
    Human A549 cells (verified by ATCC) were cultured in RPMI 1640 (Gibco catalog no. 11875) supplemented with 10% FBS, 100 U/ml of penicillin, and 100 μg/ml streptomycin.
    A549
    suggested: None
    Human HEK 293T cells were cultured in DMEM supplemented with 10% FBS and 1 mM sodium pyruvate.
    HEK 293T
    suggested: None
    Human Calu-3 cells (clone HTB-55) were cultured in MEM supplemented with 20% FBS without antibiotics.
    Calu-3
    suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)

    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 49 and 50. 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.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

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  2. Version published to 10.1101/2020.09.24.312553 on bioRxiv