Type I and Type III IFN Restrict SARS-CoV-2 Infection of Human Airway Epithelial Cultures

  1. Abigail Vanderheiden
  2. Philipp Ralfs
  3. Tatiana Chirkova
  4. Amit A. Upadhyay
  5. Matthew G. Zimmerman
  6. Shamika Bedoya
  7. Hadj Aoued
  8. Gregory M. Tharp
  9. Kathryn L. Pellegrini
  10. Anice C. Lowen
  11. Vineet D. Menachery
  12. Larry J. Anderson
  13. Arash Grakoui
  14. Steven E. Bosinger
  15. Mehul S. Suthar

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Abstract

The newly emerged human coronavirus, SARS-CoV-2, has caused a pandemic of respiratory illness. The innate immune response is critical for protection against Coronaviruses. However, little is known about the interplay between the innate immune system and SARS-CoV-2. Here, we modeled SARS-CoV-2 infection using primary human airway epithelial (pHAE) cultures, which are maintained in an air-liquid interface. We found that SARS-CoV-2 infects and replicates in pHAE cultures and is directionally released on the apical, but not basolateral surface. Transcriptional profiling studies found that infected pHAE cultures had a molecular signature dominated by pro-inflammatory cytokines and chemokine induction, including IL-6, TNFα, CXCL8. We also identified NF-κB and ATF4 transcription factors as key drivers of this pro-inflammatory cytokine response. Surprisingly, we observed a complete lack of a type I or III IFN induction during SARS-CoV-2 infection. Pre-treatment or post-treatment with type I and III IFNs dramatically reduced virus replication in pHAE cultures and this corresponded with an upregulation of antiviral effector genes. Our findings demonstrate that SARS-CoV-2 induces a strong pro-inflammatory cytokine response yet blocks the production of type I and III IFNs. Further, SARS-CoV-2 is sensitive to the effects of type I and III IFNs, demonstrating their potential utility as therapeutic options to treat COVID-19 patients.

IMPORTANCE

The current pandemic of respiratory illness, COVID-19, is caused by a recently emerged coronavirus named SARS-CoV-2. This virus infects airway and lung cells causing fever, dry cough, and shortness of breath. Severe cases of COVID-19 can result in lung damage, low blood oxygen levels, and even death. As there are currently no vaccines or antivirals approved for use in humans, studies of the mechanisms of SARS-CoV-2 infection are urgently needed. SARS-CoV-2 infection of primary human airway epithelial cultures induces a strong pro-inflammatory cytokine response yet blocks the production of type I and III IFNs. Further, SARS-CoV-2 is sensitive to the effects of type I and III IFNs, demonstrating their potential utility as therapeutic options to treat COVID-19 patients.

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  1. ScreenIT

    SciScore for 10.1101/2020.05.19.105437: (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

    Antibodies
    SentencesResources
    Cells were incubated with an anti-SARS-CoV-2 spike protein primary antibody conjugated to biotin (generously provided by Dr. Jens Wrammert, Emory University) for 2 hours at room temperature (RT), then with avidin-HRP conjugated secondary antibody for 1 hour at RT.
    anti-SARS-CoV-2 spike protein
    suggested: None
    avidin-HRP
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Viral titers were determined by plaque assay on VeroE6 cells (ATCC).
    VeroE6
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Vero cells were cultured in complete DMEM medium consisting of 1x DMEM (Corning Cellgro), 10% FBS, 25 mM HEPES Buffer (Corning Cellgro), 2 mM L-glutamine, 1mM sodium pyruvate, 1x Non-essential Amino Acids, and 1x antibiotics.
    Vero
    suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
    Software and Algorithms
    SentencesResources
    Viral genes were mapped to the FDAARGOS_983 strain of the 2019-nCoV/USA-WA1/2020 SARS-CoV2 isolate (GenBank Accession: MT246667.1), using STAR v2.7.3a (41).
    STAR
    suggested: (STAR, RRID:SCR_015899)
    Reads were normalized and differentially expressed genes were analyzed using DESeq2.
    DESeq2
    suggested: (DESeq, RRID:SCR_000154)
    Pathway analysis was performed using Cytoscape software.
    Cytoscape
    suggested: (Cytoscape, RRID:SCR_003032)
    The raw data of all RNA sequencing will be deposited into the Gene Expression Omnibus (GEO) repository and the accession number will be available following acceptance of this manuscript.
    Gene Expression Omnibus
    suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
    Statistical Analysis: Statistical analyses were performed using Graphpad Prism 8, ggplot2 R package, and GSEA software.
    Graphpad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    GSEA
    suggested: (SeqGSEA, RRID:SCR_005724)

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: We did not find any issues relating to colormaps.

    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

    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 10.1101/2020.05.19.105437 on bioRxiv