A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets

  1. Annika Kratzel
  2. Jenna N. Kelly
  3. Yannick Brueggemann
  4. Jasmine Portmann
  5. Philip V’kovski
  6. Daniel Todt
  7. Nadine Ebert
  8. Eike Steinmann
  9. Ronald Dijkman
  10. Gert Zimmer
  11. Stephanie Pfaender
  12. Volker Thiel

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Abstract

Over the past 20 years, the emergence of three highly pathogenic coronaviruses (CoV) – SARS-CoV, MERS-CoV, and most recently SARS-CoV-2 – has shown that CoVs pose a serious risk to human health and highlighted the importance of developing effective therapies against them. Similar to other viruses, CoVs are dependent on host factors for their survival and replication. We hypothesized that evolutionarily distinct CoVs may exploit similar host factors and pathways to support their replication cycle. Here, we conducted two independent genome-wide CRISPR/Cas9 knockout screens to identify pan-CoV host factors required for the replication of both endemic and emerging CoVs, including the novel CoV SARS-CoV-2. Strikingly, we found that several autophagy-related genes, including the immunophilin FKBP8, TMEM41B, and MINAR1, were common host factors required for CoV replication. Importantly, inhibition of the immunophilin family with the compounds Tacrolimus, Cyclosporin A, and the non-immunosuppressive derivative Alisporivir, resulted in dose-dependent inhibition of CoV replication in primary human nasal epithelial cell cultures that resemble the natural site of virus replication. Overall, we identified host factors that are crucial for CoV replication and demonstrate that these factors constitute potential targets for therapeutic intervention by clinically approved drugs.

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    SciScore for 10.1101/2021.02.24.432634: (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.

    Table 2: Resources

    No key resources detected.

    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: We detected the following sentences addressing limitations in the study:
    To address these limitations, we also tested these drugs on primary human nasal epithelial cell cultures and found that both Alisporivir and Cyclosporin A potently inhibit SARS-CoV-2 replication at concentrations known to be achievable and efficacious in patients. Together these findings depict a promising path towards the repurposing of Cyclosporin A and Alisporivir as COVID-19 treatment options. Infection with highly pathogenic CoVs is frequently accompanied by inflammatory immunopathogenesis, including the virus-induced destruction of lung tissue and subsequent triggering of a host immune response. Importantly, in certain cases a dysregulated immune response is associated with severe lung pathology and systemic pathogenesis34. The latter highlights the need for dual-acting antiviral drugs that also target inflammation and/or cell death. Of interest, Alisporivir also blocks mitochondrial cyclophilin-D, a key regulator of mitochondrial permeability transition pore (mPTP) opening, which is a mechanism involved in triggering cell death. Hence, besides its antiviral properties, it is possible that Alisporivir also reduces CoV-induced lung tissue damage65. Trials using either Cyclosporin in patients with moderate COVID-19 (ClinicalTrials.gov Identifier: NCT04412785 and NCT04540926) or Alisporivir (ClinicalTrials.gov Identifier: NCT04608214) for the treatment of hospitalized COVID19 patients have been registered. The identification of MINAR1, TMEM41 and FKBP8 as conserved HCoVs H...

    Results from TrialIdentifier: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT04412785RecruitingCyclosporine in Patients With Moderate COVID-19
    NCT04540926Not yet recruitingCyclosporine A Plus Low-steroid Treatment in COVID-19 Pneumo…
    NCT04608214Not yet recruitingEvaluation of Alisporivir for the Treatment of Hospitalised …

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

    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

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  2. Version published to 10.1101/2021.02.24.432634 on bioRxiv