BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2

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Abstract

SARS-CoV-2 infection of human cells is initiated by the binding of the viral Spike protein to its cell-surface receptor ACE2. We conducted a targeted CRISPRi screen to uncover druggable pathways controlling Spike protein binding to human cells. We found that the protein BRD2 is required for ACE2 transcription in human lung epithelial cells and cardiomyocytes, and BRD2 inhibitors currently evaluated in clinical trials potently block endogenous ACE2 expression and SARS-CoV-2 infection of human cells, including those of human nasal epithelia. Moreover, pharmacological BRD2 inhibition with the drug ABBV-744 inhibited SARS-CoV-2 replication in Syrian hamsters. We also found that BRD2 controls transcription of several other genes induced upon SARS-CoV-2 infection, including the interferon response, which in turn regulates the antiviral response. Together, our results pinpoint BRD2 as a potent and essential regulator of the host response to SARS-CoV-2 infection and highlight the potential of BRD2 as a novel therapeutic target for COVID-19.

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  1. SciScore for 10.1101/2021.01.19.427194: (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 AuthenticationAuthentication: A vial of STR authenticated Caco-2 cells was obtained from the UCSF Cell and Genome Engineering Core (

    Table 2: Resources

    Antibodies
    SentencesResources
    CD81 expression was measured 7 days post-transduction by dislodging cells with TrypLE and live cells were stained with APC-conjugated anti-human CD81 antibody (Biolegend 349509).
    anti-human CD81
    suggested: (BioLegend Cat# 349509, RRID:AB_2564020)
    Membranes were washed 4x with TBS + 0.1% Tween-20 and incubated with secondary antibodies (1:10,000 Donkey Anti-Goat-800 [LICOR 926-32214]
    Anti-Goat-800
    suggested: None
    The experiment was performed with the included IgG and H3K4Me control antibodies and the BRD2 antibody (abcam 197865) as well as E.coli spike-in DNA according to the kit protocol.
    H3K4Me control
    suggested: None
    BRD2
    suggested: (Abcam Cat# ab197865, RRID:AB_2868601)
    Experimental Models: Cell Lines
    SentencesResources
    Cell Culture: Calu-3 cells were cultured in RPMI 1640 (Life Technologies 22400-105) with 10% FBS (VWR 89510-186), 1% Pen/Strep (Life Technologies 15140122), and 5 mM Glutamine (Life Technologies 25030081) at 37 °C and 5% CO2 Cells were split by treating with TrypLE (Life Technologies 12604013) for 15 minutes, quenching with media and spun down at 200xg for 5 minutes.
    Calu-3
    suggested: KCLB Cat# 30055, RRID:CVCL_0609)
    HEK293 cell culture and production of lentivirus was performed as previously described39.
    HEK293
    suggested: None
    A vial of STR authenticated Caco-2 cells was obtained from the UCSF Cell and Genome Engineering Core (
    Caco-2
    suggested: None
    A549 cells were cultured in DMEM (Thermo Fisher Scientific, 10313-039) with 10% FBS (VWR 89510-186), 1% Pen/Strep (Life Technologies 15140122), and 5 mM Glutamine (Life Technologies 25030081) at 37 °C and 5% CO2.
    A549
    suggested: None
    To validate the CRISPRi line, Calu-3-CRISPRi cells were transduced with lentiviral particles expressing non-targeting sgRNA (protospacer 5’-GCTCCCAGTCGGCACCACAG-3’) or CD81-targeting sgRNA (protospacer 5’-GGCCTGGCAGGATGCGCGG-3’)
    Calu-3-CRISPRi
    suggested: None
    Virus: The SARS-CoV-2 strain used (BetaCoV/France/IDF0372/2020 strain) was propagated once in Vero-E6 cells and is a kind gift from the National Reference Centre for Respiratory Viruses at Institut Pasteur, Paris, originally supplied through the European Virus Archive goes Global platform.
    Vero-E6
    suggested: None
    Software and Algorithms
    SentencesResources
    Subsequently, differential gene-expression analyses were performed using the glmQLFTest method implemented in the edgeR package47(v3.28.1).
    edgeR
    suggested: (edgeR, RRID:SCR_012802)
    Briefly, paired-end reads were mapped to the human genome GRCh38 using Bowtie2 (v2.3.4.1) with options: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 1000.
    Bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    Published BRD2 ChIP-seq data in human lung cells was obtained from ChIP-Atlas (https://chip-atlas.org/).
    ChIP-Atlas
    suggested: (ChIP-Atlas, RRID:SCR_015511)

    Results from OddPub: Thank you for sharing your data.


    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: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT03360006RecruitingA Study Evaluating the Safety and Pharmacokinetics of ABBV-7…
    NCT04454658RecruitingSafety and Tolerability Study of Oral ABBV-744 Tablet Alone …


    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

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