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

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.

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 Statement	not detected.
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Sex as a biological variable	not detected.
Cell Line Authentication	Authentication: A vial of STR authenticated Caco-2 cells was obtained from the UCSF Cell and Genome Engineering Core (

Table 2: Resources

Antibodies
Sentences	Resources
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 …

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 Statement	not detected.
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Sex as a biological variable	not detected.
Cell Line Authentication	Authentication: A vial of STR authenticated Caco-2 cells was obtained from the UCSF Cell and Genome Engineering Core (

Table 2: Resources

Antibodies
Sentences	Resources
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
Sentences	Resources
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
Sentences	Resources
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:

Identifier	Status	Title
NCT03360006	Recruiting	A Study Evaluating the Safety and Pharmacokinetics of ABBV-7…
NCT04454658	Recruiting	Safety 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.

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