CRISPR screens for host factors critical for infection by SARS-CoV-2 variants of concern identify GATA6 as a central modulator of ACE2

Abstract

The global spread of SARS-CoV-2 lead to the most challenging pandemic in this century, posing major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SASR-CoV-2 can provide insights into the virus pathogenesis, and facilitates the development of novel broad-spectrum host-directed therapeutics. Here, employing genome-scale CRISPR screens, we provide a comprehensive data-set of cellular factors that are exploited by WT-SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. These screens identified known and novel host factors critical for SARS-CoV-2 infection, including various components belonging to the Clathrin-dependent transport pathway, ubiquitination and Heparan sulfate biogenesis. In addition, the host metabolic pathways pertaining to mitochondrial activity as well as phosphatidylglycerol biosynthesis processes appeared to have major anti-viral functions. Comparative analysis between the different VOCs revealed the receptor KREMEN2 as unique gene required only to the Alpha variant, providing a possible explanation for the increased infectivity of this variant. Furthermore, the analysis identified GATA6, a zinc finger transcription factor, as an essential pro-viral gene for all variants inspected. We reveal that GATA6 directly regulates ACE2 transcription and is accordingly, critical for SARS-CoV-2 cell entry. Analysis of clinical samples collected from SARS-CoV-2 infected individuals showed an elevated level of GATA6, indicating the important role GATA6 may be playing in COVID-19 pathogenesis. Finally, pharmacological inhibition of GATA6 results in down-modulation of ACE2 and consequently to inhibition of the viral infectivity. Overall, we show GATA6 represents a target for the development of anti-SARS-CoV-2 therapeutic strategies and reaffirm the value of the CRISPR loss-of-function screens in providing a list of potential new targets for therapeutic interventions.

LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein

“…Both screens identified ACE2 as the top-ranked gene as expected, along with other known spike-binding receptors including CLEC4M in the arrayed screen (Fig 1C and S2 Data) and the transcription factor GATA6 in the CRISPR activation screen [20] (Fig 1D and S3 Data). The CRISPR activation (CRISPRa) screen was able to detect even weak spike binding signals, identifying the transcription factor EBF1 despite causing only a small increase in ACE2 levels (S2 Fig and S1 Table and S4 Data).…”

LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein

“…Both screens identified ACE2 as the top-ranked gene as expected, along with other known spikebinding receptors including CLEC4M in the arrayed screen (Figure 1C) and the transcription factor GATA6 in the CRISPR activation screen (Israeli et al, 2021) (Figure 1D). The CRISPRa screen was able to detect even weak spike binding signals, identifying the transcription factor EBF1 despite causing only a small increase in ACE2 levels (Supplemental Figure 2, Supplementary Table 1).…”

PCIF1-mediated deposition of 5′-cap N 6 ,2′- O -dimethyladenosine in ACE2 and TMPRSS2 mRNA regulates susceptibility to SARS-CoV-2 infection

“…Several studies have shown ACE2 transcription in human cells is regulated by multiple factors ( 31 – 33 ). Wei et al.…”

“…found that bromodomain-containing protein 2 (BRD2), a transcriptional regulator, promotes ACE2 transcription, and the authors further demonstrated that the BRD2 inhibitor ABBV-774 inhibited SARS-CoV-2 infection in vitro and in vivo ( 32 ). The transcriptional regulator GATA-binding protein 6 (GATA6) was shown to affect the susceptibility of Calu-3 cells to SARS-CoV-2 infection by directly binding to the ACE2 promoter ( 33 ). Thus, multiple host factors have been implicated in regulating cellular susceptibility to SARS-CoV-2 infection through modulation of ACE2 transcription.…”