Genome-wide CRISPR screens identify GATA6 as a proviral host factor for SARS-CoV-2 via modulation of ACE2

Abstract

The global spread of SARS-CoV-2 led to major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SARS-CoV-2 can provide insights into the virus pathogenesis, and facilitate the development of novel therapeutics. Here, employing a genome-scale CRISPR screen, we provide a comprehensive data-set of cellular factors that are exploited by wild type SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. We identified several host factors critical for SARS-CoV-2 infection, including various components belonging to the Clathrin-dependent transport pathway, ubiquitination, Heparan sulfate biogenesis and host phosphatidylglycerol biosynthesis. Comparative analysis of the different VOCs revealed the host factors KREMEN2 and SETDB1 as potential unique candidates required only to the Alpha variant. Furthermore, the analysis identified GATA6, a zinc finger transcription factor, as an essential proviral gene for all variants inspected. We show that GATA6 directly regulates ACE2 transcription and accordingly, is critical for SARS-CoV-2 cell entry. Analysis of clinical samples collected from SARS-CoV-2 infected individuals shows elevated levels of GATA6, suggesting a role in COVID-19 pathogenesis. Finally, pharmacological inhibition of GATA6 resulted in down-modulation of ACE2 and inhibition of viral infectivity. Overall, we show GATA6 may represent 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.

MaGplotR: a software for the analysis and visualization of multiple MaGeCK screen datasets through aggregation

“…This tool has been tested using multiple datasets to offer robust and wide applicability [16–20]. Of note, this tool can be used to detect hits that were previously unnoticed, by aggregating common hits from different experiments, as is the case of GATA6 proviral gene for SARS-CoV-2, which we identified as the 4 th hit using rearranged Biering et al datasets [19], and has been confirmed by Israeli et al [21].…”

Kinase-independent activity of DYRK1A promotes viral entry of highly pathogenic human coronaviruses

“…Located on chromosome Xp22 , ACE2 is an X-linked, dosage-sensitive gene known to be transcriptionally regulated by EP300, SP-1, CEBP, GATA3, and HNF1/4 115,116 . Recent efforts have aimed to identify novel ACE2 modifiers, uncovering PIAS1, SMAD4, BAMBI , KDM6A , and GATA6 111,117 . DPP4 , which is situated on chromosome 2q24, e ncodes a serine exopeptidase that regulates glucose homeostasis 118,119 .…”

SARS-CoV-2 pandemics: An update of CRISPR in diagnosis and host–virus interaction studies

“…The performance of the CRISPR screens was robust, as indicated by the top resistance hits of viral entry receptors identified, such as dipeptidyl peptidase-4 (DPP4) for MERS-CoV, human aminopeptidase N (ANPEP) for HCoV-229E, and ACE2 for SARS-CoV, SARS-CoV-2, and HCoV-NL63 [ [69] , [70] , [71] , [72] , [73] , [74] ]. Unlike other coronaviruses, HCoV-OC43 lacks a recognized proteinaceous receptor, but alternatively relies on sialic acid [ 75 ] or glycosaminoglycans (Neu5, 9Ac2) for cell entry [ 76 ].…”