Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection

Cell. 2021 Jan 7;184(1):76-91.e13. doi: 10.1016/j.cell.2020.10.028. Epub 2020 Oct 20.

Abstract

Identification of host genes essential for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may reveal novel therapeutic targets and inform our understanding of coronavirus disease 2019 (COVID-19) pathogenesis. Here we performed genome-wide CRISPR screens in Vero-E6 cells with SARS-CoV-2, Middle East respiratory syndrome CoV (MERS-CoV), bat CoV HKU5 expressing the SARS-CoV-1 spike, and vesicular stomatitis virus (VSV) expressing the SARS-CoV-2 spike. We identified known SARS-CoV-2 host factors, including the receptor ACE2 and protease Cathepsin L. We additionally discovered pro-viral genes and pathways, including HMGB1 and the SWI/SNF chromatin remodeling complex, that are SARS lineage and pan-coronavirus specific, respectively. We show that HMGB1 regulates ACE2 expression and is critical for entry of SARS-CoV-2, SARS-CoV-1, and NL63. We also show that small-molecule antagonists of identified gene products inhibited SARS-CoV-2 infection in monkey and human cells, demonstrating the conserved role of these genetic hits across species. This identifies potential therapeutic targets for SARS-CoV-2 and reveals SARS lineage-specific and pan-CoV host factors that regulate susceptibility to highly pathogenic CoVs.

Keywords: COVID-19; CRISPR screen; Epigenetics; HMGB1; MERS-CoV; Middle East Respiratory Syndrome; SARS-CoV-2; SWI/SNF complex; Severe Acute Respiratory Syndrome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Angiotensin-Converting Enzyme 2 / metabolism
  • Animals
  • COVID-19 / immunology
  • COVID-19 / virology
  • Cell Line
  • Chlorocebus aethiops
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Coronavirus / classification
  • Coronavirus Infections / drug therapy
  • Coronavirus Infections / genetics*
  • Coronavirus Infections / immunology
  • Gene Knockout Techniques
  • Gene Regulatory Networks
  • Genome-Wide Association Study*
  • HEK293 Cells
  • HMGB1 Protein / genetics
  • HMGB1 Protein / metabolism
  • Host-Pathogen Interactions* / drug effects
  • Humans
  • SARS-CoV-2 / physiology*
  • Vero Cells
  • Virus Internalization

Substances

  • HMGB1 Protein
  • Angiotensin-Converting Enzyme 2