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Identification of Required Host Factors for SARSCoV-2 Infection in Human Cells

To identify potential therapeutic targets for SARS-CoV-2, Daniloski and collaborators from New York University in US, conducted a genome-wide CRISPR screen in human lung epithelial cells. They identify genes and pathways required for SARS-CoV-2 infection, including the vacuolar ATPase proton pump, Retromer, and Commander complexes. Using single-cell transcriptomics, they identify the upregulation of cholesterol biosynthesis as a common mechanism underlying viral resistance, in addition to ACE2 sequestration. 


Highlights


  • Genome-wide CRISPR knockout screen identifies host factors for SARS-CoV-2 infection
  • Top-ranked genes include vacuolar ATPases, Retromer, Commander, and Arp2/3 complex 
  • Validation using CRISPR knockout, RNA interference, and small molecule inhibitors Reduced infection via increased cholesterol biosynthesis and sequestration of ACE2

As of October 2020, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has infected 40 million people worldwide and led to the deaths of more than 1 million people, according to the John Hopkins Research Center. 

Given that SARS-CoV-2 has already taken a major toll on human life and livelihoods worldwide, many research institutions, governmental organizations, and pharmaceutical companies are working to identify antiviral drugs and develop vaccines. 

This article shows a genome-scale loss-of-function screen—to identify targets among host genes required for SARS-CoV-2 infection. These gene targets (and inhibitors of these genes) may aid in developing new therapies for COVID-19. SARS-CoV-2 is an enveloped positive-sense RNA virus that relies on host factors for its life cycle stages.

To date, there are no genome-wide studies that directly identify human genes required for viral infection, which will be of great interest and utility for the broader scientific community. This paper shows the genome-scale CRISPR loss-of-function screen in human alveolar basal epithelial carcinoma cells to identify genes whose loss confers resistance to SARS-CoV-2 viral infection. 

They validate that these genes reduce SARS-CoV-2 infection using multiple orthogonal cell perturbations (CRISPR knockout, RNA interference knockdown, and small-molecule inhibitors). They explored potential mechanisms of their antiviral activity using single-cell transcriptomics, flow cytometry, and immunofluorescence for the top gene hits. 

This work provides a quantitative resource of the impact of each gene’s loss on response to viral infection for every protein-coding gene in the human genome.

 

Source: Daniloski et al., Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells, Cell (2021), https://doi.org/10.1016/j.cell.2020.10.030