Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses

Ruofan Wang; Camille R Simoneau; Jessie Kulsuptrakul; Mehdi Bouhaddou; Katherine A Travisano; Jennifer M Hayashi; Jared Carlson-Stevermer; James R Zengel; Christopher M Richards; Parinaz Fozouni; Jennifer Oki; Lauren Rodriguez; Bastian Joehnk; Keith Walcott; Kevin Holden; Anita Sil; Jan E Carette; Nevan J Krogan; Melanie Ott; Andreas S Puschnik

doi:10.1016/j.cell.2020.12.004

Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses

Cell. 2021 Jan 7;184(1):106-119.e14. doi: 10.1016/j.cell.2020.12.004. Epub 2020 Dec 9.

Authors

Ruofan Wang¹, Camille R Simoneau², Jessie Kulsuptrakul¹, Mehdi Bouhaddou³, Katherine A Travisano¹, Jennifer M Hayashi⁴, Jared Carlson-Stevermer⁵, James R Zengel⁶, Christopher M Richards⁶, Parinaz Fozouni⁷, Jennifer Oki⁵, Lauren Rodriguez⁸, Bastian Joehnk⁹, Keith Walcott⁹, Kevin Holden⁵, Anita Sil⁹, Jan E Carette⁶, Nevan J Krogan³, Melanie Ott¹⁰, Andreas S Puschnik¹¹

Affiliations

¹ Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
² Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA.
³ Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
⁴ Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA.
⁵ Synthego Corporation, Menlo Park, CA 94025, USA.
⁶ Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
⁷ Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA.
⁸ UCSF CoLabs, Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
⁹ Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
¹⁰ Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: [email protected].
¹¹ Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address: [email protected].

Abstract

The Coronaviridae are a family of viruses that cause disease in humans ranging from mild respiratory infection to potentially lethal acute respiratory distress syndrome. Finding host factors common to multiple coronaviruses could facilitate the development of therapies to combat current and future coronavirus pandemics. Here, we conducted genome-wide CRISPR screens in cells infected by SARS-CoV-2 as well as two seasonally circulating common cold coronaviruses, OC43 and 229E. This approach correctly identified the distinct viral entry factors ACE2 (for SARS-CoV-2), aminopeptidase N (for 229E), and glycosaminoglycans (for OC43). Additionally, we identified phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis as critical host pathways supporting infection by all three coronaviruses. By contrast, the lysosomal protein TMEM106B appeared unique to SARS-CoV-2 infection. Pharmacological inhibition of phosphatidylinositol kinases and cholesterol homeostasis reduced replication of all three coronaviruses. These findings offer important insights for the understanding of the coronavirus life cycle and the development of host-directed therapies.

Keywords: 229E; COVID-19; CRISPR; OC43; SARS-CoV-2; coronavirus; genetic screen; host factors; host-targeted antivirals; virus-host interactions.

Publication types

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

MeSH terms

A549 Cells
Animals
Biosynthetic Pathways / drug effects
COVID-19 / genetics*
COVID-19 / virology
Cell Line
Chlorocebus aethiops
Cholesterol / biosynthesis
Cholesterol / metabolism
Cluster Analysis
Clustered Regularly Interspaced Short Palindromic Repeats
Common Cold / genetics
Common Cold / virology
Coronavirus / classification
Coronavirus / physiology*
Coronavirus Infections / genetics*
Coronavirus Infections / virology
Gene Knockout Techniques
Genome-Wide Association Study*
Host-Pathogen Interactions* / drug effects
Humans
Mice
Phosphatidylinositols / biosynthesis
SARS-CoV-2 / physiology*
Vero Cells
Virus Internalization / drug effects
Virus Replication

Substances

Phosphatidylinositols
Cholesterol

Abstract

Publication types

MeSH terms

Substances

Grants and funding