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

Cell. 2021 Jan 7;184(1):92-105.e16. doi: 10.1016/j.cell.2020.10.030.

Zharko Daniloski ¹, Tristan X Jordan ², Hans-Hermann Wessels ¹, Daisy A Hoagland ², Silva Kasela ³, Mateusz Legut ¹, Silas Maniatis ⁴, Eleni P Mimitou ⁵, Lu Lu ¹, Evan Geller ¹, Oded Danziger ², Brad R Rosenberg ², Hemali Phatnani ⁶, Peter Smibert ⁵, Tuuli Lappalainen ³, Benjamin R tenOever ⁷, Neville E Sanjana ⁸

Affiliations

1 New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA.
2 Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
3 New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA.
4 New York Genome Center, New York, NY, USA.
5 Technology Innovation Lab, New York Genome Center, New York, NY, USA.
6 New York Genome Center, New York, NY, USA; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
7 Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Electronic address: benjamin.tenoever@mssm.edu.
8 New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA. Electronic address: neville@sanjanalab.org.

PMID: 33147445 DOI: 10.1016/j.cell.2020.10.030

Abstract

To better understand host-virus genetic dependencies and find potential therapeutic targets for COVID-19, we performed a genome-scale CRISPR loss-of-function screen to identify host factors required for SARS-CoV-2 viral Infection of human alveolar epithelial cells. Top-ranked genes cluster into distinct pathways, including the vacuolar ATPase Proton Pump, Retromer, and Commander complexes. We validate these gene targets using several orthogonal methods such as CRISPR knockout, RNA interference knockdown, and small-molecule inhibitors. Using single-cell RNA-sequencing, we identify shared transcriptional changes in Cholesterol biosynthesis upon loss of top-ranked genes. In addition, given the key role of the ACE2 receptor in the early stages of viral entry, we show that loss of RAB7A reduces viral entry by sequestering the ACE2 receptor inside cells. Overall, this work provides a genome-scale, quantitative resource of the impact of the loss of each host gene on fitness/response to viral Infection.

Keywords

COVID-19; CRISPR; Cas9; ECCITE-seq; SARS-CoV-2; cholesterol; endosome; genome-wide screen; human lung; loss of function.

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