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

Zharko Daniloski; Tristan X. Jordan; Hans Hermann Wessels; Daisy A. Hoagland; Silva Kasela; Mateusz Legut; Silas Maniatis; Eleni P. Mimitou; Lu Lu; Evan Geller; Oded Danziger; Brad R. Rosenberg; Hemali Phatnani; Peter Smibert; Tuuli Lappalainen; Benjamin R. tenOever; Neville E. Sanjana

doi:10.1016/j.cell.2020.10.030

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

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

Research output: Contribution to journal › Article › peer-review

309 Scopus citations

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.

Original language	English
Pages (from-to)	92-105.e16
Journal	Cell
Volume	184
Issue number	1
DOIs	https://doi.org/10.1016/j.cell.2020.10.030
State	Published - 7 Jan 2021

Keywords

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

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10.1016/j.cell.2020.10.030

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Daniloski, Z., Jordan, T. X., Wessels, H. H., Hoagland, D. A., Kasela, S., Legut, M., Maniatis, S., Mimitou, E. P., Lu, L., Geller, E., Danziger, O., Rosenberg, B. R., Phatnani, H., Smibert, P., Lappalainen, T., tenOever, B. R., & Sanjana, N. E. (2021). Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells. Cell, 184(1), 92-105.e16. https://doi.org/10.1016/j.cell.2020.10.030

@article{3e0e2152339546b39f8d81be845b8af3,

title = "Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells",

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",

author = "Zharko Daniloski and Jordan, {Tristan X.} and Wessels, {Hans Hermann} and Hoagland, {Daisy A.} and Silva Kasela and Mateusz Legut and Silas Maniatis and Mimitou, {Eleni P.} and Lu Lu and Evan Geller and Oded Danziger and Rosenberg, {Brad R.} and Hemali Phatnani and Peter Smibert and Tuuli Lappalainen and tenOever, {Benjamin R.} and Sanjana, {Neville E.}",

note = "Funding Information: We thank the entire Sanjana and tenOever laboratories for support and advice. We also thank the New York Genome Center for flow cytometry and confocal microscopy resources and T. Maniatis for advice. Z.D. is supported by an American Heart Association postdoctoral fellowship ( 20POST35220040 ). Postdoctoral fellowship support for T.X.J. is provided by the NIH ( R01AI123155 ). M.L. is supported by the Hope Funds for Cancer Research postdoctoral fellowship . T.L. is supported by NIH/NIMH ( R01MH106842 ) and NIH/NHGRI ( UM1HG008901 ). S.K. and T.L. are supported by NIH/NHLBI ( R01HL142028 ). B.R.t. is supported by the Marc Haas Foundation , the NIH , and DARPA{\textquoteright}s PREPARE Program ( HR0011-20-2-0040 ). N.E.S. is supported by NYU and NYGC startup funds, NIH/NHGRI ( DP2HG010099 ), NIH/NCI ( R01CA218668 ), DARPA ( D18AP00053 ), the Sidney Kimmel Foundation , and the Brain and Behavior Foundation . Publisher Copyright: {\textcopyright} 2020 Elsevier Inc.",

year = "2021",

month = jan,

day = "7",

doi = "10.1016/j.cell.2020.10.030",

language = "English",

volume = "184",

pages = "92--105.e16",

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Daniloski, Z, Jordan, TX, Wessels, HH, Hoagland, DA, Kasela, S, Legut, M, Maniatis, S, Mimitou, EP, Lu, L, Geller, E, Danziger, O, Rosenberg, BR, Phatnani, H, Smibert, P, Lappalainen, T, tenOever, BR & Sanjana, NE 2021, 'Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells', Cell, vol. 184, no. 1, pp. 92-105.e16. https://doi.org/10.1016/j.cell.2020.10.030

TY - JOUR

T1 - Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

AU - Daniloski, Zharko

AU - Jordan, Tristan X.

AU - Wessels, Hans Hermann

AU - Hoagland, Daisy A.

AU - Kasela, Silva

AU - Legut, Mateusz

AU - Maniatis, Silas

AU - Mimitou, Eleni P.

AU - Lu, Lu

AU - Geller, Evan

AU - Danziger, Oded

AU - Rosenberg, Brad R.

AU - Phatnani, Hemali

AU - Smibert, Peter

AU - Lappalainen, Tuuli

AU - tenOever, Benjamin R.

AU - Sanjana, Neville E.

N1 - Funding Information: We thank the entire Sanjana and tenOever laboratories for support and advice. We also thank the New York Genome Center for flow cytometry and confocal microscopy resources and T. Maniatis for advice. Z.D. is supported by an American Heart Association postdoctoral fellowship ( 20POST35220040 ). Postdoctoral fellowship support for T.X.J. is provided by the NIH ( R01AI123155 ). M.L. is supported by the Hope Funds for Cancer Research postdoctoral fellowship . T.L. is supported by NIH/NIMH ( R01MH106842 ) and NIH/NHGRI ( UM1HG008901 ). S.K. and T.L. are supported by NIH/NHLBI ( R01HL142028 ). B.R.t. is supported by the Marc Haas Foundation , the NIH , and DARPA’s PREPARE Program ( HR0011-20-2-0040 ). N.E.S. is supported by NYU and NYGC startup funds, NIH/NHGRI ( DP2HG010099 ), NIH/NCI ( R01CA218668 ), DARPA ( D18AP00053 ), the Sidney Kimmel Foundation , and the Brain and Behavior Foundation . Publisher Copyright: © 2020 Elsevier Inc.

PY - 2021/1/7

Y1 - 2021/1/7

N2 - 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.

AB - 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.

KW - COVID-19

KW - CRISPR

KW - Cas9

KW - ECCITE-seq

KW - SARS-CoV-2

KW - cholesterol

KW - endosome

KW - genome-wide screen

KW - human lung

KW - loss of function

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U2 - 10.1016/j.cell.2020.10.030

DO - 10.1016/j.cell.2020.10.030

M3 - Article

C2 - 33147445

AN - SCOPUS:85095819080

SN - 0092-8674

VL - 184

SP - 92-105.e16

JO - Cell

JF - Cell

IS - 1

ER -

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

Abstract

Keywords

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