Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors

Katherine Chan; Adrian Granda Farias; Hunsang Lee; Furkan Guvenc; Patricia Mero; Kevin R. Brown; Henry N Ward; Maximilian Billmann; Kamaldeep Aulakh; Audrey Astori; Shahan Haider; Edyta Marcon; Ulrich Braunschweig; Shuye Pu; Andrea Habsid; Amy Hin Yan Tong; Natasha Christie-Holmes; Patrick Budylowski; Ayoob Ghalami; Samira Mubareka; Finlay Maguire; Arinjay Banerjee; Karen L. Mossman; Jack Greenblatt; Scott D. Gray-Owen; Brian Raught; Benjamin J. Blencowe; Mikko Taipale; Chad Myers; Jason Moffat

doi:10.1016/j.heliyon.2022.e12744

Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors

Katherine Chan, Adrian Granda Farias, Hunsang Lee, Furkan Guvenc, Patricia Mero, Kevin R. Brown, Henry N Ward, Maximilian Billmann, Kamaldeep Aulakh, Audrey Astori, Shahan Haider, Edyta Marcon, Ulrich Braunschweig, Shuye Pu, Andrea Habsid, Amy Hin Yan Tong, Natasha Christie-Holmes, Patrick Budylowski, Ayoob Ghalami, Samira MubarekaFinlay Maguire, Arinjay Banerjee, Karen L. Mossman, Jack Greenblatt, Scott D. Gray-Owen, Brian Raught, Benjamin J. Blencowe, Mikko Taipale, Chad Myers, Jason Moffat

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

7 Scopus citations

Abstract

SARS-CoV-2 depends on host cell components for infection and replication. Identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection and replication. If druggable, host factor dependencies may present an attractive strategy for anti-viral therapy. In this study, we performed genome wide CRISPR knockout screens in Vero E6 cells and four human cell lines including Calu-3, UM-UC-4, HEK-293 and HuH-7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while other host genes identified were largely cell line specific, including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, immune-related pathways, and chromatin modification. Notably, the chromatin modifier gene KMT2C in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed.

Original language	English (US)
Article number	e12744
Journal	Heliyon
Volume	9
Issue number	1
DOIs	https://doi.org/10.1016/j.heliyon.2022.e12744
State	Published - Jan 2023

Bibliographical note

Funding Information:
We would like to acknowledge Anne-Claude Gingras and Payman Samavarchi-Tehrani for sharing HEK-293 +A+T cell line and Betty Poon for assistance in the C-CL3 facility. This work was supported by the University of Toronto COVID-19 Action Initiative Fund to J.M., B.J.B., S.G.O., J.G., K.M., and S.M. Indirect support was also received from the University of Toronto and the Temerty Foundation to support enhanced capacity and operations of the Toronto Combined Containment Level 3 Facility during the COVID-19 pandemic. This work was also partially supported from a Canadian Institutes for Health Research Project Grant to J.M. ( MOP142375 ) and a Disruptive Innovations Phase 2 Grant from Genome Canada to J.M.

Publisher Copyright:
© 2023 The Authors

Keywords

ACE2
CRISPR screens
Genome-wide loss-of-function
Host factors
SARS-CoV-2

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.heliyon.2022.e12744

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Chan, K., Farias, A. G., Lee, H., Guvenc, F., Mero, P., Brown, K. R., Ward, H. N., Billmann, M., Aulakh, K., Astori, A., Haider, S., Marcon, E., Braunschweig, U., Pu, S., Habsid, A., Yan Tong, A. H., Christie-Holmes, N., Budylowski, P., Ghalami, A., ... Moffat, J. (2023). Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors. Heliyon, 9(1), Article e12744. https://doi.org/10.1016/j.heliyon.2022.e12744

Chan, K, Farias, AG, Lee, H, Guvenc, F, Mero, P, Brown, KR, Ward, HN, Billmann, M, Aulakh, K, Astori, A, Haider, S, Marcon, E, Braunschweig, U, Pu, S, Habsid, A, Yan Tong, AH, Christie-Holmes, N, Budylowski, P, Ghalami, A, Mubareka, S, Maguire, F, Banerjee, A, Mossman, KL, Greenblatt, J, Gray-Owen, SD, Raught, B, Blencowe, BJ, Taipale, M, Myers, C & Moffat, J 2023, 'Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors', Heliyon, vol. 9, no. 1, e12744. https://doi.org/10.1016/j.heliyon.2022.e12744

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title = "Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors",

abstract = "SARS-CoV-2 depends on host cell components for infection and replication. Identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection and replication. If druggable, host factor dependencies may present an attractive strategy for anti-viral therapy. In this study, we performed genome wide CRISPR knockout screens in Vero E6 cells and four human cell lines including Calu-3, UM-UC-4, HEK-293 and HuH-7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while other host genes identified were largely cell line specific, including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, immune-related pathways, and chromatin modification. Notably, the chromatin modifier gene KMT2C in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed.",

keywords = "ACE2, CRISPR screens, Genome-wide loss-of-function, Host factors, SARS-CoV-2",

author = "Katherine Chan and Farias, {Adrian Granda} and Hunsang Lee and Furkan Guvenc and Patricia Mero and Brown, {Kevin R.} and Ward, {Henry N} and Maximilian Billmann and Kamaldeep Aulakh and Audrey Astori and Shahan Haider and Edyta Marcon and Ulrich Braunschweig and Shuye Pu and Andrea Habsid and {Yan Tong}, {Amy Hin} and Natasha Christie-Holmes and Patrick Budylowski and Ayoob Ghalami and Samira Mubareka and Finlay Maguire and Arinjay Banerjee and Mossman, {Karen L.} and Jack Greenblatt and Gray-Owen, {Scott D.} and Brian Raught and Blencowe, {Benjamin J.} and Mikko Taipale and Chad Myers and Jason Moffat",

note = "Funding Information: We would like to acknowledge Anne-Claude Gingras and Payman Samavarchi-Tehrani for sharing HEK-293 +A+T cell line and Betty Poon for assistance in the C-CL3 facility. This work was supported by the University of Toronto COVID-19 Action Initiative Fund to J.M., B.J.B., S.G.O., J.G., K.M., and S.M. Indirect support was also received from the University of Toronto and the Temerty Foundation to support enhanced capacity and operations of the Toronto Combined Containment Level 3 Facility during the COVID-19 pandemic. This work was also partially supported from a Canadian Institutes for Health Research Project Grant to J.M. ( MOP142375 ) and a Disruptive Innovations Phase 2 Grant from Genome Canada to J.M. Publisher Copyright: {\textcopyright} 2023 The Authors",

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language = "English (US)",

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T1 - Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors

AU - Chan, Katherine

AU - Farias, Adrian Granda

AU - Lee, Hunsang

AU - Guvenc, Furkan

AU - Mero, Patricia

AU - Brown, Kevin R.

AU - Ward, Henry N

AU - Billmann, Maximilian

AU - Aulakh, Kamaldeep

AU - Astori, Audrey

AU - Haider, Shahan

AU - Marcon, Edyta

AU - Braunschweig, Ulrich

AU - Pu, Shuye

AU - Habsid, Andrea

AU - Yan Tong, Amy Hin

AU - Christie-Holmes, Natasha

AU - Budylowski, Patrick

AU - Ghalami, Ayoob

AU - Mubareka, Samira

AU - Maguire, Finlay

AU - Banerjee, Arinjay

AU - Mossman, Karen L.

AU - Greenblatt, Jack

AU - Gray-Owen, Scott D.

AU - Raught, Brian

AU - Blencowe, Benjamin J.

AU - Taipale, Mikko

AU - Myers, Chad

AU - Moffat, Jason

N1 - Funding Information: We would like to acknowledge Anne-Claude Gingras and Payman Samavarchi-Tehrani for sharing HEK-293 +A+T cell line and Betty Poon for assistance in the C-CL3 facility. This work was supported by the University of Toronto COVID-19 Action Initiative Fund to J.M., B.J.B., S.G.O., J.G., K.M., and S.M. Indirect support was also received from the University of Toronto and the Temerty Foundation to support enhanced capacity and operations of the Toronto Combined Containment Level 3 Facility during the COVID-19 pandemic. This work was also partially supported from a Canadian Institutes for Health Research Project Grant to J.M. ( MOP142375 ) and a Disruptive Innovations Phase 2 Grant from Genome Canada to J.M. Publisher Copyright: © 2023 The Authors

PY - 2023/1

Y1 - 2023/1

N2 - SARS-CoV-2 depends on host cell components for infection and replication. Identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection and replication. If druggable, host factor dependencies may present an attractive strategy for anti-viral therapy. In this study, we performed genome wide CRISPR knockout screens in Vero E6 cells and four human cell lines including Calu-3, UM-UC-4, HEK-293 and HuH-7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while other host genes identified were largely cell line specific, including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, immune-related pathways, and chromatin modification. Notably, the chromatin modifier gene KMT2C in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed.

AB - SARS-CoV-2 depends on host cell components for infection and replication. Identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection and replication. If druggable, host factor dependencies may present an attractive strategy for anti-viral therapy. In this study, we performed genome wide CRISPR knockout screens in Vero E6 cells and four human cell lines including Calu-3, UM-UC-4, HEK-293 and HuH-7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while other host genes identified were largely cell line specific, including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, immune-related pathways, and chromatin modification. Notably, the chromatin modifier gene KMT2C in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed.

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ER -

Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors

Abstract

Bibliographical note

Keywords

UN SDGs

Publisher link

Find It

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