Genome-wide loss-of-function screen using human pluripotent stem cells to study virus-host interactions for SARS-CoV-2

Ariel Pagis; Or Alfi; Shay Kinreich; Atilgan Yilmaz; Marah Hamdan; Aseel Gadban; Amos Panet; Dana G. Wolf; Nissim Benvenisty

doi:10.1016/j.stemcr.2023.07.003

Genome-wide loss-of-function screen using human pluripotent stem cells to study virus-host interactions for SARS-CoV-2

Ariel Pagis, Or Alfi, Shay Kinreich, Atilgan Yilmaz, Marah Hamdan, Aseel Gadban, Amos Panet, Dana G. Wolf^*, Nissim Benvenisty^*

^*Corresponding author for this work

Department of Genetics

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

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019, has become a global health concern. Therefore, there is an immense need to understand the network of virus-host interactions by using human disease-relevant cells. We have thus conducted a loss-of-function genome-wide screen using haploid human embryonic stem cells (hESCs) to identify genes involved in SARS-CoV-2 infection. Although the undifferentiated hESCs are resistant to SARS-CoV-2, their differentiated definitive endoderm (DE) progenies, which express high levels of ACE2, are highly sensitive to the virus. Our genetic screening was able to identify the well-established entry receptor ACE2 as a host factor, along with additional potential novel modulators of SARS-CoV-2. Two such novel screen hits, the transcription factor MAFG and the transmembrane protein TMEM86A, were further validated as conferring resistance against SARS-CoV-2 by using CRISPR-mediated mutagenesis in hESCs, followed by differentiation of mutant lines into DE cells and infection by SARS-CoV-2. Our genome-wide genetic screening investigated SARS-CoV-2 host factors in non-cancerous human cells with endogenous ACE2 expression, providing a unique platform to identify novel modulators of SARS-CoV-2 cytopathology in human cells.

Original language	American English
Pages (from-to)	1766-1774
Number of pages	9
Journal	Stem Cell Reports
Volume	18
Issue number	9
DOIs	https://doi.org/10.1016/j.stemcr.2023.07.003
State	Published - 12 Sep 2023

Bibliographical note

Funding Information:
The authors would like to thank Dr. Ofra Yanuka and Tamar Golan-Lev for their help with tissue culture experiments and all the members of The Azrieli Center for Stem Cells and Genetic Research for their input and critically reading the manuscript. The study was partially supported by the Azrieli Foundation , by the Rosetrees Trust , by the ISF-Israel Precision Medicine Partnership (IPMP) Program (no. 3605/21 ), and by the Israel Science Foundation (grant nos. 3687/19 and 2054/22 ). N.B. is the Herbert Cohn Chair in Cancer Research .

Publisher Copyright:
© 2023 The Author(s)

Keywords

Genome-wide screening
Human pluripoptent stem cells
SARS-CoV-2

UN SDGs

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

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10.1016/j.stemcr.2023.07.003

Cite this

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title = "Genome-wide loss-of-function screen using human pluripotent stem cells to study virus-host interactions for SARS-CoV-2",

abstract = "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019, has become a global health concern. Therefore, there is an immense need to understand the network of virus-host interactions by using human disease-relevant cells. We have thus conducted a loss-of-function genome-wide screen using haploid human embryonic stem cells (hESCs) to identify genes involved in SARS-CoV-2 infection. Although the undifferentiated hESCs are resistant to SARS-CoV-2, their differentiated definitive endoderm (DE) progenies, which express high levels of ACE2, are highly sensitive to the virus. Our genetic screening was able to identify the well-established entry receptor ACE2 as a host factor, along with additional potential novel modulators of SARS-CoV-2. Two such novel screen hits, the transcription factor MAFG and the transmembrane protein TMEM86A, were further validated as conferring resistance against SARS-CoV-2 by using CRISPR-mediated mutagenesis in hESCs, followed by differentiation of mutant lines into DE cells and infection by SARS-CoV-2. Our genome-wide genetic screening investigated SARS-CoV-2 host factors in non-cancerous human cells with endogenous ACE2 expression, providing a unique platform to identify novel modulators of SARS-CoV-2 cytopathology in human cells.",

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note = "Funding Information: The authors would like to thank Dr. Ofra Yanuka and Tamar Golan-Lev for their help with tissue culture experiments and all the members of The Azrieli Center for Stem Cells and Genetic Research for their input and critically reading the manuscript. The study was partially supported by the Azrieli Foundation , by the Rosetrees Trust , by the ISF-Israel Precision Medicine Partnership (IPMP) Program (no. 3605/21 ), and by the Israel Science Foundation (grant nos. 3687/19 and 2054/22 ). N.B. is the Herbert Cohn Chair in Cancer Research . Publisher Copyright: {\textcopyright} 2023 The Author(s)",

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AU - Hamdan, Marah

AU - Gadban, Aseel

AU - Panet, Amos

AU - Wolf, Dana G.

AU - Benvenisty, Nissim

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N2 - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019, has become a global health concern. Therefore, there is an immense need to understand the network of virus-host interactions by using human disease-relevant cells. We have thus conducted a loss-of-function genome-wide screen using haploid human embryonic stem cells (hESCs) to identify genes involved in SARS-CoV-2 infection. Although the undifferentiated hESCs are resistant to SARS-CoV-2, their differentiated definitive endoderm (DE) progenies, which express high levels of ACE2, are highly sensitive to the virus. Our genetic screening was able to identify the well-established entry receptor ACE2 as a host factor, along with additional potential novel modulators of SARS-CoV-2. Two such novel screen hits, the transcription factor MAFG and the transmembrane protein TMEM86A, were further validated as conferring resistance against SARS-CoV-2 by using CRISPR-mediated mutagenesis in hESCs, followed by differentiation of mutant lines into DE cells and infection by SARS-CoV-2. Our genome-wide genetic screening investigated SARS-CoV-2 host factors in non-cancerous human cells with endogenous ACE2 expression, providing a unique platform to identify novel modulators of SARS-CoV-2 cytopathology in human cells.

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ER -

Genome-wide loss-of-function screen using human pluripotent stem cells to study virus-host interactions for SARS-CoV-2

Abstract

Bibliographical note

Keywords

UN SDGs

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