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

Research output: Contribution to journalArticlepeer-review


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 languageAmerican English
Pages (from-to)1766-1774
Number of pages9
JournalStem Cell Reports
Issue number9
StatePublished - 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)


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


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