Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

Sara Sunshine; Andreas S Puschnik; Joseph M Replogle; Matthew T Laurie; Jamin Liu; Beth Shoshana Zha; James K Nuñez; Janie R Byrum; Aidan H McMorrow; Matthew B Frieman; Juliane Winkler; Xiaojie Qiu; Oren S Rosenberg; Manuel D Leonetti; Chun Jimmie Ye; Jonathan S Weissman; Joseph L DeRisi; Marco Y Hein

doi:10.1038/s41467-023-41788-4

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

Nat Commun. 2023 Oct 6;14(1):6245. doi: 10.1038/s41467-023-41788-4.

Authors

Sara Sunshine¹, Andreas S Puschnik², Joseph M Replogle^{3

4}, Matthew T Laurie¹, Jamin Liu^{1

5}, Beth Shoshana Zha⁶, James K Nuñez^{3

7}, Janie R Byrum², Aidan H McMorrow², Matthew B Frieman⁸, Juliane Winkler^{9

10}, Xiaojie Qiu^{4

11}, Oren S Rosenberg¹², Manuel D Leonetti², Chun Jimmie Ye^{13

14

15

16

17}, Jonathan S Weissman^{18

19

20

21}, Joseph L DeRisi^{22

23}, Marco Y Hein^{24

25

26

27

28}

Affiliations

¹ Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
² Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
³ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
⁴ Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
⁵ University of California, Berkeley-UCSF Joint Graduate Program in Bioengineering, San Francisco, CA, USA.
⁶ Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA.
⁷ Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
⁸ Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA.
⁹ Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA.
¹⁰ Center for Cancer Research, Medical University of Vienna, Vienna, Austria.
¹¹ Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹² Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
¹³ Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
¹⁴ Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA.
¹⁵ Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
¹⁶ Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
¹⁷ Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
¹⁸ Whitehead Institute for Biomedical Research, Cambridge, MA, USA. weissman@wi.mit.edu.
¹⁹ Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. weissman@wi.mit.edu.
²⁰ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. weissman@wi.mit.edu.
²¹ David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. weissman@wi.mit.edu.
²² Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA. joe@derisilab.ucsf.edu.
²³ Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA. joe@derisilab.ucsf.edu.
²⁴ Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA. marco.hein@maxperutzlabs.ac.at.
²⁵ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA. marco.hein@maxperutzlabs.ac.at.
²⁶ Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA. marco.hein@maxperutzlabs.ac.at.
²⁷ Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria. marco.hein@maxperutzlabs.ac.at.
²⁸ Medical University of Vienna, Center for Medical Biochemistry, Vienna, Austria. marco.hein@maxperutzlabs.ac.at.

Abstract

Genomic and proteomic screens have identified numerous host factors of SARS-CoV-2, but efficient delineation of their molecular roles during infection remains a challenge. Here we use Perturb-seq, combining genetic perturbations with a single-cell readout, to investigate how inactivation of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our high-dimensional data resolve complex phenotypes such as shifts in the stages of infection and modulations of the interferon response. However, only a small percentage of host factors showed such phenotypes upon perturbation. We further identified the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides massively parallel functional characterization of host factors of SARS-CoV-2 and quantitatively defines their roles both in virus-infected and bystander cells.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / genetics
Epithelial Cells
Humans
Lung
Proteomics
SARS-CoV-2* / genetics

Grants and funding

F31 AI150007/AI/NIAID NIH HHS/United States