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

Sara Sunshine¹, Andreas S Puschnik², Joseph M Replogle^3,4

¹Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.

Nature Communications

|October 6, 2023

Summary

This study used Perturb-seq to functionally characterize SARS-CoV-2 host factors in lung cells. It identified key factors like IκBα, EIF4E2, and EIF4H essential for early viral infection.

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Area of Science:

Virology
Genomics
Cell Biology

Background:

Genomic and proteomic screens have identified numerous host factors for SARS-CoV-2.
Delineating the molecular roles of these host factors during infection is challenging.

Purpose of the Study:

To investigate how inactivating host factors impacts SARS-CoV-2 infection and host response using Perturb-seq.
To functionally characterize SARS-CoV-2 host factors in human lung epithelial cells.

Main Methods:

Utilized Perturb-seq, a method combining genetic perturbations with single-cell RNA sequencing.
Analyzed high-dimensional data to resolve complex infection phenotypes and host responses.

Main Results:

Identified specific host factors that, upon perturbation, alter infection stages and interferon responses.
Discovered IκBα (NFKBIA), EIF4E2, and EIF4H as critical host dependency factors for early SARS-CoV-2 infection.
Quantitatively defined the roles of host factors in both infected and bystander cells.

Conclusions:

Perturb-seq enables massively parallel functional characterization of SARS-CoV-2 host factors.
This study quantitatively defines the roles of host factors in viral infection and host cell responses.