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

• Published in: Nature communications Vol. 14; no. 1; pp. 6245 - 13
• Main Authors: Sunshine, Sara, Puschnik, Andreas S., Replogle, Joseph M., Laurie, Matthew T., Liu, Jamin, Zha, Beth Shoshana, Nuñez, James K., Byrum, Janie R., McMorrow, Aidan H., Frieman, Matthew B., Winkler, Juliane, Qiu, Xiaojie, Rosenberg, Oren S., Leonetti, Manuel D., Ye, Chun Jimmie, Weissman, Jonathan S., DeRisi, Joseph L., Hein, Marco Y.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06.10.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 45/47; 49; 631/208/191; 631/250/255/2514; 631/326/596/2557; COVID-19; COVID-19 - genetics; Deactivation; Epithelial Cells; Epithelium; Humanities and Social Sciences; Humans; Inactivation; Infections; Interrogation; Lung; multidisciplinary; NF-κB protein; Perturbation; Phenotypes; Proteomics; SARS-CoV-2 - genetics; Science; Science (multidisciplinary); Severe acute respiratory syndrome coronavirus 2; Viral diseases
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-41788-4

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. Sunshine et al. use Perturb-seq to study host dependencies of SARS-CoV-2 by inactivating host factors genetically and monitoring the course of infection by single-cell sequencing, characterizing global host phenotypes. They identified NFKBIA, EIF4E2 and EIF4H as strong host dependency factors.