Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions

Ryan A Flynn; Julia A Belk; Yanyan Qi; Yuki Yasumoto; Jin Wei; Mia Madel Alfajaro; Quanming Shi; Maxwell R Mumbach; Aditi Limaye; Peter C DeWeirdt; Cameron O Schmitz; Kevin R Parker; Elizabeth Woo; Howard Y Chang; Tamas L Horvath; Jan E Carette; Carolyn R Bertozzi; Craig B Wilen; Ansuman T Satpathy

doi:10.1016/j.cell.2021.03.012

Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions

Cell. 2021 Apr 29;184(9):2394-2411.e16. doi: 10.1016/j.cell.2021.03.012. Epub 2021 Mar 11.

Authors

Ryan A Flynn¹, Julia A Belk², Yanyan Qi³, Yuki Yasumoto⁴, Jin Wei⁵, Mia Madel Alfajaro⁵, Quanming Shi⁶, Maxwell R Mumbach⁶, Aditi Limaye³, Peter C DeWeirdt⁷, Cameron O Schmitz⁵, Kevin R Parker⁶, Elizabeth Woo⁸, Howard Y Chang⁹, Tamas L Horvath⁴, Jan E Carette¹⁰, Carolyn R Bertozzi¹¹, Craig B Wilen¹², Ansuman T Satpathy¹³

Affiliations

¹ Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA, USA. Electronic address: ryan.flynn@childrens.harvard.edu.
² Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA.
³ Department of Pathology, Stanford University, Stanford, CA, USA.
⁴ Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT, USA.
⁵ Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
⁶ Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
⁷ Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁸ Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
⁹ Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
¹⁰ Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
¹¹ Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
¹² Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA. Electronic address: craig.wilen@yale.edu.
¹³ Department of Pathology, Stanford University, Stanford, CA, USA. Electronic address: satpathy@stanford.edu.

Abstract

SARS-CoV-2 is the cause of a pandemic with growing global mortality. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with ChIRP-MS data from three other RNA viruses defined viral specificity of RNA-host protein interactions. Targeted CRISPR screens revealed that the majority of functional RNA-binding proteins protect the host from virus-induced cell death, and comparative CRISPR screens across seven RNA viruses revealed shared and SARS-specific antiviral factors. Finally, by combining the RNA-centric approach and functional CRISPR screens, we demonstrated a physical and functional connection between SARS-CoV-2 and mitochondria, highlighting this organelle as a general platform for antiviral activity. Altogether, these data provide a comprehensive catalog of functional SARS-CoV-2 RNA-host protein interactions, which may inform studies to understand the host-virus interface and nominate host pathways that could be targeted for therapeutic benefit.

Keywords: CRISPR; ChIRP-MS; RNA virus; RNA-binding proteins; SARS-CoV-2; host-pathogen interactions; mitochondria.

Publication types

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

MeSH terms

Animals
COVID-19 / virology
CRISPR-Cas Systems / genetics
Cell Line, Tumor
Chlorocebus aethiops
Female
Genome, Viral
Host-Pathogen Interactions*
Humans
Lung / virology
Male
Mass Spectrometry
Mitochondria / metabolism
Mitochondria / ultrastructure
Proteome / metabolism
RNA, Viral / genetics*
RNA-Binding Proteins / metabolism
SARS-CoV-2 / genetics*
SARS-CoV-2 / ultrastructure
Vero Cells

Substances

Proteome
RNA, Viral
RNA-Binding Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding