Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection.
Defining the subset of cellular factors governing SARS-CoV-2 replication can provide critical insights into viral pathogenesis and identify targets for host-directed antiviral therapies. While a number of genetic screens have previously reported SARS-CoV-2 host dependency factors, most of these appr...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2025-06-01
|
| Series: | PLoS Biology |
| Online Access: | https://doi.org/10.1371/journal.pbio.3002738 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850116360874491904 |
|---|---|
| author | Xin Yin Yuan Pu Shuofeng Yuan Lars Pache Christopher Churas Stuart Weston Laura Riva Lacy M Simons William J Cisneros Thomas Clausen Grace Biddle Simon Doss-Gollin Meagan Deming Paul D De Jesus Ha Na Kim Daniel Fuentes John M Whitelock Jeffrey D Esko Megan S Lord Ignacio Mena Adolfo García-Sastre Judd F Hultquist Matthew B Frieman Trey Ideker Dexter Pratt Laura Martin-Sancho Sumit K Chanda |
| author_facet | Xin Yin Yuan Pu Shuofeng Yuan Lars Pache Christopher Churas Stuart Weston Laura Riva Lacy M Simons William J Cisneros Thomas Clausen Grace Biddle Simon Doss-Gollin Meagan Deming Paul D De Jesus Ha Na Kim Daniel Fuentes John M Whitelock Jeffrey D Esko Megan S Lord Ignacio Mena Adolfo García-Sastre Judd F Hultquist Matthew B Frieman Trey Ideker Dexter Pratt Laura Martin-Sancho Sumit K Chanda |
| author_sort | Xin Yin |
| collection | DOAJ |
| description | Defining the subset of cellular factors governing SARS-CoV-2 replication can provide critical insights into viral pathogenesis and identify targets for host-directed antiviral therapies. While a number of genetic screens have previously reported SARS-CoV-2 host dependency factors, most of these approaches relied on utilizing pooled genome-scale CRISPR libraries, which are biased toward the discovery of host proteins impacting early stages of viral replication. To identify host factors involved throughout the SARS-CoV-2 infectious cycle, we conducted an arrayed genome-scale siRNA screen. Resulting data were integrated with published functional screens and proteomics data to reveal (i) common pathways that were identified in all OMICs datasets-including regulation of Wnt signaling and gap junctions, (ii) pathways uniquely identified in this screen-including NADH oxidation, or (iii) pathways supported by this screen and proteomics data but not published functional screens-including arachionate production and MAPK signaling. The identified proviral host factors were mapped into the SARS-CoV-2 infectious cycle, including 32 proteins that were determined to impact viral replication and 27 impacting late stages of infection, respectively. Additionally, a subset of proteins was tested across other coronaviruses revealing a subset of proviral factors that were conserved across pandemic SARS-CoV-2, epidemic SARS-CoV-1 and MERS-CoV, and the seasonal coronavirus OC43-CoV. Further studies illuminated a role for the heparan sulfate proteoglycan perlecan in SARS-CoV-2 viral entry and found that inhibition of the non-canonical NF-kB pathway through targeting of BIRC2 restricts SARS-CoV-2 replication both in vitro and in vivo. These studies provide critical insight into the landscape of virus-host interactions driving SARS-CoV-2 replication as well as valuable targets for host-directed antivirals. |
| format | Article |
| id | doaj-art-1ab0ff39590944df975161f024ece3aa |
| institution | OA Journals |
| issn | 1544-9173 1545-7885 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Biology |
| spelling | doaj-art-1ab0ff39590944df975161f024ece3aa2025-08-20T02:36:20ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852025-06-01236e300273810.1371/journal.pbio.3002738Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection.Xin YinYuan PuShuofeng YuanLars PacheChristopher ChurasStuart WestonLaura RivaLacy M SimonsWilliam J CisnerosThomas ClausenGrace BiddleSimon Doss-GollinMeagan DemingPaul D De JesusHa Na KimDaniel FuentesJohn M WhitelockJeffrey D EskoMegan S LordIgnacio MenaAdolfo García-SastreJudd F HultquistMatthew B FriemanTrey IdekerDexter PrattLaura Martin-SanchoSumit K ChandaDefining the subset of cellular factors governing SARS-CoV-2 replication can provide critical insights into viral pathogenesis and identify targets for host-directed antiviral therapies. While a number of genetic screens have previously reported SARS-CoV-2 host dependency factors, most of these approaches relied on utilizing pooled genome-scale CRISPR libraries, which are biased toward the discovery of host proteins impacting early stages of viral replication. To identify host factors involved throughout the SARS-CoV-2 infectious cycle, we conducted an arrayed genome-scale siRNA screen. Resulting data were integrated with published functional screens and proteomics data to reveal (i) common pathways that were identified in all OMICs datasets-including regulation of Wnt signaling and gap junctions, (ii) pathways uniquely identified in this screen-including NADH oxidation, or (iii) pathways supported by this screen and proteomics data but not published functional screens-including arachionate production and MAPK signaling. The identified proviral host factors were mapped into the SARS-CoV-2 infectious cycle, including 32 proteins that were determined to impact viral replication and 27 impacting late stages of infection, respectively. Additionally, a subset of proteins was tested across other coronaviruses revealing a subset of proviral factors that were conserved across pandemic SARS-CoV-2, epidemic SARS-CoV-1 and MERS-CoV, and the seasonal coronavirus OC43-CoV. Further studies illuminated a role for the heparan sulfate proteoglycan perlecan in SARS-CoV-2 viral entry and found that inhibition of the non-canonical NF-kB pathway through targeting of BIRC2 restricts SARS-CoV-2 replication both in vitro and in vivo. These studies provide critical insight into the landscape of virus-host interactions driving SARS-CoV-2 replication as well as valuable targets for host-directed antivirals.https://doi.org/10.1371/journal.pbio.3002738 |
| spellingShingle | Xin Yin Yuan Pu Shuofeng Yuan Lars Pache Christopher Churas Stuart Weston Laura Riva Lacy M Simons William J Cisneros Thomas Clausen Grace Biddle Simon Doss-Gollin Meagan Deming Paul D De Jesus Ha Na Kim Daniel Fuentes John M Whitelock Jeffrey D Esko Megan S Lord Ignacio Mena Adolfo García-Sastre Judd F Hultquist Matthew B Frieman Trey Ideker Dexter Pratt Laura Martin-Sancho Sumit K Chanda Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection. PLoS Biology |
| title | Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection. |
| title_full | Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection. |
| title_fullStr | Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection. |
| title_full_unstemmed | Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection. |
| title_short | Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection. |
| title_sort | global sirna screen identifies human host factors critical for sars cov 2 replication and late stages of infection |
| url | https://doi.org/10.1371/journal.pbio.3002738 |
| work_keys_str_mv | AT xinyin globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT yuanpu globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT shuofengyuan globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT larspache globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT christopherchuras globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT stuartweston globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT laurariva globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT lacymsimons globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT williamjcisneros globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT thomasclausen globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT gracebiddle globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT simondossgollin globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT meagandeming globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT paulddejesus globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT hanakim globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT danielfuentes globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT johnmwhitelock globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT jeffreydesko globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT meganslord globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT ignaciomena globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT adolfogarciasastre globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT juddfhultquist globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT matthewbfrieman globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT treyideker globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT dexterpratt globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT lauramartinsancho globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection AT sumitkchanda globalsirnascreenidentifieshumanhostfactorscriticalforsarscov2replicationandlatestagesofinfection |