TY - JOUR
T1 - Single-cell image-based screens identify host regulators of Ebola virus infection dynamics
AU - Carlson, Rebecca J.
AU - Patten, J. J.
AU - Stefanakis, George
AU - Soong, Brian Y.
AU - Radhakrishnan, Adityanarayanan
AU - Singh, Avtar
AU - Thakur, Naveen
AU - Sheehan, Kathleen C.F.
AU - Amarasinghe, Gaya K.
AU - Hacohen, Nir
AU - Basler, Christopher F.
AU - Leung, Daisy W.
AU - Uhler, Caroline
AU - Davey, Robert A.
AU - Blainey, Paul C.
N1 - Publisher Copyright:
© The Author(s), under exclusive licence to Springer Nature Limited 2025.
PY - 2025/8
Y1 - 2025/8
N2 - Filoviruses such as Ebola virus (EBOV) give rise to frequent epidemics with high case fatality rates while therapeutic options remain limited. Earlier genetic screens aimed to identify potential drug targets for EBOV relied on systems that may not fully recapitulate the virus life cycle. Here we applied an image-based genome-wide CRISPR screen to identify 998 host regulators of EBOV infection in 39,085,093 cells. A deep learning model associated each host factor with a distinct viral replication step. From this we confirmed UQCRB as a post-entry regulator of EBOV RNA replication and show that small-molecule UQCRB inhibition reduced virus infection in vitro. Using a random forest model, we found that perturbations on STRAP (a spliceosome-associated factor) disrupted the equilibrium between viral RNA and protein. STRAP was associated with VP35, a viral RNA processing protein. This genome-wide screen coupled with 12 secondary screens including validation experiments with Sudan and Marburg virus, presents a rich resource for host regulators of virus replication and potential targets for therapeutic intervention.
AB - Filoviruses such as Ebola virus (EBOV) give rise to frequent epidemics with high case fatality rates while therapeutic options remain limited. Earlier genetic screens aimed to identify potential drug targets for EBOV relied on systems that may not fully recapitulate the virus life cycle. Here we applied an image-based genome-wide CRISPR screen to identify 998 host regulators of EBOV infection in 39,085,093 cells. A deep learning model associated each host factor with a distinct viral replication step. From this we confirmed UQCRB as a post-entry regulator of EBOV RNA replication and show that small-molecule UQCRB inhibition reduced virus infection in vitro. Using a random forest model, we found that perturbations on STRAP (a spliceosome-associated factor) disrupted the equilibrium between viral RNA and protein. STRAP was associated with VP35, a viral RNA processing protein. This genome-wide screen coupled with 12 secondary screens including validation experiments with Sudan and Marburg virus, presents a rich resource for host regulators of virus replication and potential targets for therapeutic intervention.
UR - https://www.scopus.com/pages/publications/105011372379
U2 - 10.1038/s41564-025-02034-3
DO - 10.1038/s41564-025-02034-3
M3 - Article
C2 - 40707832
AN - SCOPUS:105011372379
SN - 2058-5276
VL - 10
SP - 1989
EP - 2002
JO - Nature microbiology
JF - Nature microbiology
IS - 8
ER -