Single-cell image-based screens identify host regulators of Ebola virus infection dynamics

Rebecca J Carlson^#^{1

2}, J J Patten^#^{3

4}, George Stefanakis⁵, Brian Y Soong^{2

6}, Adityanarayanan Radhakrishnan^{2

7}, Avtar Singh^{2

8}, Naveen Thakur⁹, Kathleen C F Sheehan¹⁰, Gaya K Amarasinghe¹⁰, Nir Hacohen^{2

11}, Christopher F Basler⁹, Daisy W Leung¹², Caroline Uhler^{2

5}, Robert A Davey^{13

14}, Paul C Blainey^{15

16

17}

Affiliations

¹ Massachusetts Institute of Technology, Department of Health Sciences and Technology, Cambridge, MA, USA.
² Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³ Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA, USA.
⁴ National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
⁵ Laboratory for Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁶ Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁷ Harvard School of Engineering and Applied Sciences, Cambridge, MA, USA.
⁸ Department of Cell and Tissue Genomics, Genentech, San Francisco, CA, USA.
⁹ Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
¹⁰ Department of Pathology and immunology, Washington University School of Medicine, St Louis, MO, USA.
¹¹ Massachusetts General Hospital Cancer Center, Boston, MA, USA.
¹² Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
¹³ Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA, USA. radavey@bu.edu.
¹⁴ National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA. radavey@bu.edu.
¹⁵ Broad Institute of MIT and Harvard, Cambridge, MA, USA. pblainey@broadinstitute.org.
¹⁶ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. pblainey@broadinstitute.org.
¹⁷ Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. pblainey@broadinstitute.org.

^# Contributed equally.

PMID: 40707832
DOI: 10.1038/s41564-025-02034-3

Single-cell image-based screens identify host regulators of Ebola virus infection dynamics

Rebecca J Carlson et al. Nat Microbiol. 2025 Aug.

. 2025 Aug;10(8):1989-2002.

doi: 10.1038/s41564-025-02034-3. Epub 2025 Jul 24.

Authors

Affiliations

¹ Massachusetts Institute of Technology, Department of Health Sciences and Technology, Cambridge, MA, USA.
² Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³ Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA, USA.
⁴ National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
⁵ Laboratory for Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁶ Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁷ Harvard School of Engineering and Applied Sciences, Cambridge, MA, USA.
⁸ Department of Cell and Tissue Genomics, Genentech, San Francisco, CA, USA.
⁹ Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
¹⁰ Department of Pathology and immunology, Washington University School of Medicine, St Louis, MO, USA.
¹¹ Massachusetts General Hospital Cancer Center, Boston, MA, USA.
¹² Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
¹³ Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA, USA. radavey@bu.edu.
¹⁴ National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA. radavey@bu.edu.
¹⁵ Broad Institute of MIT and Harvard, Cambridge, MA, USA. pblainey@broadinstitute.org.
¹⁶ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. pblainey@broadinstitute.org.
¹⁷ Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. pblainey@broadinstitute.org.

^# Contributed equally.

PMID: 40707832
DOI: 10.1038/s41564-025-02034-3

Abstract

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.

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Conflict of interest statement

Competing interests: P.C.B. is a consultant to or holds equity in 10X Genomics, General Automation Lab Technologies/Isolation Bio, Next Gen Diagnostics, Cache DNA, Concerto Biosciences, Stately, Ramona Optics, Bifrost Biosystems, and Amber Bio. His laboratory received research funding from Calico Life Sciences, Merck, and Genentech for work related to genetic screening. N.H. holds equity in and advises Danger Bio/Related Sciences, owns equity in BioNtech and receives research funding from Bristol Myers Squibb. C.U. serves on the Scientific Advisory Board of Immunai, Relation Therapeutics, and Focal Biosciences, and receives research funding from AstraZeneca and Janssen Pharmaceuticals. The Broad Institute and MIT may seek to commercialize aspects of this work, and related applications for intellectual property have been filed. A.S. is an employee at Genentech and R.J.C. is an employee at Flagship Pioneering. The remaining authors declare no competing interests.

Update of

Single-cell image-based genetic screens systematically identify regulators of Ebola virus subcellular infection dynamics.
Carlson RJ, Patten JJ, Stefanakis G, Soong BY, Radhakrishnan A, Singh A, Thakur N, Amarasinghe GK, Hacohen N, Basler CF, Leung D, Uhler C, Davey RA, Blainey PC. Carlson RJ, et al. bioRxiv [Preprint]. 2024 Apr 7:2024.04.06.588168. doi: 10.1101/2024.04.06.588168. bioRxiv. 2024. Update in: Nat Microbiol. 2025 Aug;10(8):1989-2002. doi: 10.1038/s41564-025-02034-3. PMID: 38617272 Free PMC article. Updated. Preprint.

References

1. Hoenen, T., Groseth, A. & Feldmann, H. Therapeutic strategies to target the Ebola virus life cycle. Nat. Rev. Microbiol. 17, 593–606 (2019). - PubMed
1. Hoenen, T. et al. Inclusion bodies are a site of Ebolavirus replication. J. Virol. 86, 11779–11788 (2012). - PubMed - PMC
1. Nanbo, A., Watanabe, S., Halfmann, P. & Kawaoka, Y. The spatio-temporal distribution dynamics of Ebola virus proteins and RNA in infected cells. Sci. Rep. 3, 1206 (2013). - PubMed - PMC
1. Bruchez, A. et al. MHC class II transactivator CIITA induces cell resistance to Ebola virus and SARS-like coronaviruses. Science 370, 241–247 (2020). - PubMed - PMC
1. Carette, J. E. et al. Ebola virus entry requires the cholesterol transporter Niemann-Pick C1. Nature 477, 340–343 (2011). - PubMed - PMC

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Single-cell image-based screens identify host regulators of Ebola virus infection dynamics

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Single-cell image-based screens identify host regulators of Ebola virus infection dynamics

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