Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways PMID: 41332698

ADC Targets in Oncology

2026-04-10

Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways

bioRxiv. 2025 Nov 17:2025.11.17.687821. doi: 10.1101/2025.11.17.687821.

Tomas Pachano ¹ , He Leng ² , Guillaume Dugied ² , Travis Tribble ² ³ , Vincent Loubiere ¹ , Felix Rauh ¹ , Yeojin Lee ⁴ , Alexander Schleiffer ¹ , Veronika Young ⁵ , Benjamin Weller ⁵ , Eleanor A Lyons ⁶ , Matthew R Hass ⁷ , Leah C Kottayan ⁷ ⁸ , Matthew T Weirauch ⁷ ⁸ , Juan I Fuxman Bass ⁹ , Hayley J Newton ¹⁰ , Alexander W Ensminger ³ ¹¹ , Pascal Falter Braun ⁵ ¹² , Daniel Schramek ³ ⁴ , Alexander Stark ¹ ¹³ , Mikko Taipale ² ³

Affiliations

1. Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
2. Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada.
3. Department of Molecular Genetics, University of Toronto, Ontario M5S 3E1, Canada.
4. Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
5. Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany.
6. Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
7. Center for Autoimmune Genomics and Etiology, Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
8. Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
9. Biology Department and Bioinformatics Program, Boston University, Boston, MA, USA.
10. Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia.
11. Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
12. Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-Universität (LMU) Mu nchen, Planegg-Martinsried, Germany.
13. Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.

Abstract

Pathogens deploy effector proteins to exploit host Cell Biology, and most pathogen open reading frames (ORFs) are rapidly evolving and lack functional annotation. We developed the eORFeome, a scalable functional genomics platform encompassing 3,835 effector ORFs from diverse viruses, bacteria, and parasites. High-throughput barcoded screens across NFκB, Apoptosis, p53, cGAS-STING and MHC-I pathways revealed functions for hundreds of uncharacterized eORFs, unexpected new activities for known effectors, and distinct pathway-specific functions encoded by single ORFs. Illustrating the power of the approach, we identify HHV6A U14 as a p53 antagonist, HHV7 U21 as a dual-function STING antagonist and MHC-I antigen display inhibitor, and adenoviral 13.6K/i-leader protein as a de novo evolved TAP inhibitor that suppresses MHC-I display. These results establish a general framework for systematic effector annotation, uncover new mechanisms of host-pathogen interaction across kingdoms, and highlight pathogen effectors as a versatile toolkit for rewiring and probing human cellular pathways.