A Chemical-Genetic Interaction Matrix Reveals Drug Mechanism and Genetic Architecture

bioRxiv. 2026 Jan 30:2026.01.28.701823. doi: 10.64898/2026.01.28.701823.

Jasmin Coulombe-Huntington ¹ ², Thierry Bertomeu ¹ ³, Caroline Huard ¹, Andrew Chatr-Aryamontri ¹ ³, Daniel J St-Cyr ¹ ⁴, María Sánchez-Osuna ⁵, David Papadopoli ⁶, Karine Normandin ¹, Mohammadjavad Paydar ¹, Shannon McLaughlan ⁷, Corinne St-Denis ¹, Li Zhang ¹ ³, Henry Say ⁵, Roger Palou ⁵, Chris Stark ⁵, Bobby-Joe Breitkreutz ⁵, Almer M van der Sloot ⁸, Sandhya Manohar ⁹, Hugo Lavoie ¹, Katherine L B Borden ¹ ¹⁰, Brian Raught ¹¹ ¹², Damien D'Amours ¹³, Frank Sicheri ¹⁴ ¹⁵, Alain Verreault ¹ ¹⁶, Sylvie Mader ¹ ¹⁷, Sylvain Meloche ¹ ¹⁸, Marc Therrien ¹ ¹⁶, Pierre Thibault ¹ ¹⁹, Brian Wilhelm ¹ ²⁰, Peter B Dirks ²¹, John D Aitchison ²², Elizabeth Patton ²³, Randall W King ²⁴, Philippe P Roux ¹ ¹⁶, Guy Sauvageau ¹ ²⁰, Trang Hoang ¹ ¹⁶, Anne Marinier ¹ ¹⁹, Lea Harrington ²⁵, Benjamin Kwok ²⁶, Vincent Archambault ¹ ¹⁷, Ivan Topisirovic ⁶ ⁷, Mike Tyers ⁵ ¹⁵

Affiliations

1 Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada.
2 Department of Bioengineering, McGill University, Montreal, QC, Canada.
3 ChemoGenix CRISPR Screening Platform, Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada.
4 X-Chem, Inc., 4800 Rue Levy, Montréal, QC, Canada, H4R 2P7.
5 Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, Canada.
6 Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.
7 Department of Biochemistry, McGill University, Montreal, QC, Canada.
8 The Québec Artificial Intelligence Institute, Mila, Montréal, QC, Canada.
9 Department of Molecular Mechanisms of Disease, Universität Zürich, Zurich, Switzerland.
10 Department of Pharmacology, The Robert H Lurie Comprehensive Cancer Centre, Northwestern University, IL, USA.
11 Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
12 Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
13 Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
14 The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
15 Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
16 Department of Pathology and Cell Biology, Université de Montréal, Montreal, QC, Canada.
17 Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada.
18 Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada.
19 Department of Chemistry, Université de Montréal, Montréal, QC, Canada.
20 Department of Medicine, Université de Montréal, Montréal, QC, Canada.
21 Program in Developmental, Stem Cell & Cancer Biology, Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada.
22 Center for Global Infectious Disease Research, Seattle Children's Research Institute, Departments of Pediatrics and Biochemistry, University of Washington, WA, USA.
23 MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom.
24 Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
25 Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
26 Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE, USA.

PMID: 41659671 DOI: 10.64898/2026.01.28.701823

Abstract

To probe drug mechanism of action (MOA) and interrogate the genetic architecture of human cells, we carried out isogenic genome-wide CRISPR/Cas9 knockout screens against 310 diverse drugs, bioactive compounds, and stress conditions. Stringent statistical correction for gene knockout fitness defects yielded a large-scale matrix of >12,000 high confidence chemical-genetic interactions (CGIs). This dataset revealed many previously unappreciated off-target effects for well-characterized compounds and novel MOAs for uncharacterized compounds. The CGI matrix uncovered dense genetic modules that yielded new biological insights into phospholipidosis, mitotic regulation, metabolism, the DNA damage response, and mTOR signaling. The dataset allowed identification of multi-drug sensitization and resistance mechanisms, inference of gene function, elaboration of cross-process connectivity, evaluation of the cell type specificity of CGIs, prediction of chemical synergism, and extensive annotation of understudied genes. This resource provides a map of the genetic landscape in human cells and a framework to help guide drug discovery.

Keywords

CRISPR/Cas9; DNA damage response; chemical synergy; chemical-genetic interaction; chemogenomic profile; drug mechanism; gene function; mTOR; mitosis; phospholipidosis.

Products

Cat. No.

Product Name

Category/Application
HY-K0010

Protease Inhibitor Cocktail (EDTA-Free, 100× in DMSO)

Protease Inhibitor Cocktail

Name
Email *

	Sorry, but the email address you supplied was invalid.