Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens
Iñigo Ayestaran,
Ana Galhoz,
Elmar Spiegel,
Ben Sidders,
Jonathan R. Dry,
Frank Dondelinger,
Andreas Bender,
Ultan McDermott,
Francesco Iorio,
Michael P. Menden
Affiliations
Iñigo Ayestaran
Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany; CRUK Cambridge Centre Early Detection Programme, Department of Oncology, University of Cambridge, Cambridge, UK
Ana Galhoz
Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany; Department of Biology, Ludwig-Maximilians University Munich, Martinsried 82152, Germany
Elmar Spiegel
Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany
Ben Sidders
Research and Early Development, Oncology, AstraZeneca, Cambridge CB4 0WG, UK
Jonathan R. Dry
Research and Early Development, Oncology, AstraZeneca, Boston, MA 02451, USA; Tempus Labs, Boston, MA, USA
Frank Dondelinger
Centre for Health Informatics, Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster LA1 4YW, UK
Andreas Bender
Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
Ultan McDermott
Research and Early Development, Oncology, AstraZeneca, Cambridge CB4 0WG, UK
Francesco Iorio
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1RQ, UK; Human Technopole, Palazzo Italia Via Cristina Belgioioso 171, Milano 20157, Italy
Michael P. Menden
Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany; Department of Biology, Ludwig-Maximilians University Munich, Martinsried 82152, Germany; German Centre for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany; Corresponding author
Summary: High-throughput drug screens in cancer cell lines test compounds at low concentrations, thereby enabling the identification of drug-sensitivity biomarkers, while resistance biomarkers remain underexplored. Dissecting meaningful drug responses at high concentrations is challenging due to cytotoxicity, i.e., off-target effects, thus limiting resistance biomarker discovery to frequently mutated cancer genes. To address this, we interrogate subpopulations carrying sensitivity biomarkers and consecutively investigate unexpectedly resistant (UNRES) cell lines for unique genetic alterations that may drive resistance. By analyzing the GDSC and CTRP datasets, we find 53 and 35 UNRES cases, respectively. For 24 and 28 of them, we highlight putative resistance biomarkers. We find clinically relevant cases such as EGFRT790M mutation in NCI-H1975 or PTEN loss in NCI-H1650 cells, in lung adenocarcinoma treated with EGFR inhibitors. Interrogating the underpinnings of drug resistance with publicly available CRISPR phenotypic assays assists in prioritizing resistance drivers, offering hypotheses for drug combinations. The Bigger Picture: Cancer drug resistance is the major challenge of modern oncology. Identifying resistance and its biomarkers will empower the next generation of precision medicines. High-throughput pharmacology screens in cancer cell lines have successfully identified drug-sensitivity biomarkers, but drug-resistance biomarkers are underexplored. Intrinsic drug-resistance events are often rare and experimentally indistinguishable from cytotoxicity or artifacts without prior knowledge. To address this, we investigate cell-line populations sensitized to a drug treatment (i.e., carrying established sensitivity biomarkers) and characterize those cell lines that do not respond as expected. We highlight unique genetic features harbored by these cell lines and confirm their linkage to drug resistance using CRISPR gene essentiality data. Our analysis and results pave the way for enhanced precision medicine, guide further CRISPR screens, and identify potential drug combinations to tackle resistance.
