1. Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins.
- Author
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Shirasaki R, Matthews GM, Gandolfi S, de Matos Simoes R, Buckley DL, Raja Vora J, Sievers QL, Brüggenthies JB, Dashevsky O, Poarch H, Tang H, Bariteau MA, Sheffer M, Hu Y, Downey-Kopyscinski SL, Hengeveld PJ, Glassner BJ, Dhimolea E, Ott CJ, Zhang T, Kwiatkowski NP, Laubach JP, Schlossman RL, Richardson PG, Culhane AC, Groen RWJ, Fischer ES, Vazquez F, Tsherniak A, Hahn WC, Levy J, Auclair D, Licht JD, Keats JJ, Boise LH, Ebert BL, Bradner JE, Gray NS, and Mitsiades CS
- Subjects
- Animals, CRISPR-Cas Systems, Cell Line, Tumor, Cyclin-Dependent Kinase 9 metabolism, Drug Resistance, Neoplasm, Gene Editing, Gene Expression Regulation, Neoplastic, Genes, Overlapping, Genome-Wide Association Study, Genomics methods, Humans, Mice, Multiple Myeloma drug therapy, Oncogene Proteins metabolism, Proteins antagonists & inhibitors, Proteins metabolism, Proteolysis, Tumor Cells, Cultured, Adaptor Proteins, Signal Transducing metabolism, Antineoplastic Agents pharmacology, Multiple Myeloma genetics, Multiple Myeloma metabolism, Ubiquitin-Protein Ligases metabolism, Von Hippel-Lindau Tumor Suppressor Protein metabolism
- Abstract
Heterobifunctional proteolysis-targeting chimeric compounds leverage the activity of E3 ligases to induce degradation of target oncoproteins and exhibit potent preclinical antitumor activity. To dissect the mechanisms regulating tumor cell sensitivity to different classes of pharmacological "degraders" of oncoproteins, we performed genome-scale CRISPR-Cas9-based gene editing studies. We observed that myeloma cell resistance to degraders of different targets (BET bromodomain proteins, CDK9) and operating through CRBN (degronimids) or VHL is primarily mediated by prevention of, rather than adaptation to, breakdown of the target oncoprotein; and this involves loss of function of the cognate E3 ligase or interactors/regulators of the respective cullin-RING ligase (CRL) complex. The substantial gene-level differences for resistance mechanisms to CRBN- versus VHL-based degraders explains mechanistically the lack of cross-resistance with sequential administration of these two degrader classes. Development of degraders leveraging more diverse E3 ligases/CRLs may facilitate sequential/alternating versus combined uses of these agents toward potentially delaying or preventing resistance., Competing Interests: Declaration of Interests F.V. receives research funding from Novo Ventures. P.G.R. reports research support from Oncopeptides, Celgene/BMS, and Takeda and is an advisory committee member for Karyopharm, Oncopeptides, Celgene/BMS, Takeda, Janssen, Sanofi, Secura Bio, and GSK. E.S.F. is a founder, science advisory board member, and equity holder in Civetta, Jengu (board member), and Neomorph; an equity holder in C4; and a consultant to Astellas, Novartis, Deerfield, and EcoR1. The Fischer lab receives or has received research funding from Novartis, Astellas, Ajax, and Deerfield. N.P.K. is a consultant to Epiphanes, Inc. W.C.H. is a consultant for Thermo Fisher, Solvasta, MPM Capital, Tyra Biosciences, Jubilant Therapeutics, Frontier Medicines, RAPPTA Therapeutics, and Parexel and is a founder of and advisor to KSQ Therapeutics. L.H.B. receives research funding from AstraZeneca and is a consultant for AstraZeneca and Genentech. B.L.E. has received research funding from Celgene and Deerfield. He has received consulting fees from GRAIL, and he serves on the scientific advisory boards for and holds equity in Skyhawk Therapeutics and Exo Therapeutics. J.E.B. is an author on United States patent applications licensed from the Dana-Farber Cancer Institute to C4 Therapeutics (TPD) and Tensha Therapeutics (now Roche; BRD4 inhibition). He is now an executive of and shareholder in Novartis AG. N.S.G. is a scientific founder, member of the scientific advisory board and equity holder in C4 Therapeutics, Syros Pharmaceuticals, Petra Pharmaceuticals, Ravenna, Inception, Allorion, Jengu, and Soltego (board member) and is the inventor on intellectual property licensed to these entities. R.S., G.M.M., S.G., R.d.M.S., and C.S.M. are authors on a patent application on the use of degraders. C.S.M. also discloses consultant/honoraria from Fate Therapeutics, Ionis Pharmaceuticals and FIMECS; employment of a relative with Takeda; and research funding from Janssen/Johnson & Johnson, TEVA, EMD Serono, Abbvie, Arch Oncology, Karyopharm, Sanofi, and Nurix., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
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