Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins

Ryosuke Shirasaki; Geoffrey M Matthews; Sara Gandolfi; Ricardo de Matos Simoes; Dennis L Buckley; Joseline Raja Vora; Quinlan L Sievers; Johanna B Brüggenthies; Olga Dashevsky; Haley Poarch; Huihui Tang; Megan A Bariteau; Michal Sheffer; Yiguo Hu; Sondra L Downey-Kopyscinski; Paul J Hengeveld; Brian J Glassner; Eugen Dhimolea; Christopher J Ott; Tinghu Zhang; Nicholas P Kwiatkowski; Jacob P Laubach; Robert L Schlossman; Paul G Richardson; Aedin C Culhane; Richard W J Groen; Eric S Fischer; Francisca Vazquez; Aviad Tsherniak; William C Hahn; Joan Levy; Daniel Auclair; Jonathan D Licht; Jonathan J Keats; Lawrence H Boise; Benjamin L Ebert; James E Bradner; Nathanael S Gray; Constantine S Mitsiades

doi:10.1016/j.celrep.2020.108532

Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins

Cell Rep. 2021 Jan 5;34(1):108532. doi: 10.1016/j.celrep.2020.108532.

Authors

Ryosuke Shirasaki¹, Geoffrey M Matthews², Sara Gandolfi¹, Ricardo de Matos Simoes¹, Dennis L Buckley², Joseline Raja Vora², Quinlan L Sievers², Johanna B Brüggenthies², Olga Dashevsky¹, Haley Poarch³, Huihui Tang¹, Megan A Bariteau², Michal Sheffer¹, Yiguo Hu⁴, Sondra L Downey-Kopyscinski², Paul J Hengeveld⁴, Brian J Glassner¹, Eugen Dhimolea¹, Christopher J Ott⁵, Tinghu Zhang⁶, Nicholas P Kwiatkowski⁶, Jacob P Laubach⁴, Robert L Schlossman⁴, Paul G Richardson⁴, Aedin C Culhane⁷, Richard W J Groen⁸, Eric S Fischer⁶, Francisca Vazquez⁹, Aviad Tsherniak⁹, William C Hahn², Joan Levy¹⁰, Daniel Auclair¹⁰, Jonathan D Licht¹¹, Jonathan J Keats¹², Lawrence H Boise¹³, Benjamin L Ebert², James E Bradner², Nathanael S Gray⁶, Constantine S Mitsiades¹⁴

Affiliations

¹ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA.
² Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
⁴ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
⁵ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁶ Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
⁷ Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA.
⁸ Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands.
⁹ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
¹⁰ Multiple Myeloma Research Foundation, Norwalk, CT, USA.
¹¹ University of Florida Health Cancer Center, Gainesville, FL, USA.
¹² Translational Genomics Research Institute, Phoenix, AZ, USA.
¹³ Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA.
¹⁴ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: constantine_mitsiades@dfci.harvard.edu.

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.

Keywords: CRBN; CRISPR; CRISPR activation; E3 ligase; PROTAC; VHL; heterobifunctional proteolysis-targeting chimeric compounds; myeloma; pharmacological degraders; resistance.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Adaptor Proteins, Signal Transducing / metabolism*
Animals
Antineoplastic Agents / pharmacology*
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
Multiple Myeloma / genetics*
Multiple Myeloma / metabolism*
Oncogene Proteins / metabolism
Proteins / antagonists & inhibitors
Proteins / metabolism
Proteolysis
Tumor Cells, Cultured
Ubiquitin-Protein Ligases / metabolism*
Von Hippel-Lindau Tumor Suppressor Protein / metabolism*

Substances

Adaptor Proteins, Signal Transducing
Antineoplastic Agents
CRBN protein, human
Oncogene Proteins
Proteins
bromodomain and extra-terminal domain protein, human
CULL-RING ligase, human
Ubiquitin-Protein Ligases
Von Hippel-Lindau Tumor Suppressor Protein
CDK9 protein, human
Cyclin-Dependent Kinase 9

Abstract

Publication types

MeSH terms

Substances

Grants and funding