1
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Souroullas GP, Jeck WR, Parker JS, Simon JM, Liu JY, Paulk J, Xiong J, Clark KS, Fedoriw Y, Qi J, Burd CE, Bradner JE, Sharpless NE. Author Correction: An oncogenic Ezh2 mutation induces tumors through global redistribution of histone 3 lysine 27 trimethylation. Nat Med 2024:10.1038/s41591-024-02867-1. [PMID: 38383796 DOI: 10.1038/s41591-024-02867-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Affiliation(s)
- George P Souroullas
- Department of Genetics, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - William R Jeck
- Department of Genetics, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jeremy M Simon
- Department of Genetics, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jie-Yu Liu
- Department of Genetics, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jessie Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Kelly S Clark
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Yuri Fedoriw
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Christin E Burd
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio, USA
- Department of Molecular Virology, Immunology and Medical Genetics, Ohio State University, Columbus, Ohio, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Norman E Sharpless
- Department of Genetics, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
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2
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Hudson L, Mason JW, Westphal MV, Richter MJR, Thielman JR, Hua BK, Gerry CJ, Xia G, Osswald HL, Knapp JM, Tan ZY, Kokkonda P, Tresco BIC, Liu S, Reidenbach AG, Lim KS, Poirier J, Capece J, Bonazzi S, Gampe CM, Smith NJ, Bradner JE, Coley CW, Clemons PA, Melillo B, Hon CSY, Ottl J, Dumelin CE, Schaefer JV, Faust AME, Berst F, Schreiber SL, Zécri FJ, Briner K. Author Correction: Diversity-oriented synthesis encoded by deoxyoligonucleotides. Nat Commun 2023; 14:7589. [PMID: 37989745 PMCID: PMC10663570 DOI: 10.1038/s41467-023-43518-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Affiliation(s)
- Liam Hudson
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jeremy W Mason
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthias V Westphal
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthieu J R Richter
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jonathan R Thielman
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher J Gerry
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Guoqin Xia
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Heather L Osswald
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - John M Knapp
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Zher Yin Tan
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Ben I C Tresco
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Shuang Liu
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Katherine S Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jennifer Poirier
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - John Capece
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Simone Bonazzi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Christian M Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Nichola J Smith
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - James E Bradner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Connor W Coley
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, 02139, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - C Suk-Yee Hon
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Christoph E Dumelin
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jonas V Schaefer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Ann Marie E Faust
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Frédéric Berst
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Frédéric J Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | - Karin Briner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
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3
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Hudson L, Mason JW, Westphal MV, Richter MJR, Thielman JR, Hua BK, Gerry CJ, Xia G, Osswald HL, Knapp JM, Tan ZY, Kokkonda P, Tresco BIC, Liu S, Reidenbach AG, Lim KS, Poirier J, Capece J, Bonazzi S, Gampe CM, Smith NJ, Bradner JE, Coley CW, Clemons PA, Melillo B, Hon CSY, Ottl J, Dumelin CE, Schaefer JV, Faust AME, Berst F, Schreiber SL, Zécri FJ, Briner K. Diversity-oriented synthesis encoded by deoxyoligonucleotides. Nat Commun 2023; 14:4930. [PMID: 37582753 PMCID: PMC10427684 DOI: 10.1038/s41467-023-40575-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
Diversity-oriented synthesis (DOS) is a powerful strategy to prepare molecules with underrepresented features in commercial screening collections, resulting in the elucidation of novel biological mechanisms. In parallel to the development of DOS, DNA-encoded libraries (DELs) have emerged as an effective, efficient screening strategy to identify protein binders. Despite recent advancements in this field, most DEL syntheses are limited by the presence of sensitive DNA-based constructs. Here, we describe the design, synthesis, and validation experiments performed for a 3.7 million-member DEL, generated using diverse skeleton architectures with varying exit vectors and derived from DOS, to achieve structural diversity beyond what is possible by varying appendages alone. We also show screening results for three diverse protein targets. We will make this DEL available to the academic scientific community to increase access to novel structural features and accelerate early-phase drug discovery.
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Affiliation(s)
- Liam Hudson
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jeremy W Mason
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthias V Westphal
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthieu J R Richter
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jonathan R Thielman
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher J Gerry
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Guoqin Xia
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Heather L Osswald
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - John M Knapp
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Zher Yin Tan
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Ben I C Tresco
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Shuang Liu
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Katherine S Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jennifer Poirier
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - John Capece
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Simone Bonazzi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Christian M Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Nichola J Smith
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - James E Bradner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Connor W Coley
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, 02139, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - C Suk-Yee Hon
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Christoph E Dumelin
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jonas V Schaefer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Ann Marie E Faust
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Frédéric Berst
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Frédéric J Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | - Karin Briner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
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4
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de Matos Simoes R, Shirasaki R, Downey-Kopyscinski SL, Matthews GM, Barwick BG, Gupta VA, Dupéré-Richer D, Yamano S, Hu Y, Sheffer M, Dhimolea E, Dashevsky O, Gandolfi S, Ishiguro K, Meyers RM, Bryan JG, Dharia NV, Hengeveld PJ, Brüggenthies JB, Tang H, Aguirre AJ, Sievers QL, Ebert BL, Glassner BJ, Ott CJ, Bradner JE, Kwiatkowski NP, Auclair D, Levy J, Keats JJ, Groen RWJ, Gray NS, Culhane AC, McFarland JM, Dempster JM, Licht JD, Boise LH, Hahn WC, Vazquez F, Tsherniak A, Mitsiades CS. Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias. Nat Cancer 2023; 4:754-773. [PMID: 37237081 PMCID: PMC10918623 DOI: 10.1038/s43018-023-00550-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/29/2023] [Indexed: 05/28/2023]
Abstract
Clinical progress in multiple myeloma (MM), an incurable plasma cell (PC) neoplasia, has been driven by therapies that have limited applications beyond MM/PC neoplasias and do not target specific oncogenic mutations in MM. Instead, these agents target pathways critical for PC biology yet largely dispensable for malignant or normal cells of most other lineages. Here we systematically characterized the lineage-preferential molecular dependencies of MM through genome-scale clustered regularly interspaced short palindromic repeats (CRISPR) studies in 19 MM versus hundreds of non-MM lines and identified 116 genes whose disruption more significantly affects MM cell fitness compared with other malignancies. These genes, some known, others not previously linked to MM, encode transcription factors, chromatin modifiers, endoplasmic reticulum components, metabolic regulators or signaling molecules. Most of these genes are not among the top amplified, overexpressed or mutated in MM. Functional genomics approaches thus define new therapeutic targets in MM not readily identifiable by standard genomic, transcriptional or epigenetic profiling analyses.
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Affiliation(s)
- Ricardo de Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Sondra L Downey-Kopyscinski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Geoffrey M Matthews
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Vikas A Gupta
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | | | - Shizuka Yamano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Sara Gandolfi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Kazuya Ishiguro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Robin M Meyers
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jordan G Bryan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Neekesh V Dharia
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul J Hengeveld
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Johanna B Brüggenthies
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Huihui Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Quinlan L Sievers
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Brian J Glassner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Nicholas P Kwiatkowski
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Joan Levy
- Multiple Myeloma Research Foundation, Norwalk, CT, USA
| | | | - Richard W J Groen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Nathanael S Gray
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aedin C Culhane
- Department of Data Sciences, Dana-Farber Cancer Institute & Harvard School of Public Health, Boston, MA, USA
- Limerick Digital Cancer Research Center, Health Research Institute, School of Medicine, University of Limerick, Limerick, Ireland
| | - James M McFarland
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Joshua M Dempster
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jonathan D Licht
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Francisca Vazquez
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center at Harvard, Boston, MA, USA.
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5
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Bonazzi S, d'Hennezel E, Beckwith REJ, Xu L, Fazal A, Magracheva A, Ramesh R, Cernijenko A, Antonakos B, Bhang HEC, Caro RG, Cobb JS, Ornelas E, Ma X, Wartchow CA, Clifton MC, Forseth RR, Fortnam BH, Lu H, Csibi A, Tullai J, Carbonneau S, Thomsen NM, Larrow J, Chie-Leon B, Hainzl D, Gu Y, Lu D, Meyer MJ, Alexander D, Kinyamu-Akunda J, Sabatos-Peyton CA, Dales NA, Zécri FJ, Jain RK, Shulok J, Wang YK, Briner K, Porter JA, Tallarico JA, Engelman JA, Dranoff G, Bradner JE, Visser M, Solomon JM. Discovery and characterization of a selective IKZF2 glue degrader for cancer immunotherapy. Cell Chem Biol 2023; 30:235-247.e12. [PMID: 36863346 DOI: 10.1016/j.chembiol.2023.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 12/15/2022] [Accepted: 02/09/2023] [Indexed: 03/04/2023]
Abstract
Malignant tumors can evade destruction by the immune system by attracting immune-suppressive regulatory T cells (Treg) cells. The IKZF2 (Helios) transcription factor plays a crucial role in maintaining function and stability of Treg cells, and IKZF2 deficiency reduces tumor growth in mice. Here we report the discovery of NVP-DKY709, a selective molecular glue degrader of IKZF2 that spares IKZF1/3. We describe the recruitment-guided medicinal chemistry campaign leading to NVP-DKY709 that redirected the degradation selectivity of cereblon (CRBN) binders from IKZF1 toward IKZF2. Selectivity of NVP-DKY709 for IKZF2 was rationalized by analyzing the DDB1:CRBN:NVP-DKY709:IKZF2(ZF2 or ZF2-3) ternary complex X-ray structures. Exposure to NVP-DKY709 reduced the suppressive activity of human Treg cells and rescued cytokine production in exhausted T-effector cells. In vivo, treatment with NVP-DKY709 delayed tumor growth in mice with a humanized immune system and enhanced immunization responses in cynomolgus monkeys. NVP-DKY709 is being investigated in the clinic as an immune-enhancing agent for cancer immunotherapy.
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Affiliation(s)
- Simone Bonazzi
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
| | - Eva d'Hennezel
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
| | | | - Lei Xu
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Aleem Fazal
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Anna Magracheva
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Radha Ramesh
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | - Hyo-Eun C Bhang
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Jennifer S Cobb
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Xiaolei Ma
- Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | | | | | - Ry R Forseth
- Novartis Institutes for Biomedical Research, East Hanover, NJ, USA
| | | | - Hongbo Lu
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Alfredo Csibi
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jennifer Tullai
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Seth Carbonneau
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Noel M Thomsen
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jay Larrow
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Dominik Hainzl
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Yi Gu
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Darlene Lu
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Matthew J Meyer
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Dylan Alexander
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | - Natalie A Dales
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Rishi K Jain
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Janine Shulok
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Y Karen Wang
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Karin Briner
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | | | - Glenn Dranoff
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - James E Bradner
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Michael Visser
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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6
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O'Donnell CJ, Bradner JE. Bridging the Gap to Translating Genome-Wide Discoveries Into Therapies to Prevent and Treat Atherosclerotic Cardiovascular Disease. Circulation 2022; 146:930-933. [PMID: 36121912 DOI: 10.1161/circulationaha.122.060998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Christopher J O'Donnell
- Novartis Institutes for BioMedical Research, Cambridge, MA (C.J.O., J.E.B.).,Cardiology Section, VA Boston Healthcare System, Harvard Medical School, MA (C.J.O.)
| | - James E Bradner
- Novartis Institutes for BioMedical Research, Cambridge, MA (C.J.O., J.E.B.)
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7
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Zaiken MC, Flynn R, Paz KG, Rhee SY, Jin S, Mohamed FA, Saha A, Thangavelu G, Park PMC, Hemming ML, Sage PT, Sharpe AH, DuPage M, Bluestone JA, Panoskaltsis-Mortari A, Cutler CS, Koreth J, Antin JH, Soiffer RJ, Ritz J, Luznik L, Maillard I, Hill GR, MacDonald KPA, Munn DH, Serody JS, Murphy WJ, Kean LS, Zhang Y, Bradner JE, Qi J, Blazar BR. BET-bromodomain and EZH2 inhibitor-treated chronic GVHD mice have blunted germinal centers with distinct transcriptomes. Blood 2022; 139:2983-2997. [PMID: 35226736 PMCID: PMC9101246 DOI: 10.1182/blood.2021014557] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/09/2022] [Indexed: 01/26/2023] Open
Abstract
Despite advances in the field, chronic graft-versus-host-disease (cGVHD) remains a leading cause of morbidity and mortality following allogenic hematopoietic stem cell transplant. Because treatment options remain limited, we tested efficacy of anticancer, chromatin-modifying enzyme inhibitors in a clinically relevant murine model of cGVHD with bronchiolitis obliterans (BO). We observed that the novel enhancer of zeste homolog 2 (EZH2) inhibitor JQ5 and the BET-bromodomain inhibitor JQ1 each improved pulmonary function; impaired the germinal center (GC) reaction, a prerequisite in cGVHD/BO pathogenesis; and JQ5 reduced EZH2-mediated H3K27me3 in donor T cells. Using conditional EZH2 knockout donor cells, we demonstrated that EZH2 is obligatory for the initiation of cGVHD/BO. In a sclerodermatous cGVHD model, JQ5 reduced the severity of cutaneous lesions. To determine how the 2 drugs could lead to the same physiological improvements while targeting unique epigenetic processes, we analyzed the transcriptomes of splenic GCB cells (GCBs) from transplanted mice treated with either drug. Multiple inflammatory and signaling pathways enriched in cGVHD/BO GCBs were reduced by each drug. GCBs from JQ5- but not JQ1-treated mice were enriched for proproliferative pathways also seen in GCBs from bone marrow-only transplanted mice, likely reflecting their underlying biology in the unperturbed state. In conjunction with in vivo data, these insights led us to conclude that epigenetic targeting of the GC is a viable clinical approach for the treatment of cGVHD, and that the EZH2 inhibitor JQ5 and the BET-bromodomain inhibitor JQ1 demonstrated clinical potential for EZH2i and BETi in patients with cGVHD/BO.
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Affiliation(s)
- Michael C Zaiken
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Ryan Flynn
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Katelyn G Paz
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Stephanie Y Rhee
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Sujeong Jin
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Fathima A Mohamed
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Asim Saha
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Govindarajan Thangavelu
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Paul M C Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Matthew L Hemming
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Peter T Sage
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Evergrande Center for Immunologic Diseases, Harvard Medical School-Brigham and Women's Hospital, Boston, MA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Evergrande Center for Immunologic Diseases, Harvard Medical School-Brigham and Women's Hospital, Boston, MA
| | - Michel DuPage
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA
| | | | - Angela Panoskaltsis-Mortari
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | | | | | | | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | - Leo Luznik
- Department of Oncology, Sidney Kimmel Cancer Center, Baltimore, MD
| | - Ivan Maillard
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Geoffrey R Hill
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Medical Oncology, University of Washington, Seattle, WA
| | - Kelli P A MacDonald
- Department of Immunology, Queensland Institute of Medical Research (QIMR), University of Queensland, Brisbane, QLD, Australia
| | - David H Munn
- Georgia Cancer Center, Augusta University, Augusta, GA
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - William J Murphy
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA
| | - Leslie S Kean
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA
| | - Yi Zhang
- Fels Institute for Cancer Research and Molecular Biology, Department of Microbiology and Immunology, Temple University, Philadelphia, PA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; and
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Bruce R Blazar
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
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8
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Liao Y, Chen CH, Xiao T, de la Peña Avalos B, Dray EV, Cai C, Gao S, Shah N, Zhang Z, Feit A, Xue P, Liu Z, Yang M, Lee JH, Xu H, Li W, Mei S, Pierre RS, Shu S, Fei T, Duarte M, Zhao J, Bradner JE, Polyak K, Kantoff PW, Long H, Balk SP, Liu XS, Brown M, Xu K. Inhibition of EZH2 transactivation function sensitizes solid tumors to genotoxic stress. Proc Natl Acad Sci U S A 2022; 119:e2105898119. [PMID: 35031563 PMCID: PMC8784159 DOI: 10.1073/pnas.2105898119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Drugs that block the activity of the methyltransferase EZH2 are in clinical development for the treatment of non-Hodgkin lymphomas harboring EZH2 gain-of-function mutations that enhance its polycomb repressive function. We have previously reported that EZH2 can act as a transcriptional activator in castration-resistant prostate cancer (CRPC). Now we show that EZH2 inhibitors can also block the transactivation activity of EZH2 and inhibit the growth of CRPC cells. Gene expression and epigenomics profiling of cells treated with EZH2 inhibitors demonstrated that in addition to derepressing gene expression, these compounds also robustly down-regulate a set of DNA damage repair (DDR) genes, especially those involved in the base excision repair (BER) pathway. Methylation of the pioneer factor FOXA1 by EZH2 contributes to the activation of these genes, and interaction with the transcriptional coactivator P300 via the transactivation domain on EZH2 directly turns on the transcription. In addition, CRISPR-Cas9-mediated knockout screens in the presence of EZH2 inhibitors identified these BER genes as the determinants that underlie the growth-inhibitory effect of EZH2 inhibitors. Interrogation of public data from diverse types of solid tumors expressing wild-type EZH2 demonstrated that expression of DDR genes is significantly correlated with EZH2 dependency and cellular sensitivity to EZH2 inhibitors. Consistent with these findings, treatment of CRPC cells with EZH2 inhibitors dramatically enhances their sensitivity to genotoxic stress. These studies reveal a previously unappreciated mechanism of action of EZH2 inhibitors and provide a mechanistic basis for potential combination cancer therapies.
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Affiliation(s)
- Yiji Liao
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Chen-Hao Chen
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Tengfei Xiao
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Bárbara de la Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Eloise V Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Changmeng Cai
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA 02125
| | - Shuai Gao
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA 02125
| | - Neel Shah
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Zhao Zhang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Avery Feit
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Pengya Xue
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Zhijie Liu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Mei Yang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Ji Hoon Lee
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Han Xu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Wei Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Shenglin Mei
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Roodolph S Pierre
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
- Biological and Biomedical Science Program, Harvard Medical School, Boston, MA 02115
| | - Shaokun Shu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Teng Fei
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Melissa Duarte
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Jin Zhao
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - James E Bradner
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
- Biological and Biomedical Science Program, Harvard Medical School, Boston, MA 02115
| | - Kornelia Polyak
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Philip W Kantoff
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Steven P Balk
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115;
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115;
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Kexin Xu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229;
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115
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9
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Gill T, Wang H, Bandaru R, Lawlor M, Lu C, Nieman LT, Tao J, Zhang Y, Anderson DG, Ting DT, Chen X, Bradner JE, Ott CJ. Selective targeting of MYC mRNA by stabilized antisense oligonucleotides. Oncogene 2021; 40:6527-6539. [PMID: 34650218 PMCID: PMC8627489 DOI: 10.1038/s41388-021-02053-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 09/07/2021] [Accepted: 09/30/2021] [Indexed: 12/30/2022]
Abstract
MYC is a prolific proto-oncogene driving the malignant behaviors of numerous common cancers, yet potent and selective cell-permeable inhibitors of MYC remain elusive. In order to ultimately realize the goal of therapeutic MYC inhibition in cancer, we have initiated discovery chemistry efforts aimed at inhibiting MYC translation. Here we describe a series of conformationally stabilized synthetic antisense oligonucleotides designed to target MYC mRNA (MYCASOs). To support bioactivity, we designed and synthesized this focused library of MYCASOs incorporating locked nucleic acid (LNA) bases at the 5'- and 3'-ends, a phosphorothioate backbone, and internal DNA bases. Treatment of MYC-expressing cancer cells with MYCASOs leads to a potent decrease in MYC mRNA and protein levels. Cleaved MYC mRNA in MYCASO-treated cells is detected with a sensitive 5' Rapid Amplification of cDNA Ends (RACE) assay. MYCASO treatment of cancer cell lines leads to significant inhibition of cellular proliferation while specifically perturbing MYC-driven gene expression signatures. In a MYC-induced model of hepatocellular carcinoma, MYCASO treatment decreases MYC protein levels within tumors, decreases tumor burden, and improves overall survival. MYCASOs represent a new chemical tool for in vitro and in vivo modulation of MYC activity, and promising therapeutic agents for MYC-addicted tumors.
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Affiliation(s)
- Taylor Gill
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA
| | - Haichuan Wang
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, CA, 94143, USA
| | - Raj Bandaru
- ENZON Pharmaceuticals, Cranford, NJ, 07016, USA
| | - Matthew Lawlor
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
| | - Chenyue Lu
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
| | - Linda T Nieman
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
| | - Junyan Tao
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, CA, 94143, USA
| | | | - Daniel G Anderson
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - David T Ting
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, CA, 94143, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA.
| | - Christopher J Ott
- Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA.
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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10
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Bill M, Goda C, Pepe F, Ozer HG, McNeil B, Zhang X, Karunasiri M, Kulkarni R, Kalyan S, Papaioannou D, Ferenchak G, Garzon R, Bradner JE, Marcucci G, Caligiuri MA, Dorrance AM. Targeting BRD4 in acute myeloid leukemia with partial tandem duplication of the MLL gene. Haematologica 2021; 106:2527-2532. [PMID: 33979989 PMCID: PMC8409020 DOI: 10.3324/haematol.2020.271627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Indexed: 12/24/2022] Open
Affiliation(s)
- Marius Bill
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA; Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus Dresden, Dresden
| | - Chinmayee Goda
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH
| | - Felice Pepe
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH
| | - Hatice Gulcin Ozer
- The Ohio State University, Department of Biomedical Informatics, Columbus, OH
| | - Betina McNeil
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH
| | - Xiaoli Zhang
- The Ohio State University, Department of Biomedical Informatics, Columbus, OH
| | - Malith Karunasiri
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH
| | - Rohan Kulkarni
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH
| | - Sonu Kalyan
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH
| | - Dimitrios Papaioannou
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA; Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Gregory Ferenchak
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH
| | - Ramiro Garzon
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA; Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | | | - Guido Marcucci
- City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010
| | - Michael A Caligiuri
- City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA 91010
| | - Adrienne M Dorrance
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA; Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH.
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11
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Hideshima T, Mazitschek R, Qi J, Mimura N, Tseng JC, Kung AL, Bradner JE, Anderson KC. Correction: HDAC6 inhibitor WT161 downregulates growth factor receptors in breast cancer. Oncotarget 2021; 12:1736. [PMID: 34434504 PMCID: PMC8378766 DOI: 10.18632/oncotarget.28051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Teru Hideshima
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Naoya Mimura
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Department of Hematology, Chiba University Hospital, Chiba, Japan
| | - Jen-Chieh Tseng
- Lurie Family Imaging Center, Dana-Farber Cancer Institute, Boston, MA, USA.,PerkinElmer Inc., Hopkinton, MA, USA
| | - Andrew L Kung
- Lurie Family Imaging Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children's Hospital Boston, Boston, MA, USA.,Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
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12
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Kong W, Dimitri A, Wang W, Jung IY, Ott CJ, Fasolino M, Wang Y, Kulikovskaya I, Gupta M, Yoder T, DeNizio JE, Everett JK, Williams EF, Xu J, Scholler J, Reich TJ, Bhoj VG, Haines KM, Maus MV, Melenhorst JJ, Young RM, Jadlowsky JK, Marcucci KT, Bradner JE, Levine BL, Porter DL, Bushman FD, Kohli RM, June CH, Davis MM, Lacey SF, Vahedi G, Fraietta JA. BET bromodomain protein inhibition reverses chimeric antigen receptor extinction and reinvigorates exhausted T cells in chronic lymphocytic leukemia. J Clin Invest 2021; 131:e145459. [PMID: 34396987 DOI: 10.1172/jci145459] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 07/06/2021] [Indexed: 12/17/2022] Open
Abstract
Chimeric antigen receptor (CAR) T cells have induced remarkable antitumor responses in B cell malignancies. Some patients do not respond because of T cell deficiencies that hamper the expansion, persistence, and effector function of these cells. We used longitudinal immune profiling to identify phenotypic and pharmacodynamic changes in CD19-directed CAR T cells in patients with chronic lymphocytic leukemia (CLL). CAR expression maintenance was also investigated because this can affect response durability. CAR T cell failure was accompanied by preexisting T cell-intrinsic defects or dysfunction acquired after infusion. In a small subset of patients, CAR silencing was observed coincident with leukemia relapse. Using a small molecule inhibitor, we demonstrated that the bromodomain and extra-terminal (BET) family of chromatin adapters plays a role in downregulating CAR expression. BET protein blockade also ameliorated CAR T cell exhaustion as manifested by inhibitory receptor reduction, enhanced metabolic fitness, increased proliferative capacity, and enriched transcriptomic signatures of T cell reinvigoration. BET inhibition decreased levels of the TET2 methylcytosine dioxygenase, and forced expression of the TET2 catalytic domain eliminated the potency-enhancing effects of BET protein targeting in CAR T cells, providing a mechanism linking BET proteins and T cell dysfunction. Thus, modulating BET epigenetic readers may improve the efficacy of cell-based immunotherapies.
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Affiliation(s)
- Weimin Kong
- Department of Microbiology.,Center for Cellular Immunotherapies.,Abramson Cancer Center, and
| | - Alexander Dimitri
- Department of Microbiology.,Center for Cellular Immunotherapies.,Abramson Cancer Center, and
| | - Wenliang Wang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - In-Young Jung
- Department of Microbiology.,Center for Cellular Immunotherapies.,Abramson Cancer Center, and
| | - Christopher J Ott
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Maria Fasolino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yan Wang
- Center for Cellular Immunotherapies
| | | | | | | | - Jamie E DeNizio
- Department of Medicine and.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Erik F Williams
- Department of Microbiology.,Center for Cellular Immunotherapies.,Abramson Cancer Center, and
| | - Jun Xu
- Center for Cellular Immunotherapies
| | | | | | - Vijay G Bhoj
- Center for Cellular Immunotherapies.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Marcela V Maus
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts, USA
| | - J Joseph Melenhorst
- Center for Cellular Immunotherapies.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - James E Bradner
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Bruce L Levine
- Center for Cellular Immunotherapies.,Abramson Cancer Center, and.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David L Porter
- Abramson Cancer Center, and.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Rahul M Kohli
- Department of Medicine and.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carl H June
- Center for Cellular Immunotherapies.,Abramson Cancer Center, and.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Megan M Davis
- Center for Cellular Immunotherapies.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Simon F Lacey
- Center for Cellular Immunotherapies.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Golnaz Vahedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph A Fraietta
- Department of Microbiology.,Center for Cellular Immunotherapies.,Abramson Cancer Center, and.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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13
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Yi JS, Sias-Garcia O, Nasholm N, Hu X, Iniguez AB, Hall MD, Davis M, Guha R, Moreno-Smith M, Barbieri E, Duong K, Koach J, Qi J, Bradner JE, Stegmaier K, Weiss WA, Gustafson WC. The synergy of BET inhibitors with aurora A kinase inhibitors in MYCN-amplified neuroblastoma is heightened with functional TP53. Neoplasia 2021; 23:624-633. [PMID: 34107377 PMCID: PMC8192452 DOI: 10.1016/j.neo.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/29/2022] Open
Abstract
Amplification of MYCN is a poor prognostic feature in neuroblastoma (NBL) indicating aggressive disease. We and others have shown BET bromodomain inhibitors (BETi) target MYCN indirectly by downregulating its transcription. Here we sought to identify agents that synergize with BETi and to identify biomarkers of resistance. We previously performed a viability screen of ∼1,900 oncology-focused compounds combined with BET bromodomain inhibitors against MYCN-amplified NBL cell lines. Reanalysis of our screening results prominently identified inhibitors of aurora kinase A (AURKAi) to be highly synergistic with BETi. We confirmed the anti-proliferative effects of several BETi+AURKAi combinations in MYCN-amplified NBL cell lines. Compared to single agents, these combinations cooperated to decrease levels of N-myc. We treated both TP53-wild type and mutant, MYCN-amplified cell lines with the BETi JQ1 and the AURKAi Alisertib. The combination had improved efficacy in the TP53-WT context, notably driving apoptosis in both genetic backgrounds. JQ1+Alisertib combination treatment of a MYCN-amplified, TP53-null or TP53-restored genetically engineered mouse model of NBL prolonged survival better than either single agent. This was most profound with TP53 restored, with marked tumor shrinkage and apoptosis induction in response to combination JQ1+Alisertib. BETi+AURKAi in MYCN-amplified NBL, particularly in the context of functional TP53, provided anti-tumor benefits in preclinical models. This combination should be studied more closely in a pediatric clinical trial.
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Affiliation(s)
- Joanna S Yi
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.
| | - Oscar Sias-Garcia
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Nicole Nasholm
- Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - Xiaoyu Hu
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Amanda Balboni Iniguez
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA; Broad Institute, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Mindy Davis
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Rajarshi Guha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Myrthala Moreno-Smith
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Eveline Barbieri
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Kevin Duong
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Jessica Koach
- Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; Department of Neurology and Neurological Surgery, University of California, San Francisco, California, USA
| | - Jun Qi
- Broad Institute, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - James E Bradner
- Broad Institute, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA; Broad Institute, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - William A Weiss
- Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; Department of Neurology and Neurological Surgery, University of California, San Francisco, California, USA
| | - W Clay Gustafson
- Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA.
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14
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Carbonneau S, Sharma S, Peng L, Rajan V, Hainzl D, Henault M, Yang C, Hale J, Shulok J, Tallarico J, Porter J, Brogdon JL, Dranoff G, Bradner JE, Hild M, Guimaraes CP. An IMiD-inducible degron provides reversible regulation for chimeric antigen receptor expression and activity. Cell Chem Biol 2021; 28:583. [PMID: 33861956 DOI: 10.1016/j.chembiol.2021.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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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, Mitsiades CS. Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins. Cell Rep 2021; 34:108532. [PMID: 33406420 DOI: 10.1016/j.celrep.2020.108532] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 06/14/2019] [Accepted: 11/25/2020] [Indexed: 12/15/2022] Open
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.
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Affiliation(s)
- Ryosuke Shirasaki
- 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
| | - Geoffrey M Matthews
- 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
| | - Sara Gandolfi
- 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
| | - Ricardo de Matos Simoes
- 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
| | - Dennis L Buckley
- 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
| | - Joseline Raja Vora
- 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
| | - Quinlan L Sievers
- 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
| | - Johanna B Brüggenthies
- 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
| | - Olga Dashevsky
- 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
| | - Haley Poarch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Huihui Tang
- 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
| | - Megan A Bariteau
- 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
| | - Michal Sheffer
- 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
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Sondra L Downey-Kopyscinski
- 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
| | - Paul J Hengeveld
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Brian J Glassner
- 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
| | - Eugen Dhimolea
- 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
| | - Christopher J Ott
- 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
| | - Tinghu Zhang
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicholas P Kwiatkowski
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob P Laubach
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Robert L Schlossman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Paul G Richardson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Richard W J Groen
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Eric S Fischer
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - William C Hahn
- 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
| | - Joan Levy
- Multiple Myeloma Research Foundation, Norwalk, CT, USA
| | | | - Jonathan D Licht
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | | | - Lawrence H Boise
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Benjamin L Ebert
- 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
| | - James E Bradner
- 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
| | - Nathanael S Gray
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Constantine S Mitsiades
- 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.
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16
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Dowling CM, Hollinshead KER, Di Grande A, Pritchard J, Zhang H, Dillon ET, Haley K, Papadopoulos E, Mehta AK, Bleach R, Lindner AU, Mooney B, Düssmann H, O'Connor D, Prehn JHM, Wynne K, Hemann M, Bradner JE, Kimmelman AC, Guerriero JL, Cagney G, Wong KK, Letai AG, Chonghaile TN. Multiple screening approaches reveal HDAC6 as a novel regulator of glycolytic metabolism in triple-negative breast cancer. Sci Adv 2021; 7:7/3/eabc4897. [PMID: 33523897 PMCID: PMC7810372 DOI: 10.1126/sciadv.abc4897] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/23/2020] [Indexed: 06/10/2023]
Abstract
Triple-negative breast cancer (TNBC) is a subtype of breast cancer without a targeted form of therapy. Unfortunately, up to 70% of patients with TNBC develop resistance to treatment. A known contributor to chemoresistance is dysfunctional mitochondrial apoptosis signaling. We set up a phenotypic small-molecule screen to reveal vulnerabilities in TNBC cells that were independent of mitochondrial apoptosis. Using a functional genetic approach, we identified that a "hit" compound, BAS-2, had a potentially similar mechanism of action to histone deacetylase inhibitors (HDAC). An in vitro HDAC inhibitor assay confirmed that the compound selectively inhibited HDAC6. Using state-of-the-art acetylome mass spectrometry, we identified glycolytic substrates of HDAC6 in TNBC cells. We confirmed that inhibition or knockout of HDAC6 reduced glycolytic metabolism both in vitro and in vivo. Through a series of unbiased screening approaches, we have identified a previously unidentified role for HDAC6 in regulating glycolytic metabolism.
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Affiliation(s)
- Catríona M Dowling
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Kate E R Hollinshead
- Department of Radiation Oncology, Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Alessandra Di Grande
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Justin Pritchard
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Hua Zhang
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science, Conway Institute of Biomedical and Biomolecular Sciences, University College Dublin, Dublin, Ireland
| | - Kathryn Haley
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Eleni Papadopoulos
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Anita K Mehta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Rachel Bleach
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Andreas U Lindner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Brian Mooney
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Heiko Düssmann
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Darran O'Connor
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, Conway Institute of Biomedical and Biomolecular Sciences, University College Dublin, Dublin, Ireland
| | - Michael Hemann
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alec C Kimmelman
- Department of Radiation Oncology, Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Jennifer L Guerriero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute of Biomedical and Biomolecular Sciences, University College Dublin, Dublin, Ireland
| | - Kwok-Kin Wong
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Anthony G Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tríona Ní Chonghaile
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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17
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Carbonneau S, Sharma S, Peng L, Rajan V, Hainzl D, Henault M, Yang C, Hale J, Shulok J, Tallarico J, Porter J, Brogdon JL, Dranoff G, Bradner JE, Hild M, Guimaraes CP. An IMiD-inducible degron provides reversible regulation for chimeric antigen receptor expression and activity. Cell Chem Biol 2020; 28:802-812.e6. [PMID: 33333026 DOI: 10.1016/j.chembiol.2020.11.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/02/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022]
Abstract
The recent development of successful CAR (chimeric antigen receptor) T cell therapies has been accompanied by a need to better control potentially fatal toxicities that can arise from adverse immune reactions. Here we present a ligand-controlled CAR system, based on the IKZF3 ZF2 β-hairpin IMiD-inducible degron, which allows for the reversible control of expression levels of type I membrane proteins, including CARs. Testing this system in an established mouse xenotransplantation model for acute lymphoblastic leukemia, we validate the ability of the CAR19-degron to target and kill CD19-positive cells displaying complete control/clearance of the tumor. We also demonstrate that the activity of CAR19-degron can be regulated in vivo when dosing a US Food and Drug Administration-approved drug, lenalidomide.
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Affiliation(s)
- Seth Carbonneau
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Sujata Sharma
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Liaomin Peng
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Vaisakh Rajan
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Dominik Hainzl
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Martin Henault
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Chian Yang
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jacob Hale
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Janine Shulok
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - John Tallarico
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jeff Porter
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Glenn Dranoff
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - James E Bradner
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Marc Hild
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
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18
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Poon E, Liang T, Jamin Y, Walz S, Kwok C, Hakkert A, Barker K, Urban Z, Thway K, Zeid R, Hallsworth A, Box G, Ebus ME, Licciardello MP, Sbirkov Y, Lazaro G, Calton E, Costa BM, Valenti M, De Haven Brandon A, Webber H, Tardif N, Almeida GS, Christova R, Boysen G, Richards MW, Barone G, Ford A, Bayliss R, Clarke PA, De Bono J, Gray NS, Blagg J, Robinson SP, Eccles SA, Zheleva D, Bradner JE, Molenaar J, Vivanco I, Eilers M, Workman P, Lin CY, Chesler L. Orally bioavailable CDK9/2 inhibitor shows mechanism-based therapeutic potential in MYCN-driven neuroblastoma. J Clin Invest 2020; 130:5875-5892. [PMID: 33016930 PMCID: PMC7598076 DOI: 10.1172/jci134132] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/29/2020] [Indexed: 01/23/2023] Open
Abstract
The undruggable nature of oncogenic Myc transcription factors poses a therapeutic challenge in neuroblastoma, a pediatric cancer in which MYCN amplification is strongly associated with unfavorable outcome. Here, we show that CYC065 (fadraciclib), a clinical inhibitor of CDK9 and CDK2, selectively targeted MYCN-amplified neuroblastoma via multiple mechanisms. CDK9 - a component of the transcription elongation complex P-TEFb - bound to the MYCN-amplicon superenhancer, and its inhibition resulted in selective loss of nascent MYCN transcription. MYCN loss led to growth arrest, sensitizing cells for apoptosis following CDK2 inhibition. In MYCN-amplified neuroblastoma, MYCN invaded active enhancers, driving a transcriptionally encoded adrenergic gene expression program that was selectively reversed by CYC065. MYCN overexpression in mesenchymal neuroblastoma was sufficient to induce adrenergic identity and sensitize cells to CYC065. CYC065, used together with temozolomide, a reference therapy for relapsed neuroblastoma, caused long-term suppression of neuroblastoma growth in vivo, highlighting the clinical potential of CDK9/2 inhibition in the treatment of MYCN-amplified neuroblastoma.
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Affiliation(s)
- Evon Poon
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Tong Liang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Yann Jamin
- Division of Radiotherapy and Imaging, ICR, London, United Kingdom
| | - Susanne Walz
- Core Unit Bioinformatics, Comprehensive Cancer Center Mainfranken and Theodor Boveri Institute, Biocenter, University of Wurzburg, Wurzburg, Germany
| | - Colin Kwok
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Anne Hakkert
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Karen Barker
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Zuzanna Urban
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Khin Thway
- Division of Molecular Pathology, ICR, London, and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Albert Hallsworth
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Gary Box
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | - Marli E. Ebus
- Prinses Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Marco P. Licciardello
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | - Yordan Sbirkov
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Glori Lazaro
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Elizabeth Calton
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Barbara M. Costa
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Melanie Valenti
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | - Alexis De Haven Brandon
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | - Hannah Webber
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Nicolas Tardif
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Gilberto S. Almeida
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Division of Radiotherapy and Imaging, ICR, London, United Kingdom
| | | | | | - Mark W. Richards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Giuseppe Barone
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Anthony Ford
- Division of Molecular Pathology, ICR, London, and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Richard Bayliss
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Paul A. Clarke
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | | | - Nathanael S. Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Julian Blagg
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | | | - Suzanne A. Eccles
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | | | - James E. Bradner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jan Molenaar
- Prinses Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Igor Vivanco
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Martin Eilers
- Comprehensive Cancer Center Mainfranken and Theodor Boveri Institute, Biocenter, University of Wurzburg, Wurzburg, Germany
| | - Paul Workman
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | - Charles Y. Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Louis Chesler
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
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19
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Nabet B, Ferguson FM, Seong BKA, Kuljanin M, Leggett AL, Mohardt ML, Robichaud A, Conway AS, Buckley DL, Mancias JD, Bradner JE, Stegmaier K, Gray NS. Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules. Nat Commun 2020; 11:4687. [PMID: 32948771 PMCID: PMC7501296 DOI: 10.1038/s41467-020-18377-w] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Chemical biology strategies for directly perturbing protein homeostasis including the degradation tag (dTAG) system provide temporal advantages over genetic approaches and improved selectivity over small molecule inhibitors. We describe dTAGV-1, an exclusively selective VHL-recruiting dTAG molecule, to rapidly degrade FKBP12F36V-tagged proteins. dTAGV-1 overcomes a limitation of previously reported CRBN-recruiting dTAG molecules to degrade recalcitrant oncogenes, supports combination degrader studies and facilitates investigations of protein function in cells and mice.
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Affiliation(s)
- Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bo Kyung A Seong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Miljan Kuljanin
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alan L Leggett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mikaela L Mohardt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amanda Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy S Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Joseph D Mancias
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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20
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Antolic A, Wakimoto H, Jiao Z, Gorham JM, DePalma SR, Lemieux ME, Conner DA, Lee DY, Qi J, Seidman JG, Bradner JE, Brown JD, Haldar SM, Seidman CE, Burke MA. BET bromodomain proteins regulate transcriptional reprogramming in genetic dilated cardiomyopathy. JCI Insight 2020; 5:138687. [PMID: 32603312 DOI: 10.1172/jci.insight.138687] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/17/2020] [Indexed: 01/20/2023] Open
Abstract
The bromodomain and extraterminal (BET) family comprises epigenetic reader proteins that are important regulators of inflammatory and hypertrophic gene expression in the heart. We previously identified the activation of proinflammatory gene networks as a key early driver of dilated cardiomyopathy (DCM) in transgenic mice expressing a mutant form of phospholamban (PLNR9C) - a genetic cause of DCM in humans. We hypothesized that BETs coactivate this inflammatory process, representing a critical node in the progression of DCM. To test this hypothesis, we treated PLNR9C or age-matched WT mice longitudinally with the small molecule BET bromodomain inhibitor JQ1 or vehicle. BET inhibition abrogated adverse cardiac remodeling, reduced cardiac fibrosis, and prolonged survival in PLNR9C mice by inhibiting expression of proinflammatory gene networks at all stages of disease. Specifically, JQ1 had profound effects on proinflammatory gene network expression in cardiac fibroblasts, while having little effect on gene expression in cardiomyocytes. Cardiac fibroblast proliferation was also substantially reduced by JQ1. Mechanistically, we demonstrated that BRD4 serves as a direct and essential regulator of NF-κB-mediated proinflammatory gene expression in cardiac fibroblasts. Suppressing proinflammatory gene expression via BET bromodomain inhibition could be a novel therapeutic strategy for chronic DCM in humans.
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Affiliation(s)
- Andrew Antolic
- Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Zhe Jiao
- Emory University School of Medicine, Atlanta, Georgia, USA
| | | | | | | | | | - Da Young Lee
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jun Qi
- Bioinfo, Plantagenet, Ontario, Canada
| | | | - James E Bradner
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Saptarsi M Haldar
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA.,Department of Medicine, Cardiology Division, UCSF School of Medicine, San Francisco, California, USA.,Amgen Research, South San Francisco, California, USA
| | - Christine E Seidman
- Harvard Medical School, Boston, Massachusetts, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Howard Hughes Medical Institute
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21
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Sahni JM, Gayle SS, Bonk KLW, Vite LC, Yori JL, Webb B, Ramos EK, Seachrist DD, Landis MD, Chang JC, Bradner JE, Keri RA. Correction: Bromodomain and extraterminal protein inhibition blocks growth of triple-negative breast cancers through the suppression of aurora kinases. J Biol Chem 2020; 295:9266. [PMID: 32620694 DOI: 10.1074/jbc.aac120.014699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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22
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Gaub A, Sheikh BN, Basilicata MF, Vincent M, Nizon M, Colson C, Bird MJ, Bradner JE, Thevenon J, Boutros M, Akhtar A. Evolutionary conserved NSL complex/BRD4 axis controls transcription activation via histone acetylation. Nat Commun 2020; 11:2243. [PMID: 32382029 PMCID: PMC7206058 DOI: 10.1038/s41467-020-16103-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
Cells rely on a diverse repertoire of genes for maintaining homeostasis, but the transcriptional networks underlying their expression remain poorly understood. The MOF acetyltransferase-containing Non-Specific Lethal (NSL) complex is a broad transcription regulator. It is essential in Drosophila, and haploinsufficiency of the human KANSL1 subunit results in the Koolen-de Vries syndrome. Here, we perform a genome-wide RNAi screen and identify the BET protein BRD4 as an evolutionary conserved co-factor of the NSL complex. Using Drosophila and mouse embryonic stem cells, we characterise a recruitment hierarchy, where NSL-deposited histone acetylation enables BRD4 recruitment for transcription of constitutively active genes. Transcriptome analyses in Koolen-de Vries patient-derived fibroblasts reveals perturbations with a cellular homeostasis signature that are evoked by the NSL complex/BRD4 axis. We propose that BRD4 represents a conserved bridge between the NSL complex and transcription activation, and provide a new perspective in the understanding of their functions in healthy and diseased states.
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Affiliation(s)
- Aline Gaub
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Bilal N Sheikh
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - M Felicia Basilicata
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Marie Vincent
- CHU Nantes, Service de Génétique Médicale, 38 Boulevard Jean Monnet, 44000, Nantes, France
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, 38 Boulevard Jean Monnet, 44000, Nantes, France
| | - Cindy Colson
- Service Génétique, Génétique Clinique, CHU, Avenue Georges Clemenceau CS 30001, 14033, Caen, France.,Normandy University, UNICAEN, BIOTARGEN, Esplanade de la Paix CS 14032, 14032, Caen, France
| | - Matthew J Bird
- Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - James E Bradner
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Julien Thevenon
- CNRS UMR 5309, INSERM, U1209, Institute of Advanced Biosciences, Université Grenoble-Alpes CHU Grenoble, Allée des Alpes, 38700, La Tronche Grenoble, France
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.,Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.
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23
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Remillard D, Buckley DL, Seo HS, Ferguson FM, Dhe-Paganon S, Bradner JE, Gray NS. Dual Inhibition of TAF1 and BET Bromodomains from the BI-2536 Kinase Inhibitor Scaffold. ACS Med Chem Lett 2019; 10:1443-1449. [PMID: 31620231 DOI: 10.1021/acsmedchemlett.9b00243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
Recent reports have highlighted the dual bromodomains of TAF1 (TAF1(1,2)) as synergistic with BET inhibition in cellular cancer models, engendering interest in TAF/BET polypharmacology. Here, we examine structure activity relationships within the BI-2536 PLK1 kinase inhibitor scaffold, previously reported to bind BRD4. We examine binding by this ligand to TAF1(2) and apply structure guided design strategies to discriminate binding to both the PLK1 kinase and BRD4(1) bromodomain while retaining activity on TAF1(2). Through this effort we discover potent dual inhibitors of TAF1(2)/BRD4(1), as well as biased derivatives showing marked TAF1 selectivity. We resolve X-ray crystallographic data sets to examine the mechanisms of the observed TAF1 selectivity and to provide a resource for further development of this scaffold.
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Affiliation(s)
- David Remillard
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
| | - Dennis L. Buckley
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
| | - Fleur M. Ferguson
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston Massachusetts 02115, United States
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
| | - James E. Bradner
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston Massachusetts 02115, United States
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24
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Labbé DP, Zadra G, Yang M, Reyes JM, Lin CY, Cacciatore S, Ebot EM, Creech AL, Giunchi F, Fiorentino M, Elfandy H, Syamala S, Karoly ED, Alshalalfa M, Erho N, Ross A, Schaeffer EM, Gibb EA, Takhar M, Den RB, Lehrer J, Karnes RJ, Freedland SJ, Davicioni E, Spratt DE, Ellis L, Jaffe JD, DʼAmico AV, Kantoff PW, Bradner JE, Mucci LA, Chavarro JE, Loda M, Brown M. High-fat diet fuels prostate cancer progression by rewiring the metabolome and amplifying the MYC program. Nat Commun 2019; 10:4358. [PMID: 31554818 PMCID: PMC6761092 DOI: 10.1038/s41467-019-12298-z] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 08/23/2019] [Indexed: 12/16/2022] Open
Abstract
Systemic metabolic alterations associated with increased consumption of saturated fat and obesity are linked with increased risk of prostate cancer progression and mortality, but the molecular underpinnings of this association are poorly understood. Here, we demonstrate in a murine prostate cancer model, that high-fat diet (HFD) enhances the MYC transcriptional program through metabolic alterations that favour histone H4K20 hypomethylation at the promoter regions of MYC regulated genes, leading to increased cellular proliferation and tumour burden. Saturated fat intake (SFI) is also associated with an enhanced MYC transcriptional signature in prostate cancer patients. The SFI-induced MYC signature independently predicts prostate cancer progression and death. Finally, switching from a high-fat to a low-fat diet, attenuates the MYC transcriptional program in mice. Our findings suggest that in primary prostate cancer, dietary SFI contributes to tumour progression by mimicking MYC over expression, setting the stage for therapeutic approaches involving changes to the diet.
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Affiliation(s)
- David P Labbé
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Urology, Department of Surgery, McGill University and Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Giorgia Zadra
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Meng Yang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jaime M Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Stefano Cacciatore
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Ericka M Ebot
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amanda L Creech
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Francesca Giunchi
- Pathology Service, Addarii Institute of Oncology, S-Orsola-Malpighi Hospital, Bologna, IT, Italy
| | - Michelangelo Fiorentino
- Pathology Service, Addarii Institute of Oncology, S-Orsola-Malpighi Hospital, Bologna, IT, Italy
| | - Habiba Elfandy
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sudeepa Syamala
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - Ashley Ross
- James Buchanan Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | | | | | - Robert B Den
- Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | | | - R Jeffrey Karnes
- Department of Urology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Stephen J Freedland
- Department of Surgery, Division of Urology, Center for Integrated Research on Cancer and Lifestyle, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Surgery Section, Durham Veteran Affairs Medical Center, Durham, NC, USA
| | | | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Leigh Ellis
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Jacob D Jaffe
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Anthony V DʼAmico
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Philip W Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jorge E Chavarro
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA.
- Department of Pathology and Laboratory Medicine, Weil Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, NY, USA.
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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25
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Bandopadhayay P, Piccioni F, O'Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin JR, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun 2019; 10:2400. [PMID: 31160565 PMCID: PMC6546744 DOI: 10.1038/s41467-019-10307-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/25/2019] [Indexed: 12/26/2022] Open
Abstract
BET-bromodomain inhibition (BETi) has shown pre-clinical promise for MYC-amplified medulloblastoma. However, the mechanisms for its action, and ultimately for resistance, have not been fully defined. Here, using a combination of expression profiling, genome-scale CRISPR/Cas9-mediated loss of function and ORF/cDNA driven rescue screens, and cell-based models of spontaneous resistance, we identify bHLH/homeobox transcription factors and cell-cycle regulators as key genes mediating BETi's response and resistance. Cells that acquire drug tolerance exhibit a more neuronally differentiated cell-state and expression of lineage-specific bHLH/homeobox transcription factors. However, they do not terminally differentiate, maintain expression of CCND2, and continue to cycle through S-phase. Moreover, CDK4/CDK6 inhibition delays acquisition of resistance. Therefore, our data provide insights about the mechanisms underlying BETi effects and the appearance of resistance and support the therapeutic use of combined cell-cycle inhibitors with BETi in MYC-amplified medulloblastoma.
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Affiliation(s)
- Pratiti Bandopadhayay
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | - Ryan O'Rourke
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Patricia Ho
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Elizabeth M Gonzalez
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Graham Buchan
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Kenin Qian
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Gabrielle Gionet
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Emily Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Margo Coxon
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | | | - Lisa Brenan
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Frank Dubois
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Ofer Shapira
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Noah F Greenwald
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, USA
| | - Melanie Pages
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Amanda Balboni Iniguez
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Brenton R Paolella
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Alice Meng
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Claire Sinai
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Giovanni Roti
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine and Surgery, Hematology and BMT, University of Parma, Parma, Italy
| | - Neekesh V Dharia
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | | | - Prasidda Khadka
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Adam Tracy
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Hong L Tiv
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Boston, USA
| | - Andrew L Hong
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Shannon Coy
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - Rumana Rashid
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, USA
| | - Glenn S Cowley
- Broad Institute of MIT and Harvard, Cambridge, USA
- Discovery Science, Janssen Research and Development (Johnson & Johnson), Spring House, PA, USA
| | - Fred C Lam
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Yenarae Lee
- Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
| | | | - James E Bradner
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Michael B Yaffe
- Broad Institute of MIT and Harvard, Cambridge, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Center for Child and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jun Qi
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pathology, Boston Children's Hospital, Boston, USA
| | - Mark W Kieran
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Sandro Santagata
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Boston, USA
| | | | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Kimberly Stegmaier
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | - Rameen Beroukhim
- Broad Institute of MIT and Harvard, Cambridge, USA.
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA.
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA.
- Department of Medicine, Harvard Medical School, Boston, USA.
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Miller AL, Fehling SC, Garcia PL, Gamblin TL, Council LN, van Waardenburg RCAM, Yang ES, Bradner JE, Yoon KJ. The BET inhibitor JQ1 attenuates double-strand break repair and sensitizes models of pancreatic ductal adenocarcinoma to PARP inhibitors. EBioMedicine 2019; 44:419-430. [PMID: 31126889 PMCID: PMC6604668 DOI: 10.1016/j.ebiom.2019.05.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND DNA repair deficiency accumulates DNA damage and sensitizes tumor cells to PARP inhibitors (PARPi). Based on our observation that the BET inhibitor JQ1 increases levels of DNA damage, we evaluated the efficacy of JQ1 + the PARPi olaparib in preclinical models of pancreatic ductal adenocarcinoma (PDAC). We also addressed the mechanism by which JQ1 increased DNA damage. METHODS The effect of JQ1 + olaparib on in vivo tumor growth was assessed with patient-derived xenograft (PDX) models of PDAC. Changes in protein expression were detected by immunohistochemistry and immunoblot. In vitro growth inhibition and mechanistic studies were done using alamarBlue, qRT-PCR, immunoblot, immunofluorescence, ChIP, and shRNA knockdown assays. FINDINGS Tumors exposed in vivo to JQ1 had higher levels of the DNA damage marker γH2AX than tumors exposed to vehicle only. Increases in γH2AX was concomitant with decreased expression of DNA repair proteins Ku80 and RAD51. JQ1 + olaparib inhibited the growth of PDX tumors greater than either drug alone. Mechanistically, ChIP assays demonstrated that JQ1 decreased the association of BRD4 and BRD2 with promoter loci of Ku80 and RAD51, and shRNA data showed that expression of Ku80 and RAD51 was BRD4- and BRD2-dependent in PDAC cell lines. INTERPRETATION The data are consistent with the hypothesis that JQ1 confers a repair deficient phenotype and the consequent accumulation of DNA damage sensitizes PDAC cells to PARPi. Combinations of BET inhibitors with PARPi may provide a novel strategy for treating PDAC. FUND: NIH grants R01CA208272 and R21CA205501; UAB CMB T32 predoctoral training grant.
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Affiliation(s)
- Aubrey L Miller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 1670 University Blvd, Birmingham, AL, USA
| | - Samuel C Fehling
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 1670 University Blvd, Birmingham, AL, USA
| | - Patrick L Garcia
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 1670 University Blvd, Birmingham, AL, USA
| | - Tracy L Gamblin
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 1670 University Blvd, Birmingham, AL, USA
| | - Leona N Council
- Department of Pathology, Division of Anatomic Pathology, University of Alabama at Birmingham, NP3551 North Pavilion UAB Hospital, Birmingham, AL, USA; The Birmingham Veterans Administration Medical Center, 700 19(th) St S, Birmingham, AL, USA
| | - Robert C A M van Waardenburg
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 1670 University Blvd, Birmingham, AL, USA
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama at Birmingham, Hazelrig Salter Radiation Oncology Center, 1700 6(th) Avenue S, Birmingham, AL, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Karina J Yoon
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 1670 University Blvd, Birmingham, AL, USA.
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27
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Sharifnia T, Wawer MJ, Chen T, Huang QY, Weir BA, Sizemore A, Lawlor MA, Goodale A, Cowley GS, Vazquez F, Ott CJ, Francis JM, Sassi S, Cogswell P, Sheppard HE, Zhang T, Gray NS, Clarke PA, Blagg J, Workman P, Sommer J, Hornicek F, Root DE, Hahn WC, Bradner JE, Wong KK, Clemons PA, Lin CY, Kotz JD, Schreiber SL. Small-molecule targeting of brachyury transcription factor addiction in chordoma. Nat Med 2019; 25:292-300. [PMID: 30664779 PMCID: PMC6633917 DOI: 10.1038/s41591-018-0312-3] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Chordoma is a primary bone cancer with no approved therapy1. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors2,3. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation. In other cancer types, transcriptional CDK inhibitors have been observed to downregulate highly expressed, enhancer-associated oncogenic transcription factors4,5. In chordoma, we find that T is associated with a 1.5-Mb region containing 'super-enhancers' and is the most highly expressed super-enhancer-associated transcription factor. Notably, transcriptional CDK inhibition leads to preferential and concentration-dependent downregulation of cellular brachyury protein levels in all models tested. In vivo, CDK7/12/13-inhibitor treatment substantially reduces tumor growth. Together, these data demonstrate small-molecule targeting of brachyury transcription factor addiction in chordoma, identify a mechanism of T gene regulation that underlies this therapeutic strategy, and provide a blueprint for applying systematic genetic and chemical screening approaches to discover vulnerabilities in genomically quiet cancers.
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Affiliation(s)
| | | | - Ting Chen
- New York University Langone Medical Center, New York, NY, USA
| | - Qing-Yuan Huang
- New York University Langone Medical Center, New York, NY, USA
- Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Barbara A Weir
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Janssen R&D, Cambridge, MA, USA
| | - Ann Sizemore
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew A Lawlor
- Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital, Charlestown, MA, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Janssen R&D, Spring House, PA, USA
| | | | - Christopher J Ott
- Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital, Charlestown, MA, USA
| | - Joshua M Francis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Gritstone Oncology, Cambridge, MA, USA
| | - Slim Sassi
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | | | - Francis Hornicek
- Massachusetts General Hospital, Boston, MA, USA
- UCLA Medical Center, Santa Monica, CA, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Dana-Farber Cancer Institute, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Kwok K Wong
- New York University Langone Medical Center, New York, NY, USA
| | | | | | - Joanne D Kotz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Jnana Therapeutics, Boston, MA, USA.
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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28
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Hemming ML, Lawlor MA, Andersen JL, Hagan T, Chipashvili O, Scott TG, Raut CP, Sicinska E, Armstrong SA, Demetri GD, Bradner JE. Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and Are Targetable by BET Bromodomain Inhibition. Cancer Res 2019; 79:994-1009. [PMID: 30630822 DOI: 10.1158/0008-5472.can-18-1888] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 12/04/2018] [Accepted: 01/07/2019] [Indexed: 12/31/2022]
Abstract
Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutations in the related receptor tyrosine kinases KIT and PDGFRA. GIST relies on expression of these unamplified receptor tyrosine kinase (RTK) genes through a large enhancer domain, resulting in high expression levels of the oncogene required for tumor growth. Although kinase inhibition is an effective therapy for many patients with GIST, disease progression from kinase-resistant mutations is common and no other effective classes of systemic therapy exist. In this study, we identify regulatory regions of the KIT enhancer essential for KIT gene expression and GIST cell viability. Given the dependence of GIST upon enhancer-driven expression of RTKs, we hypothesized that the enhancer domains could be therapeutically targeted by a BET bromodomain inhibitor (BBI). Treatment of GIST cells with BBIs led to cell-cycle arrest, apoptosis, and cell death, with unique sensitivity in GIST cells arising from attenuation of the KIT enhancer domain and reduced KIT gene expression. BBI treatment in KIT-dependent GIST cells produced genome-wide changes in the H3K27ac enhancer landscape and gene expression program, which was also seen with direct KIT inhibition using a tyrosine kinase inhibitor (TKI). Combination treatment with BBI and TKI led to superior cytotoxic effects in vitro and in vivo, with BBI preventing tumor growth in TKI-resistant xenografts. Resistance to select BBI in GIST was attributable to drug efflux pumps. These results define a therapeutic vulnerability and clinical strategy for targeting oncogenic kinase dependency in GIST. SIGNIFICANCE: Expression and activity of mutant KIT is essential for driving the majority of GIST neoplasms, which can be therapeutically targeted using BET bromodomain inhibitors.
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Affiliation(s)
- Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Matthew A Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jessica L Andersen
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Timothy Hagan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Otari Chipashvili
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Thomas G Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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29
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Hemming ML, Lawlor MA, Andersen JL, Hagan T, Chipashvili O, Scott TG, Raut CP, Sicinska E, Armstrong SA, Demetri GD, Bradner JE, Ganz PA, Tomlinson G, Olopade OI, Couch FJ, Wang X, Lindor NM, Pankratz VS, Radice P, Manoukian S, Peissel B, Zaffaroni D, Barile M, Viel A, Allavena A, Dall'Olio V, Peterlongo P, Szabo CI, Zikan M, Claes K, Poppe B, Foretova L, Mai PL, Greene MH, Rennert G, Lejbkowicz F, Glendon G, Ozcelik H, Andrulis IL, Thomassen M, Gerdes AM, Sunde L, Cruger D, Birk Jensen U, Caligo M, Friedman E, Kaufman B, Laitman Y, Milgrom R, Dubrovsky M, Cohen S, Borg A, Jernström H, Lindblom A, Rantala J, Stenmark-Askmalm M, Melin B, Nathanson K, Domchek S, Jakubowska A, Lubinski J, Huzarski T, Osorio A, Lasa A, Durán M, Tejada MI, Godino J, Benitez J, Hamann U, Kriege M, Hoogerbrugge N, van der Luijt RB, van Asperen CJ, Devilee P, Meijers-Heijboer EJ, Blok MJ, Aalfs CM, Hogervorst F, Rookus M, Cook M, Oliver C, Frost D, Conroy D, Evans DG, Lalloo F, Pichert G, Davidson R, Cole T, Cook J, Paterson J, Hodgson S, Morrison PJ, Porteous ME, Walker L, Kennedy MJ, Dorkins H, Peock S, Godwin AK, Stoppa-Lyonnet D, de Pauw A, Mazoyer S, Bonadona V, Lasset C, Dreyfus H, Leroux D, Hardouin A, Berthet P, Faivre L, Loustalot C, Noguchi T, Sobol H, Rouleau E, Nogues C, Frénay M, Vénat-Bouvet L, Hopper JL, Daly MB, Terry MB, John EM, Buys SS, Yassin Y, Miron A, Goldgar D, Singer CF, Dressler AC, Gschwantler-Kaulich D, Pfeiler G, Hansen TVO, Jønson L, Agnarsson BA, Kirchhoff T, Offit K, Devlin V, Dutra-Clarke A, Piedmonte M, Rodriguez GC, Wakeley K, Boggess JF, Basil J, Schwartz PE, Blank SV, Toland AE, Montagna M, Casella C, Imyanitov E, Tihomirova L, Blanco I, Lazaro C, Ramus SJ, Sucheston L, Karlan BY, Gross J, Schmutzler R, Wappenschmidt B, Engel C, Meindl A, Lochmann M, Arnold N, Heidemann S, Varon-Mateeva R, Niederacher D, Sutter C, Deissler H, Gadzicki D, Preisler-Adams S, Kast K, Schönbuchner I, Caldes T, de la Hoya M, Aittomäki K, Nevanlinna H, Simard J, Spurdle AB, Holland H, Chen X, Platte R, Chenevix-Trench G, Easton DF. Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and Are Targetable by BET Bromodomain Inhibition. Cancer Res 2019. [PMID: 18483246 DOI: 10.1158/0008-5472] [Citation(s) in RCA: 655] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutations in the related receptor tyrosine kinases KIT and PDGFRA. GIST relies on expression of these unamplified receptor tyrosine kinase (RTK) genes through a large enhancer domain, resulting in high expression levels of the oncogene required for tumor growth. Although kinase inhibition is an effective therapy for many patients with GIST, disease progression from kinase-resistant mutations is common and no other effective classes of systemic therapy exist. In this study, we identify regulatory regions of the KIT enhancer essential for KIT gene expression and GIST cell viability. Given the dependence of GIST upon enhancer-driven expression of RTKs, we hypothesized that the enhancer domains could be therapeutically targeted by a BET bromodomain inhibitor (BBI). Treatment of GIST cells with BBIs led to cell-cycle arrest, apoptosis, and cell death, with unique sensitivity in GIST cells arising from attenuation of the KIT enhancer domain and reduced KIT gene expression. BBI treatment in KIT-dependent GIST cells produced genome-wide changes in the H3K27ac enhancer landscape and gene expression program, which was also seen with direct KIT inhibition using a tyrosine kinase inhibitor (TKI). Combination treatment with BBI and TKI led to superior cytotoxic effects in vitro and in vivo, with BBI preventing tumor growth in TKI-resistant xenografts. Resistance to select BBI in GIST was attributable to drug efflux pumps. These results define a therapeutic vulnerability and clinical strategy for targeting oncogenic kinase dependency in GIST. SIGNIFICANCE: Expression and activity of mutant KIT is essential for driving the majority of GIST neoplasms, which can be therapeutically targeted using BET bromodomain inhibitors.
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Affiliation(s)
- Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Matthew A Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jessica L Andersen
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Timothy Hagan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Otari Chipashvili
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Thomas G Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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30
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Ott CJ, Federation AJ, Schwartz LS, Kasar S, Klitgaard JL, Lenci R, Li Q, Lawlor M, Fernandes SM, Souza A, Polaski D, Gadi D, Freedman ML, Brown JR, Bradner JE. Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia. Cancer Cell 2018; 34:982-995.e7. [PMID: 30503705 PMCID: PMC6298230 DOI: 10.1016/j.ccell.2018.11.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 08/16/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022]
Abstract
Enhancer profiling is a powerful approach for discovering cis-regulatory elements that define the core transcriptional regulatory circuits of normal and malignant cells. Gene control through enhancer activity is often dominated by a subset of lineage-specific transcription factors. By integrating measures of chromatin accessibility and enrichment for H3K27 acetylation, we have generated regulatory landscapes of chronic lymphocytic leukemia (CLL) samples and representative cell lines. With super enhancer-based modeling of regulatory circuits and assessments of transcription factor dependencies, we discover that the essential super enhancer factor PAX5 dominates CLL regulatory nodes and is essential for CLL cell survival. Targeting enhancer signaling via BET bromodomain inhibition disrupts super enhancer-dependent gene expression with selective effects on CLL core regulatory circuitry, conferring potent anti-tumor activity.
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MESH Headings
- Acetylation
- Animals
- Azepines/pharmacology
- Cell Line, Tumor
- Chromatin/drug effects
- Chromatin/genetics
- Chromatin/metabolism
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic/drug effects
- Gene Expression Regulation, Leukemic/genetics
- Histones/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Mice, Knockout
- PAX5 Transcription Factor/genetics
- PAX5 Transcription Factor/metabolism
- Protein Binding
- Proteins/antagonists & inhibitors
- Proteins/genetics
- Proteins/metabolism
- Triazoles/pharmacology
- Xenograft Model Antitumor Assays/methods
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Affiliation(s)
- Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th St. Charlestown, Boston, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA.
| | - Alexander J Federation
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Logan S Schwartz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th St. Charlestown, Boston, MA 02129, USA
| | - Siddha Kasar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Josephine L Klitgaard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Romina Lenci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Qiyuan Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Medical School, Xiamen University, Xiamen 361102, China
| | - Matthew Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th St. Charlestown, Boston, MA 02129, USA
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Amanda Souza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Donald Polaski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Deepti Gadi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA; Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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31
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Brien GL, Remillard D, Shi J, Hemming ML, Chabon J, Wynne K, Dillon ET, Cagney G, Van Mierlo G, Baltissen MP, Vermeulen M, Qi J, Fröhling S, Gray NS, Bradner JE, Vakoc CR, Armstrong SA. Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma. eLife 2018; 7:41305. [PMID: 30431433 PMCID: PMC6277197 DOI: 10.7554/elife.41305] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/11/2018] [Indexed: 12/14/2022] Open
Abstract
Synovial sarcoma tumours contain a characteristic fusion protein, SS18-SSX, which drives disease development. Targeting oncogenic fusion proteins presents an attractive therapeutic opportunity. However, SS18-SSX has proven intractable for therapeutic intervention. Using a domain-focused CRISPR screen we identified the bromodomain of BRD9 as a critical functional dependency in synovial sarcoma. BRD9 is a component of SS18-SSX containing BAF complexes in synovial sarcoma cells; and integration of BRD9 into these complexes is critical for cell growth. Moreover BRD9 and SS18-SSX co-localize extensively on the synovial sarcoma genome. Remarkably, synovial sarcoma cells are highly sensitive to a novel small molecule degrader of BRD9, while other sarcoma subtypes are unaffected. Degradation of BRD9 induces downregulation of oncogenic transcriptional programs and inhibits tumour progression in vivo. We demonstrate that BRD9 supports oncogenic mechanisms underlying the SS18-SSX fusion in synovial sarcoma and highlight targeted degradation of BRD9 as a potential therapeutic opportunity in this disease.
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Affiliation(s)
- Gerard L Brien
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - David Remillard
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Junwei Shi
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Matthew L Hemming
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Jonathon Chabon
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Eugène T Dillon
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Guido Van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jun Qi
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Stefan Fröhling
- German Cancer Consortium, Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Translational Oncology, National Center for Tumor Diseases Heidelberg and German Cancer Research Center, Heidelberg, Germany
| | - Nathanael S Gray
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - James E Bradner
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | | | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
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32
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Wang J, Erazo T, Ferguson FM, Buckley DL, Gomez N, Muñoz-Guardiola P, Diéguez-Martínez N, Deng X, Hao M, Massefski W, Fedorov O, Offei-Addo NK, Park PM, Dai L, DiBona A, Becht K, Kim ND, McKeown MR, Roberts JM, Zhang J, Sim T, Alessi DR, Bradner JE, Lizcano JM, Blacklow SC, Qi J, Xu X, Gray NS. Structural and Atropisomeric Factors Governing the Selectivity of Pyrimido-benzodiazipinones as Inhibitors of Kinases and Bromodomains. ACS Chem Biol 2018; 13:2438-2448. [PMID: 30102854 PMCID: PMC6333101 DOI: 10.1021/acschembio.7b00638] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bromodomains have been pursued intensively over the past several years as emerging targets for the development of anticancer and anti-inflammatory agents. It has recently been shown that some kinase inhibitors are able to potently inhibit the bromodomains of BRD4. The clinical activities of PLK inhibitor BI-2536 and JAK2-FLT3 inhibitor TG101348 have been attributed to this unexpected polypharmacology, indicating that dual-kinase/bromodomain activity may be advantageous in a therapeutic context. However, for target validation and biological investigation, a more selective target profile is desired. Here, we report that benzo[e]pyrimido-[5,4- b]diazepine-6(11H)-ones, versatile ATP-site directed kinase pharmacophores utilized in the development of inhibitors of multiple kinases, including several previously reported kinase chemical probes, are also capable of exhibiting potent BRD4-dependent pharmacology. Using a dual kinase-bromodomain inhibitor of the kinase domains of ERK5 and LRRK2, and the bromodomain of BRD4 as a case study, we define the structure-activity relationships required to achieve dual kinase/BRD4 activity, as well as how to direct selectivity toward inhibition of either ERK5 or BRD4. This effort resulted in identification of one of the first reported kinase-selective chemical probes for ERK5 (JWG-071), a BET selective inhibitor with 1 μM BRD4 IC50 (JWG-115), and additional inhibitors with rationally designed polypharmacology (JWG-047, JWG-069). Co-crystallography of seven representative inhibitors with the first bromodomain of BRD4 demonstrate that distinct atropisomeric conformers recognize the kinase ATP-site and the BRD4 acetyl lysine binding site, conformational preferences supported by rigid docking studies.
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Affiliation(s)
- Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Tatiana Erazo
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina. Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain
| | - Fleur M. Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis L. Buckley
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nestor Gomez
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina. Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain
| | - Pau Muñoz-Guardiola
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina. Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain
| | - Nora Diéguez-Martínez
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina. Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain
| | - Xianming Deng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Mingfeng Hao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Walter Massefski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Oleg Fedorov
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Paul M. Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Lingling Dai
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amy DiBona
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kelly Becht
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nam Doo Kim
- NDBio Therapeutics Inc., 32 Songdogwahak-ro, Yeonsu-gu, Incheon 21984, Republic of Korea
| | - Michael R. McKeown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Justin M. Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jinwei Zhang
- MRC Protein Phosphorylation and Ubiquitination Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - Taebo Sim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul, Korea and KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Korea
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitination Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - James E. Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jose M. Lizcano
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina. Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain
| | - Stephen C. Blacklow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Xiang Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding Author,
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding Author,
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33
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Liu S, Yosief HO, Dai L, Huang H, Dhawan G, Zhang X, Muthengi AM, Roberts J, Buckley DL, Perry JA, Wu L, Bradner JE, Qi J, Zhang W. Structure-Guided Design and Development of Potent and Selective Dual Bromodomain 4 (BRD4)/Polo-like Kinase 1 (PLK1) Inhibitors. J Med Chem 2018; 61:7785-7795. [PMID: 30125504 PMCID: PMC6309379 DOI: 10.1021/acs.jmedchem.8b00765] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The simultaneous inhibition of polo-like kinase 1 (PLK1) and BRD4 bromodomain by a single molecule could lead to the development of an effective therapeutic strategy for a variety of diseases in which PLK1 and BRD4 are implicated. Compound 23 has been found to be a potent dual kinase-bromodomain inhibitor (BRD4-BD1 IC50 = 28 nM, PLK1 IC50 = 40 nM). Compound 6 was found to be the most selective PLK1 inhibitor over BRD4 in our series (BRD4-BD1 IC50 = 2579 nM, PLK1 IC50 = 9.9 nM). Molecular docking studies with 23 and BRD4-BD1/PLK1 as well as with 6 corroborate the biochemical assay results.
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Affiliation(s)
- Shuai Liu
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Hailemichael O Yosief
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Lingling Dai
- Phase I Clinical Trial Center & Department of Clinical Pharmacology, Xiangya Hospital , Central South University , Changsha , Hunan 410008 , P.R. China
| | - He Huang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , United States
| | - Gagan Dhawan
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
- Department of Biomedical Science, Acharya Narendra Dev College , University of Delhi , New Delhi 110019 , India
| | - Xiaofeng Zhang
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Alex M Muthengi
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | | | | | | | | | - James E Bradner
- Novartis Institutes for Biomedical Research , Cambridge , Massachusetts 02139 , United States
| | - Jun Qi
- Department of Medicine , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Wei Zhang
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
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34
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Adeegbe DO, Liu S, Hattersley MM, Bowden M, Zhou CW, Li S, Vlahos R, Grondine M, Dolgalev I, Ivanova EV, Quinn MM, Gao P, Hammerman PS, Bradner JE, Diehl JA, Rustgi AK, Bass AJ, Tsirigos A, Freeman GJ, Chen H, Wong KK. BET Bromodomain Inhibition Cooperates with PD-1 Blockade to Facilitate Antitumor Response in Kras-Mutant Non-Small Cell Lung Cancer. Cancer Immunol Res 2018; 6:1234-1245. [PMID: 30087114 DOI: 10.1158/2326-6066.cir-18-0077] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/22/2018] [Accepted: 08/02/2018] [Indexed: 12/24/2022]
Abstract
KRAS mutation is present in approximately 30% of human lung adenocarcinomas. Although recent advances in targeted therapy have shown great promise, effective targeting of KRAS remains elusive, and concurrent alterations in tumor suppressors render KRAS-mutant tumors even more resistant to existing therapies. Contributing to the refractoriness of KRAS-mutant tumors are immunosuppressive mechanisms, such as increased presence of suppressive regulatory T cells (Treg) in tumors and elevated expression of the inhibitory receptor PD-1 on tumor-infiltrating T cells. Treatment with BET bromodomain inhibitors is beneficial for hematologic malignancies, and they have Treg-disruptive effects in a non-small cell lung cancer (NSCLC) model. Targeting PD-1-inhibitory signals through PD-1 antibody blockade also has substantial therapeutic impact in lung cancer, although these outcomes are limited to a minority of patients. We hypothesized that the BET bromodomain inhibitor JQ1 would synergize with PD-1 blockade to promote a robust antitumor response in lung cancer. In the present study, using Kras+/LSL-G12D ; Trp53L/L (KP) mouse models of NSCLC, we identified cooperative effects between JQ1 and PD-1 antibody. The numbers of tumor-infiltrating Tregs were reduced and activation of tumor-infiltrating T cells, which had a T-helper type 1 (Th1) cytokine profile, was enhanced, underlying their improved effector function. Furthermore, lung tumor-bearing mice treated with this combination showed robust and long-lasting antitumor responses compared with either agent alone, culminating in substantial improvement in the overall survival of treated mice. Thus, combining BET bromodomain inhibition with immune checkpoint blockade offers a promising therapeutic approach for solid malignancies such as lung adenocarcinoma. Cancer Immunol Res; 6(10); 1234-45. ©2018 AACR.
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Affiliation(s)
- Dennis O Adeegbe
- Laura & Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York.
| | - Shengwu Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Maureen M Hattersley
- Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, Massachusetts
| | - Michaela Bowden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Chensheng W Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Shuai Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Raven Vlahos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Michael Grondine
- Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, Massachusetts
| | - Igor Dolgalev
- Applied Bioinformatics Laboratories and Department of Pathology, New York University School of Medicine, New York, New York
| | - Elena V Ivanova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Max M Quinn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Peng Gao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Peter S Hammerman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - James E Bradner
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - J Alan Diehl
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina
| | - Anil K Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories and Department of Pathology, New York University School of Medicine, New York, New York
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Huawei Chen
- Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, Massachusetts
| | - Kwok-Kin Wong
- Laura & Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York.
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35
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Burke MA, Wakimoto H, Jiao Z, Gorham JM, DePalma SR, Conner DA, Qi J, Seidman JG, Bradner JE, Brown JD, Haldar SM, Seidman CE. Epigenomic Control of Cardiac Fibrosis by Bet Bromodomain Proteins in Dilated Cardiomyopathy. J Card Fail 2018. [DOI: 10.1016/j.cardfail.2018.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Adeegbe DO, Liu S, Bowden M, Hammerman PS, Bradner JE, Rustgi AK, Bass AJ, Freeman GJ, Chen H, Wong KK. Abstract 4713: BET bromodomain inhibition synergizes with PD-1 blockade to facilitate anti-tumor response in Kras-mutant non-small cell lung cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
KRAS mutation is present in about 30% of human lung adenocarcinomas. While recent advances in targeted therapy have shown great promise, KRAS remains undruggable and concurrent alterations in tumor suppressors render KRAS mutant tumors even more resistant to existing therapies. Contributing to the refractoriness of KRAS mutant tumors harboring these co-mutations are immunosuppressive mechanisms such as increased presence of suppressive Tregs in tumors and elevated expression of the inhibitory receptor PD-1 on tumor-infiltrating T cells. BET bromodomain inhibitors demonstrate clinical benefit in hematologic malignancies, and prior reports demonstrate their Treg-disruptive effects in a NSCLC model. Targeting PD-1 inhibitory signals through anti-PD-1 antibody blockade has also shown substantial therapeutic impact in lung cancer although these outcomes are still limited to a minor pool of patients. We therefore hypothesized that the BET bromodomain inhibitor JQ1 would synergize with PD-1 blockade to promote robust anti-tumor response in lung cancer. In the present study, using Kras+/LSL-G12D; Trp53L/L (KP) mouse models of non-small cell lung cancer, we identified cooperative effects among JQ1 and anti-PD-1 that included reduced numbers of tumor-infiltrated Tregs and enhanced activation of tumor-infiltrating T cells, which exhibited a Th1 cytokine profile that favored their demonstrated improved effector function. Furthermore, lung-tumor-bearing mice under this combinatorial treatment regimen showed robust and long-lasting anti-tumor responses compared to either agent alone, culminating in substantial improvement in the survival of treated mice. Thus, combining BET bromodomain inhibition with immune checkpoint blockade offers a promising therapeutic approach for solid malignancies such as lung adenocarcinoma.
Citation Format: Dennis O. Adeegbe, Shengwu Liu, Michaela Bowden, Peter S. Hammerman, James E. Bradner, Anil K. Rustgi, Adam J. Bass, Gordon J. Freeman, Huawei Chen, kwok-Kin Wong. BET bromodomain inhibition synergizes with PD-1 blockade to facilitate anti-tumor response in Kras-mutant non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4713.
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Affiliation(s)
| | | | | | | | | | - Anil K. Rustgi
- 4University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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37
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Kim SK, Knight DA, Jones LR, Vervoort S, Ng AP, Seymour JF, Bradner JE, Waibel M, Kats L, Johnstone RW. JAK2 is dispensable for maintenance of JAK2 mutant B-cell acute lymphoblastic leukemias. Genes Dev 2018; 32:849-864. [PMID: 29907650 PMCID: PMC6049517 DOI: 10.1101/gad.307504.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 05/07/2018] [Indexed: 11/24/2022]
Abstract
Kim et al. show that while expression of mutant Jak2 is necessary for B-cell acute lymphoblastic leukemia induction, neither its continued expression nor enzymatic activity is required to maintain leukemia survival and rapid proliferation. Activating JAK2 point mutations are implicated in the pathogenesis of myeloid and lymphoid malignancies, including high-risk B-cell acute lymphoblastic leukemia (B-ALL). In preclinical studies, treatment of JAK2 mutant leukemias with type I JAK2 inhibitors (e.g., Food and Drug Administration [FDA]-approved ruxolitinib) provided limited single-agent responses, possibly due to paradoxical JAK2Y1007/1008 hyperphosphorylation induced by these agents. To determine the importance of mutant JAK2 in B-ALL initiation and maintenance, we developed unique genetically engineered mouse models of B-ALL driven by overexpressed Crlf2 and mutant Jak2, recapitulating the genetic aberrations found in human B-ALL. While expression of mutant Jak2 was necessary for leukemia induction, neither its continued expression nor enzymatic activity was required to maintain leukemia survival and rapid proliferation. CRLF2/JAK2 mutant B-ALLs with sustained depletion or pharmacological inhibition of JAK2 exhibited enhanced expression of c-Myc and prominent up-regulation of c-Myc target genes. Combined indirect targeting of c-Myc using the BET bromodomain inhibitor JQ1 and direct targeting of JAK2 with ruxolitinib potently killed JAK2 mutant B-ALLs.
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Affiliation(s)
- Sang-Kyu Kim
- The Peter MacCallum Cancer Centre, Melbourne, 3000 Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 Victoria, Australia
| | - Deborah A Knight
- The Peter MacCallum Cancer Centre, Melbourne, 3000 Victoria, Australia
| | - Lisa R Jones
- The Peter MacCallum Cancer Centre, Melbourne, 3000 Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 Victoria, Australia
| | - Stephin Vervoort
- The Peter MacCallum Cancer Centre, Melbourne, 3000 Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 Victoria, Australia
| | - Ashley P Ng
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, 3010 Victoria, Australia
| | - John F Seymour
- The Peter MacCallum Cancer Centre, Melbourne, 3000 Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 Victoria, Australia
| | - James E Bradner
- Novartis Institutes for BioMedical (NIBR) Research, Cambridge, Massachusetts 02139, USA
| | - Michaela Waibel
- The Peter MacCallum Cancer Centre, Melbourne, 3000 Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 Victoria, Australia
| | - Lev Kats
- The Peter MacCallum Cancer Centre, Melbourne, 3000 Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 Victoria, Australia
| | - Ricky W Johnstone
- The Peter MacCallum Cancer Centre, Melbourne, 3000 Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 Victoria, Australia
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38
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Nowak RP, DeAngelo SL, Buckley D, He Z, Donovan KA, An J, Safaee N, Jedrychowski MP, Ponthier CM, Ishoey M, Zhang T, Mancias JD, Gray NS, Bradner JE, Fischer ES. Plasticity in binding confers selectivity in ligand-induced protein degradation. Nat Chem Biol 2018; 14:706-714. [PMID: 29892083 PMCID: PMC6202246 DOI: 10.1038/s41589-018-0055-y] [Citation(s) in RCA: 324] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 03/13/2018] [Indexed: 11/09/2022]
Abstract
Heterobifunctional small-molecule degraders that induce protein degradation through ligase-mediated ubiquitination have shown considerable promise as a new pharmacological modality. However, we currently lack a detailed understanding of the molecular basis for target recruitment and selectivity, which is critically required to enable rational design of degraders. Here we utilize a comprehensive characterization of the ligand-dependent CRBN-BRD4 interaction to demonstrate that binding between proteins that have not evolved to interact is plastic. Multiple X-ray crystal structures show that plasticity results in several distinct low-energy binding conformations that are selectively bound by ligands. We demonstrate that computational protein-protein docking can reveal the underlying interprotein contacts and inform the design of a BRD4 selective degrader that can discriminate between highly homologous BET bromodomains. Our findings that plastic interprotein contacts confer selectivity for ligand-induced protein dimerization provide a conceptual framework for the development of heterobifunctional ligands.
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Affiliation(s)
- Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Stephen L DeAngelo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dennis Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Zhixiang He
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jian An
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nozhat Safaee
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mark P Jedrychowski
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Charles M Ponthier
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mette Ishoey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Joseph D Mancias
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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39
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Liu Y, Li Y, Liu S, Adeegbe DO, Christensen CL, Quinn MM, Dries R, Han S, Buczkowski K, Wang X, Chen T, Gao P, Zhang H, Li F, Hammerman PS, Bradner JE, Quayle SN, Wong KK. NK Cells Mediate Synergistic Antitumor Effects of Combined Inhibition of HDAC6 and BET in a SCLC Preclinical Model. Cancer Res 2018; 78:3709-3717. [PMID: 29760044 DOI: 10.1158/0008-5472.can-18-0161] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/03/2018] [Accepted: 05/04/2018] [Indexed: 01/18/2023]
Abstract
Small-cell lung cancer (SCLC) has the highest malignancy among all lung cancers, exhibiting aggressive growth and early metastasis to distant sites. For 30 years, treatment options for SCLC have been limited to chemotherapy, warranting the need for more effective treatments. Frequent inactivation of TP53 and RB1 as well as histone dysmodifications in SCLC suggest that transcriptional and epigenetic regulations play a major role in SCLC disease evolution. Here we performed a synthetic lethal screen using the BET inhibitor JQ1 and an shRNA library targeting 550 epigenetic genes in treatment-refractory SCLC xenograft models and identified HDAC6 as a synthetic lethal target in combination with JQ1. Combined treatment of human and mouse SCLC cell line-derived xenograft tumors with the HDAC6 inhibitor ricolinostat (ACY-1215) and JQ1 demonstrated significant inhibition of tumor growth; this effect was abolished upon depletion of NK cells, suggesting that these innate immune lymphoid cells play a role in SCLC tumor treatment response. Collectively, these findings suggest a potential new treatment for recurrent SCLC.Significance: These findings identify a novel therapeutic strategy for SCLC using a combination of HDAC6 and BET inhibitors. Cancer Res; 78(13); 3709-17. ©2018 AACR.
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Affiliation(s)
- Yan Liu
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Yuyang Li
- Shandong Provincial Hospital affiliated to Shandong University, Jinan, China
| | - Shengwu Liu
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Dennis O Adeegbe
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | | | - Max M Quinn
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Ruben Dries
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Shiwei Han
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Kevin Buczkowski
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Xiaoen Wang
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Ting Chen
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Peng Gao
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Hua Zhang
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Fei Li
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Peter S Hammerman
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - James E Bradner
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | | | - Kwok-Kin Wong
- Laura & Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York.
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40
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Kleppe M, Koche R, Zou L, van Galen P, Hill CE, Dong L, De Groote S, Papalexi E, Hanasoge Somasundara AV, Cordner K, Keller M, Farnoud N, Medina J, McGovern E, Reyes J, Roberts J, Witkin M, Rapaport F, Teruya-Feldstein J, Qi J, Rampal R, Bernstein BE, Bradner JE, Levine RL. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell 2018; 33:785-787. [PMID: 29634952 PMCID: PMC5908465 DOI: 10.1016/j.ccell.2018.03.024] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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41
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Zeid R, Lawlor MA, Poon E, Reyes JM, Fulciniti M, Lopez MA, Scott TG, Nabet B, Erb MA, Winter GE, Jacobson Z, Polaski DR, Karlin KL, Hirsch RA, Munshi NP, Westbrook TF, Chesler L, Lin CY, Bradner JE. Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma. Nat Genet 2018; 50:515-523. [PMID: 29379199 PMCID: PMC6310397 DOI: 10.1038/s41588-018-0044-9] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/18/2017] [Indexed: 11/08/2022]
Abstract
Amplification of the locus encoding the oncogenic transcription factor MYCN is a defining feature of high-risk neuroblastoma. Here we present the first dynamic chromatin and transcriptional landscape of MYCN perturbation in neuroblastoma. At oncogenic levels, MYCN associates with E-box binding motifs in an affinity-dependent manner, binding to strong canonical E-boxes at promoters and invading abundant weaker non-canonical E-boxes clustered at enhancers. Loss of MYCN leads to a global reduction in transcription, which is most pronounced at MYCN target genes with the greatest enhancer occupancy. These highly occupied MYCN target genes show tissue-specific expression and are linked to poor patient survival. The activity of genes with MYCN-occupied enhancers is dependent on the tissue-specific transcription factor TWIST1, which co-occupies enhancers with MYCN and is required for MYCN-dependent proliferation. These data implicate tissue-specific enhancers in defining often highly tumor-specific 'MYC target gene signatures' and identify disruption of the MYCN enhancer regulatory axis as a promising therapeutic strategy in neuroblastoma.
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Affiliation(s)
- Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew A Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Jaime M Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mariateresa Fulciniti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael A Lopez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thomas G Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Behnam Nabet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael A Erb
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Georg E Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoe Jacobson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donald R Polaski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristen L Karlin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rachel A Hirsch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Nikhil P Munshi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thomas F Westbrook
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Novartis Institute for Biomedical Research, Cambridge, MA, USA.
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42
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Oran AR, Adams CM, Zhang XY, Gennaro VJ, Pfeiffer HK, Mellert HS, Seidel HE, Mascioli K, Kaplan J, Gaballa MR, Shen C, Rigoutsos I, King MP, Cotney JL, Arnold JJ, Sharma SD, Martinez-Outschoorn UE, Vakoc CR, Chodosh LA, Thompson JE, Bradner JE, Cameron CE, Shadel GS, Eischen CM, McMahon SB. Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer. Oncotarget 2018; 7:72395-72414. [PMID: 27590350 PMCID: PMC5340124 DOI: 10.18632/oncotarget.11718] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/25/2016] [Indexed: 12/14/2022] Open
Abstract
Despite ubiquitous activation in human cancer, essential downstream effector pathways of the MYC transcription factor have been difficult to define and target. Using a structure/function-based approach, we identified the mitochondrial RNA polymerase (POLRMT) locus as a critical downstream target of MYC. The multifunctional POLRMT enzyme controls mitochondrial gene expression, a process required both for mitochondrial function and mitochondrial biogenesis. We further demonstrate that inhibition of this newly defined MYC effector pathway causes robust and selective tumor cell apoptosis, via an acute, checkpoint-like mechanism linked to aberrant electron transport chain complex assembly and mitochondrial reactive oxygen species (ROS) production. Fortuitously, MYC-dependent tumor cell death can be induced by inhibiting the mitochondrial gene expression pathway using a variety of strategies, including treatment with FDA-approved antibiotics. In vivo studies using a mouse model of Burkitt's Lymphoma provide pre-clinical evidence that these antibiotics can successfully block progression of MYC-dependent tumors.
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Affiliation(s)
- Amanda R Oran
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Clare M Adams
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Xiao-Yong Zhang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Victoria J Gennaro
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Harla K Pfeiffer
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hestia S Mellert
- Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA, USA
| | - Hans E Seidel
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Kirsten Mascioli
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jordan Kaplan
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mahmoud R Gaballa
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Chen Shen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY, USA
| | - Isidore Rigoutsos
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Michael P King
- Department of Biochemistry, Thomas Jefferson University, Philadelphia, PA, USA
| | - Justin L Cotney
- Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT, USA
| | - Jamie J Arnold
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Suresh D Sharma
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Lewis A Chodosh
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - James E Thompson
- Leukemia Service, Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA,USA
| | - Craig E Cameron
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Gerald S Shadel
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Christine M Eischen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Steven B McMahon
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
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43
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Ishoey M, Chorn S, Singh N, Jaeger MG, Brand M, Paulk J, Bauer S, Erb MA, Parapatics K, Müller AC, Bennett KL, Ecker GF, Bradner JE, Winter GE. Translation Termination Factor GSPT1 Is a Phenotypically Relevant Off-Target of Heterobifunctional Phthalimide Degraders. ACS Chem Biol 2018; 13:553-560. [PMID: 29356495 DOI: 10.1021/acschembio.7b00969] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein degradation is an emerging therapeutic strategy with a unique molecular pharmacology that enables the disruption of all functions associated with a target. This is particularly relevant for proteins depending on molecular scaffolding, such as transcription factors or receptor tyrosine kinases (RTKs). To address tractability of multiple RTKs for chemical degradation by the E3 ligase CUL4-RBX1-DDB1-CRBN (CRL4CRBN), we synthesized a series of phthalimide degraders based on the promiscuous kinase inhibitors sunitinib and PHA665752. While both series failed to induce degradation of their consensus targets, individual molecules displayed pronounced efficacy in leukemia cell lines. Orthogonal target identification supported by molecular docking led us to identify the translation termination factor G1 to S phase transition 1 (GSPT1) as a converging off-target, resulting from inadvertent E3 ligase modulation. This research highlights the importance of monitoring degradation events that are independent of the respective targeting ligand as a unique feature of small-molecule degraders.
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Affiliation(s)
- Mette Ishoey
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Someth Chorn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Natesh Singh
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - Martin G. Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Matthias Brand
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Sophie Bauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Michael A. Erb
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Gerhard F. Ecker
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - James E. Bradner
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Georg E. Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
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44
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Duan Q, McMahon S, Anand P, Shah H, Thomas S, Salunga HT, Huang Y, Zhang R, Sahadevan A, Lemieux ME, Brown JD, Srivastava D, Bradner JE, McKinsey TA, Haldar SM. BET bromodomain inhibition suppresses innate inflammatory and profibrotic transcriptional networks in heart failure. Sci Transl Med 2018; 9:9/390/eaah5084. [PMID: 28515341 DOI: 10.1126/scitranslmed.aah5084] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 01/18/2017] [Accepted: 03/30/2017] [Indexed: 12/13/2022]
Abstract
Despite current standard of care, the average 5-year mortality after an initial diagnosis of heart failure (HF) is about 40%, reflecting an urgent need for new therapeutic approaches. Previous studies demonstrated that the epigenetic reader protein bromodomain-containing protein 4 (BRD4), an emerging therapeutic target in cancer, functions as a critical coactivator of pathologic gene transactivation during cardiomyocyte hypertrophy. However, the therapeutic relevance of these findings to human disease remained unknown. We demonstrate that treatment with the BET bromodomain inhibitor JQ1 has therapeutic effects during severe, preestablished HF from prolonged pressure overload, as well as after a massive anterior myocardial infarction in mice. Furthermore, JQ1 potently blocks agonist-induced hypertrophy in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). Integrated transcriptomic analyses across animal models and human iPSC-CMs reveal that BET inhibition preferentially blocks transactivation of a common pathologic gene regulatory program that is robustly enriched for NFκB and TGF-β signaling networks, typified by innate inflammatory and profibrotic myocardial genes. As predicted by these specific transcriptional mechanisms, we found that JQ1 does not suppress physiological cardiac hypertrophy in a mouse swimming model. These findings establish that pharmacologically targeting innate inflammatory and profibrotic myocardial signaling networks at the level of chromatin is effective in animal models and human cardiomyocytes, providing the critical rationale for further development of BET inhibitors and other epigenomic medicines for HF.
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Affiliation(s)
- Qiming Duan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Sarah McMahon
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Priti Anand
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Hirsh Shah
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Sean Thomas
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Hazel T Salunga
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Yu Huang
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Rongli Zhang
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Aarathi Sahadevan
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | | | - Jonathan D Brown
- Division of Cardiovascular Medicine, Department of Medicine, and Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.,Division of Cardiology, Department of Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA 94158, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Timothy A McKinsey
- Division of Cardiology, Department of Medicine, Consortium for Fibrosis Research & Translation, University of Colorado, Anschutz Medical Campus, Denver, CO 80204, USA
| | - Saptarsi M Haldar
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA. .,Division of Cardiology, Department of Medicine, and Cardiovascular Research Institute, University of California San Francisco School of Medicine, San Francisco, CA 94158, USA
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45
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Koo SJ, Fernández-Montalván AE, Badock V, Ott CJ, Holton SJ, von Ahsen O, Toedling J, Vittori S, Bradner JE, Gorjánácz M. ATAD2 is an epigenetic reader of newly synthesized histone marks during DNA replication. Oncotarget 2018; 7:70323-70335. [PMID: 27612420 PMCID: PMC5342555 DOI: 10.18632/oncotarget.11855] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/21/2016] [Indexed: 02/02/2023] Open
Abstract
ATAD2 (ATPase family AAA domain-containing protein 2) is a chromatin regulator harboring an AAA+ ATPase domain and a bromodomain, previously proposed to function as an oncogenic transcription co-factor. Here we suggest that ATAD2 is also required for DNA replication. ATAD2 is co-expressed with genes involved in DNA replication in various cancer types and predominantly expressed in S phase cells where it localized on nascent chromatin (replication sites). Our extensive biochemical and cellular analyses revealed that ATAD2 is recruited to replication sites through a direct interaction with di-acetylated histone H4 at K5 and K12, indicative of newly synthesized histones during replication-coupled chromatin reassembly. Similar to ATAD2-depletion, ectopic expression of ATAD2 mutants that are deficient in binding to these di-acetylation marks resulted in reduced DNA replication and impaired loading of PCNA onto chromatin, suggesting relevance of ATAD2 in DNA replication. Taken together, our data show a novel function of ATAD2 in cancer and for the first time identify a reader of newly synthesized histone di-acetylation-marks during replication.
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Affiliation(s)
| | | | | | - Christopher J Ott
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Sarah Vittori
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Present address: Novartis Institute for BioMedical Research, Cambridge, MA, USA
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46
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Jacques C, Lamoureux F, Baud'huin M, Rodriguez Calleja L, Quillard T, Amiaud J, Tirode F, Rédini F, Bradner JE, Heymann D, Ory B. Targeting the epigenetic readers in Ewing sarcoma inhibits the oncogenic transcription factor EWS/Fli1. Oncotarget 2018; 7:24125-40. [PMID: 27006472 PMCID: PMC5029689 DOI: 10.18632/oncotarget.8214] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/02/2016] [Indexed: 11/25/2022] Open
Abstract
Ewing Sarcoma is a rare bone and soft tissue malignancy affecting children and young adults. Chromosomal translocations in this cancer produce fusion oncogenes as characteristic molecular signatures of the disease. The most common case is the translocation t (11; 22) (q24;q12) which yields the EWS-Fli1 chimeric transcription factor. Finding a way to directly target EWS-Fli1 remains a central therapeutic approach to eradicate this aggressive cancer. Here we demonstrate that treating Ewing Sarcoma cells with JQ1(+), a BET bromodomain inhibitor, represses directly EWS-Fli1 transcription as well as its transcriptional program. Moreover, the Chromatin Immuno Precipitation experiments demonstrate for the first time that these results are a consequence of the depletion of BRD4, one of the BET bromodomains protein from the EWS-Fli1 promoter. In vitro, JQ1(+) treatment reduces the cell viability, impairs the cell clonogenic and the migratory abilities, and induces a G1-phase blockage as well as a time- and a dose-dependent apoptosis. Furthermore, in our in vivo model, we observed a tumor burden delay, an inhibition of the global vascularization and an increase of the mice overall survival. Taken together, our data indicate that inhibiting the BET bromodomains interferes with EWS-FLi1 transcription and could be a promising strategy in the Ewing tumors context.
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Affiliation(s)
- Camille Jacques
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | - François Lamoureux
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | - Marc Baud'huin
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France.,Nantes University Hospital, Nantes, France
| | - Lidia Rodriguez Calleja
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | - Thibaut Quillard
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | - Jérôme Amiaud
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | | | - Françoise Rédini
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Dominique Heymann
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France.,Nantes University Hospital, Nantes, France
| | - Benjamin Ory
- INSERM, UMR 957, Équipe Labellisée Ligue 2012, Nantes, France.,Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes, Nantes Atlantique Universités, EA3822, Nantes, France
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47
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Kleppe M, Koche R, Zou L, van Galen P, Hill CE, Dong L, De Groote S, Papalexi E, Hanasoge Somasundara AV, Cordner K, Keller M, Farnoud N, Medina J, McGovern E, Reyes J, Roberts J, Witkin M, Rapaport F, Teruya-Feldstein J, Qi J, Rampal R, Bernstein BE, Bradner JE, Levine RL. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell 2018; 33:29-43.e7. [PMID: 29249691 PMCID: PMC5760343 DOI: 10.1016/j.ccell.2017.11.009] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 07/13/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022]
Abstract
Genetic and functional studies underscore the central role of JAK/STAT signaling in myeloproliferative neoplasms (MPNs). However, the mechanisms that mediate transformation in MPNs are not fully delineated, and clinically utilized JAK inhibitors have limited ability to reduce disease burden or reverse myelofibrosis. Here we show that MPN progenitor cells are characterized by marked alterations in gene regulation through differential enhancer utilization, and identify nuclear factor κB (NF-κB) signaling as a key pathway activated in malignant and non-malignant cells in MPN. Inhibition of BET bromodomain proteins attenuated NF-κB signaling and reduced cytokine production in vivo. Most importantly, combined JAK/BET inhibition resulted in a marked reduction in the serum levels of inflammatory cytokines, reduced disease burden, and reversed bone marrow fibrosis in vivo.
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Affiliation(s)
- Maria Kleppe
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lihua Zou
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Peter van Galen
- Department of Pathology Massachusetts General Hospital, Harvard Medical School, Broad Institute of Harvard and MIT, Boston, MA, USA
| | - Corinne E Hill
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA
| | - Lauren Dong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA
| | - Sofie De Groote
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA
| | - Efthymia Papalexi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA
| | - Amritha V Hanasoge Somasundara
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA
| | - Keith Cordner
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA
| | - Matthew Keller
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA
| | - Noushin Farnoud
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Juan Medina
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erin McGovern
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jaime Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
| | - Justin Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
| | - Matthew Witkin
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Franck Rapaport
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
| | - Raajit Rampal
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bradley E Bernstein
- Department of Pathology Massachusetts General Hospital, Harvard Medical School, Broad Institute of Harvard and MIT, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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48
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Kalin JH, Wu M, Gomez AV, Song Y, Das J, Hayward D, Adejola N, Wu M, Panova I, Chung HJ, Kim E, Roberts HJ, Roberts JM, Prusevich P, Jeliazkov JR, Roy Burman SS, Fairall L, Milano C, Eroglu A, Proby CM, Dinkova-Kostova AT, Hancock WW, Gray JJ, Bradner JE, Valente S, Mai A, Anders NM, Rudek MA, Hu Y, Ryu B, Schwabe JWR, Mattevi A, Alani RM, Cole PA. Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors. Nat Commun 2018; 9:53. [PMID: 29302039 PMCID: PMC5754352 DOI: 10.1038/s41467-017-02242-4] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/14/2017] [Indexed: 01/08/2023] Open
Abstract
Here we report corin, a synthetic hybrid agent derived from the class I HDAC inhibitor (entinostat) and an LSD1 inhibitor (tranylcypromine analog). Enzymologic analysis reveals that corin potently targets the CoREST complex and shows more sustained inhibition of CoREST complex HDAC activity compared with entinostat. Cell-based experiments demonstrate that corin exhibits a superior anti-proliferative profile against several melanoma lines and cutaneous squamous cell carcinoma lines compared to its parent monofunctional inhibitors but is less toxic to melanocytes and keratinocytes. CoREST knockdown, gene expression, and ChIP studies suggest that corin's favorable pharmacologic effects may rely on an intact CoREST complex. Corin was also effective in slowing tumor growth in a melanoma mouse xenograft model. These studies highlight the promise of a new class of two-pronged hybrid agents that may show preferential targeting of particular epigenetic regulatory complexes and offer unique therapeutic opportunities.
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Affiliation(s)
- Jay H Kalin
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Muzhou Wu
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Andrea V Gomez
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Yun Song
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK
| | - Jayanta Das
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Dawn Hayward
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nkosi Adejola
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mingxuan Wu
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Izabela Panova
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Hye Jin Chung
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Edward Kim
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Holly J Roberts
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Polina Prusevich
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Shourya S Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Louise Fairall
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK
| | - Charles Milano
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK
| | - Abdulkerim Eroglu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Charlotte M Proby
- Division of Cancer Research, Jacqui Wood Cancer Centre, University of Dundee, Dundee, DD1 9SY, UK
| | - Albena T Dinkova-Kostova
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Division of Cancer Research, Jacqui Wood Cancer Centre, University of Dundee, Dundee, DD1 9SY, UK
| | - Wayne W Hancock
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Jeffrey J Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sergio Valente
- Pasteur Institute, Cenci-Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Antonello Mai
- Pasteur Institute, Cenci-Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Nicole M Anders
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Michelle A Rudek
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yong Hu
- Department of Oncology, BioDuro LLC, Shanghai, 200131, China
| | - Byungwoo Ryu
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - John W R Schwabe
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 9HN, UK.
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy.
| | - Rhoda M Alani
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Philip A Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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49
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Erwin GS, Grieshop MP, Ali A, Qi J, Lawlor M, Kumar D, Ahmad I, McNally A, Teider N, Worringer K, Sivasankaran R, Syed DN, Eguchi A, Ashraf M, Jeffery J, Xu M, Park PMC, Mukhtar H, Srivastava AK, Faruq M, Bradner JE, Ansari AZ. Synthetic transcription elongation factors license transcription across repressive chromatin. Science 2017; 358:1617-1622. [PMID: 29192133 PMCID: PMC6037176 DOI: 10.1126/science.aan6414] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022]
Abstract
The release of paused RNA polymerase II into productive elongation is highly regulated, especially at genes that affect human development and disease. To exert control over this rate-limiting step, we designed sequence-specific synthetic transcription elongation factors (Syn-TEFs). These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that engages the transcription elongation machinery. By limiting activity to targeted loci, Syn-TEFs convert constituent modules from broad-spectrum inhibitors of transcription into gene-specific stimulators. Here we present Syn-TEF1, a molecule that actively enables transcription across repressive GAA repeats that silence frataxin expression in Friedreich's ataxia, a terminal neurodegenerative disease with no effective therapy. The modular design of Syn-TEF1 defines a general framework for developing a class of molecules that license transcription elongation at targeted genomic loci.
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Affiliation(s)
- Graham S Erwin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew P Grieshop
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Asfa Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deepak Kumar
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Istaq Ahmad
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Anna McNally
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Natalia Teider
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Katie Worringer
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Rajeev Sivasankaran
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Deeba N Syed
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Asuka Eguchi
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Md Ashraf
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Justin Jeffery
- Small Animal Imaging Facility, University of Wisconsin Carbone Cancer Center, Madison, WI 53792, USA
| | - Mousheng Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hasan Mukhtar
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Achal K Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
- The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
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50
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Mack SC, Pajtler KW, Chavez L, Okonechnikov K, Bertrand KC, Wang X, Erkek S, Federation A, Song A, Lee C, Wang X, McDonald L, Morrow JJ, Saiakhova A, Sin-Chan P, Wu Q, Michaelraj KA, Miller TE, Hubert CG, Ryzhova M, Garzia L, Donovan L, Dombrowski S, Factor DC, Luu B, Valentim CLL, Gimple RC, Morton A, Kim L, Prager BC, Lee JJY, Wu X, Zuccaro J, Thompson Y, Holgado BL, Reimand J, Ke SQ, Tropper A, Lai S, Vijayarajah S, Doan S, Mahadev V, Miñan AF, Gröbner SN, Lienhard M, Zapatka M, Huang Z, Aldape KD, Carcaboso AM, Houghton PJ, Keir ST, Milde T, Witt H, Li Y, Li CJ, Bian XW, Jones DTW, Scott I, Singh SK, Huang A, Dirks PB, Bouffet E, Bradner JE, Ramaswamy V, Jabado N, Rutka JT, Northcott PA, Lupien M, Lichter P, Korshunov A, Scacheri PC, Pfister SM, Kool M, Taylor MD, Rich JN. Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling. Nature 2017; 553:101-105. [PMID: 29258295 PMCID: PMC5993422 DOI: 10.1038/nature25169] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 11/22/2017] [Indexed: 12/26/2022]
Abstract
Genomic sequencing has driven precision-based oncology therapy; however, genetic drivers remain unknown or non-targetable for many malignancies, demanding alternative approaches to identify therapeutic leads. Ependymomas are chemotherapy-resistant brain tumours, which, despite genomic sequencing, lack effective molecular targets. Intracranial ependymomas are segregated based on anatomical location – supratentorial region (ST) or posterior fossa (PF) – and further divided into distinct molecular subgroups that reflect differences in age of onset, gender predominance, and response to therapy1–3. The most common and aggressive subgroup, Posterior Fossa Ependymoma Group A (PF-EPN-A), occurs in young children and appears to lack recurrent somatic mutations2. Conversely, Posterior Fossa Ependymoma Group B (PF-EPN-B) tumours display frequent large-scale copy number gains and losses yet favourable clinical outcomes1,3. Greater than 70% of supratentorial ependymomas are defined by highly recurrent gene fusions in the NFκB subunit RELA (ST-EPN-RELA), and less frequently involve fusion of the gene encoding the transcriptional activator YAP1 (ST-EPN-YAP1).1,3,4 Subependymomas, a distinct histologic variant, can also be found within the ST and PF compartments accounting for the majority of tumours in the molecular subgroups ST-EPN-SE and PF-EPN-SE, respectively1. Here, we mapped active chromatin landscapes in 42 primary ependymomas in two non-overlapping primary ependymoma cohorts with the goal of identifying essential super enhancer associated genes on which tumour cells were dependent. Enhancer regions revealed putative oncogenes, molecular targets, and pathways, which when subjected to small molecule inhibitor or shRNA treatment, diminished proliferation of patient-derived neurospheres and increased survival in mouse models of ependymomas. Through profiling of transcriptional enhancers, our study provides a framework for target and drug discovery in other cancers recalcitrant to therapeutic development because of their lack of known genetic drivers.
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Affiliation(s)
- Stephen C Mack
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatric Hematolgy and Oncology, Texas Children's Cancer and Hematology Centers, Houston, Texas, USA.,Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Lukas Chavez
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Medicine, Division of Medical Genetics, University of California - San Diego School of Medicine, La Jolla, California 92093, USA
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Kelsey C Bertrand
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatric Hematolgy and Oncology, Texas Children's Cancer and Hematology Centers, Houston, Texas, USA.,Department of Pediatrics, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Xiuxing Wang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA.,Department of Medicine, Division of Regenerative Medicine, University of California - San Diego School of Medicine, La Jolla, California, USA
| | - Serap Erkek
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Alexander Federation
- Department of Genomic Sciences, University of Washington, Seattle, Washington 355065, USA
| | - Anne Song
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Christine Lee
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Xin Wang
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Laura McDonald
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - James J Morrow
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Patrick Sin-Chan
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Qiulian Wu
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA.,Department of Medicine, Division of Regenerative Medicine, University of California - San Diego School of Medicine, La Jolla, California, USA
| | - Kulandaimanuvel Antony Michaelraj
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Tyler E Miller
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA.,Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Christopher G Hubert
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, 4th Tverskaya-Yamskaya 16, Moscow 125047, Russia
| | - Livia Garzia
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Laura Donovan
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Stephen Dombrowski
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA.,Rose Ella Burkhardt Brain Tumor & Neuro-Oncology Center, Cleveland Clinic Neurological Institute, Department of Neurosurgery, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Daniel C Factor
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Betty Luu
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Claudia L L Valentim
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Ryan C Gimple
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA.,Department of Medicine, Division of Regenerative Medicine, University of California - San Diego School of Medicine, La Jolla, California, USA.,Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Andrew Morton
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Leo Kim
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA.,Department of Medicine, Division of Regenerative Medicine, University of California - San Diego School of Medicine, La Jolla, California, USA
| | - Briana C Prager
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA.,Department of Medicine, Division of Regenerative Medicine, University of California - San Diego School of Medicine, La Jolla, California, USA
| | - John J Y Lee
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Xiaochong Wu
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Jennifer Zuccaro
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Yuan Thompson
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Borja L Holgado
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Susan Q Ke
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Adam Tropper
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Sisi Lai
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Senthuran Vijayarajah
- Department of Pediatrics, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Pediatrics, Division of Critical Care, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Sylvia Doan
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Vaidehi Mahadev
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Ana Fernandez Miñan
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Susanne N Gröbner
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Matthias Lienhard
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Zhiqin Huang
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Kenneth D Aldape
- Department of Pathology, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Angel M Carcaboso
- Preclinical Therapeutics and Drug Delivery Research Program, Fundacio Sant Joan de Deu, 08950 Barcelona, Spain
| | - Peter J Houghton
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, Ohio
| | - Stephen T Keir
- Duke University Medical Center, Department of Surgery, Durham, North Carolina, USA
| | - Till Milde
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), INF 280, D-69120 Heidelberg, Germany
| | - Hendrik Witt
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Yan Li
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Chao-Jun Li
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, National Resource Centre for Mutant Mice, Nanjing, China
| | - Xiu-Wu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, The Third Military Medical University, and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing, China
| | - David T W Jones
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Ian Scott
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Sheila K Singh
- Department of Surgery, Division of Neurosurgery, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Annie Huang
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Peter B Dirks
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Eric Bouffet
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - James E Bradner
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Vijay Ramaswamy
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Division of Hematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Nada Jabado
- Departments of Paediatrics and Human Genetics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec H3Z 2Z3, Canada
| | - James T Rutka
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Paul A Northcott
- Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Mathieu Lupien
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Michael D Taylor
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Jeremy N Rich
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA.,Department of Medicine, Division of Regenerative Medicine, University of California - San Diego School of Medicine, La Jolla, California, USA.,Rose Ella Burkhardt Brain Tumor & Neuro-Oncology Center, Cleveland Clinic Neurological Institute, Department of Neurosurgery, Cleveland Clinic, Cleveland, Ohio 44195, USA
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