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Irani S, Tan W, Li Q, Toy W, Jones C, Gadiya M, Marra A, Katzenellenbogen JA, Carlson KE, Katzenellenbogen BS, Karimi M, Segu Rajappachetty R, Del Priore IS, Reis-Filho JS, Shen Y, Chandarlapaty S. Somatic estrogen receptor α mutations that induce dimerization promote receptor activity and breast cancer proliferation. J Clin Invest 2024; 134:e163242. [PMID: 37883178 PMCID: PMC10760953 DOI: 10.1172/jci163242] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/06/2022] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
Physiologic activation of estrogen receptor α (ERα) is mediated by estradiol (E2) binding in the ligand-binding pocket of the receptor, repositioning helix 12 (H12) to facilitate binding of coactivator proteins in the unoccupied coactivator binding groove. In breast cancer, activation of ERα is often observed through point mutations that lead to the same H12 repositioning in the absence of E2. Through expanded genetic sequencing of breast cancer patients, we identified a collection of mutations located far from H12 but nonetheless capable of promoting E2-independent transcription and breast cancer cell growth. Using machine learning and computational structure analyses, this set of mutants was inferred to act distinctly from the H12-repositioning mutants and instead was associated with conformational changes across the ERα dimer interface. Through both in vitro and in-cell assays of full-length ERα protein and isolated ligand-binding domain, we found that these mutants promoted ERα dimerization, stability, and nuclear localization. Point mutations that selectively disrupted dimerization abrogated E2-independent transcriptional activity of these dimer-promoting mutants. The results reveal a distinct mechanism for activation of ERα function through enforced receptor dimerization and suggest dimer disruption as a potential therapeutic strategy to treat ER-dependent cancers.
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Affiliation(s)
- Seema Irani
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
| | - Qing Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Weiyi Toy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Catherine Jones
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mayur Gadiya
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Antonio Marra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - John A. Katzenellenbogen
- Department of Chemistry and Molecular and Integrative Physiology, and the Cancer Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kathryn E. Carlson
- Department of Chemistry and Molecular and Integrative Physiology, and the Cancer Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Benita S. Katzenellenbogen
- Department of Chemistry and Molecular and Integrative Physiology, and the Cancer Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mostafa Karimi
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
| | - Ramya Segu Rajappachetty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Isabella S. Del Priore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
- Department of Computer Science and Engineering and
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
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Dorso M, Patel PT, Pankov A, Boyer JA, Soni RK, Del Priore IS, Hayatt O, Kulick A, Hagen CJ, de Stanchina E, Junttila MR, Daemen A, Friedman LS, Hendrickson RC, Chandarlapaty S. A Druggable FOXA1-Glucocorticoid Receptor Transcriptional Axis Drives Tumor Growth in a Subset of Non-Small Cell Lung Cancer. Cancer Res Commun 2023; 3:1788-1799. [PMID: 37691854 PMCID: PMC10484118 DOI: 10.1158/2767-9764.crc-23-0310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
The FOXA1 pioneer factor is an essential mediator of steroid receptor function in multiple hormone-dependent cancers, including breast and prostate cancers, enabling nuclear receptors such as estrogen receptor (ER) and androgen receptor (AR) to activate lineage-specific growth programs. FOXA1 is also highly expressed in non-small cell lung cancer (NSCLC), but whether and how it regulates tumor growth in this context is not known. Analyzing data from loss-of-function screens, we identified a subset of NSCLC tumor lines where proliferation is FOXA1 dependent. Using rapid immunoprecipitation and mass spectrometry of endogenous protein, we identified chromatin-localized interactions between FOXA1 and glucocorticoid receptor (GR) in these tumor cells. Knockdown of GR inhibited proliferation of FOXA1-dependent, but not FOXA1-independent NSCLC cells. In these FOXA1-dependent models, FOXA1 and GR cooperate to regulate gene targets involved in EGF signaling and G1-S cell-cycle progression. To investigate the therapeutic potential for targeting this complex, we examined the effects of highly selective inhibitors of the GR ligand-binding pocket and found that GR antagonism with ORIC-101 suppressed FOXA1/GR target expression, activation of EGF signaling, entry into the S-phase, and attendant proliferation in vitro and in vivo. Taken together, our findings point to a subset of NSCLCs harboring a dependence on the FOXA1/GR growth program and provide rationale for its therapeutic targeting. Significance NSCLC is the leading cause of cancer deaths worldwide. There is a need to identify novel druggable dependencies. We identify a subset of NSCLCs dependent on FOXA1-GR and sensitive to GR antagonism.
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Affiliation(s)
- M. Dorso
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, New York
| | - Payal T. Patel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, New York
| | | | - Jacob A. Boyer
- Gerstner Sloan Kettering Graduate Program, Sloan Kettering Institute, New York, New York
| | - Rajesh K. Soni
- Microchemistry and Proteomics Core, Sloan Kettering Institute, New York, New York
| | - Isabella S. Del Priore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Omar Hayatt
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amanda Kulick
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Connor J. Hagen
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | | | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Li Q, Jiang B, Guo J, Shao H, Del Priore IS, Chang Q, Kudo R, Li Z, Razavi P, Liu B, Boghossian AS, Rees MG, Ronan MM, Roth JA, Donovan KA, Palafox M, Reis-Filho JS, de Stanchina E, Fischer ES, Rosen N, Serra V, Koff A, Chodera JD, Gray NS, Chandarlapaty S. INK4 Tumor Suppressor Proteins Mediate Resistance to CDK4/6 Kinase Inhibitors. Cancer Discov 2022; 12:356-371. [PMID: 34544752 PMCID: PMC8831444 DOI: 10.1158/2159-8290.cd-20-1726] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [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: 12/01/2020] [Revised: 07/13/2021] [Accepted: 09/15/2021] [Indexed: 01/22/2023]
Abstract
Cyclin-dependent kinases 4 and 6 (CDK4/6) represent a major therapeutic vulnerability for breast cancer. The kinases are clinically targeted via ATP competitive inhibitors (CDK4/6i); however, drug resistance commonly emerges over time. To understand CDK4/6i resistance, we surveyed over 1,300 breast cancers and identified several genetic alterations (e.g., FAT1, PTEN, or ARID1A loss) converging on upregulation of CDK6. Mechanistically, we demonstrate CDK6 causes resistance by inducing and binding CDK inhibitor INK4 proteins (e.g., p18INK4C). In vitro binding and kinase assays together with physical modeling reveal that the p18INK4C-cyclin D-CDK6 complex occludes CDK4/6i binding while only weakly suppressing ATP binding. Suppression of INK4 expression or its binding to CDK6 restores CDK4/6i sensitivity. To overcome this constraint, we developed bifunctional degraders conjugating palbociclib with E3 ligands. Two resulting lead compounds potently degraded CDK4/6, leading to substantial antitumor effects in vivo, demonstrating the promising therapeutic potential for retargeting CDK4/6 despite CDK4/6i resistance. SIGNIFICANCE: CDK4/6 kinase activation represents a common mechanism by which oncogenic signaling induces proliferation and is potentially targetable by ATP competitive inhibitors. We identify a CDK6-INK4 complex that is resilient to current-generation inhibitors and develop a new strategy for more effective inhibition of CDK4/6 kinases.This article is highlighted in the In This Issue feature, p. 275.
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Affiliation(s)
- Qing Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Baishan Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Jiaye Guo
- Computational & Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hong Shao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Isabella S Del Priore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Qing Chang
- Anti-Tumor Assessment, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rei Kudo
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zhiqiang Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pedram Razavi
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Matthew G Rees
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Melissa M Ronan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Marta Palafox
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Anti-Tumor Assessment, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Neal Rosen
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Andrew Koff
- Program in Molecular Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John D Chodera
- Computational & Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
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