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Li W, Garcia-Rivera EM, Mitchell DC, Chick JM, Maetani M, Knapp JM, Matthews GM, Shirasaki R, de Matos Simoes R, Viswanathan V, Pulice JL, Rees MG, Roth JA, Gygi SP, Mitsiades CS, Kadoch C, Schreiber SL, Ostrem JML. Highly specific intracellular ubiquitination of a small molecule. bioRxiv 2024:2024.01.26.577493. [PMID: 38328167 PMCID: PMC10849632 DOI: 10.1101/2024.01.26.577493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Ubiquitin is a small, highly conserved protein that acts as a posttranslational modification in eukaryotes. Ubiquitination of proteins frequently serves as a degradation signal, marking them for disposal by the proteasome. Here, we report a novel small molecule from a diversity-oriented synthesis library, BRD1732, that is directly ubiquitinated in cells, resulting in dramatic accumulation of inactive ubiquitin monomers and polyubiquitin chains causing broad inhibition of the ubiquitin-proteasome system. Ubiquitination of BRD1732 and its associated cytotoxicity are stereospecific and dependent upon two homologous E3 ubiquitin ligases, RNF19A and RNF19B. Our finding opens the possibility for indirect ubiquitination of a target through a ubiquitinated bifunctional small molecule, and more broadly raises the potential for posttranslational modification in trans .
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2
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Pulice JL, Meyerson M. Dosage amplification dictates oncogenic regulation by the NKX2-1 lineage factor in lung adenocarcinoma. bioRxiv 2023:2023.10.26.563996. [PMID: 37994369 PMCID: PMC10664179 DOI: 10.1101/2023.10.26.563996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Amplified oncogene expression is a critical and widespread driver event in cancer, yet our understanding of how amplification-mediated elevated dosage mediates oncogenic regulation is limited. Here, we find that the most significant focal amplification event in lung adenocarcinoma (LUAD) targets a lineage super-enhancer near the NKX2-1 lineage transcription factor. The NKX2-1 super-enhancer is targeted by focal and co-amplification with NKX2-1, and activation or repression controls NKX2-1 expression. We find that NKX2-1 is a widespread dependency in LUAD cell lines, where NKX2-1 pioneers enhancer accessibility to drive a lineage addicted state in LUAD, and NKX2-1 confers persistence to EGFR inhibitors. Notably, we find that oncogenic NKX2-1 regulation requires expression above a minimum dosage threshold-NKX2-1 dosage below this threshold is insufficient for cell viability, enhancer remodeling, and TKI persistence. Our data suggest that copy-number amplification can be a gain-of-function alteration, wherein amplification elevates oncogene expression above a critical dosage required for oncogenic regulation and cancer cell survival.
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Affiliation(s)
- John L. Pulice
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Lead contact
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3
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Pulice JL, Meyerson M. Abstract A003: Enhancer amplification defines lineage addiction in human lung adenocarcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.cancepi22-a003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Abstract
Lung cancer is the most common cause of death from cancer worldwide, and lung adenocarcinoma (LUAD) is the most common subtype of lung cancer. NKX2-1 (also known as TTF-1, TITF-1) is a lineage defining transcription factor throughout normal lung development. In LUAD, NKX2-1 is a highly specific and sensitive marker for 85-90% of both primary and metastatic LUADs. We and others identified NKX2-1 as the most significantly amplified gene in LUAD. NKX2-1 is amplified as the earliest stages of LUAD development, and NKX2-1 amplification is a truncal event in multi-region LUAD evolution. Despite strong evidence for an oncogenic role for NKX2-1, little is known about the mechanisms of NKX2-1 activation, or how its oncogenic regulation drives LUAD. Here, we identify recurrent focal amplification targeting a super-enhancer (SE) of NKX2-1 as a driving event in LUAD. Using epigenomic data from LUAD cell lines and primary samples, we identify this region as a lineage super-enhancer that is specifically active in NKX2-1(+) cell lines and patients. Notably, this region is co-amplified with NKX2-1 in 95.9% (143/149) of NKX2-1-amplified samples, suggesting this region is a hallmark of NKX2-1 activation, through focal or co-amplification with NKX2-1. Using endogenous ChIP-seq and exogenous luciferase assays, we show the enhancer activity of the NKX2-1 SE is comprised of three constituent enhancers, and map the transcriptional activity of the strongest enhancer to individual binding motifs for AP-1 and ETS. Using CRISPR inhibition (CRISPRi) and CRISPR activation (CRISPRa) in LUAD cell lines expressing high or low levels of NKX2-1, we show that activity of the NKX2-1 SE defines endogenous NKX2-1 expression. Using genome-wide shRNA and CRISPR screens, we identify a NKX2-1 dependency in NKX2-1 positive LUAD cell lines, and validate this dependency in clonogenic and proliferation assays. Using RNA sequencing (RNA-seq), we find that NKX2-1 knockdown activates an epithelial-mesenchymal transition (EMT) gene signature and downregulates an alveolar differentiation signature, including critical markers of LUAD differentiation, such as NAPSA, LMO3, and SLC34A2. Using a global clustering approach to CCLE RNA-seq of LUAD cell lines, we find that NKX2-1(+) LUAD cell lines cluster apart from NKX2-1(–), and that NKX2-1 knockdown regulates the majority (57/97) of genes that distinguish NKX2-1(+) LUADs. Similarly, we find that global clustering of H3K27ac ChIP-seq in LUAD cell lines separates NKX2-1(+) cells, and identify enhancers that are uniquely active NKX2-1(+) LUAD cell lines. We find these enhancers are bound and activated by NKX2-1, regulating genes we identified above such as NAPSA and LMO3. Our data demonstrates that enhancer amplification is a hallmark of oncogenic NKX2-1 activation in LUAD, through which NKX2-1 drives a lineage addicted state and oncogenic cell proliferation. This suggests that NKX2-1 is a critical defining oncogene for LUAD, and that targeting of NKX2-1 or its enhancer may suppress LUAD.
Citation Format: John L. Pulice, Matthew Meyerson. Enhancer amplification defines lineage addiction in human lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A003.
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Sandoval GJ, Pulice JL, Pakula H, Schenone M, Takeda DY, Pop M, Boulay G, Williamson KE, McBride MJ, Pan J, St Pierre R, Hartman E, Garraway LA, Carr SA, Rivera MN, Li Z, Ronco L, Hahn WC, Kadoch C. Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis. Mol Cell 2018; 71:554-566.e7. [PMID: 30078722 DOI: 10.1016/j.molcel.2018.06.040] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [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: 03/19/2018] [Revised: 06/04/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022]
Abstract
Chromosomal rearrangements resulting in the fusion of TMPRSS2, an androgen-regulated gene, and the ETS family transcription factor ERG occur in over half of prostate cancers. However, the mechanism by which ERG promotes oncogenic gene expression and proliferation remains incompletely understood. Here, we identify a binding interaction between ERG and the mammalian SWI/SNF (BAF) ATP-dependent chromatin remodeling complex, which is conserved among other oncogenic ETS factors, including ETV1, ETV4, and ETV5. We find that ERG drives genome-wide retargeting of BAF complexes in a manner dependent on binding of ERG to the ETS DNA motif. Moreover, ERG requires intact BAF complexes for chromatin occupancy and BAF complex ATPase activity for target gene regulation. In a prostate organoid model, BAF complexes are required for ERG-mediated basal-to-luminal transition, a hallmark of ERG activity in prostate cancer. These observations suggest a fundamental interdependence between ETS transcription factors and BAF chromatin remodeling complexes in cancer.
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Affiliation(s)
- Gabriel J Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - John L Pulice
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hubert Pakula
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - David Y Takeda
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Marius Pop
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gaylor Boulay
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Kaylyn E Williamson
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Matthew J McBride
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Chemical Biology Program, Harvard Medical School, Boston, MA, USA
| | - Joshua Pan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Roodolph St Pierre
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Chemical Biology Program, Harvard Medical School, Boston, MA, USA
| | - Emily Hartman
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Steven A Carr
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Miguel N Rivera
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Zhe Li
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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McBride MJ, Pulice JL, Beird HC, Ingram DR, D'Avino AR, Shern JF, Charville GW, Hornick JL, Nakayama RT, Garcia-Rivera EM, Araujo DM, Wang WL, Tsai JW, Yeagley M, Wagner AJ, Futreal PA, Khan J, Lazar AJ, Kadoch C. The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma. Cancer Cell 2018; 33:1128-1141.e7. [PMID: 29861296 PMCID: PMC6791822 DOI: 10.1016/j.ccell.2018.05.002] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/26/2018] [Accepted: 05/02/2018] [Indexed: 12/22/2022]
Abstract
Synovial sarcoma (SS) is defined by the hallmark SS18-SSX fusion oncoprotein, which renders BAF complexes aberrant in two manners: gain of SSX to the SS18 subunit and concomitant loss of BAF47 subunit assembly. Here we demonstrate that SS18-SSX globally hijacks BAF complexes on chromatin to activate an SS transcriptional signature that we define using primary tumors and cell lines. Specifically, SS18-SSX retargets BAF complexes from enhancers to broad polycomb domains to oppose PRC2-mediated repression and activate bivalent genes. Upon suppression of SS18-SSX, reassembly of BAF47 restores enhancer activation, but is not required for proliferative arrest. These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations.
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Affiliation(s)
- Matthew J McBride
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Chemical Biology, Harvard University, Cambridge, MA, USA
| | - John L Pulice
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hannah C Beird
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Davis R Ingram
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew R D'Avino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Gregory W Charville
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert T Nakayama
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; Ludwig Center at Dana-Farber/Harvard and Center for Sarcoma and Bone Oncology, Department of Medical Oncology, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Enrique M Garcia-Rivera
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dejka M Araujo
- Department of Sarcoma Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Wei-Lien Wang
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Jen-Wei Tsai
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Michelle Yeagley
- Department of Sarcoma Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew J Wagner
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Javed Khan
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA; Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA; Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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McBride MJ, Pulice JL, Nakayama RT, Mashtalir N, Ingram DR, Jaffe JD, Shern JF, Khan J, Hornick JL, Lazar AJ, Kadoch C. Abstract PR11: SSX-mediated chromatin engagement and targeting of BAF complexes activates oncogenic transcription in synovial sarcoma. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.sarcomas17-pr11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Synovial sarcoma (SS) is a soft-tissue malignancy driven by a recurrent chromosomal translocation (t(X;18)) that uniformly produces the SS18-SSX oncogenic fusion protein. SS18 is a core subunit of the mammalian SWI/SNF (BAF) complexes, which remodel nucleosomes in an ATP-dependent manner and antagonistically oppose gene-silencing activity of polycomb-repressive complexes to maintain transcriptional control throughout development and differentiation. We previously discovered that in SS, incorporation of the oncogenic SS18-SSX fusion into BAF complexes leads to eviction of the tumor-suppressor BAF47 (INI1/SMARCB1) subunit, and aberrant activation of polycomb target genes by displacement of H3K27me3-mediated repression. However, uncoupling the oncogenic consequences of two co-occurrent BAF complex perturbations, gain of 78- amino acids of SSX to SS18 and loss of BAF47, has remained a challenge for the field. To identify effective targeted therapeutics for this patient population, it is critical that we understand the contribution of the gain- versus loss-of-function properties of these molecular events in this malignancy.
Here we demonstrate that the SSX 78aa tail engages mononucleosomes and targeted, quantitative mass spectrometry proteomics reveals preferential engagement to nucleosomes decorated with histone modifications associated with transcriptional repression. Using biochemical affinity assays, we find that SSX dramatically increases the affinity of SS18-SSX-containing BAF complexes for chromatin, thereby decreasing the dynamic mobility of BAF complexes. Furthermore, we show that SS18-SSX-containing BAF complexes possess a broader genomic footprint and exhibit distinct chromatin localization in that expression of SS18-SSX drives a near complete retargeting of BAF complexes genome-wide. SS18-SSX directs BAF complexes to polycomb-repressed sites to activate embryonic development and neuronal gene pathways hallmark to SS primary tumors. This targeting by SSX results in a transcriptional signature markedly distinct from sarcomas such as malignant rhabdoid tumors, which are driven solely by biallelic loss of BAF47. Moreover, using CRISPR/Cas9-mediated KO of BAF47 in SS cell lines, we show that the proliferative arrest of SS cell lines upon suppression of SS18-SSX is independent of BAF47 reassembly into BAF complexes, thereby demonstrating that SSX targeting of BAF complexes drives oncogenesis in a manner distinct from BAF47 loss. Taken together, these studies uncover a novel functionality of the SSX tail that is required for SS oncogenesis, and inform the selection of appropriate targeted therapeutic agents for this gain-of-function BAF complex-driven cancer.
This abstract is also being presented as Poster B25.
Citation Format: Matthew J. McBride, John L. Pulice, Robert T. Nakayama, Nazar Mashtalir, Davis R. Ingram, Jacob D. Jaffe, Jack F. Shern, Javed Khan, Jason L. Hornick, Alexander J. Lazar, Cigall Kadoch. SSX-mediated chromatin engagement and targeting of BAF complexes activates oncogenic transcription in synovial sarcoma [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr PR11.
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Affiliation(s)
| | - John L. Pulice
- 1Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA,
| | | | - Nazar Mashtalir
- 1Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA,
| | - Davis R. Ingram
- 2The University of Texas MD Anderson Cancer Center, Houston, TX,
| | | | | | - Javed Khan
- 4National Institutes of Health, Bethesda, MD,
| | | | | | - Cigall Kadoch
- 1Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA,
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Nakayama RT, Pulice JL, Valencia AM, McBride MJ, McKenzie ZM, Gillespie MA, Ku WL, Teng M, Cui K, Williams RT, Cassel SH, Qing H, Widmer CJ, Demetri GD, Irizarry RA, Zhao K, Ranish JA, Kadoch C. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nat Genet 2017; 49:1613-1623. [PMID: 28945250 PMCID: PMC5803080 DOI: 10.1038/ng.3958] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [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: 11/17/2016] [Accepted: 08/29/2017] [Indexed: 12/15/2022]
Abstract
Perturbations to mammalian SWI/SNF (BAF) complexes contribute to over 20% of human cancers, with driving roles first identified in malignant rhabdoid tumor (MRT), an aggressive pediatric cancer characterized by biallelic inactivation of the core BAF complex subunit SMARCB1 (BAF47). However, the mechanism by which this alteration contributes to tumorigenesis remains poorly understood. We find that BAF47 loss destabilizes BAF complexes on chromatin, absent significant changes in intra-complex integrity. Rescue of BAF47 in BAF47-deficient sarcoma cell lines results in increased genome-wide BAF complex occupancy, facilitating widespread enhancer activation and opposition of polycomb-mediated repression at bivalent promoters. We demonstrate differential regulation by BAF and PBAF complexes at enhancers and promoters, respectively, suggesting distinct functions of each complex which are perturbed upon BAF47 loss. Our results demonstrate collaborative mechanisms of mSWI/SNF-mediated gene activation, identifying functions that are coopted or abated to drive human cancers and developmental disorders.
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Affiliation(s)
- Robert T Nakayama
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.,Ludwig Center at Dana-Farber/Harvard and Center for Sarcoma and Bone Oncology, Department of Medical Oncology, Harvard Medical School, Boston, Massachusetts, USA
| | - John L Pulice
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alfredo M Valencia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.,Program in Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Matthew J McBride
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.,Program in Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Zachary M McKenzie
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Wai Lim Ku
- Systems Biology Center, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Mingxiang Teng
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kairong Cui
- Systems Biology Center, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert T Williams
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Seth H Cassel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.,Medical Scientist Training Program, Harvard Medical School, Boston, Massachusetts, USA
| | - He Qing
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Christian J Widmer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - George D Demetri
- Ludwig Center at Dana-Farber/Harvard and Center for Sarcoma and Bone Oncology, Department of Medical Oncology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rafael A Irizarry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Keji Zhao
- Systems Biology Center, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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McBride MJ, Pulice JL, Nakayama RT, Mashtalir N, Ingram DR, Shern JF, Khan J, Hornick JL, Lazar AJ, Kadoch C. Abstract 3875: SSX drives gain-of-function BAF complex chromatin affinity and genomic targeting in synovial sarcoma. Tumour Biol 2017. [DOI: 10.1158/1538-7445.am2017-3875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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9
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Kadoch C, Williams RT, Calarco JP, Miller EL, Weber CM, Braun SG, Pulice JL, Chory EJ, Crabtree GR. Dynamics of BAF-Polycomb complex opposition on heterochromatin in normal and oncogenic states. Nat Genet 2017; 49:213-222. [PMID: 27941796 PMCID: PMC5285326 DOI: 10.1038/ng.3734] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [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: 07/21/2016] [Accepted: 11/01/2016] [Indexed: 12/14/2022]
Abstract
The opposition between Polycomb repressive complexes (PRCs) and BAF (mSWI/SNF) complexes has a critical role in both development and disease. Mutations in the genes encoding BAF subunits contribute to more than 20% of human malignancies, yet the underlying mechanisms remain unclear, owing largely to a lack of assays to assess BAF function in living cells. To address this, we have developed a widely applicable recruitment assay system through which we find that BAF opposes PRC by rapid, ATP-dependent eviction, leading to the formation of accessible chromatin. The reversal of this process results in reassembly of facultative heterochromatin. Surprisingly, BAF-mediated PRC eviction occurs in the absence of RNA polymerase II (Pol II) occupancy, transcription, and replication. Further, we find that tumor-suppressor and oncogenic mutant BAF complexes have different effects on PRC eviction. The results of these studies define a mechanistic sequence underlying the resolution and formation of facultative heterochromatin, and they demonstrate that BAF opposes PRC on a minute-by-minute basis to provide epigenetic plasticity.
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Affiliation(s)
- Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert T. Williams
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Joseph P. Calarco
- Howard Hughes Medical Institute and Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erik L. Miller
- Howard Hughes Medical Institute and Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher M. Weber
- Howard Hughes Medical Institute and Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Simon G. Braun
- Howard Hughes Medical Institute and Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - John L. Pulice
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma J. Chory
- Howard Hughes Medical Institute and Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gerald R. Crabtree
- Howard Hughes Medical Institute and Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
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10
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Sandoval GJ, Pulice JL, Takeda DY, Schenone MA, Pop M, Boulay G, Rivera MN, Ronco L, Hahn WC, Kadoch C. Abstract 882: TMPRSS2-ERG drives global mistargeting of mammalian SWI/SNF (BAF) complexes in prostate cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Prostate cancer remains one of the leading causes of cancer-related death in men. Chromosomal rearrangements resulting in the fusion of the androgen regulated gene TMPRSS2 and the ETS-family transcription factor ERG occur in over 50% of all prostate cancer cases. Recent studies enabled by genome-wide methodologies have implicated altered epigenomic landscapes and changes in DNA accessibility as major contributors to ERG-driven oncogenesis, however the precise mechanism underlying the ERG transcriptional signature has to date remained unclear. Here we performed the first endogenous purification and SILAC-mass spectrometric analysis of ERG in TMPRSS2-ERG prostate cancer cells. Remarkably, we demonstrate that ERG directly interacts with the mammalian SWI/SNF (BAF) ATP-dependent chromatin remodeling complex, which was recently shown to be mutated in >20% of human malignancies. ERG co-localizes with BAF complexes genome-wide, resulting in specific ERG-dependent BAF complex targeting to sites enriched in known ERG, FOXA1, and HOXB13 motifs; additionally, loss of ERG in TMPRSS2-ERG driven cell lines results in dramatic retargeting of BAF complexes away from ERG-dependent sites, to sites enriched in known AR and CTCF motifs. Importantly, ERG-driven BAF complex retargeting contributes to activation of TMPRSS2-ERG prostate cancer gene expression signatures. We map the ERG-BAF interaction to a specific region within the ERG amino acid sequence and find that this region is required to bind BAF complexes. These studies reveal a novel, unexpected mechanism of action of ERG-driven oncogenesis and offers new strategies for therapeutic intervention.
Citation Format: Gabriel J. Sandoval, John L. Pulice, David Y. Takeda, Monica A. Schenone, Marius Pop, Gaylor Boulay, Miguel N. Rivera, Lucienne Ronco, William C. Hahn, Cigall Kadoch. TMPRSS2-ERG drives global mistargeting of mammalian SWI/SNF (BAF) complexes in prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 882.
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Affiliation(s)
| | | | | | | | - Marius Pop
- 2The Broad Institute of Harvard and MIT, Boston, MA
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Abstract
Mammalian SWI/SNF (BAF) chromatin remodeling complexes play critical roles in maintaining chromatin architecture and gene expression. Genomic sequencing efforts over the past several years have unveiled a major role for these complexes in the development of human cancer as well as neurologic disease, prompting the need to interrogate underlying mechanisms and to develop new methods to comprehensively understand mSWI/SNF complex function. Here we discuss the emerging insights from genetic, biochemical, and functional genomic studies in the field and suggest approaches toward further basic investigations, as well as therapeutic targeting of chromatin remodeling machinery.
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Affiliation(s)
- John L Pulice
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02215
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02215
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
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