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Bracken AP, Pasini D, Capra M, Prosperini E, Colli E, Helin K. Author Correction: EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J 2024; 43:886. [PMID: 38347304 PMCID: PMC10907575 DOI: 10.1038/s44318-024-00033-4] [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: 03/03/2024] Open
Affiliation(s)
- Adrian P Bracken
- European Institute of Oncology, Department of Experimental Oncology, Via Ripamonti 435, 20141, Milan, Italy
| | - Diego Pasini
- European Institute of Oncology, Department of Experimental Oncology, Via Ripamonti 435, 20141, Milan, Italy
| | - Maria Capra
- European Institute of Oncology, Department of Experimental Oncology, Via Ripamonti 435, 20141, Milan, Italy
- FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Elena Prosperini
- European Institute of Oncology, Department of Experimental Oncology, Via Ripamonti 435, 20141, Milan, Italy
| | - Elena Colli
- European Institute of Oncology, Department of Experimental Oncology, Via Ripamonti 435, 20141, Milan, Italy
| | - Kristian Helin
- European Institute of Oncology, Department of Experimental Oncology, Via Ripamonti 435, 20141, Milan, Italy.
- FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy.
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2
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Bracken AP, Kleine-Kohlbrecher D, Dietrich N, Pasini D, Gargiulo G, Beekman C, Theilgaard-Mönch K, Minucci S, Porse BT, Marine JC, Hansen KH, Helin K. Corrigendum: The Polycomb group proteins bind throughout the INK4A-ARF locus and are disassociated in senescent cells. Genes Dev 2023; 37:861. [PMID: 37852794 PMCID: PMC10620040 DOI: 10.1101/gad.351178.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
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3
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Glancy E, Wang C, Tuck E, Healy E, Amato S, Neikes HK, Mariani A, Mucha M, Vermeulen M, Pasini D, Bracken AP. PRC2.1- and PRC2.2-specific accessory proteins drive recruitment of different forms of canonical PRC1. Mol Cell 2023; 83:1393-1411.e7. [PMID: 37030288 PMCID: PMC10168607 DOI: 10.1016/j.molcel.2023.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 07/10/2022] [Revised: 01/19/2023] [Accepted: 03/16/2023] [Indexed: 04/10/2023]
Abstract
Polycomb repressive complex 2 (PRC2) mediates H3K27me3 deposition, which is thought to recruit canonical PRC1 (cPRC1) via chromodomain-containing CBX proteins to promote stable repression of developmental genes. PRC2 forms two major subcomplexes, PRC2.1 and PRC2.2, but their specific roles remain unclear. Through genetic knockout (KO) and replacement of PRC2 subcomplex-specific subunits in naïve and primed pluripotent cells, we uncover distinct roles for PRC2.1 and PRC2.2 in mediating the recruitment of different forms of cPRC1. PRC2.1 catalyzes the majority of H3K27me3 at Polycomb target genes and is sufficient to promote recruitment of CBX2/4-cPRC1 but not CBX7-cPRC1. Conversely, while PRC2.2 is poor at catalyzing H3K27me3, we find that its accessory protein JARID2 is essential for recruitment of CBX7-cPRC1 and the consequent 3D chromatin interactions at Polycomb target genes. We therefore define distinct contributions of PRC2.1- and PRC2.2-specific accessory proteins to Polycomb-mediated repression and uncover a new mechanism for cPRC1 recruitment.
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Affiliation(s)
- Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Cheng Wang
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Ellen Tuck
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Simona Amato
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Hannah K Neikes
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Andrea Mariani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Marlena Mucha
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands; The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Diego Pasini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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4
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Gu L, Casserly D, Brady G, Carpenter S, Bracken AP, Fitzgerald KA, Unterholzner L, Bowie AG. Myeloid cell nuclear differentiation antigen controls the pathogen-stimulated type I interferon cascade in human monocytes by transcriptional regulation of IRF7. Nat Commun 2022; 13:14. [PMID: 35013241 PMCID: PMC8748983 DOI: 10.1038/s41467-021-27701-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/04/2020] [Accepted: 12/02/2021] [Indexed: 12/19/2022] Open
Abstract
Type I interferons (IFNs) are critical for anti-viral responses, and also drive autoimmunity when dysregulated. Upon viral sensing, monocytes elicit a sequential cascade of IFNβ and IFNα production involving feedback amplification, but how exactly this cascade is regulated in human cells is incompletely understood. Here we show that the PYHIN protein myeloid cell nuclear differentiation antigen (MNDA) is required for IFNα induction in monocytes. Unlike other PYHINs, this is not due to a pathogen sensing role, but rather MNDA regulated expression of IRF7, a transcription factor essential for IFNα induction. Mechanistically, MNDA is required for recruitment of STAT2 and RNA polymerase II to the IRF7 gene promoter, and in fact MNDA is itself recruited to the IRF7 promoter after type I IFN stimulation. These data implicate MNDA as a critical regulator of the type I IFN cascade in human myeloid cells and reveal a new role for human PYHINs in innate immune gene induction. The interferon response is a critical component of the innate immune response. Here the authors implicate MNDA in the regulation of type I interferon responses to pathogen infection.
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Affiliation(s)
- Lili Gu
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - David Casserly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Gareth Brady
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Susan Carpenter
- Division of Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Katherine A Fitzgerald
- Division of Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Leonie Unterholzner
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.,Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Andrew G Bowie
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.
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5
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Lundahl MLE, Mitermite M, Ryan DG, Case S, Williams NC, Yang M, Lynch RI, Lagan E, Lebre FM, Gorman AL, Stojkovic B, Bracken AP, Frezza C, Sheedy FJ, Scanlan EM, O'Neill LAJ, Gordon SV, Lavelle EC. Macrophage innate training induced by IL-4 and IL-13 activation enhances OXPHOS driven anti-mycobacterial responses. eLife 2022; 11:74690. [PMID: 36173104 PMCID: PMC9555863 DOI: 10.7554/elife.74690] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 09/28/2022] [Indexed: 01/05/2023] Open
Abstract
Macrophages are a highly adaptive population of innate immune cells. Polarization with IFNγ and LPS into the 'classically activated' M1 macrophage enhances pro-inflammatory and microbicidal responses, important for eradicating bacteria such as Mycobacterium tuberculosis. By contrast, 'alternatively activated' M2 macrophages, polarized with IL-4, oppose bactericidal mechanisms and allow mycobacterial growth. These activation states are accompanied by distinct metabolic profiles, where M1 macrophages favor near exclusive use of glycolysis, whereas M2 macrophages up-regulate oxidative phosphorylation (OXPHOS). Here, we demonstrate that activation with IL-4 and IL-13 counterintuitively induces protective innate memory against mycobacterial challenge. In human and murine models, prior activation with IL-4/13 enhances pro-inflammatory cytokine secretion in response to a secondary stimulation with mycobacterial ligands. In our murine model, enhanced killing capacity is also demonstrated. Despite this switch in phenotype, IL-4/13 trained murine macrophages do not demonstrate M1-typical metabolism, instead retaining heightened use of OXPHOS. Moreover, inhibition of OXPHOS with oligomycin, 2-deoxy glucose or BPTES all impeded heightened pro-inflammatory cytokine responses from IL-4/13 trained macrophages. Lastly, this work identifies that IL-10 attenuates protective IL-4/13 training, impeding pro-inflammatory and bactericidal mechanisms. In summary, this work provides new and unexpected insight into alternative macrophage activation states in the context of mycobacterial infection.
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Affiliation(s)
- Mimmi LE Lundahl
- School of Biochemistry and Immunology, Adjuvant Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland,School of Chemistry, Scanlan Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Morgane Mitermite
- School of Veterinary Medicine, UCD Veterinary Sciences Centre, University College DublinDublinIreland
| | - Dylan Gerard Ryan
- School of Biochemistry and Immunology, Inflammation Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland,Hutchison/MRC Research centre, MRC Cancer Unit, University of CambridgeCambridgeUnited Kingdom
| | - Sarah Case
- School of Biochemistry and Immunology, Macrophage Homeostasis Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Niamh C Williams
- School of Biochemistry and Immunology, Inflammation Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Ming Yang
- Hutchison/MRC Research centre, MRC Cancer Unit, University of CambridgeCambridgeUnited Kingdom
| | - Roisin I Lynch
- School of Biochemistry and Immunology, Adjuvant Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Eimear Lagan
- School of Genetics and Microbiology, Department of Genetics, Trinity College DublinDublinIreland
| | - Filipa M Lebre
- School of Biochemistry and Immunology, Adjuvant Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Aoife L Gorman
- School of Biochemistry and Immunology, Adjuvant Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Bojan Stojkovic
- School of Veterinary Medicine, UCD Veterinary Sciences Centre, University College DublinDublinIreland
| | - Adrian P Bracken
- School of Genetics and Microbiology, Department of Genetics, Trinity College DublinDublinIreland
| | - Christian Frezza
- Hutchison/MRC Research centre, MRC Cancer Unit, University of CambridgeCambridgeUnited Kingdom
| | - Frederick J Sheedy
- School of Biochemistry and Immunology, Macrophage Homeostasis Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Eoin M Scanlan
- School of Chemistry, Scanlan Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Luke AJ O'Neill
- School of Biochemistry and Immunology, Inflammation Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Stephen V Gordon
- School of Veterinary Medicine, UCD Veterinary Sciences Centre, University College DublinDublinIreland
| | - Ed C Lavelle
- School of Biochemistry and Immunology, Adjuvant Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
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6
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Brien GL, Bressan RB, Monger C, Gannon D, Lagan E, Doherty AM, Healy E, Neikes H, Fitzpatrick DJ, Deevy O, Grant V, Marqués-Torrejón MA, Alfazema N, Pollard SM, Bracken AP. Simultaneous disruption of PRC2 and enhancer function underlies histone H3.3-K27M oncogenic activity in human hindbrain neural stem cells. Nat Genet 2021; 53:1221-1232. [PMID: 34294917 DOI: 10.1038/s41588-021-00897-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 05/21/2020] [Accepted: 06/11/2021] [Indexed: 01/10/2023]
Abstract
Driver mutations in genes encoding histone H3 proteins resulting in p.Lys27Met substitutions (H3-K27M) are frequent in pediatric midline brain tumors. However, the precise mechanisms by which H3-K27M causes tumor initiation remain unclear. Here, we use human hindbrain neural stem cells to model the consequences of H3.3-K27M on the epigenomic landscape in a relevant developmental context. Genome-wide mapping of epitope-tagged histone H3.3 revealed that both the wild type and the K27M mutant incorporate abundantly at pre-existing active enhancers and promoters, and to a lesser extent at Polycomb repressive complex 2 (PRC2)-bound regions. At active enhancers, H3.3-K27M leads to focal H3K27ac loss, decreased chromatin accessibility and reduced transcriptional expression of nearby neurodevelopmental genes. In addition, H3.3-K27M deposition at a subset of PRC2 target genes leads to increased PRC2 and PRC1 binding and augmented transcriptional repression that can be partially reversed by PRC2 inhibitors. Our work suggests that, rather than imposing de novo transcriptional circuits, H3.3-K27M drives tumorigenesis by locking initiating cells in their pre-existing, immature epigenomic state, via disruption of PRC2 and enhancer functions.
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Affiliation(s)
- Gerard L Brien
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
| | - Raul Bardini Bressan
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Craig Monger
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Dáire Gannon
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Eimear Lagan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Anthony M Doherty
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Hannah Neikes
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Orla Deevy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Vivien Grant
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Maria-Angeles Marqués-Torrejón
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Neza Alfazema
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Steven M Pollard
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK.
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK.
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
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7
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Seoighe C, Bracken AP, Buckley P, Doran P, Green R, Healy S, Kavanagh D, Kenny E, Lawler M, Lowery M, Morris D, Morrissey D, O'Byrne JJ, Shields D, Smith O, Steward CA, Sweeney B, Kolch W. The future of genomics in Ireland - focus on genomics for health. HRB Open Res 2020; 3:89. [PMID: 33855271 PMCID: PMC7993626 DOI: 10.12688/hrbopenres.13187.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
Genomics is revolutionizing biomedical research, medicine and healthcare globally in academic, public and industry sectors alike. Concrete examples around the world show that huge benefits for patients, society and economy can be accrued through effective and responsible genomic research and clinical applications. Unfortunately, Ireland has fallen behind and needs to act now in order to catch up. Here, we identify key issues that have resulted in Ireland lagging behind, describe how genomics can benefit Ireland and its people and outline the measures needed to make genomics work for Ireland and Irish patients. There is now an urgent need for a national genomics strategy that enables an effective, collaborative, responsible, well-regulated, and patient centred environment where genome research and clinical genomics can thrive. We present eight recommendations that could be the pillars of a national genomics health strategy.
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Affiliation(s)
- Cathal Seoighe
- National University of Ireland Galway, Galway, H91 TK33, Ireland
| | | | | | - Peter Doran
- University College Dublin, Dublin, 4, Ireland
- Mater Misericordiae University Hospital, Dublin, 7, Ireland
| | - Robert Green
- Brigham Health, Broad Institute, Ariadne Labs, Harvard Medical School, Boston, MA, 02115, USA
| | - Sandra Healy
- National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - David Kavanagh
- Genuity Science (Ireland) Ltd., Dublin, D18 K7W4, Ireland
| | - Elaine Kenny
- Trinity College Dublin, Dublin, 2, Ireland
- ELDA Biotech, Trinity Translational Medicine Institute, St James's Hospital, Dublin, D08 W9RT, Ireland
| | - Mark Lawler
- Queen's University Belfast, Belfast, Northern Ireland, BT7 1NN, Ireland
| | - Maeve Lowery
- Trinity College Dublin, Dublin, 2, Ireland
- Saint James' Hospital, Dublin, D08 NHY1, Ireland
| | - Derek Morris
- National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - Darrin Morrissey
- National Institute for Bioprocessing Research and Training, Blackrock, A94 X099, Ireland
| | | | | | - Owen Smith
- University College Dublin, Dublin, 4, Ireland
- Children’s Health Ireland, Crumlin, Dublin, D12 N512, Ireland
| | | | | | - Walter Kolch
- National University of Ireland Galway, Galway, H91 TK33, Ireland
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8
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Abstract
To delineate the roles of variant (vPRC1) and canonical (cPRC1) Polycomb repressive complex 1, Blackledge et al. (2020) and Tamburri et al. (2020) elegantly disrupt RING1A/B catalytic activity without affecting stability of either complex and then explore the precise contribution of vPRC1-mediated H2AK119ub1 to Polycomb-mediated gene repression.
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Affiliation(s)
- Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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9
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Volpari T, De Santis F, Bracken AP, Pupa SM, Buschbeck M, Wegner A, Di Cosimo S, Lisanti MP, Dotti G, Massaia M, Pruneri G, Anichini A, Fortunato O, De Braud F, Del Vecchio M, Di Nicola M. Anticancer innovative therapy: Highlights from the ninth annual meeting. Cytokine Growth Factor Rev 2019; 51:1-9. [PMID: 31862236 DOI: 10.1016/j.cytogfr.2019.12.002] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Ninth Annual Conference of "Anticancer Innovative Therapy", organized by Fondazione IRCCS Istituto Nazionale dei Tumori di Milano (Fondazione IRCCS INT) and hosted by Hotel Michelangelo, was held in Milan on 25 January 2019. Cutting-edge science was presented in two main scientific sessions: i) pre-clinical evidences and new targets, and ii) clinical translation. The Keynote lecture entitled "Cancer stem cells (CSCs): metabolic strategies for their identification and eradication" presented by M. Lisanti, was one of the highlights of the conference. One key concept of the meeting was how the continuous advances in our knowledge about molecular mechanisms in various fields of research (cancer metabolism reprogramming, epigenetic regulation, transformation/invasiveness, and immunology, among others) are driving cancer research towards more effective personalized antineoplastic strategies. Specifically, recent preclinical data on the following topics were discussed: 1. Polycomb group proteins in cancer; 2. A d16HER2 splice variant is a flag of HER2 addiction across HER2-positive cancers; 3. Studying chromatin as a nexus between translational and basic research; 4. Metabolomic analysis in cancer patients; 5. CDK4-6 cyclin inhibitors: clinical activity and future perspectives as immunotherapy adjuvant; and 6. Cancer stem cells (CSCs): metabolic strategies for their identification and eradication. In terms of clinical translation, several novel approaches were presented: 1. Developing CAR-T cell therapies: an update of preclinical and clinical development at University of North Carolina; 2. Vγ9Vδ2 T-cell activation and immune suppression in multiple myeloma; 3. Predictive biomarkers for real-world immunotherapy: the cancer immunogram model in the clinical arena; and 4. Mechanisms of resistance to immune checkpoint blockade in solid tumors. Overall, the pre-clinical and clinical findings presented could pave the way to identify novel actionable therapeutic targets to significantly enhance the care of persons with cancer.
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Affiliation(s)
- T Volpari
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - F De Santis
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - A P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - S M Pupa
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Buschbeck
- Josep Carreras Leukemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - A Wegner
- Technische Universiät Braunschweig, Department of Bioinfomatics and Biochemistry and Braunschweig Integrated Center of Systems Biology (BRICS), Rebenring 56, 38106, Braunschweig, Germany
| | - S Di Cosimo
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M P Lisanti
- Translational Medicine, Biomedical Research Centre, School of Environment and Life Sciences, University of Salford, Greater Manchester, United Kingdom
| | - G Dotti
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - M Massaia
- Laboratorio di Immunologia dei Tumori del Sangue, Centro Interdipartimentale di Ricerca in Biologia Molecolare, Università degli Studi di Torino, Turin, Italy; SC Ematologia, AO S. Croce e Carle, Cuneo, Italy
| | - G Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS - Istituto Nazionale dei Tumori, Milan, Italy
| | - A Anichini
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - O Fortunato
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - F De Braud
- Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Del Vecchio
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Unit of Melanoma Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Di Nicola
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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10
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Abstract
Polycomb repressive complex 2 (PRC2) is a conserved chromatin regulator that is responsible for the methylation of histone H3 lysine 27 (H3K27). PRC2 is essential for normal development and its loss of function thus results in a range of developmental phenotypes. Here, we review the latest advances in our understanding of mammalian PRC2 activity and present an updated summary of the phenotypes associated with its loss of function in mice. We then discuss recent studies that have highlighted regulatory interplay between the modifications laid down by PRC2 and other chromatin modifiers, including NSD1 and DNMT3A. Finally, we propose a model in which the dysregulation of these modifications at intergenic regions is a shared molecular feature of genetically distinct but highly phenotypically similar overgrowth syndromes in humans.
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Affiliation(s)
- Orla Deevy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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11
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Healy E, Mucha M, Glancy E, Fitzpatrick DJ, Conway E, Neikes HK, Monger C, Van Mierlo G, Baltissen MP, Koseki Y, Vermeulen M, Koseki H, Bracken AP. PRC2.1 and PRC2.2 Synergize to Coordinate H3K27 Trimethylation. Mol Cell 2019; 76:437-452.e6. [PMID: 31521505 DOI: 10.1016/j.molcel.2019.08.012] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [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: 03/07/2019] [Revised: 06/28/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is composed of EED, SUZ12, and EZH1/2 and mediates mono-, di-, and trimethylation of histone H3 at lysine 27. At least two independent subcomplexes exist, defined by their specific accessory proteins: PRC2.1 (PCL1-3, EPOP, and PALI1/2) and PRC2.2 (AEBP2 and JARID2). We show that PRC2.1 and PRC2.2 share the majority of target genes in mouse embryonic stem cells. The loss of PCL1-3 is sufficient to evict PRC2.1 from Polycomb target genes but only leads to a partial reduction of PRC2.2 and H3K27me3. Conversely, disruption of PRC2.2 function through the loss of either JARID2 or RING1A/B is insufficient to completely disrupt targeting of SUZ12 by PCLs. Instead, the combined loss of both PRC2.1 and PRC2.2 is required, leading to the global mislocalization of SUZ12. This supports a model in which the specific accessory proteins within PRC2.1 and PRC2.2 cooperate to direct H3K27me3 via both synergistic and independent mechanisms.
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Affiliation(s)
- Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Marlena Mucha
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Hannah K Neikes
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Craig Monger
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Guido Van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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12
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Abstract
In this review, Bracken et al. discuss the functional organization and biochemical activities of remodelers and Polycomb and explore how they work together to control cell differentiation and the maintenance of cell identity. They also discuss how mutations in the genes encoding these various chromatin regulators contribute to oncogenesis by disrupting the chromatin equilibrium. Changes in chromatin structure mediated by ATP-dependent nucleosome remodelers and histone modifying enzymes are integral to the process of gene regulation. Here, we review the roles of the SWI/SNF (switch/sucrose nonfermenting) and NuRD (nucleosome remodeling and deacetylase) and the Polycomb system in chromatin regulation and cancer. First, we discuss the basic molecular mechanism of nucleosome remodeling, and how this controls gene transcription. Next, we provide an overview of the functional organization and biochemical activities of SWI/SNF, NuRD, and Polycomb complexes. We describe how, in metazoans, the balance of these activities is central to the proper regulation of gene expression and cellular identity during development. Whereas SWI/SNF counteracts Polycomb, NuRD facilitates Polycomb repression on chromatin. Finally, we discuss how disruptions of this regulatory equilibrium contribute to oncogenesis, and how new insights into the biological functions of remodelers and Polycombs are opening avenues for therapeutic interventions on a broad range of cancer types.
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Affiliation(s)
- Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Gerard L Brien
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - C Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, 3000 DR Rotterdam, the Netherlands
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13
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O'Connor D, Kelly CM, Crown J, Russell N, Barron S, Loughman T, Lynch S, O'Grady A, Sheehan KM, Fay J, Saha A, Dynoodt P, Fender B, Wang CJA, O'Leary D, Bracken AP, Rahman A, Gonzalez CA, Attar NA, Gallagher WM. Additional prognostic value of OncoMasTR multigene prognostic signature to clinicopathological information in patients with HR-positive, HER2-negative, lymph node-negative breast cancer from the TAILORx Tissue Bank, Ireland. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
535 Background: Multigene prognostic signatures (MGPS) can identify early stage breast cancer patients who may require less aggressive treatment. To be clinically useful, MGPSs must provide additional prognostic information to clinicopathological information routinely used by clinicians. The OncoMasTR MGPS was discovered via a novel bioinformatic transcriptional network analysis. OncoMasTR consists of genes – Master Transcription Regulators (MTRs) – that regulate previously known prognostic genes and have identified functional roles in several hallmarks of cancer including proliferation, invasion and metastasis. The OncoMasTR Molecular Score (OM) consists of just 3 MTRs. The OncoMasTR Risk Score (OncoMasTR) combines OM with lymph node status and tumour size, and categorises patients as low or high risk. The OncoMasTR Test has been analytically and clinically validated. Methods: MTR expression was measured by RT-qPCR in tissue from 404 patients enrolled in an independent translational trial (NCT02050750) that collected tissue and clinical data from patients enrolled in TAILORx in Ireland. OM, OncoMasTR and Oncotype DX Recurrence Score (RS) were compared on the additional prognostic value they provided to Ki67, Nottingham Prognostic Index (NPI) and other clinicopathological information for distant recurrence (DR) and invasive disease (ID). Results: OM (LRχ2 = 20.3, p < 0.00001, c-index = 0.84) and OncoMasTR (LRχ2 = 22.6, p < 0.00001, c-index = 0.85) were significantly prognostic, and more prognostic than RS (LRχ2 = 8.4, p = 0.004, c-index = 0.73) for DR. OM and OncoMasTR provided more additional prognostic information than RS to Ki67, NPI, tumour size, tumour grade, and age for DR. Similar results were found when OM, OncoMasTR and RS were compared on prognostic performance for ID. Conclusions: OM and OncoMasTR were significantly prognostic for DR and ID and added significant prognostic value to Ki67, NPI, and other clinicopathological information. Furthermore, OM and OncoMasTR showed superior prognostic performance to RS.
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Affiliation(s)
- Darran O'Connor
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - John Crown
- NSABP/NRG Oncology, and The Irish Cooperative Oncology Research Group, Dublin, Ireland
| | - Niamh Russell
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, Dublin, Ireland
| | | | | | - Seodhna Lynch
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, Dublin, Ireland
| | - Anthony O'Grady
- Department of Histopathology, Beaumont Hospital, Dublin, Ireland
| | | | - Joanna Fay
- RCSI Education and Research Centre, Dublin, Ireland
| | | | | | | | | | | | | | | | - Claudia Aura Gonzalez
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, Dublin, Ireland
| | - Nebras Al Attar
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, Dublin, Ireland
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14
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Abstract
EZH2 is an oncogene in non-Hodgkin lymphoma. Understanding the underlying pathogenic mechanisms will be essential to improve treatments for patients with EZH2 mutant lymphomas. Recently Donaldson-Collier and colleagues (Nat. Genet. 2019; published online January 28, https://doi.org/10.1038/s41588-018-0338-y) examined the effects of mutant EZH2 on the 3D architecture of the lymphoma genome, highlighting the potential relevance of chromatin folding dynamics.
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Affiliation(s)
- Gerard L Brien
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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15
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Conway E, Jerman E, Healy E, Ito S, Holoch D, Oliviero G, Deevy O, Glancy E, Fitzpatrick DJ, Mucha M, Watson A, Rice AM, Chammas P, Huang C, Pratt-Kelly I, Koseki Y, Nakayama M, Ishikura T, Streubel G, Wynne K, Hokamp K, McLysaght A, Ciferri C, Di Croce L, Cagney G, Margueron R, Koseki H, Bracken AP. A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities. Mol Cell 2018; 70:408-421.e8. [PMID: 29628311 DOI: 10.1016/j.molcel.2018.03.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [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: 07/06/2017] [Revised: 01/11/2018] [Accepted: 03/02/2018] [Indexed: 12/18/2022]
Abstract
The polycomb repressive complex 2 (PRC2) consists of core subunits SUZ12, EED, RBBP4/7, and EZH1/2 and is responsible for mono-, di-, and tri-methylation of lysine 27 on histone H3. Whereas two distinct forms exist, PRC2.1 (containing one polycomb-like protein) and PRC2.2 (containing AEBP2 and JARID2), little is known about their differential functions. Here, we report the discovery of a family of vertebrate-specific PRC2.1 proteins, "PRC2 associated LCOR isoform 1" (PALI1) and PALI2, encoded by the LCOR and LCORL gene loci, respectively. PALI1 promotes PRC2 methyltransferase activity in vitro and in vivo and is essential for mouse development. Pali1 and Aebp2 define mutually exclusive, antagonistic PRC2 subtypes that exhibit divergent H3K27-tri-methylation activities. The balance of these PRC2.1/PRC2.2 activities is required for the appropriate regulation of polycomb target genes during differentiation. PALI1/2 potentially link polycombs with transcriptional co-repressors in the regulation of cellular identity during development and in cancer.
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Affiliation(s)
- Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Emilia Jerman
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Daniel Holoch
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS UMR 3215, INSERM U934, 75248 Paris Cedex 05, France
| | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Orla Deevy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Marlena Mucha
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Alan M Rice
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Paul Chammas
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Christine Huang
- Department of Structural Biology, Genentech, San Francisco, CA 94080, USA
| | - Indigo Pratt-Kelly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Manabu Nakayama
- Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan
| | - Tomoyuki Ishikura
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Kieran Wynne
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Claudio Ciferri
- Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan
| | - Luciano Di Croce
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Raphaël Margueron
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS UMR 3215, INSERM U934, 75248 Paris Cedex 05, France
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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16
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Streubel G, Watson A, Jammula SG, Scelfo A, Fitzpatrick DJ, Oliviero G, McCole R, Conway E, Glancy E, Negri GL, Dillon E, Wynne K, Pasini D, Krogan NJ, Bracken AP, Cagney G. The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells. Mol Cell 2018; 70:371-379.e5. [PMID: 29606589 DOI: 10.1016/j.molcel.2018.02.027] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [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] [Received: 06/05/2017] [Revised: 12/22/2017] [Accepted: 02/23/2018] [Indexed: 12/12/2022]
Abstract
The Polycomb repressor complex 2 (PRC2) is composed of the core subunits Ezh1/2, Suz12, and Eed, and it mediates all di- and tri-methylation of histone H3 at lysine 27 in higher eukaryotes. However, little is known about how the catalytic activity of PRC2 is regulated to demarcate H3K27me2 and H3K27me3 domains across the genome. To address this, we mapped the endogenous interactomes of Ezh2 and Suz12 in embryonic stem cells (ESCs), and we combined this with a functional screen for H3K27 methylation marks. We found that Nsd1-mediated H3K36me2 co-locates with H3K27me2, and its loss leads to genome-wide expansion of H3K27me3. These increases in H3K27me3 occurred at PRC2/PRC1 target genes and as de novo accumulation within what were previously broad H3K27me2 domains. Our data support a model in which Nsd1 is a key modulator of PRC2 function required for regulating the demarcation of genome-wide H3K27me2 and H3K27me3 domains in ESCs.
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Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland; School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sri Ganesh Jammula
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Rachel McCole
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Gian Luca Negri
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Eugene Dillon
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Health Sciences, University of Milan, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94148, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland.
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17
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Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP. Fam60a defines a variant Sin3a‐Hdac complex in embryonic stem cells required for self‐renewal. EMBO J 2017. [DOI: https://doi.org/10.15252/embj.201696307] [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: 11/06/2022] Open
Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Andrea Scelfo
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Bruce Moran
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin 2 Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Gian Luca Negri
- Department of Molecular Oncology British Columbia Cancer Research Center Vancouver BC Canada
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - SriGanesh Jammula
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Karsten Hokamp
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin 2 Ireland
| | - Diego Pasini
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
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18
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Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP. Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal. EMBO J 2017; 36:2216-2232. [PMID: 28554894 DOI: 10.15252/embj.201696307] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 12/16/2016] [Revised: 04/18/2017] [Accepted: 04/22/2017] [Indexed: 12/15/2022] Open
Abstract
Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex, crucially required during early embryonic development for the growth of pluripotent cells of the inner cell mass. Here, we compare the composition of the Sin3a-Hdac complex between pluripotent embryonic stem (ES) and differentiated cells by establishing a method that couples two independent endogenous immunoprecipitations with quantitative mass spectrometry. We define the precise composition of the Sin3a complex in multiple cell types and identify the Fam60a subunit as a key defining feature of a variant Sin3a complex present in ES cells, which also contains Ogt and Tet1. Fam60a binds on H3K4me3-positive promoters in ES cells, together with Ogt, Tet1 and Sin3a, and is essential to maintain the complex on chromatin. Finally, we show that depletion of Fam60a phenocopies the loss of Sin3a, leading to reduced proliferation, an extended G1-phase and the deregulation of lineage genes. Taken together, Fam60a is an essential core subunit of a variant Sin3a complex in ES cells that is required to promote rapid proliferation and prevent unscheduled differentiation.
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Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Bruce Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC, Canada
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - SriGanesh Jammula
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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19
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Moran B, Lanigan F, Russell N, Barron S, Wang CJ, Jirstrom K, Bracken AP, Gallagher WM. Evaluation of the prognostic value of the OncoMasTR RNA panel in diverse tumor types. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e23201] [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: 11/20/2022] Open
Abstract
e23201 Background: Master transcriptional regulators (MTRs) are genes that are highly connected with many other genes and which can contribute to a specific cellular phenotype. The OncoMasTR panel, a set of 10 proliferation-linked MTRs and the key regulator of senescence CDKN2A, was identified in lymph node-negative breast cancer patients using publicly available data (Lanigan et al FEBS 2015 10.1111/febs.13354). Using two prognostic gene signatures and an experimentally defined ‘proliferative’ signature, highly concordant results for the top ranking sets of MTRs were found. One advantage of this process was the distillation of gene signatures into a discrete, mechanistically anchored biomarker set shown to be prognostically relevant, particularly in ER-positive patients, and with an ability to discriminate patients into low versus high risk of recurrence. Our aim here was to determine if the OncoMasTR panel was similarly useful in multiple other cancer types using publicly available transcriptomic data. Methods: The Gene Expression Omnibus was queried for datasets with relevant overall-, disease free- and/or recurrence free-survival information alongside microarray gene expression data. Survival analysis was conducted on 34 datasets using the R statistical environment package ‘survival’. Patient samples were scored based on median or tertile expression which were summed to give a final OncoMasTR RNA score, used to divide the patient samples into two groups (low and high risk) for analysis. Results: Using all 2,047 possible combinations of genes, a total of 23 datasets had significant prognostic associations. Following appropriate correction via multiple testing, this was reduced to 4 datasets representing bladder, lung and colorectal cancers, and multiple myeloma. Hazard ratios for the top 100 combinations in each data set were 1.8 – 2.1, 1.6 – 1.9, 1.1 – 1.3, 1.3 – 1.5 (standard error ±0.2, 0.1, 0.2, 0.1) respectively. All genes were found in the top ten combinations in all 4 datasets, and no specific combination was found to be prevalent across datasets, indicating that every MTR in the OncoMasTR panel contributes to its utility. Conclusions: The OncoMasTR panel is potentially prognostically useful in multiple cancer types.
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Affiliation(s)
| | | | | | | | | | - Karin Jirstrom
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | | | - William M. Gallagher
- University College Dublin School of Biomolecular and Biomedical Science, Dublin, Ireland
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20
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Erceg J, Pakozdi T, Marco-Ferreres R, Ghavi-Helm Y, Girardot C, Bracken AP, Furlong EEM. Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements. Genes Dev 2017; 31:590-602. [PMID: 28381411 PMCID: PMC5393054 DOI: 10.1101/gad.292870.116] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [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: 10/28/2016] [Accepted: 03/03/2017] [Indexed: 11/24/2022]
Abstract
Here, Erceg et al. studied the occupancy of the Drosophila PhoRC during embryogenesis and revealed extensive co-occupancy at developmental enhancers. By using an established in vivo assay for Polycomb response element (PRE) activity, they show that a subset of characterized developmental enhancers can function as PREs and silence transcription in a Polycomb-dependent manner, thereby suggesting that reuse of the same elements by the PcG system may help fine-tune gene expression and ensure the timely maintenance of cell identities. Developmental gene expression is tightly regulated through enhancer elements, which initiate dynamic spatio–temporal expression, and Polycomb response elements (PREs), which maintain stable gene silencing. These two cis-regulatory functions are thought to operate through distinct dedicated elements. By examining the occupancy of the Drosophila pleiohomeotic repressive complex (PhoRC) during embryogenesis, we revealed extensive co-occupancy at developmental enhancers. Using an established in vivo assay for PRE activity, we demonstrated that a subset of characterized developmental enhancers can function as PREs, silencing transcription in a Polycomb-dependent manner. Conversely, some classic Drosophila PREs can function as developmental enhancers in vivo, activating spatio–temporal expression. This study therefore uncovers elements with dual function: activating transcription in some cells (enhancers) while stably maintaining transcriptional silencing in others (PREs). Given that enhancers initiate spatio–temporal gene expression, reuse of the same elements by the Polycomb group (PcG) system may help fine-tune gene expression and ensure the timely maintenance of cell identities.
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Affiliation(s)
- Jelena Erceg
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
| | - Tibor Pakozdi
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
| | - Raquel Marco-Ferreres
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
| | - Yad Ghavi-Helm
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
| | - Charles Girardot
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eileen E M Furlong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
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21
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Oliviero G, Brien GL, Waston A, Streubel G, Jerman E, Andrews D, Doyle B, Munawar N, Wynne K, Crean J, Bracken AP, Cagney G. Dynamic Protein Interactions of the Polycomb Repressive Complex 2 during Differentiation of Pluripotent Cells. Mol Cell Proteomics 2016. [DOI: https://doi.org/10.1074/mcp.m116.062240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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22
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Oliviero G, Brien GL, Waston A, Streubel G, Jerman E, Andrews D, Doyle B, Munawar N, Wynne K, Crean J, Bracken AP, Cagney G. Dynamic Protein Interactions of the Polycomb Repressive Complex 2 during Differentiation of Pluripotent Cells. Mol Cell Proteomics 2016; 15:3450-3460. [PMID: 27634302 DOI: 10.1074/mcp.m116.062240] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Indexed: 01/08/2023] Open
Abstract
Polycomb proteins assemble to form complexes with important roles in epigenetic regulation. The Polycomb Repressive Complex 2 (PRC2) modulates the di- and tri-methylation of lysine 27 on histone H3, each of which are associated with gene repression. Although three subunits, EZH1/2, SUZ12, and EED, form the catalytic core of PRC2, a wider group of proteins associate with low stoichiometry. This raises the question of whether dynamic variation of the PRC2 interactome results in alternative forms of the complex during differentiation. Here we compared the physical interactions of PRC2 in undifferentiated and differentiated states of NTERA2 pluripotent embryonic carcinoma cells. Label-free quantitative proteomics was used to assess endogenous immunoprecipitation of the EZH2 and SUZ12 subunits of PRC2. A high stringency data set reflecting the endogenous state of PRC2 was produced that included all previously reported core and associated PRC2 components, and several novel interacting proteins. Comparison of the interactomes obtained in undifferentiated and differentiated cells revealed candidate proteins that were enriched in complexes isolated from one of the two states. For example, SALL4 and ZNF281 associate with PRC2 in pluripotent cells, whereas PCL1 and SMAD3 preferentially associate with PRC2 in differentiating cells. Analysis of the mRNA and protein levels of these factors revealed that their association with PRC2 correlated with their cell state-specific expression. Taken together, we propose that dynamic changes to the PRC2 interactome during differentiation may contribute to directing its activity during cell fate transitions.
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Affiliation(s)
- Giorgio Oliviero
- From the ‡School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gerard L Brien
- §Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115.,¶Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Ariane Waston
- From the ‡School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gundula Streubel
- ¶Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Emilia Jerman
- ¶Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Darrell Andrews
- From the ‡School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Benjamin Doyle
- From the ‡School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nayla Munawar
- From the ‡School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kieran Wynne
- From the ‡School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - John Crean
- From the ‡School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Adrian P Bracken
- ¶Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Gerard Cagney
- From the ‡School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland;
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23
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Oliviero G, Munawar N, Watson A, Streubel G, Manning G, Bardwell V, Bracken AP, Cagney G. The variant Polycomb Repressor Complex 1 component PCGF1 interacts with a pluripotency sub-network that includes DPPA4, a regulator of embryogenesis. Sci Rep 2015. [DOI: https://doi.org/10.1038/srep18388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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24
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Oliviero G, Munawar N, Watson A, Streubel G, Manning G, Bardwell V, Bracken AP, Cagney G. The variant Polycomb Repressor Complex 1 component PCGF1 interacts with a pluripotency sub-network that includes DPPA4, a regulator of embryogenesis. Sci Rep 2015; 5:18388. [PMID: 26687479 PMCID: PMC4685312 DOI: 10.1038/srep18388] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 08/06/2015] [Accepted: 11/06/2015] [Indexed: 01/21/2023] Open
Abstract
PCGF1 encodes one of six human Polycomb RING finger homologs that are linked to transcriptional repression and developmental gene regulation. Individual PCGF proteins define discrete Polycomb Repressor Complex 1 (PRC1) multi-protein complexes with diverse subunit composition whose functions are incompletely understood. PCGF1 is a component of a variant PRC1 complex that also contains the BCL6 co-repressor BCOR and the histone demethylase KDM2B. To further investigate the role of PCGF1, we mapped the physical interactions of the protein under endogenous conditions in a cell model of neuronal differentiation. Using stringent statistical cut-offs, 83 highly enriched interacting proteins were identified, including all previously reported members of the variant PRC1 complex containing PCGF1, as well as proteins linked to diverse cellular pathways such as chromatin and cell cycle regulation. Notably, a sub-network of proteins associated with the establishment and maintenance of pluripotency (NANOG, OCT4, PATZ1, and the developmental regulator DPPA4) were found to independently interact with PCGF1 in a subsequent round of physical interaction mapping experiments. Furthermore, knockdown of PCGF1 results in reduced expression of DPPA4 and other subunits of the variant PRC1 complex at both mRNA and protein levels. Thus, PCGF1 represents a physical and functional link between Polycomb function and pluripotency.
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Affiliation(s)
- Giorgio Oliviero
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND
| | - Gundula Streubel
- Department of Genetics, Trinity College Dublin, Dublin 2, IRELAND
| | - Gwendolyn Manning
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND
| | - Vivian Bardwell
- Developmental Biology Center, Masonic Cancer Center, and Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 USA
| | - Adrian P Bracken
- Department of Genetics, Trinity College Dublin, Dublin 2, IRELAND
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND
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25
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Affiliation(s)
- Gerard L Brien
- a The Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center , New York , NY , USA.,b Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center , New York , NY , USA
| | - Adrian P Bracken
- c The Smurfit Institute of Genetics, Trinity College Dublin , Dublin 2 , Ireland
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26
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Conway E, Healy E, Bracken AP. PRC2 mediated H3K27 methylations in cellular identity and cancer. Curr Opin Cell Biol 2015; 37:42-8. [PMID: 26497635 DOI: 10.1016/j.ceb.2015.10.003] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
The Polycomb Repressive Complex 2 (PRC2) is a multiprotein chromatin modifying complex that is essential for vertebrate development and differentiation. It is composed of a trimeric core of SUZ12, EED and EZH1/2 and is responsible for catalysing both di-methylation and tri-methylation of Histone H3 at lysine 27 (H3K27me2/3). Both H3K27 methylations contribute to the role of PRC2 in maintaining cellular identity. In all cell types, the H3K27me3 modification is associated with repression of genes encoding regulators of alternative lineages. The less well-characterised H3K27me2 modification is ubiquitous throughout the genome and is thought to act like a protective blanket to maintain the repression of non-H3K27me3 associated genes and cell-type-specific enhancers of alternative lineages. Recent cancer genome sequencing studies highlighted that several genes encoding PRC2 components as well as Histone H3 are mutated in multiple cancer types. Intriguingly, these cancers have changes in the global levels of the H3K27me2 and H3K27me3 modifications as well as genome-wide redistributions. Exciting new studies suggest that these changes confer context dependent blocks in cellular differentiation and increased vulnerability to aberrant cancer signalling pathways.
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Affiliation(s)
- Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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27
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Brien GL, Healy E, Jerman E, Conway E, Fadda E, O'Donovan D, Krivtsov AV, Rice AM, Kearney CJ, Flaus A, McDade SS, Martin SJ, McLysaght A, O'Connell DJ, Armstrong SA, Bracken AP. A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence. Genes Dev 2015; 29:2231-43. [PMID: 26494712 PMCID: PMC4647557 DOI: 10.1101/gad.267930.115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 06/25/2015] [Accepted: 10/02/2015] [Indexed: 12/05/2022]
Abstract
Brien et al. show that while Polycomb-like proteins PCL2 and PCL3 are E2F-regulated genes expressed in proliferating cells, PCL1 is a p53 target gene predominantly expressed in quiescent cells. PCL1 binds to and stabilizes p53 to block cellular proliferation, and depletion of PCL1 phenocopies the defects in maintaining cellular quiescence associated with p53 loss. Polycomb-like proteins 1–3 (PCL1–3) are substoichiometric components of the Polycomb-repressive complex 2 (PRC2) that are essential for association of the complex with chromatin. However, it remains unclear why three proteins with such apparent functional redundancy exist in mammals. Here we characterize their divergent roles in both positively and negatively regulating cellular proliferation. We show that while PCL2 and PCL3 are E2F-regulated genes expressed in proliferating cells, PCL1 is a p53 target gene predominantly expressed in quiescent cells. Ectopic expression of any PCL protein recruits PRC2 to repress the INK4A gene; however, only PCL2 and PCL3 confer an INK4A-dependent proliferative advantage. Remarkably, PCL1 has evolved a PRC2- and chromatin-independent function to negatively regulate proliferation. We show that PCL1 binds to and stabilizes p53 to induce cellular quiescence. Moreover, depletion of PCL1 phenocopies the defects in maintaining cellular quiescence associated with p53 loss. This newly evolved function is achieved by the binding of the PCL1 N-terminal PHD domain to the C-terminal domain of p53 through two unique serine residues, which were acquired during recent vertebrate evolution. This study illustrates the functional bifurcation of PCL proteins, which act in both a chromatin-dependent and a chromatin-independent manner to regulate the INK4A and p53 pathways.
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Affiliation(s)
- Gerard L Brien
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Emilia Jerman
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Elisa Fadda
- Department of Chemistry, National University of Ireland, Maynooth, Ireland
| | | | - Andrei V Krivtsov
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Alan M Rice
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Conor J Kearney
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Andrew Flaus
- Centre for Chromosome Biology, School of Life Sciences, National University of Ireland Galway, Galway, Ireland
| | - Simon S McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Seamus J Martin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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28
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Abstract
The Mediator multiprotein complex physically links transcription factors to RNA polymerase II and the basal transcription machinery. While the Mediator complex has been shown to be required for transcriptional initiation and elongation, the understanding of its interplay with histone modifying enzymes and post‐translational modifications remains elusive. In this issue of The EMBO Journal, Yao et al (2015) report that the MED23 subunit of the Mediator complex physically associates with the heterodimeric RNF20/40 E3‐ligase complex to facilitate the monoubiquitylation of histone H2B on gene bodies of actively transcribed genes.
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Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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29
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Lanigan F, Brien GL, Fan Y, Madden SF, Jerman E, Maratha A, Aloraifi F, Hokamp K, Dunne EJ, Lohan AJ, Flanagan L, Garbe JC, Stampfer MR, Fridberg M, Jirstrom K, Quinn CM, Loftus B, Gallagher WM, Geraghty J, Bracken AP. Delineating transcriptional networks of prognostic gene signatures refines treatment recommendations for lymph node-negative breast cancer patients. FEBS J 2015; 282:3455-73. [DOI: 10.1111/febs.13354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/02/2015] [Accepted: 06/17/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Fiona Lanigan
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Gerard L. Brien
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Yue Fan
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - Stephen F. Madden
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - Emilia Jerman
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Ashwini Maratha
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - Fatima Aloraifi
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Karsten Hokamp
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Eiseart J. Dunne
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Amanda J. Lohan
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - Louise Flanagan
- Department of Histopathology; St Vincent's University Hospital; Dublin Ireland
| | - James C. Garbe
- Life Science Division; Lawrence Berkeley National Laboratory; Berkeley CA USA
| | - Martha R. Stampfer
- Life Science Division; Lawrence Berkeley National Laboratory; Berkeley CA USA
| | - Marie Fridberg
- Department of Clinical Sciences, Division of Oncology and Pathology; Lund University; Sweden
| | - Karin Jirstrom
- Department of Clinical Sciences, Division of Oncology and Pathology; Lund University; Sweden
| | - Cecily M. Quinn
- Department of Histopathology; St Vincent's University Hospital; Dublin Ireland
| | - Brendan Loftus
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - William M. Gallagher
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - James Geraghty
- Department of Histopathology; St Vincent's University Hospital; Dublin Ireland
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30
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Aloraifi F, McDevitt T, Martiniano R, McGreevy J, McLaughlin R, Egan CM, Cody N, Meany M, Kenny E, Green AJ, Bradley DG, Geraghty JG, Bracken AP. Detection of novel germline mutations for breast cancer in non-BRCA1/2 families. FEBS J 2015; 282:3424-37. [PMID: 26094658 DOI: 10.1111/febs.13352] [Citation(s) in RCA: 34] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/12/2015] [Accepted: 06/17/2015] [Indexed: 01/22/2023]
Abstract
The identification of the breast cancer susceptibility genes BRCA1 and BRCA2 enhanced clinicians' ability to select high-risk individuals for aggressive surveillance and prevention, and led to the development of targeted therapies. However, BRCA1/2 mutations account for only 25% of familial breast cancer cases. To systematically identify rare, probably pathogenic variants in familial cases of breast cancer without BRCA1/2 mutations, we developed a list of 312 genes, and performed targeted DNA enrichment coupled to multiplex next-generation sequencing on 104 'BRCAx' patients and 101 geographically matched controls in Ireland. As expected, this strategy allowed us to identify mutations in several well-known high-susceptibility and moderate-susceptibility genes, including ATM (~ 5%), RAD50 (~ 3%), CHEK2 (~ 2%), TP53 (~ 1%), PALB2 (~ 1%), and MRE11A (~ 1%). However, we also identified novel pathogenic variants in 30 other genes, which, when taken together, potentially explain the etiology of the missing heritability in up to 35% of BRCAx patients. These included novel potential pathogenic mutations in MAP3K1, CASP8, RAD51B, ZNF217, CDKN2B-AS1, and ERBB2, including a splice site mutation, which we predict would generate a constitutively active HER2 protein. Taken together, this work extends our understanding of the genetics of familial breast cancer, and supports the need to implement hereditary multigene panel testing to more appropriately orientate clinical management.
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Affiliation(s)
- Fatima Aloraifi
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Trudi McDevitt
- National Centre for Medical Genetics, Our Lady's Hospital, Crumlin, Dublin 12, Ireland
| | - Rui Martiniano
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Jonah McGreevy
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | | | - Chris M Egan
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Nuala Cody
- National Centre for Medical Genetics, Our Lady's Hospital, Crumlin, Dublin 12, Ireland
| | - Marie Meany
- National Centre for Medical Genetics, Our Lady's Hospital, Crumlin, Dublin 12, Ireland
| | | | - Andrew J Green
- National Centre for Medical Genetics, Our Lady's Hospital, Crumlin, Dublin 12, Ireland
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31
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32
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Lanigan FT, Dunne EJ, Brien GL, Al Oraifi F, Fan Y, Quinn C, Flanagan L, Fridberg M, Jirstrom K, Geraghty JG, Gallagher WM, Bracken AP. High levels of proliferation regulators and an impaired senescence response pathway to identify early-stage breast tumors with a poor prognosis. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.26_suppl.43] [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: 11/20/2022] Open
Abstract
43 Background: Predicting the risk of tumour recurrence, and thus the need for chemotherapy, for lymph node-negative breast cancer patients is a significant problem for clinicians and patients. Methods: We have identified a ‘core proliferation signature,’ which is consistently high in proliferating primary cultures, and is downregulated during cellular senescence. Using a reverse engineering approach on a breast cancer-specific regulatory network, and confirmed by ChIP-seq analysis, we have identified a hierarchy of several highly interconnected Master Transcriptional Regulators upstream of these core proliferation genes. Results: Further analysis of the expression of these factors in breast cancer cohorts at the mRNA and protein levels reveals a remarkable ability to reliably predict recurrence risk for early-stage breast cancer. Strikingly, in our analyses, a combination of just two of these factors outperforms the currently used clinical biomarkers for breast cancer recurrence risk, as well as recently developed multi-gene prognostic assays. Moreover, the addition of the senescence regulator p16INK4A to this panel further increases its prognostic capability. Conclusions: We propose that this novel approach has succeeded in identifying ‘drivers’ of breast cancer proliferation which, when combined with a marker of senescence such as p16INK4A, successfully identify actively proliferating tumours with an impaired senescence response pathway. Furthermore, we suggest that this gene combination has the potential to become an improved prognostic assay for early-stage breast cancer.
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Affiliation(s)
| | | | | | | | - Yue Fan
- Smurfit Institute of Genetics, Dublin, Ireland
| | - Cecily Quinn
- Department of Pathology and Laboratory Medicine, St. Vincent's University Hospital, Dublin, Ireland
| | - Louise Flanagan
- Department of Pathology and Laboratory Medicine, St. Vincent's University Hospital, Dublin, Ireland
| | - Marie Fridberg
- Department of Clinical Sciences, Division of Pathology, Lund University, Lund, Sweden
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33
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Egan CM, Nyman U, Skotte J, Streubel G, Turner S, O'Connell DJ, Rraklli V, Dolan MJ, Chadderton N, Klaus H, Jane FG, Helin K, Holmberg J, Bracken AP. Abstract PR12: CHD5 is required for neurogenesis and has a dual role in facilitating gene expression and Polycomb gene repression. Cancer Res 2013. [DOI: 10.1158/1538-7445.cec13-pr12] [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
The chromatin remodeler CHD5 is expressed in neural tissues and is frequently deleted in aggressive neuroblastoma. Very little is known about the normal function of CHD5, its mechanism of action or how its deletion may contribute to neuroblastoma. Here we report that depletion of CHD5 in the developing murine neocortex blocks neuronal differentiation leading to an accumulation of undifferentiated progenitors. Consistent with this, ChIP-SEQ analysis of CHD5 shows it binds a large cohort of neuronal genes and is required for facilitating their activation during differentiation. However, CHD5 also binds a cohort of Polycomb target genes and is required for the maintenance of H3K27me3 on their promoters and their sustained repression during differentiation. Finally, we show that the chromodomains of CHD5 directly bind H3K27me3 and are essential for the function of CHD5 during neuronal differentiation. These findings provide new insights into the essential role of CHD5 during neurogenesis and show how the inactivation of this candidate tumor suppressor might contribute to the progression of neuroblastoma via a defect in differentiation.
This abstract is also presented as Poster A05.
Citation Format: Christopher M. Egan, Ulrika Nyman, Julie Skotte, Gundula Streubel, Siobhán Turner, David J. O'Connell, Vilma Rraklli, Michael J. Dolan, Naomi Chadderton, Hansen Klaus, Farrar Gwyneth Jane, Kristian Helin, Johan Holmberg, Adrian P. Bracken. CHD5 is required for neurogenesis and has a dual role in facilitating gene expression and Polycomb gene repression. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr PR12.
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Affiliation(s)
| | - Ulrika Nyman
- 2Ludwig Institute for Cancer Research, Stockholm, Sweden,
| | - Julie Skotte
- 3BRIC, University of Copenhagen, Copenhagen, Denmark,
| | | | | | | | - Vilma Rraklli
- 2Ludwig Institute for Cancer Research, Stockholm, Sweden,
| | | | | | - Hansen Klaus
- 3BRIC, University of Copenhagen, Copenhagen, Denmark,
| | | | | | - Johan Holmberg
- 2Ludwig Institute for Cancer Research, Stockholm, Sweden,
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34
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Mielke LA, Jones SA, Raverdeau M, Higgs R, Stefanska A, Groom JR, Misiak A, Dungan LS, Sutton CE, Streubel G, Bracken AP, Mills KH. Retinoic acid expression associates with enhanced IL-22 production by γδ T cells and innate lymphoid cells and attenuation of intestinal inflammation. J Exp Med 2013; 210:1117-24. [PMID: 23690441 PMCID: PMC3674702 DOI: 10.1084/jem.20121588] [Citation(s) in RCA: 226] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 05/01/2013] [Indexed: 11/07/2022] Open
Abstract
Retinoic acid (RA), a vitamin A metabolite, modulates mucosal T helper cell responses. Here we examined the role of RA in regulating IL-22 production by γδ T cells and innate lymphoid cells in intestinal inflammation. RA significantly enhanced IL-22 production by γδ T cells stimulated in vitro with IL-1β or IL-18 and IL-23. In vivo RA attenuated colon inflammation induced by dextran sodium sulfate treatment or Citrobacter rodentium infection. This was associated with a significant increase in IL-22 secretion by γδ T cells and innate lymphoid cells. In addition, RA treatment enhanced production of the IL-22-responsive antimicrobial peptides Reg3β and Reg3γ in the colon. The attenuating effects of RA on colitis were reversed by treatment with an anti-IL-22 neutralizing antibody, demonstrating that RA mediates protection by enhancing IL-22 production. To define the molecular events involved, we used chromatin immunoprecipitation assays and found that RA promoted binding of RA receptor to the IL-22 promoter in γδ T cells. Our findings provide novel insights into the molecular events controlling IL-22 transcription and suggest that one key outcome of RA signaling may be to shape early intestinal immune responses by promoting IL-22 synthesis by γδ T cells and innate lymphoid cells.
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MESH Headings
- Animals
- Antibodies, Neutralizing/immunology
- Citrobacter rodentium/immunology
- Colitis/genetics
- Colitis/immunology
- Colon/immunology
- Colon/metabolism
- Dextran Sulfate/adverse effects
- Enterobacteriaceae Infections/genetics
- Enterobacteriaceae Infections/immunology
- Enterobacteriaceae Infections/metabolism
- Inflammation/genetics
- Inflammation/immunology
- Inflammation/metabolism
- Interleukins/biosynthesis
- Interleukins/genetics
- Interleukins/immunology
- Lymphocytes/immunology
- Lymphocytes/metabolism
- Mice
- Mice, Inbred C57BL
- Promoter Regions, Genetic/genetics
- Promoter Regions, Genetic/immunology
- Protein Binding/genetics
- Protein Binding/immunology
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Receptors, Retinoic Acid/immunology
- Receptors, Retinoic Acid/metabolism
- T-Lymphocytes, Helper-Inducer/immunology
- T-Lymphocytes, Helper-Inducer/metabolism
- Transcription, Genetic/genetics
- Transcription, Genetic/immunology
- Tretinoin/immunology
- Tretinoin/metabolism
- Interleukin-22
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Affiliation(s)
- Lisa A. Mielke
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
| | - Sarah A. Jones
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
| | - Mathilde Raverdeau
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
| | - Rowan Higgs
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
| | - Anna Stefanska
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
| | - Joanna R. Groom
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Alicja Misiak
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
| | - Lara S. Dungan
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
| | - Caroline E. Sutton
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
| | - Gundula Streubel
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
| | - Adrian P. Bracken
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
| | - Kingston H.G. Mills
- Immunology Research Centre and Immune Regulation Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute; and Smurfit Institute of Genetics; Trinity College Dublin, Dublin 2, Ireland
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35
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Brien GL, Gambero G, O'Connell DJ, Jerman E, Turner SA, Egan CM, Dunne EJ, Jurgens MC, Wynne K, Piao L, Lohan AJ, Ferguson N, Shi X, Sinha KM, Loftus BJ, Cagney G, Bracken AP. Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation. Nat Struct Mol Biol 2012; 19:1273-81. [DOI: 10.1038/nsmb.2449] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Accepted: 10/17/2012] [Indexed: 12/21/2022]
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36
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Abstract
Cellular senescence is an irreversible arrest of proliferation. It is activated when a cell encounters stress such as DNA damage, telomere shortening or oncogene activation. Like apoptosis, it impedes tumour progression and acts as a barrier that pre-neoplastic cells must overcome during their evolution toward the full tumourigenic state. This review focuses on the role of transcriptional regulators in the control of cellular senescence, explores how their function is perturbed in cancer and discusses the potential to harness this knowledge for future cancer therapies.
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Affiliation(s)
- F Lanigan
- Smurfit Genetics Department, The Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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37
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Abstract
The Polycomb group (PcG) proteins are transcriptional repressors that regulate lineage choices during development and differentiation. Recent studies have advanced our understanding of how the PcG proteins regulate cell fate decisions and how their deregulation potentially contributes to cancer. In this Review we discuss the emerging roles of long non-coding RNAs (ncRNAs) and a subset of transcription factors, which we call cell fate transcription factors, in the regulation of PcG association with target genes. We also speculate about how their deregulation contributes to tumorigenesis.
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Affiliation(s)
- Adrian P Bracken
- The Smurfit Institute of Genetics, Trinity College Dublin and The Adelaide & Meath Hospital, including the National Children's Hospital, Dublin, Ireland.
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38
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Brien GL, Bracken AP. Transcriptomics: unravelling the biology of transcription factors and chromatin remodelers during development and differentiation. Semin Cell Dev Biol 2009; 20:835-41. [PMID: 19682593 DOI: 10.1016/j.semcdb.2009.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
Abstract
Mammalian development is a highly complex and tightly regulated process. Transcription factors and chromatin remodelers, acting downstream of cell signalling pathways, are the key intrinsic factors which control gene expression. Recent advances in transcriptomics are allowing biologists to begin to unravel the complex biological roles played by these factors. This review focuses on how genome-wide gene expression and chromatin immunoprecipitation studies are expanding our understanding of the roles played by transcription factors and chromatin remodelers during cell fate decisions in development and differentiation.
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Affiliation(s)
- Gerard L Brien
- The Smurfit Institute of Genetics, Trinity College Dublin and The Adelaide & Meath Hospital, including The National Children's Hospital, Dublin, Ireland
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39
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Hansen KH, Bracken AP, Pasini D, Dietrich N, Gehani SS, Monrad A, Rappsilber J, Lerdrup M, Helin K. Erratum: A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol 2008. [DOI: 10.1038/ncb1208-1484] [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: 11/09/2022]
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40
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Pasini D, Bracken AP, Agger K, Christensen J, Hansen K, Cloos PAC, Helin K. Regulation of stem cell differentiation by histone methyltransferases and demethylases. Cold Spring Harb Symp Quant Biol 2008; 73:253-63. [PMID: 19022750 DOI: 10.1101/sqb.2008.73.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The generation of different cell types from stem cells containing identical genetic information and their organization into tissues and organs during development is a highly complex process that requires defined transcriptional programs. Maintenance of such programs is epigenetically regulated and the factors involved in these processes are often essential for development. The activities required for cell-fate decisions are frequently deregulated in human tumors, and the elucidation of the molecular mechanisms that regulate these processes is therefore important for understanding both developmental processes and tumorigenesis.
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Affiliation(s)
- D Pasini
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmark
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41
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Krivtsov AV, Feng Z, Lemieux ME, Faber J, Vempati S, Sinha AU, Xia X, Jesneck J, Bracken AP, Silverman LB, Kutok JL, Kung AL, Armstrong SA. H3K79 methylation profiles define murine and human MLL-AF4 leukemias. Cancer Cell 2008; 14:355-68. [PMID: 18977325 PMCID: PMC2591932 DOI: 10.1016/j.ccr.2008.10.001] [Citation(s) in RCA: 451] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 08/11/2008] [Accepted: 10/02/2008] [Indexed: 11/18/2022]
Abstract
We created a mouse model wherein conditional expression of an Mll-AF4 fusion oncogene induces B precursor acute lymphoblastic (ALL) or acute myeloid leukemias (AML). Gene expression profile analysis of the ALL cells demonstrated significant overlap with human MLL-rearranged ALL. ChIP-chip analysis demonstrated histone H3 lysine 79 (H3K79) methylation profiles that correlated with Mll-AF4-associated gene expression profiles in murine ALLs and in human MLL-rearranged leukemias. Human MLL-rearranged ALLs could be distinguished from other ALLs by their H3K79 profiles, and suppression of the H3K79 methyltransferase DOT1L inhibited expression of critical MLL-AF4 target genes. We thus demonstrate that ectopic H3K79 methylation is a distinguishing feature of murine and human MLL-AF4 ALLs and is important for maintenance of MLL-AF4-driven gene expression.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Differentiation
- Cells, Cultured
- Chromatin Immunoprecipitation
- Female
- Flow Cytometry
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Gene Rearrangement
- Histone Methyltransferases
- Histone-Lysine N-Methyltransferase
- Histones/chemistry
- Histones/genetics
- Histones/metabolism
- Homeodomain Proteins/metabolism
- Humans
- Immunophenotyping
- Integrases/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Lysine/chemistry
- Lysine/genetics
- Lysine/metabolism
- Male
- Methylation
- Methyltransferases/antagonists & inhibitors
- Methyltransferases/physiology
- Mice
- Mice, Transgenic
- Myeloid-Lymphoid Leukemia Protein/physiology
- Oligonucleotide Array Sequence Analysis
- Oncogene Proteins, Fusion/physiology
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Principal Component Analysis
- Protein Methyltransferases/genetics
- Protein Methyltransferases/metabolism
- RNA, Small Interfering/pharmacology
- Transcription, Genetic
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Affiliation(s)
- Andrei V. Krivtsov
- Division of Hematology/Oncology, Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zhaohui Feng
- Division of Hematology/Oncology, Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Madeleine E. Lemieux
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joerg Faber
- Division of Hematology/Oncology, Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sridhar Vempati
- Division of Hematology/Oncology, Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Amit U. Sinha
- Division of Hematology/Oncology, Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xiaobo Xia
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonathan Jesneck
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Adrian P. Bracken
- Department of Genetics, The Smurfit Institute, Trinity College, Dublin 2, Ireland
| | - Lewis B. Silverman
- Division of Hematology/Oncology, Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jeffery L. Kutok
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Andrew L. Kung
- Division of Hematology/Oncology, Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Scott A. Armstrong
- Division of Hematology/Oncology, Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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42
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Hansen KH, Bracken AP, Pasini D, Dietrich N, Gehani SS, Monrad A, Rappsilber J, Lerdrup M, Helin K. A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol 2008; 10:1291-300. [PMID: 18931660 DOI: 10.1038/ncb1787] [Citation(s) in RCA: 538] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 09/08/2008] [Indexed: 12/14/2022]
Abstract
Organization of chromatin by epigenetic mechanisms is essential for establishing and maintaining cellular identity in developing and adult organisms. A key question that remains unresolved about this process is how epigenetic marks are transmitted to the next cell generation during cell division. Here we provide a model to explain how trimethylated Lys 27 of histone 3 (H3K27me3), which is catalysed by the EZH2-containing Polycomb Repressive Complex 2 (PRC2), is maintained in proliferating cells. We show that the PRC2 complex binds to the H3K27me3 mark and colocalizes with this mark in G1 phase and with sites of ongoing DNA replication. Efficient binding requires an intact trimeric PRC2 complex containing EZH2, EED and SUZ12, but is independent of the catalytic SET domain of EZH2. Using a heterologous reporter system, we show that transient recruitment of the PRC2 complex to chromatin, upstream of the transcriptional start site, is sufficient to maintain repression through endogenous PRC2 during subsequent cell divisions. Thus, we suggest that once the H3K27me3 is established, it recruits the PRC2 complex to maintain the mark at sites of DNA replication, leading to methylation of H3K27 on the daughter strands during incorporation of newly synthesized histones. This mechanism ensures maintenance of the H3K27me3 epigenetic mark in proliferating cells, not only during DNA replication when histones synthesized de novo are incorporated, but also outside S phase, thereby preserving chromatin structure and transcriptional programs.
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Affiliation(s)
- Klaus H Hansen
- Biotech Research & Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N., Denmark.
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43
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Abstract
Polycomb group (PcG) proteins form multiprotein complexes, called Polycomb repressive complexes (PRCs). PRC2 contains the PcG proteins EZH2, SUZ12, and EED and represses transcription through methylation of lysine (K) 27 of histone H3 (H3). Suz12 is essential for PRC2 activity and its inactivation results in early lethality of mouse embryos. Here, we demonstrate that Suz12(-/-) mouse embryonic stem (ES) cells can be established and expanded in tissue culture. The Suz12(-/-) ES cells are characterized by global loss of H3K27 trimethylation (H3K27me3) and higher expression levels of differentiation-specific genes. Moreover, Suz12(-/-) ES cells are impaired in proper differentiation, resulting in a lack of repression of ES cell markers as well as activation of differentiation-specific genes. Finally, we demonstrate that the PcGs are actively recruited to several genes during ES cell differentiation, which despite an increase in H3K27me3 levels is not always sufficient to prevent transcriptional activation. In summary, we demonstrate that Suz12 is required for the establishment of specific expression programs required for ES cell differentiation. Furthermore, we provide evidence that PcGs have different mechanisms to regulate transcription during cellular differentiation.
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Affiliation(s)
- Diego Pasini
- Centre for Epigenetics and BRIC, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
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44
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Dietrich N, Bracken AP, Trinh E, Schjerling CK, Koseki H, Rappsilber J, Helin K, Hansen KH. Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A-ARF locus. EMBO J 2007; 26:1637-48. [PMID: 17332741 PMCID: PMC1829390 DOI: 10.1038/sj.emboj.7601632] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 02/06/2007] [Indexed: 12/23/2022] Open
Abstract
The Polycomb group (PcG) proteins are essential for embryogenesis, and their expression is often found deregulated in human cancer. The PcGs form two major protein complexes, called polycomb repressive complexes 1 and 2 (PRC1 and PRC2) whose function is to maintain transcriptional repression. Here, we demonstrate that the chromodomain-containing protein, CBX8, which is part of one of the PRC1 complexes, regulates proliferation of diploid human and mouse fibroblasts through direct binding to the INK4A-ARF locus. Furthermore, we demonstrate that CBX8 is limiting for the regulation of INK4A-ARF, and that ectopic expression of CBX8 leads to repression of the Ink4a-Arf locus and bypass of senescence, leading to cellular immortalization. Gene expression and location analysis demonstrate that besides the INK4A-ARF locus, CBX8 also regulates a number of other genes important for cell growth and survival. On the basis of these results, we conclude that CBX8 is an essential component of one of the PRC1 complexes, which directly regulate the expression of numerous target genes, including the INK4A-ARF locus, involved in cell-fate decisions.
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Affiliation(s)
- Nikolaj Dietrich
- Centre for Epigenetics and Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Adrian P Bracken
- Centre for Epigenetics and Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Emmanuelle Trinh
- Centre for Epigenetics and Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Charlotte K Schjerling
- Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen, Denmark
| | - Haruhiko Koseki
- RIKEN Research Center for Allergy and Immunology, Tsurumi-ku, Yokohama, Japan
| | - Juri Rappsilber
- Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh, Scotland
| | - Kristian Helin
- Centre for Epigenetics and Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Tel.: +45 3532 5666; Fax: +45 3532 5669; E-mail:
| | - Klaus H Hansen
- Centre for Epigenetics and Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Tel.: +45 3532 5664; Fax: +45 3532 5669; E-mail:
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45
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Bracken AP, Kleine-Kohlbrecher D, Dietrich N, Pasini D, Gargiulo G, Beekman C, Theilgaard-Mönch K, Minucci S, Porse BT, Marine JC, Hansen KH, Helin K. The Polycomb group proteins bind throughout the INK4A-ARF locus and are disassociated in senescent cells. Genes Dev 2007; 21:525-30. [PMID: 17344414 PMCID: PMC1820894 DOI: 10.1101/gad.415507] [Citation(s) in RCA: 675] [Impact Index Per Article: 39.7] [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: 10/23/2006] [Accepted: 01/22/2007] [Indexed: 01/28/2023]
Abstract
The p16INK4A and p14ARF proteins, encoded by the INK4A-ARF locus, are key regulators of cellular senescence, yet the mechanisms triggering their up-regulation are not well understood. Here, we show that the ability of the oncogene BMI1 to repress the INK4A-ARF locus requires its direct association and is dependent on the continued presence of the EZH2-containing Polycomb-Repressive Complex 2 (PRC2) complex. Significantly, EZH2 is down-regulated in stressed and senescing populations of cells, coinciding with decreased levels of associated H3K27me3, displacement of BMI1, and activation of transcription. These results provide a model for how the INK4A-ARF locus is activated and how Polycombs contribute to cancer.
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Affiliation(s)
- Adrian P. Bracken
- Centre for Epigenetics, Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen 2200, Denmark
| | - Daniela Kleine-Kohlbrecher
- Centre for Epigenetics, Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen 2200, Denmark
| | - Nikolaj Dietrich
- Centre for Epigenetics, Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen 2200, Denmark
| | - Diego Pasini
- Centre for Epigenetics, Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen 2200, Denmark
| | - Gaetano Gargiulo
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Chantal Beekman
- Laboratory for Molecular Cancer Biology, Flanders Interuniversity Institute for Biotechnology, University of Ghent, Ghent B-9052 Belgium
| | - Kim Theilgaard-Mönch
- The Laboratory for Gene Therapy Research, Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Bo T. Porse
- The Laboratory for Gene Therapy Research, Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Flanders Interuniversity Institute for Biotechnology, University of Ghent, Ghent B-9052 Belgium
| | - Klaus H. Hansen
- Centre for Epigenetics, Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen 2200, Denmark
| | - Kristian Helin
- Centre for Epigenetics, Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen 2200, Denmark
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46
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Abstract
The Polycomb group (PcG) proteins form chromatin-modifying complexes that are essential for embryonic development and stem cell renewal and are commonly deregulated in cancer. Here, we identify their target genes using genome-wide location analysis in human embryonic fibroblasts. We find that Polycomb-Repressive Complex 1 (PRC1), PRC2, and tri-methylated histone H3K27 co-occupy >1000 silenced genes with a strong functional bias for embryonic development and cell fate decisions. We functionally identify 40 genes derepressed in human embryonic fibroblasts depleted of the PRC2 components (EZH2, EED, SUZ12) and the PRC1 component, BMI-1. Interestingly, several markers of osteogenesis, adipogenesis, and chrondrogenesis are among these genes, consistent with the mesenchymal origin of fibroblasts. Using a neuronal model of differentiation, we delineate two different mechanisms for regulating PcG target genes. For genes activated during differentiation, PcGs are displaced. However, for genes repressed during differentiation, we paradoxically find that they are already bound by the PcGs in nondifferentiated cells despite being actively transcribed. Our results are consistent with the hypothesis that PcGs are part of a preprogrammed memory system established during embryogenesis marking certain key genes for repressive signals during subsequent developmental and differentiation processes.
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Affiliation(s)
- Adrian P Bracken
- Biotech Research and Innovation Centre (BRIC), 2100 Copenhagen Ø, Denmark
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47
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Abstract
The Polycomb group (PcG) proteins form chromatin-modifying complexes that are essential for embryonic development and stem cell renewal and are commonly deregulated in cancer. Here, we identify their target genes using genome-wide location analysis in human embryonic fibroblasts. We find that Polycomb-Repressive Complex 1 (PRC1), PRC2, and tri-methylated histone H3K27 co-occupy >1000 silenced genes with a strong functional bias for embryonic development and cell fate decisions. We functionally identify 40 genes derepressed in human embryonic fibroblasts depleted of the PRC2 components (EZH2, EED, SUZ12) and the PRC1 component, BMI-1. Interestingly, several markers of osteogenesis, adipogenesis, and chrondrogenesis are among these genes, consistent with the mesenchymal origin of fibroblasts. Using a neuronal model of differentiation, we delineate two different mechanisms for regulating PcG target genes. For genes activated during differentiation, PcGs are displaced. However, for genes repressed during differentiation, we paradoxically find that they are already bound by the PcGs in nondifferentiated cells despite being actively transcribed. Our results are consistent with the hypothesis that PcGs are part of a preprogrammed memory system established during embryogenesis marking certain key genes for repressive signals during subsequent developmental and differentiation processes.
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Affiliation(s)
- Adrian P Bracken
- Biotech Research and Innovation Centre (BRIC), 2100 Copenhagen Ø, Denmark
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48
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Christensen J, Cloos P, Toftegaard U, Klinkenberg D, Bracken AP, Trinh E, Heeran M, Di Stefano L, Helin K. Characterization of E2F8, a novel E2F-like cell-cycle regulated repressor of E2F-activated transcription. Nucleic Acids Res 2005; 33:5458-70. [PMID: 16179649 PMCID: PMC1236722 DOI: 10.1093/nar/gki855] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The E2F family of transcription factors are downstream effectors of the retinoblastoma protein, pRB, pathway and are essential for the timely regulation of genes necessary for cell-cycle progression. Here we describe the characterization of human and murine E2F8, a new member of the E2F family. Sequence analysis of E2F8 predicts the presence of two distinct E2F-related DNA binding domains suggesting that E2F8 and, the recently, identified E2F7 form a subgroup within the E2F family. We show that E2F transcription factors bind the E2F8 promoter in vivo and that expression of E2F8 is being induced at the G1/S transition. Purified recombinant E2F8 binds specifically to a consensus E2F-DNA-binding site indicating that E2F8, like E2F7, binds DNA without the requirement of co-factors such as DP1. E2F8 inhibits E2F-driven promoters suggesting that E2F8 is transcriptional repressor like E2F7. Ectopic expression of E2F8 in diploid human fibroblasts reduces expression of E2F-target genes and inhibits cell growth consistent with a role for repressing E2F transcriptional activity. Taken together, these data suggest that E2F8 has an important role in turning of the expression of E2F-target genes in the S-phase of the cell cycle.
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Affiliation(s)
- Jesper Christensen
- Biotech Research & Innovation Centre (BRIC)Fruebjergvej 3, 2100 Copenhagen Ø, Denmark
| | - Paul Cloos
- Biotech Research & Innovation Centre (BRIC)Fruebjergvej 3, 2100 Copenhagen Ø, Denmark
| | - Ulla Toftegaard
- Biotech Research & Innovation Centre (BRIC)Fruebjergvej 3, 2100 Copenhagen Ø, Denmark
| | - David Klinkenberg
- Biotech Research & Innovation Centre (BRIC)Fruebjergvej 3, 2100 Copenhagen Ø, Denmark
| | - Adrian P. Bracken
- Biotech Research & Innovation Centre (BRIC)Fruebjergvej 3, 2100 Copenhagen Ø, Denmark
| | - Emmanuelle Trinh
- Biotech Research & Innovation Centre (BRIC)Fruebjergvej 3, 2100 Copenhagen Ø, Denmark
| | - Mel Heeran
- Biotech Research & Innovation Centre (BRIC)Fruebjergvej 3, 2100 Copenhagen Ø, Denmark
| | - Luisa Di Stefano
- European Institute of OncologyVia Ripamonti 435, 20141 Milan, Italy
| | - Kristian Helin
- Biotech Research & Innovation Centre (BRIC)Fruebjergvej 3, 2100 Copenhagen Ø, Denmark
- European Institute of OncologyVia Ripamonti 435, 20141 Milan, Italy
- Faculty of Health Sciences, University of CopenhagenBlegdamsvej 3, 2200 Copenhagen N, Denmark
- To whom correspondence should be addressed. Tel: +45 3917 9666; Fax: +45 3917 9669;
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49
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Abstract
The E2F transcription factors are downstream effectors of the retinoblastoma protein (pRB) pathway and are required for the timely regulation of numerous genes essential for DNA replication and cell cycle progression. Several laboratories have used genome-wide approaches to discover novel target genes of E2F, leading to the identification of several hundred such genes that are involved not only in DNA replication and cell cycle progression, but also in DNA damage repair, apoptosis, differentiation and development. These new findings greatly enrich our understanding of how E2F controls transcription and cellular homeostasis.
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Affiliation(s)
- Adrian P Bracken
- Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy
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50
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Pasini D, Bracken AP, Jensen MR, Denchi EL, Helin K. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J 2004; 23:4061-71. [PMID: 15385962 PMCID: PMC524339 DOI: 10.1038/sj.emboj.7600402] [Citation(s) in RCA: 675] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Accepted: 08/17/2004] [Indexed: 12/20/2022] Open
Abstract
SUZ12 is a recently identified Polycomb group (PcG) protein, which together with EZH2 and EED forms different Polycomb repressive complexes (PRC2/3). These complexes contain histone H3 lysine (K) 27/9 and histone H1 K26 methyltransferase activity specified by the EZH2 SET domain. Here we show that mice lacking Suz12, like Ezh2 and Eed mutant mice, are not viable and die during early postimplantation stages displaying severe developmental and proliferative defects. Consistent with this, we demonstrate that SUZ12 is required for proliferation of cells in tissue culture. Furthermore, we demonstrate that SUZ12 is essential for the activity and stability of the PRC2/3 complexes in mouse embryos, in tissue culture cells and in vitro. Strikingly, Suz12-deficient embryos show a specific loss of di- and trimethylated H3K27, demonstrating that Suz12 is indeed essential for EZH2 activity in vivo. In conclusion, our data demonstrate an essential role of SUZ12 in regulating the activity of the PRC2/3 complexes, which are required for regulating proliferation and embryogenesis.
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Affiliation(s)
| | | | | | | | - Kristian Helin
- European Institute of Oncology, Milan, Italy
- Biotech Research and Innovation Centre, Copenhagen, Denmark
- Biotech Research & Innovation Centre, Fruebjergvej 3, boks 1, 2100 Copenhagen, Denmark. Tel.: +45 3917 9666; Fax: +45 3917 9669; E-mail:
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