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Geyer F, Geyer M, Reuning U, Klapproth S, Wolff KD, Nieberler M. CHD4 acts as a prognostic factor and drives radioresistance in HPV negative HNSCC. Sci Rep 2024; 14:8286. [PMID: 38594331 PMCID: PMC11003975 DOI: 10.1038/s41598-024-58958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/04/2024] [Indexed: 04/11/2024] Open
Abstract
Despite great efforts in improving existing therapies, the outcome of patients with advanced radioresistant HPV-negative head and neck squamous cell carcinoma (HNSCC) remains poor. The chromatin remodeler Chromodomain helicase DNA binding protein 4 (CHD4) is involved in different DNA-repair mechanisms, but the role and potential in HNSCC has not been explored yet. In the present study, we evaluated the prognostic significance of CHD4 expression using in silico analysis of the pan-cancer dataset. Furthermore, we established a monoclonal HNSCC CHD4 knockdown cell clone utilizing the CRISPR/Cas9 system. Effects of lower CHD4 expression on radiosensitivity after increasing doses of ionizing radiation were characterized using clonogenic assays and cell numbers. The in silico analysis revealed that high CHD4 expression is associated with significant poorer overall survival of HPV-negative HNSCC patients. Additionally, the knockdown of CHD4 significantly increased the radiosensitivity of HNSCC cells. Therefore, CHD4 might be involved in promoting radioresistance in hard-to-treat HPV-negative HNSCC entities. We conclude that CHD4 could serve as a prognostic factor in HPV-negative HNSCC tumors and is a potential target protein overcoming radioresistance in HNSCC. Our results and the newly established cell clone laid the foundation to further characterize the underlying mechanisms and ultimately use CHD4 in HNSCC therapies.
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Affiliation(s)
- Fabian Geyer
- Department of Oral and Maxillofacial Surgery, Klinikum Rechts der Isar der Technischen Universität München, 81675, Munich, Germany.
| | - Maximilian Geyer
- Department of Oral and Maxillofacial Surgery, Klinikum Rechts der Isar der Technischen Universität München, 81675, Munich, Germany
| | - Ute Reuning
- Clinical Research Unit, Department of Obstetrics and Gynecology, Technical University of Munich, 81675, Munich, Germany
| | - Sarah Klapproth
- Institute of Experimental Hematology, School of Medicine, Technische Universität München, 81675, Munich, Germany
| | - Klaus-Dietrich Wolff
- Department of Oral and Maxillofacial Surgery, Klinikum Rechts der Isar der Technischen Universität München, 81675, Munich, Germany
| | - Markus Nieberler
- Department of Oral and Maxillofacial Surgery, Klinikum Rechts der Isar der Technischen Universität München, 81675, Munich, Germany
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Pendse S, Chavan S, Kale V, Vaidya A. A comprehensive analysis of cell-autonomous and non-cell-autonomous regulation of myeloid leukemic cells: The prospect of developing novel niche-targeting therapies. Cell Biol Int 2023; 47:1667-1683. [PMID: 37554060 DOI: 10.1002/cbin.12078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023]
Abstract
Leukemic cells (LCs) arise from the hematopoietic stem/and progenitor cells (HSCs/HSPCs) and utilize cues from the bone marrow microenvironment (BMM) for their regulation in the same way as their normal HSC counterparts. Mesenchymal stromal cells (MSCs), a vital component of the BMM promote leukemogenesis by creating a protective and immune-tolerant microenvironment that can support the survival of LCs, helping them escape chemotherapy, thereby resulting in the relapse of leukemia. Conversely, MSCs also induce apoptosis in the LCs and inhibit their proliferation by interfering with their self-renewal potential. This review discusses the work done so far on cell-autonomous (intrinsic) and MSCs-mediated non-cell-autonomous (extrinsic) regulation of myeloid leukemia with a special focus on the need to investigate the extrinsic regulation of myeloid leukemia to understand the contrasting role of MSCs in leukemogenesis. These mechanisms could be exploited to formulate novel therapeutic strategies that specifically target the leukemic microenvironment.
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Affiliation(s)
- Shalmali Pendse
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, Maharashtra, India
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, Maharashtra, India
| | - Sayali Chavan
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, Maharashtra, India
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, Maharashtra, India
| | - Vaijayanti Kale
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, Maharashtra, India
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, Maharashtra, India
| | - Anuradha Vaidya
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, Maharashtra, India
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, Maharashtra, India
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Kotekar A, Singh AK, Devaiah BN. BRD4 and MYC: power couple in transcription and disease. FEBS J 2023; 290:4820-4842. [PMID: 35866356 PMCID: PMC9867786 DOI: 10.1111/febs.16580] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 01/26/2023]
Abstract
The MYC proto-oncogene and BRD4, a BET family protein, are two cardinal proteins that have a broad influence in cell biology and disease. Both proteins are expressed ubiquitously in mammalian cells and play central roles in controlling growth, development, stress responses and metabolic function. As chromatin and transcriptional regulators, they play a critical role in regulating the expression of a burgeoning array of genes, maintaining chromatin architecture and genome stability. Consequently, impairment of their function or regulation leads to many diseases, with cancer being the most predominant. Interestingly, accumulating evidence indicates that regulation of the expression and functions of MYC are tightly intertwined with BRD4 at both transcriptional and post-transcriptional levels. Here, we review the mechanisms by which MYC and BRD4 are regulated, their functions in governing various molecular mechanisms and the consequences of their dysregulation that lead to disease. We present a perspective of how the regulatory mechanisms for the two proteins could be entwined at multiple points in a BRD4-MYC nexus that leads to the modulation of their functions and disease upon dysregulation.
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Affiliation(s)
- Aparna Kotekar
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Amit Kumar Singh
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
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Tan J, Shenker-Tauris N, Rodriguez-Hernaez J, Wang E, Sakellaropoulos T, Boccalatte F, Thandapani P, Skok J, Aifantis I, Fenyö D, Xia B, Tsirigos A. Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening. Nat Biotechnol 2023; 41:1140-1150. [PMID: 36624151 PMCID: PMC10329734 DOI: 10.1038/s41587-022-01612-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/14/2022] [Indexed: 01/11/2023]
Abstract
Investigating how chromatin organization determines cell-type-specific gene expression remains challenging. Experimental methods for measuring three-dimensional chromatin organization, such as Hi-C, are costly and have technical limitations, restricting their broad application particularly in high-throughput genetic perturbations. We present C.Origami, a multimodal deep neural network that performs de novo prediction of cell-type-specific chromatin organization using DNA sequence and two cell-type-specific genomic features-CTCF binding and chromatin accessibility. C.Origami enables in silico experiments to examine the impact of genetic changes on chromatin interactions. We further developed an in silico genetic screening approach to assess how individual DNA elements may contribute to chromatin organization and to identify putative cell-type-specific trans-acting regulators that collectively determine chromatin architecture. Applying this approach to leukemia cells and normal T cells, we demonstrate that cell-type-specific in silico genetic screening, enabled by C.Origami, can be used to systematically discover novel chromatin regulation circuits in both normal and disease-related biological systems.
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Affiliation(s)
- Jimin Tan
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
| | - Nina Shenker-Tauris
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- The Jackson Laboratory for Genomics Medicine, Farmington, CT, USA
| | | | - Francesco Boccalatte
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Palaniraja Thandapani
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Jane Skok
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Iannis Aifantis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Bo Xia
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA.
- Society of Fellows, Harvard University, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA.
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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O'Connor D, Demeulemeester J, Conde L, Kirkwood A, Fung K, Papaleonidopoulou F, Bloye G, Farah N, Rahman S, Hancock J, Bateman C, Inglott S, Mee J, Herrero J, Van Loo P, Moorman AV, Vora A, Mansour MR. The Clinicogenomic Landscape of Induction Failure in Childhood and Young Adult T-Cell Acute Lymphoblastic Leukemia. J Clin Oncol 2023; 41:3545-3556. [PMID: 37098241 PMCID: PMC10306434 DOI: 10.1200/jco.22.02734] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/30/2023] [Accepted: 03/06/2023] [Indexed: 04/27/2023] Open
Abstract
PURPOSE Failure to respond to induction chemotherapy portends a poor outcome in childhood acute lymphoblastic leukemia (ALL) and is more frequent in T-cell ALL (T-ALL) than B-cell ALL. We aimed to address the limited understanding of clinical and genetic factors that influence outcome in a cohort of patients with T-ALL induction failure (IF). METHODS We studied all cases of T-ALL IF on two consecutive multinational randomized trials, UKALL2003 and UKALL2011, to define risk factors, treatment, and outcomes. We performed multiomic profiling to characterize the genomic landscape. RESULTS IF occurred in 10.3% of cases and was significantly associated with increasing age, occurring in 20% of patients age 16 years and older. Five-year overall survival (OS) rates were 52.1% in IF and 90.2% in responsive patients (P < .001). Despite increased use of nelarabine-based chemotherapy consolidated by hematopoietic stem-cell transplant in UKALL2011, there was no improvement in outcome. Persistent end-of-consolidation molecular residual disease resulted in a significantly worse outcome (5-year OS, 14.3% v 68.5%; HR, 4.10; 95% CI, 1.35 to 12.45; P = .0071). Genomic profiling revealed a heterogeneous picture with 25 different initiating lesions converging on 10 subtype-defining genes. There was a remarkable abundance of TAL1 noncoding lesions, associated with a dismal outcome (5-year OS, 12.5%). Combining TAL1 lesions with mutations in the MYC and RAS pathways produces a genetic stratifier that identifies patients highly likely to fail conventional therapy (5-year OS, 23.1% v 86.4%; HR, 6.84; 95% CI, 2.78 to 16.78; P < .0001) and who should therefore be considered for experimental agents. CONCLUSION The outcome of IF in T-ALL remains poor with current therapy. The lack of a unifying genetic driver suggests alternative approaches, particularly using immunotherapy, are urgently needed.
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Affiliation(s)
- David O'Connor
- UCL Cancer Institute, University College London, London, United Kingdom
- Department of Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Jonas Demeulemeester
- The Francis Crick Institute, London, United Kingdom
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, Laboratory for Integrative Cancer Genomics, KU Leuven, Leuven, Belgium
| | - Lucia Conde
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Amy Kirkwood
- CR UK & UCL Cancer Trials Centre, UCL Cancer Institute, UCL, London, United Kingdom
| | - Kent Fung
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Foteini Papaleonidopoulou
- UCL Cancer Institute, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Gianna Bloye
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Nadine Farah
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Sunniyat Rahman
- UCL Cancer Institute, University College London, London, United Kingdom
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Jeremy Hancock
- South West Genomic Laboratory Hub, North Bristol NHS Trust, Bristol, United Kingdom
| | | | - Sarah Inglott
- Department of Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Jon Mee
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, United Kingdom
| | - Javier Herrero
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Peter Van Loo
- The Francis Crick Institute, London, United Kingdom
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Anthony V. Moorman
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ajay Vora
- Department of Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Marc R. Mansour
- UCL Cancer Institute, University College London, London, United Kingdom
- Department of Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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6
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Wenger A, Karlsson I, Kling T, Carén H. CRISPR-Cas9 knockout screen identifies novel treatment targets in childhood high-grade glioma. Clin Epigenetics 2023; 15:80. [PMID: 37161535 PMCID: PMC10170782 DOI: 10.1186/s13148-023-01498-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/03/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Brain tumours are the leading cause of cancer-related death in children, and there is no effective treatment. A growing body of evidence points to deregulated epigenetics as a tumour driver, particularly in paediatric cancers as they have relatively few genomic alterations, and key driver mutations have been identified in histone 3 (H3). Cancer stem cells (CSC) are implicated in tumour development, relapse and therapy resistance and thus particularly important to target. We therefore aimed to identify novel epigenetic treatment targets in CSC derived from H3-mutated high-grade glioma (HGG) through a CRISPR-Cas9 knockout screen. RESULTS The knockout screen identified more than 100 novel genes essential for the growth of CSC derived from paediatric HGG with H3K27M mutation. We successfully validated 12 of the 13 selected hits by individual knockout in the same two CSC lines, and for the top six hits we included two additional CSC lines derived from H3 wild-type paediatric HGG. Knockout of these genes led to a significant decrease in CSC growth, and altered stem cell and differentiation markers. CONCLUSIONS The screen robustly identified essential genes known in the literature, but also many novel genes essential for CSC growth in paediatric HGG. Six of the novel genes (UBE2N, CHD4, LSM11, KANSL1, KANSL3 and EED) were validated individually thus demonstrating their importance for CSC growth in H3-mutated and wild-type HGG. These genes should be further studied and evaluated as novel treatment targets in paediatric HGG.
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Affiliation(s)
- Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Ida Karlsson
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden.
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8
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Tirtakusuma R, Szoltysek K, Milne P, Grinev VV, Ptasinska A, Chin PS, Meyer C, Nakjang S, Hehir-Kwa JY, Williamson D, Cauchy P, Keane P, Assi SA, Ashtiani M, Kellaway SG, Imperato MR, Vogiatzi F, Schweighart EK, Lin S, Wunderlich M, Stutterheim J, Komkov A, Zerkalenkova E, Evans P, McNeill H, Elder A, Martinez-Soria N, Fordham SE, Shi Y, Russell LJ, Pal D, Smith A, Kingsbury Z, Becq J, Eckert C, Haas OA, Carey P, Bailey S, Skinner R, Miakova N, Collin M, Bigley V, Haniffa M, Marschalek R, Harrison CJ, Cargo CA, Schewe D, Olshanskaya Y, Thirman MJ, Cockerill PN, Mulloy JC, Blair HJ, Vormoor J, Allan JM, Bonifer C, Heidenreich O, Bomken S. Epigenetic regulator genes direct lineage switching in MLL/AF4 leukemia. Blood 2022; 140:1875-1890. [PMID: 35839448 PMCID: PMC10488321 DOI: 10.1182/blood.2021015036] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
The fusion gene MLL/AF4 defines a high-risk subtype of pro-B acute lymphoblastic leukemia. Relapse can be associated with a lineage switch from acute lymphoblastic to acute myeloid leukemia, resulting in poor clinical outcomes caused by resistance to chemotherapies and immunotherapies. In this study, the myeloid relapses shared oncogene fusion breakpoints with their matched lymphoid presentations and originated from various differentiation stages from immature progenitors through to committed B-cell precursors. Lineage switching is linked to substantial changes in chromatin accessibility and rewiring of transcriptional programs, including alternative splicing. These findings indicate that the execution and maintenance of lymphoid lineage differentiation is impaired. The relapsed myeloid phenotype is recurrently associated with the altered expression, splicing, or mutation of chromatin modifiers, including CHD4 coding for the ATPase/helicase of the nucleosome remodelling and deacetylation complex. Perturbation of CHD4 alone or in combination with other mutated epigenetic modifiers induces myeloid gene expression in MLL/AF4+ cell models, indicating that lineage switching in MLL/AF4 leukemia is driven and maintained by disrupted epigenetic regulation.
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Affiliation(s)
- Ricky Tirtakusuma
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Katarzyna Szoltysek
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Maria Sklodowska-Curie Institute, Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Paul Milne
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Vasily V. Grinev
- Department of Genetics, the Faculty of Biology, Belarusian State University, Minsk, Republic of Belarus
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Paulynn S. Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Claus Meyer
- Institute of Pharmaceutical Biology/DCAL, Goethe-University, Frankfurt/Main, Germany
| | - Sirintra Nakjang
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Salam A. Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Minoo Ashtiani
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sophie G. Kellaway
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Maria R. Imperato
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Fotini Vogiatzi
- ALL-BFM Study Group, Pediatric Hematology/Oncology, Christian Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Germany
| | | | - Shan Lin
- Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Mark Wunderlich
- Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | | | - Alexander Komkov
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Elena Zerkalenkova
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Paul Evans
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Hesta McNeill
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alex Elder
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Natalia Martinez-Soria
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sarah E. Fordham
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yuzhe Shi
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lisa J. Russell
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Deepali Pal
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alex Smith
- Epidemiology and Cancer Statistics Group, University of York, York, United Kingdom
| | | | - Jennifer Becq
- Illumina Cambridge Ltd., Great Abington, United Kingdom
| | - Cornelia Eckert
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Oskar A. Haas
- St Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter Carey
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - Roderick Skinner
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - Natalia Miakova
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Matthew Collin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Venetia Bigley
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Dermatology and Newcastle National Institute of Health Research (NIHR), Newcastle Biomedical Research Centre, Newcastle Hospitals National Health Service (NHS) Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology/DCAL, Goethe-University, Frankfurt/Main, Germany
| | - Christine J. Harrison
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catherine A. Cargo
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Denis Schewe
- Department of Pediatrics, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Yulia Olshanskaya
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Michael J. Thirman
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
| | - Peter N. Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - James C. Mulloy
- Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Helen J. Blair
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Josef Vormoor
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - James M. Allan
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Simon Bomken
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
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9
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Tu Z, Zheng Y. Role of ATP-dependent chromatin remodelers in hematopoietic stem and progenitor cell maintenance. Curr Opin Hematol 2022; 29:174-180. [PMID: 35787545 PMCID: PMC9257093 DOI: 10.1097/moh.0000000000000710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW ATP-dependent chromatin remodeling factors utilize energy from ATP hydrolysis to modulate DNA-histone structures and regulate gene transcription. They are essential during hematopoiesis and for hematopoietic stem and progenitor cell (HSPC) function. This review discusses the recently unveiled roles of these chromatin remodelers in HSPC regulation, with an emphasis on the mechanism of chromodomain helicase DNA-binding (CHD) family members. RECENT FINDINGS Recent studies of ATP-dependent chromatin remodelers have revealed that individual CHD family members engage in distinct mechanisms in regulating HSPC cell fate. For example, CHD8 is required for HSPC survival by restricting both P53 transcriptional activity and protein stability in steady state hematopoiesis while the related CHD7 physically interacts with RUNX family transcription factor 1 (RUNX1) and suppresses RUNX1-induced expansion of HSPCs during blood development. Moreover, other CHD subfamily members such as CHD1/CHD2 and CHD3/CHD4, as well as the switch/sucrose non-fermentable, imitation SWI, and SWI2/SNF2 related (SWR) families of chromatin modulators, have also been found important for HSPC maintenance by distinct mechanisms. SUMMARY The expanding knowledge of ATP-dependent chromatin remodelers in hematopoiesis illustrates their respective critical roles in HSPC maintenance including the regulation of HSPC differentiation, survival, and self-renewal. Further studies are warranted to elucidate how different chromatin remodeling complexes are integrated in various HSPC cell fate decisions during steady-state and stress hematopoiesis.
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Affiliation(s)
- Zhaowei Tu
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Yi Zheng
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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10
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Issah MA, Wu D, Zhang F, Zheng W, Liu Y, Fu H, Zhou H, Chen R, Shen J. Epigenetic modifications in acute myeloid leukemia: The emerging role of circular RNAs (Review). Int J Oncol 2021; 59:107. [PMID: 34792180 PMCID: PMC8651224 DOI: 10.3892/ijo.2021.5287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/13/2021] [Indexed: 11/06/2022] Open
Abstract
Canonical epigenetic modifications, which include histone modification, chromatin remodeling and DNA methylation, play key roles in numerous cellular processes. Epigenetics underlies how cells that posses DNA with similar sequences develop into different cell types with different functions in an organism. Earlier epigenetic research has primarily been focused at the chromatin level. However, the number of studies on epigenetic modifications of RNA, such as N1‑methyladenosine, 2'‑O‑ribosemethylation, inosine, 5‑methylcytidine, N6‑methyladenosine (m6A) and pseudouridine, has seen an increase. Circular RNAs (circRNAs), a type of RNA species that lacks a 5' cap or 3' poly(A) tail, are abundantly expressed in acute myeloid leukemia (AML) and may regulate disease progression. circRNAs possess various functions, including microRNA sponging, gene transcription regulation and RNA‑binding protein interaction. Furthermore, circRNAs are m6A methylated in other types of cancer, such as colorectal and hypopharyngeal squamous cell cancers. Therefore, the critical roles of circRNA epigenetic modifications, particularly m6A, and their possible involvement in AML are discussed in the present review. Epigenetic modification of circRNAs may become a diagnostic and therapeutic target for AML in the future.
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Affiliation(s)
- Mohammed Awal Issah
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Dansen Wu
- Medical Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Feng Zhang
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Weili Zheng
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Yanquan Liu
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Haiying Fu
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Huarong Zhou
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Rong Chen
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Jianzhen Shen
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
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11
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Rago F, Rodrigues LU, Bonney M, Sprouffske K, Kurth E, Elliott G, Ambrose J, Aspesi P, Oborski J, Chen JT, McDonald ER, Mapa FA, Ruddy DA, Kauffmann A, Abrams T, Bhang HEC, Jagani Z. Exquisite Sensitivity to Dual BRG1/BRM ATPase Inhibitors Reveals Broad SWI/SNF Dependencies in Acute Myeloid Leukemia. Mol Cancer Res 2021; 20:361-372. [PMID: 34799403 DOI: 10.1158/1541-7786.mcr-21-0390] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 10/03/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022]
Abstract
Various subunits of mammalian SWI/SNF chromatin remodeling complexes display loss-of-function mutations characteristic of tumor suppressors in different cancers, but an additional role for SWI/SNF supporting cell survival in distinct cancer contexts is emerging. In particular, genetic dependence on the catalytic subunit BRG1/SMARCA4 has been observed in acute myeloid leukemia (AML), yet the feasibility of direct therapeutic targeting of SWI/SNF catalytic activity in leukemia remains unknown. Here, we evaluated the activity of dual BRG1/BRM ATPase inhibitors across a genetically diverse panel of cancer cell lines and observed that hematopoietic cancer cell lines were among the most sensitive compared to other lineages. This result was striking in comparison to data from pooled short hairpin RNA screens, which showed that only a subset of leukemia cell lines display sensitivity to BRG1 knockdown. We demonstrate that combined genetic knockdown of BRG1 and BRM is required to recapitulate the effects of dual inhibitors, suggesting that SWI/SNF dependency in human leukemia extends beyond a predominantly BRG1-driven mechanism. Through gene expression and chromatin accessibility studies, we show that the dual inhibitors act at genomic loci associated with oncogenic transcription factors, and observe a downregulation of leukemic pathway genes including MYC, a well-established target of BRG1 activity in AML. Overall, small molecule inhibition of BRG1/BRM induced common transcriptional responses across leukemia models resulting in a spectrum of cellular phenotypes. Implications: Our studies reveal the breadth of SWI/SNF dependency in leukemia and support targeting SWI/SNF catalytic function as a potential therapeutic strategy in AML.
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Affiliation(s)
| | | | - Megan Bonney
- Oncology, Novartis Institutes for Biomedical Research
| | | | - Esther Kurth
- Oncology, Novartis Institutes for Biomedical Research
| | | | - Jessi Ambrose
- Oncology, Novartis Institutes for Biomedical Research
| | - Peter Aspesi
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - Justin Oborski
- High Throughput Biology, Novartis Institutes for Biomedical Research
| | - Julie T Chen
- Oncology, Novartis Institutes for Biomedical Research
| | | | - Felipa A Mapa
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - David A Ruddy
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research
| | - Audrey Kauffmann
- Oncology Disease Area, Novartis Institutes for Biomedical Research
| | - Tinya Abrams
- Disease Area Oncology, Novartis Institutes for BioMedical Research
| | | | - Zainab Jagani
- Oncology, Novartis Institutes for Biomedical Research
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12
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Sanjiv K, Calderón-Montaño JM, Pham TM, Erkers T, Tsuber V, Almlöf I, Höglund A, Heshmati Y, Seashore-Ludlow B, Nagesh Danda A, Gad H, Wiita E, Göktürk C, Rasti A, Friedrich S, Centio A, Estruch M, Våtsveen TK, Struyf N, Visnes T, Scobie M, Koolmeister T, Henriksson M, Wallner O, Sandvall T, Lehmann S, Theilgaard-Mönch K, Garnett MJ, Östling P, Walfridsson J, Helleday T, Warpman Berglund U. MTH1 Inhibitor TH1579 Induces Oxidative DNA Damage and Mitotic Arrest in Acute Myeloid Leukemia. Cancer Res 2021; 81:5733-5744. [PMID: 34593524 PMCID: PMC9397639 DOI: 10.1158/0008-5472.can-21-0061] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/25/2021] [Accepted: 09/29/2021] [Indexed: 01/07/2023]
Abstract
Acute myeloid leukemia (AML) is an aggressive hematologic malignancy, exhibiting high levels of reactive oxygen species (ROS). ROS levels have been suggested to drive leukemogenesis and is thus a potential novel target for treating AML. MTH1 prevents incorporation of oxidized nucleotides into the DNA to maintain genome integrity and is upregulated in many cancers. Here we demonstrate that hematologic cancers are highly sensitive to MTH1 inhibitor TH1579 (karonudib). A functional precision medicine ex vivo screen in primary AML bone marrow samples demonstrated a broad response profile of TH1579, independent of the genomic alteration of AML, resembling the response profile of the standard-of-care treatments cytarabine and doxorubicin. Furthermore, TH1579 killed primary human AML blast cells (CD45+) as well as chemotherapy resistance leukemic stem cells (CD45+Lin-CD34+CD38-), which are often responsible for AML progression. TH1579 killed AML cells by causing mitotic arrest, elevating intracellular ROS levels, and enhancing oxidative DNA damage. TH1579 showed a significant therapeutic window, was well tolerated in animals, and could be combined with standard-of-care treatments to further improve efficacy. TH1579 significantly improved survival in two different AML disease models in vivo. In conclusion, the preclinical data presented here support that TH1579 is a promising novel anticancer agent for AML, providing a rationale to investigate the clinical usefulness of TH1579 in AML in an ongoing clinical phase I trial. SIGNIFICANCE: The MTH1 inhibitor TH1579 is a potential novel AML treatment, targeting both blasts and the pivotal leukemic stem cells while sparing normal bone marrow cells.
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Affiliation(s)
- Kumar Sanjiv
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | - Therese M. Pham
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Tom Erkers
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Viktoriia Tsuber
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Höglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Yaser Heshmati
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Brinton Seashore-Ludlow
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Akhilesh Nagesh Danda
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Helge Gad
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Elisee Wiita
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Göktürk
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Azita Rasti
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Stefanie Friedrich
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Anders Centio
- The Finsen Laboratory, Rigshospitalet/National University Hospital, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Montserrat Estruch
- The Finsen Laboratory, Rigshospitalet/National University Hospital, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thea Kristin Våtsveen
- Department for Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,KG Jebsen Center for B cell malignancies, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Nona Struyf
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Torkild Visnes
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Scobie
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Henriksson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Olov Wallner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Teresa Sandvall
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Sören Lehmann
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Sciences, Haematology, Uppsala University, Uppsala, Sweden
| | - Kim Theilgaard-Mönch
- The Finsen Laboratory, Rigshospitalet/National University Hospital, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Hematology, Rigshospitalet/National Univ. Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Päivi Östling
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Julian Walfridsson
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Oxcia AB, Stockholm, Sweden.,Corresponding Author: Ulrika Warpman Berglund, Department of Oncology Pathology, Karolinska Institute, Tomtebodavägen 23A, Stockholm 17121, Sweden or Oxcia AB, Norrbackagatan 70C, SE-113 34 Stockholm, Sweden. Phone: 46-73-2709605; E-mail: or
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13
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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14
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Oyama Y, Shigeta S, Tokunaga H, Tsuji K, Ishibashi M, Shibuya Y, Shimada M, Yasuda J, Yaegashi N. CHD4 regulates platinum sensitivity through MDR1 expression in ovarian cancer: A potential role of CHD4 inhibition as a combination therapy with platinum agents. PLoS One 2021; 16:e0251079. [PMID: 34161330 PMCID: PMC8221472 DOI: 10.1371/journal.pone.0251079] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 04/19/2021] [Indexed: 12/20/2022] Open
Abstract
Platinum sensitivity is an important prognostic factor in patients with ovarian cancer. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a core member of the nucleosome remodeling and deacetylase complex, which functions as a chromatin remodeler. Emerging evidence indicates that CHD4 could be a potential therapeutic target for cancer therapy. The purpose of this study was to clarify the role of CHD4 in ovarian cancer and investigate its therapeutic potential focusing on platinum sensitivity. In an analysis of the Cancer Genome Atlas ovarian cancer dataset, CHD4 gene amplification was associated with worse overall survival. CHD4 mRNA expression was significantly higher in platinum-resistant samples in a subsequent clinical sample analysis, suggesting that CHD4 overexpression conferred platinum resistance to ovarian cancer cells, resulting in poor patient survival. In concordance with these findings, CHD4 knockdown enhanced the induction of apoptosis mediated by cisplatin in ovarian cancer cells TOV21G and increased cisplatin sensitivity in multiple ovarian cancer cells derived from different subtypes. However, CHD4 knockdown did not affect the expression of RAD51 or p21, the known targets of CHD4 in other cancer types that can modulate platinum sensitivity. Knockdown and overexpression assays revealed that CHD4 positively regulated the expression of multi-drug transporter MDR1 and its coding protein p-glycoprotein. In addition, a first-in-class CHD4/SMARCA5 inhibitor ED2-AD101 showed synergistic interactions with cisplatin. Our findings suggest that CHD4 mediates platinum sensitivity by modulating MDR1 expression in ovarian cancer. Further, CHD4 suppression has a potential to be a novel therapeutic strategy in combination with platinum agents.
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Affiliation(s)
- Yoshiko Oyama
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shogo Shigeta
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hideki Tokunaga
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
- * E-mail:
| | - Keita Tsuji
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masumi Ishibashi
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yusuke Shibuya
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Muneaki Shimada
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Jun Yasuda
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Miyagi, Japan
| | - Nobuo Yaegashi
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
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15
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Chang CL, Huang CR, Chang SJ, Wu CC, Chen HH, Luo CW, Yip HK. CHD4 as an important mediator in regulating the malignant behaviors of colorectal cancer. Int J Biol Sci 2021; 17:1660-1670. [PMID: 33994851 PMCID: PMC8120460 DOI: 10.7150/ijbs.56976] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/28/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) has ranked first in terms of incidence in Taiwan. Surgical resection combined with chemo-, radio-, or targeted-therapies are the main treatments for CRC patients in current clinical practice. However, many CRC patients still respond poorly to these treatments, leading to tumor recurrence and an unacceptably high incidence of metastasis and death. Therefore, appropriate diagnosis, treatment, and drug selection are pressing issues in clinical practice. The Mi-2/nucleosome remodeling and deacetylase complex is an important epigenetic regulator of chromatin structure and gene expression. An important component of this complex is chromodomain-helicase-DNA-binding protein 4 (CHD4), which is involved in DNA repair after injury. Recent studies have indicated that CHD4 has oncogenic functions that inhibit multiple tumor suppressor genes through epigenetic regulation. However, the role of CHD4 in CRC has not yet been well investigated. In this study, we compared CHD4 expression in CRC patients from The Cancer Genome Atlas database. We found higher levels of CHD4 expression in CRC patients. In a series of in vitro experiments, we found that CHD4 affected cell motility and drug sensitivity in CRC cells. In animal models, the depletion of CHD4 affected CRC tumor growth, and the combination of a histone deacetylase 1 (HDAC1) inhibitor and platinum drugs inhibited CHD4 expression and increased the cytotoxicity of platinum drugs. Moreover, CHD4 expression was also a prognostic biomarker in CRC patients. Based on the above results, we believe that CHD4 expression is a viable biomarker for predicting metastasis CRC patients, and it has the potential to become a target for drug development.
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Affiliation(s)
- Chia-Lo Chang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chi-Ruei Huang
- Center for Shockwave Medicine and Tissue Engineering, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Division of Cardiology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shu-Jyuan Chang
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Pathology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Chieh Wu
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hong-Hwa Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chi-Wen Luo
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Division of Breast Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hon-Kan Yip
- Center for Shockwave Medicine and Tissue Engineering, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Division of Cardiology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital Kaohsiung, Taiwan.,Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.,Department of Nursing, Asia University Taichung, Taiwan.,Division of Cardiology, Department of Internal Medicine, Xiamen Chang Gung Hospital, Xiamen, Fujian, China
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16
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Fang C, Rao S, Crispino JD, Ntziachristos P. Determinants and role of chromatin organization in acute leukemia. Leukemia 2020; 34:2561-2575. [PMID: 32690881 PMCID: PMC7999176 DOI: 10.1038/s41375-020-0981-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
DNA is compacted into higher order structures that have major implications in gene regulation. These structures allow for long-range interactions of DNA elements, such as the association of promoters with their cognate enhancers. In recent years, mutations in genes that control these structures, including the cohesin-complex and the insulator-binding protein CTCF, have been found in a spectrum of hematologic disorders, and especially in acute leukemias. Cohesin and CTCF are critical for mediating looping and establishing boundaries within chromatin. Cells that harbor mutations in these genes display aberrant chromatin architecture and resulting differences in gene expression that contribute to leukemia initiation and progression. Here, we provide detailed discussion of the nature of 3D interactions and the way that they are disrupted in acute leukemia. Continued research in this area will provide new insights into the mechanisms of leukemogenesis and may shed light on novel treatment strategies.
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Affiliation(s)
- Celestia Fang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sridhar Rao
- Versiti Blood Research Institute, Milwaukee, WI, 53226, USA
| | - John D Crispino
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Division of Hematology, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Division of Hematology, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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17
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Evidence-based review of genomic aberrations in B-lymphoblastic leukemia/lymphoma: Report from the cancer genomics consortium working group for lymphoblastic leukemia. Cancer Genet 2020; 243:52-72. [PMID: 32302940 DOI: 10.1016/j.cancergen.2020.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 03/04/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
Abstract
Clinical management and risk stratification of B-lymphoblastic leukemia/ lymphoma (B-ALL/LBL) depend largely on identification of chromosomal abnormalities obtained using conventional cytogenetics and Fluorescence In Situ Hybridization (FISH) testing. In the last few decades, testing algorithms have been implemented to support an optimal risk-oriented therapy, leading to a large improvement in overall survival. In addition, large scale genomic studies have identified multiple aberrations of prognostic significance that are not routinely tested by existing modalities. However, as chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) technologies are increasingly used in clinical management of hematologic malignancies, these abnormalities may be more readily detected. In this article, we have compiled a comprehensive, evidence-based review of the current B-ALL literature, focusing on known and published subtypes described to date. More specifically, we describe the role of various testing modalities in the diagnosis, prognosis, and therapeutic relevance. In addition, we propose a testing algorithm aimed at assisting laboratories in the most effective detection of the underlying genomic abnormalities.
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Shahin Varnoosfaderani F, Palau A, Dong W, Persson J, Durand-Dubief M, Svensson JP, Lennartsson A. A regulatory role for CHD2 in myelopoiesis. Epigenetics 2020; 15:702-714. [PMID: 31900031 PMCID: PMC7574388 DOI: 10.1080/15592294.2019.1710913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The transcriptional program that dictates haematopoietic cell fate and differentiation requires an epigenetic regulatory and memory function, provided by a network of epigenetic factors that regulate DNA methylation, post-translational histone modifications and chromatin structure. Disturbed epigenetic regulation causes perturbations in the blood cell differentiation program that results in various types of haematopoietic disorders. Thus, accurate epigenetic regulation is essential for functional haematopoiesis. In this study, we used a CRISPR-Cas9 screening approach to identify new epigenetic regulators in myeloid differentiation. We designed a Chromatin-UMI CRISPR guide library targeting 1092 epigenetic regulators. Phorbol 12-myristate 13-acetate (PMA) treatment of the chronic myeloid leukaemia cell line K-562 was used as a megakaryocytic myeloid differentiation model. Both previously described developmental epigenetic regulators and novel factors were identified in our screen. In this study, we validated and characterized a role for the chromatin remodeller CHD2 in myeloid proliferation and megakaryocytic differentiation.
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Affiliation(s)
| | - Anna Palau
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - Wenbo Dong
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - Jenna Persson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm, Sweden.,High Throughput Genome Engineering, Science for Life Laboratory , Stockholm, Sweden
| | - Mickaël Durand-Dubief
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
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Milan T, Canaj H, Villeneuve C, Ghosh A, Barabé F, Cellot S, Wilhelm BT. Pediatric leukemia: Moving toward more accurate models. Exp Hematol 2019; 74:1-12. [PMID: 31154068 DOI: 10.1016/j.exphem.2019.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/19/2019] [Accepted: 05/22/2019] [Indexed: 02/07/2023]
Abstract
Leukemia is a complex genetic disease caused by errors in differentiation, growth, and apoptosis of hematopoietic cells in either lymphoid or myeloid lineages. Large-scale genomic characterization of thousands of leukemia patients has produced a tremendous amount of data that have enabled a better understanding of the differences between adult and pediatric patients. For instance, although phenotypically similar, pediatric and adult myeloid leukemia patients differ in their mutational profiles, typically involving either chromosomal translocations or recurrent single-base-pair mutations, respectively. To elucidate the molecular mechanisms underlying the biology of this cancer, continual efforts have been made to develop more contextually and biologically relevant experimental models. Leukemic cell lines, for example, provide an inexpensive and tractable model but often fail to recapitulate critical aspects of tumor biology. Likewise, murine leukemia models of leukemia have been highly informative but also do not entirely reproduce the human disease. More recent advances in the development of patient-derived xenografts (PDXs) or human models of leukemias are poised to provide a more comprehensive, and biologically relevant, approach to directly assess the impact of the in vivo environment on human samples. In this review, the advantages and limitations of the various current models used to functionally define the genetic requirements of leukemogenesis are discussed.
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MESH Headings
- Adolescent
- Animals
- Cell Differentiation
- Child
- Child, Preschool
- Female
- Heterografts
- Humans
- Infant
- Infant, Newborn
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/pathology
- Leukemia, Myeloid/therapy
- Male
- Mice
- Neoplasm Transplantation
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Neoplasms, Experimental/therapy
- Translocation, Genetic
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Affiliation(s)
- Thomas Milan
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Hera Canaj
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Chloe Villeneuve
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Aditi Ghosh
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Frédéric Barabé
- Centre de recherche en infectiologie du CHUL, Centre de recherche du CHU de Québec, Quebec City, QC, Canada; CHU de Québec Hôpital Enfant-Jésus, Quebec City, QC, Canada; Department of Medicine, Université Laval, Quebec City, QC, Canada
| | - Sonia Cellot
- Division of Hematology, Department of Pediatrics, Ste-Justine Hospital, Montréal, Université de Montréal, Montréal, QC, Canada
| | - Brian T Wilhelm
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada; Department of Medicine, Université de Montréal, Montréal, QC, Canada.
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Bracken AP, Brien GL, Verrijzer CP. Dangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancer. Genes Dev 2019; 33:936-959. [PMID: 31123059 PMCID: PMC6672049 DOI: 10.1101/gad.326066.119] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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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