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Rao A, Ni Z, Suresh D, Mohanty C, Wang AR, Lee DL, Nickel KP, Varambally SRJ, Lambert PF, Kendziorski C, Iyer G. Targeted inhibition of BET proteins in HPV-16 associated head and neck squamous cell carcinoma reveals heterogeneous transcription response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560587. [PMID: 37873389 PMCID: PMC10592929 DOI: 10.1101/2023.10.02.560587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Integrated human papillomavirus (HPV-16) associated head and neck squamous cell carcinoma (HNSCC) tumors have worse survival outcomes compared to episomal HPV-16 HNSCC tumors. Therefore, there is a need to differentiate treatment for HPV-16 integrated HNSCC from other viral forms. We analyzed TCGA data and found that HPV+ HNSCC expressed higher transcript levels of the bromodomain and extra terminal domain (BET) family of transcriptional coregulators. However, the mechanism of BET protein-mediated transcription of viral-cellular genes in the integrated viral-HNSCC genomes needs to be better understood. We show that BET inhibition downregulates E6 significantly independent of the viral transcription factor, E2, and there was overall heterogeneity in the downregulation of viral transcription in response to the effects of BET inhibition across HPV-associated cell lines. Chemical BET inhibition was phenocopied with the knockdown of BRD4 and mirrored downregulation of viral E6 and E7 expression. Strikingly, there was heterogeneity in the reactivation of p53 levels despite E6 downregulation, while E7 downregulation did not alter Rb levels significantly. We identified that BET inhibition directly downregulated c-Myc and E2F expression and induced CDKN1A expression. Overall, our studies show that BET inhibition provokes a G1-cell cycle arrest with apoptotic activity and suggests that BET inhibition regulates both viral and cellular gene expression in HPV-associated HNSCC.
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Affiliation(s)
- Aakarsha Rao
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Zijian Ni
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dhruthi Suresh
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Chitrasen Mohanty
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Albert R. Wang
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Denis L Lee
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705, WI, USA
| | - Kwangok P. Nickel
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Sooryanarayana Randall J. Varambally
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705, WI, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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Yu D, Liang Y, Kim C, Jaganathan A, Ji D, Han X, Yang X, Jia Y, Gu R, Wang C, Zhang Q, Cheung KL, Zhou MM, Zeng L. Structural mechanism of BRD4-NUT and p300 bipartite interaction in propagating aberrant gene transcription in chromatin in NUT carcinoma. Nat Commun 2023; 14:378. [PMID: 36690674 PMCID: PMC9870903 DOI: 10.1038/s41467-023-36063-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/13/2023] [Indexed: 01/25/2023] Open
Abstract
BRD4-NUT, a driver fusion mutant in rare and highly aggressive NUT carcinoma, acts in aberrant transcription of anti-differentiation genes by recruiting histone acetyltransferase (HAT) p300 and promoting p300-driven histone hyperacetylation and nuclear condensation in chromatin. However, the molecular basis of how BRD4-NUT recruits and activates p300 remains elusive. Here, we report that BRD4-NUT contains two transactivation domains (TADs) in NUT that bind to the TAZ2 domain in p300. Our NMR structures reveal that NUT TADs adopt amphipathic helices when bound to the four-helical bundle TAZ2 domain. The NUT protein forms liquid-like droplets in-vitro that are enhanced by TAZ2 binding in 1:2 stoichiometry. The TAD/TAZ2 bipartite binding in BRD4-NUT/p300 triggers allosteric activation of p300 and acetylation-driven liquid-like condensation on chromatin that comprise histone H3 lysine 27 and 18 acetylation and transcription proteins BRD4L/S, CDK9, MED1, and RNA polymerase II. The BRD4-NUT/p300 chromatin condensation is key for activating transcription of pro-proliferation genes such as ALX1, resulting ALX1/Snail signaling and epithelial-to-mesenchymal transition. Our study provides a previously underappreciated structural mechanism illuminating BRD4-NUT's bipartite p300 recruitment and activation in NUT carcinoma that nucleates a feed-forward loop for propagating histone hyperacetylation and chromatin condensation to sustain aberrant anti-differentiation gene transcription and perpetual tumor cell growth.
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Affiliation(s)
- Di Yu
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Yingying Liang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Claudia Kim
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anbalagan Jaganathan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Donglei Ji
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Xinye Han
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Xuelan Yang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Yanjie Jia
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Ruirui Gu
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
- International Center of Future Science, Jilin University, Changchun, 130012, China
| | - Chunyu Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin, 130012, China
| | - Qiang Zhang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Ka Lung Cheung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Lei Zeng
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130021, China.
- International Center of Future Science, Jilin University, Changchun, 130012, China.
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Ibrahim Z, Wang T, Destaing O, Salvi N, Hoghoughi N, Chabert C, Rusu A, Gao J, Feletto L, Reynoird N, Schalch T, Zhao Y, Blackledge M, Khochbin S, Panne D. Structural insights into p300 regulation and acetylation-dependent genome organisation. Nat Commun 2022; 13:7759. [PMID: 36522330 PMCID: PMC9755262 DOI: 10.1038/s41467-022-35375-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Histone modifications are deposited by chromatin modifying enzymes and read out by proteins that recognize the modified state. BRD4-NUT is an oncogenic fusion protein of the acetyl lysine reader BRD4 that binds to the acetylase p300 and enables formation of long-range intra- and interchromosomal interactions. We here examine how acetylation reading and writing enable formation of such interactions. We show that NUT contains an acidic transcriptional activation domain that binds to the TAZ2 domain of p300. We use NMR to investigate the structure of the complex and found that the TAZ2 domain has an autoinhibitory role for p300. NUT-TAZ2 interaction or mutations found in cancer that interfere with autoinhibition by TAZ2 allosterically activate p300. p300 activation results in a self-organizing, acetylation-dependent feed-forward reaction that enables long-range interactions by bromodomain multivalent acetyl-lysine binding. We discuss the implications for chromatin organisation, gene regulation and dysregulation in disease.
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Affiliation(s)
- Ziad Ibrahim
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Tao Wang
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Olivier Destaing
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Nicola Salvi
- Institut de Biologie Structurale, CNRS, CEA, UGA, Grenoble, France
| | - Naghmeh Hoghoughi
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Clovis Chabert
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Alexandra Rusu
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Jinjun Gao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Leonardo Feletto
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Nicolas Reynoird
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Thomas Schalch
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Saadi Khochbin
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Daniel Panne
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
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Elrakaybi A, Ruess DA, Lübbert M, Quante M, Becker H. Epigenetics in Pancreatic Ductal Adenocarcinoma: Impact on Biology and Utilization in Diagnostics and Treatment. Cancers (Basel) 2022; 14:cancers14235926. [PMID: 36497404 PMCID: PMC9738647 DOI: 10.3390/cancers14235926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive malignancies with high potential of metastases and therapeutic resistance. Although genetic mutations drive PDAC initiation, they alone do not explain its aggressive nature. Epigenetic mechanisms, including aberrant DNA methylation and histone modifications, significantly contribute to inter- and intratumoral heterogeneity, disease progression and metastasis. Thus, increased understanding of the epigenetic landscape in PDAC could offer new potential biomarkers and tailored therapeutic approaches. In this review, we shed light on the role of epigenetic modifications in PDAC biology and on the potential clinical applications of epigenetic biomarkers in liquid biopsy. In addition, we provide an overview of clinical trials assessing epigenetically targeted treatments alone or in combination with other anticancer therapies to improve outcomes of patients with PDAC.
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Affiliation(s)
- Asmaa Elrakaybi
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Department of Clinical Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Dietrich A. Ruess
- Department of General and Visceral Surgery, Center of Surgery, Medical Center University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Michael Quante
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
- Department of Gastroenterology and Hepatology, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Heiko Becker
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
- Correspondence: ; Tel.: +49-761-270-36000
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NUTM1-Rearranged Neoplasms-A Heterogeneous Group of Primitive Tumors with Expanding Spectrum of Histology and Molecular Alterations-An Updated Review. Curr Oncol 2021; 28:4485-4503. [PMID: 34898574 PMCID: PMC8628659 DOI: 10.3390/curroncol28060381] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022] Open
Abstract
Nuclear protein of testis (NUT), a protein product of the NUTM1 gene (located on the long arm of chromosome 15) with highly restricted physiologic expression in post-meiotic spermatids, is the oncogenic driver of a group of emerging neoplasms when fused with genes involved in transcription regulation. Although initially identified in a group of lethal midline carcinomas in which NUT forms fusion proteins with bromodomain proteins, NUTM1-rearrangement has since been identified in tumors at non-midline locations, with non-bromodomain partners and with varied morphology. The histologic features of these tumors have also expanded to include sarcoma, skin adnexal tumors, and hematologic malignancies that harbor various fusion partners and are associated with markedly different clinical courses varying from benign to malignant. Most of these tumors have nondescript primitive morphology and therefore should be routinely considered in any undifferentiated neoplasm. The diagnosis is facilitated by the immunohistochemical use of the monoclonal C52 antibody, fluorescence in situ hybridization (FISH), and, recently, RNA-sequencing. The pathogenesis is believed to be altered expression of oncogenes or tumor suppressor genes by NUT-mediated genome-wide histone modification. NUTM1-rearranged neoplasms respond poorly to classical chemotherapy and radiation therapy. Targeted therapies such as bromodomain and extraterminal domain inhibitor (BETi) therapy are being developed. This current review provides an update on NUTM1-rearranged neoplasms, focusing on the correlation between basic sciences and clinical aspects.
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Li X, Shi H, Zhang W, Bai C, He M, Ta N, Huang H, Ning Y, Fang C, Qin H, Dong Y. Immunotherapy and Targeting the Tumor Microenvironment: Current Place and New Insights in Primary Pulmonary NUT Carcinoma. Front Oncol 2021; 11:690115. [PMID: 34660264 PMCID: PMC8515126 DOI: 10.3389/fonc.2021.690115] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Primary pulmonary nuclear protein of testis carcinoma is a rare and highly aggressive malignant tumor. It accounts for approximately 0.22% of primary thoracic tumors and is little known, so it is often misdiagnosed as pulmonary squamous cell carcinoma. No effective treatment has been formed yet, and the prognosis is extremely poor. This review aims to summarize the etiology, pathogenesis, diagnosis, treatment, and prognosis of primary pulmonary nuclear protein of testis carcinoma in order to better recognize it and discuss the current and innovative strategies to overcome it. With the increasing importance of cancer immunotherapy and tumor microenvironment, the review also discusses whether immunotherapy and targeting the tumor microenvironment can improve the prognosis of primary pulmonary nuclear protein of testis carcinoma and possible treatment strategies. We reviewed and summarized the clinicopathological features of all patients with primary pulmonary nuclear protein of testis carcinoma who received immunotherapy, including initial misdiagnosis, disease stage, immunohistochemical markers related to tumor neovascularization, and biomarkers related to immunotherapy, such as PD-L1 (programmed death-ligand 1) and TMB (tumor mutational burden). In the meanwhile, we summarized and analyzed the progression-free survival (PFS) and the overall survival (OS) of patients with primary pulmonary nuclear protein of testis carcinoma treated with PD-1 (programmed cell death protein 1)/PD-L1 inhibitors and explored potential population that may benefit from immunotherapy. To the best of our knowledge, this is the first review on the exploration of the tumor microenvironment and immunotherapy effectiveness in primary pulmonary nuclear protein of testis carcinoma.
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Affiliation(s)
- Xiang Li
- Department of Respiratory and Critical Care Medicine, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
| | - Hui Shi
- Department of Respiratory and Critical Care Medicine, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
| | - Chong Bai
- Department of Respiratory and Critical Care Medicine, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
| | - Miaoxia He
- Department of Pathology, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
| | - Na Ta
- Department of Pathology, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
| | - Haidong Huang
- Department of Respiratory and Critical Care Medicine, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yunye Ning
- Department of Respiratory and Critical Care Medicine, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
| | - Chen Fang
- Department of Respiratory and Critical Care Medicine, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
| | - Hao Qin
- Department of Respiratory and Critical Care Medicine, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yuchao Dong
- Department of Respiratory and Critical Care Medicine, Changhai Hospital (The First Affiliated Hospital of Naval Medical University), Naval Medical University (Second Military Medical University), Shanghai, China
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8
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Licht JD, Bennett RL. Leveraging epigenetics to enhance the efficacy of immunotherapy. Clin Epigenetics 2021; 13:115. [PMID: 34001289 PMCID: PMC8130138 DOI: 10.1186/s13148-021-01100-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022] Open
Abstract
Background Epigenetic mechanisms regulate chromatin accessibility patterns that govern interaction of transcription machinery with genes and their cis-regulatory elements. Mutations that affect epigenetic mechanisms are common in cancer. Because epigenetic modifications are reversible many anticancer strategies targeting these mechanisms are currently under development and in clinical trials. Main body Here we review evidence suggesting that epigenetic therapeutics can deactivate immunosuppressive gene expression or reprogram tumor cells to activate antigen presentation mechanisms. In addition, the dysregulation of epigenetic mechanisms commonly observed in cancer may alter the immunogenicity of tumor cells and effectiveness of immunotherapies. Conclusions Therapeutics targeting epigenetic mechanisms may be helpful to counter immune evasion and improve the effectiveness of immunotherapies.
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Affiliation(s)
- Jonathan D Licht
- Division of Hematology/Oncology, Department of Medicine, University of Florida Health Cancer Center, Cancer Genetics Research Complex, University of Florida, 2033 Mowry Road, Box 103633, Gainesville, FL, 32610, USA
| | - Richard L Bennett
- Division of Hematology/Oncology, Department of Medicine, University of Florida Health Cancer Center, Cancer Genetics Research Complex, University of Florida, 2033 Mowry Road, Box 103633, Gainesville, FL, 32610, USA.
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9
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Rosencrance CD, Ammouri HN, Yu Q, Ge T, Rendleman EJ, Marshall SA, Eagen KP. Chromatin Hyperacetylation Impacts Chromosome Folding by Forming a Nuclear Subcompartment. Mol Cell 2020; 78:112-126.e12. [PMID: 32243828 DOI: 10.1016/j.molcel.2020.03.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 02/04/2020] [Accepted: 03/12/2020] [Indexed: 12/24/2022]
Abstract
Delineating how chromosomes fold at length scales beyond one megabase remains obscure relative to smaller-scale folding into TADs, loops, and nucleosomes. We find that rather than simply unfolding chromatin, histone hyperacetylation results in interactions between distant genomic loci separated by tens to hundreds of megabases, even in the absence of transcription. These hyperacetylated "megadomains" are formed by the BRD4-NUT fusion oncoprotein, interact both within and between chromosomes, and form a specific nuclear subcompartment that has elevated gene activity with respect to other subcompartments. Pharmacological degradation of BRD4-NUT results in collapse of megadomains and attenuation of the interactions between them. In contrast, these interactions persist and contacts between newly acetylated regions are formed after inhibiting RNA polymerase II initiation. Our structure-function approach thus reveals that broad chromatin domains of identical biochemical composition, independent of transcription, form nuclear subcompartments, and also indicates the potential of altering chromosome structure for treating human disease.
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Affiliation(s)
- Celeste D Rosencrance
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Haneen N Ammouri
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Qi Yu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Tiffany Ge
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kyle P Eagen
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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10
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Wang R, Yang JF, Ho F, Robertson ES, You J. Bromodomain-Containing Protein BRD4 Is Hyperphosphorylated in Mitosis. Cancers (Basel) 2020; 12:E1637. [PMID: 32575711 PMCID: PMC7353023 DOI: 10.3390/cancers12061637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/06/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022] Open
Abstract
The epigenetic reader BRD4 binds acetylated histones and plays a central role in controlling cellular gene transcription and proliferation. Dysregulation of BRD4's activity has been implicated in the pathogenesis of a wide variety of cancers. While blocking BRD4 interaction with acetylated histones using BET inhibitors (BETis) has been tested in clinical trials, many cancers have acquired BETi resistance. However, the underlying mechanisms are poorly understood and BETi resistance remains a pressing clinical problem. We previously showed that BRD4 phosphorylation supports stronger chromatin binding and target oncogene expression. In this study, we discovered that BRD4 is hyperphosphorylated by CDK1 during mitosis and determined the major CDK1 phosphorylation sites in BRD4. Using CRISPR/Cas9 gene editing, we replaced endogenous BRD4 with a non-phosphorylatable mutant and demonstrated that CDK1-mediated BRD4 phosphorylation contributes to BETi resistance. CDK1 over-activation frequently observed in cancers has the potential to cause aberrant BRD4 hyperphosphorylation persisting outside of mitosis to strengthen its target gene binding and confer BETi resistance. We found that dual CDK1 and BET inhibition generates a synergistic effect in killing BETi-resistant cancer cells. Our study therefore suggests that CDK1 inhibition can be employed to overcome tumor BETi resistance and improve treatments for BRD4-associated cancers.
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Affiliation(s)
- Ranran Wang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (R.W.); (J.F.Y.); (F.H.)
| | - June F. Yang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (R.W.); (J.F.Y.); (F.H.)
| | - Flora Ho
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (R.W.); (J.F.Y.); (F.H.)
| | - Erle S. Robertson
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Jianxin You
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (R.W.); (J.F.Y.); (F.H.)
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11
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Therapeutic targeting of p300/CBP HAT domain for the treatment of NUT midline carcinoma. Oncogene 2020; 39:4770-4779. [PMID: 32366905 PMCID: PMC7286816 DOI: 10.1038/s41388-020-1301-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 11/09/2022]
Abstract
Nuclear protein of the testis (NUT) midline carcinoma (NMC), is a rare and highly aggressive form of undifferentiated squamous cell carcinoma. NMC is molecularly characterized by chromosomal rearrangement of the NUT gene to another gene, most commonly the bromodomain and extraterminal domain (BET) gene BRD4, forming the BRD4-NUT fusion oncogene. Therefore, inhibiting BRD4-NUT oncogenic function directly by BET inhibitors represents an attractive therapeutic approach but toxicity may limit the use of pan-BET inhibitors treating this cancer. We thus performed a drug screening approach using a library consisting of epigenetic compounds and ‘Donated Chemical Probes’ collated by the Structural Genomics Consortium (SGC) and identified the p300/CBP HAT inhibitor A-485, in addition to the well-known BET inhibitor JQ1, to be the most active candidate for NMC treatment. In contrast to JQ1, A-485 was selectively potent in NMC compared to other cell lines tested. Mechanistically, A-485 inhibited p300-mediated histone acetylation, leading to disruption of BRD4-NUT binding to hyperacetylated megadomains. Consistently, BRD4-NUT megadomain-associated genes MYC, CCAT1 and TP63 were downregulated by A-485. A-485 strongly induced squamous differentiation, cell cycle arrest and apoptosis. Combined inhibition of p300/CBP and BET showed synergistic effects. In summary, we identified the p300/CBP HAT domain as a putative therapeutic target in highly therapy-resistant NMC.
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12
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Douglas JK, Callahan RE, Hothem ZA, Cousineau CS, Kawak S, Thibodeau BJ, Bergeron S, Li W, Peeples CE, Wasvary HJ. Genomic variation as a marker of response to neoadjuvant therapy in locally advanced rectal cancer. Mol Cell Oncol 2020; 7:1716618. [PMID: 32391418 PMCID: PMC7199754 DOI: 10.1080/23723556.2020.1716618] [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: 10/14/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 02/07/2023]
Abstract
There is variation in the responsiveness of locally advanced rectal cancer to neoadjuvant chemoradiation, from complete response to total resistance. This study compared genetic variation in rectal cancer patients who had a complete response to chemoradiation versus poor response, using tumor tissue samples sequenced with genomics analysis software. Rectal cancer patients treated with chemoradiation and proctectomy June 2006-March 2017 were grouped based on response to chemoradiation: those with no residual tumor after surgery (CR, complete responders, AJCC-CPR tumor grade 0, n = 8), and those with poor response (PR, AJCC-CPR tumor grade two or three on surgical resection, n = 8). We identified 195 variants in 83 genes in tissue specimens implicated in colorectal cancer biopathways. PR patients showed mutations in four genes not mutated in complete responders: KDM6A, ABL1, DAXX-ZBTB22, and KRAS. Ten genes were mutated only in the CR group, including ARID1A, PMS2, JAK1, CREBBP, MTOR, RB1, PRKAR1A, FBXW7, ATM C11orf65, and KMT2D, with specific discriminating variants noted in DMNT3A, KDM6A, MTOR, APC, and TP53. Although conclusions may be limited by small sample size in this pilot study, we identified multiple genetic variations in tumor DNA from rectal cancer patients who are poor responders to neoadjuvant chemoradiation, compared to complete responders.
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Affiliation(s)
| | - Rose E. Callahan
- Department of Surgical Research, Beaumont Research Institute, Royal Oak, MI, USA
| | | | | | - Samer Kawak
- Department of Surgery, Beaumont Health, Royal Oak, MI, USA
| | | | | | - Wei Li
- Department of Pathology, Beaumont Health, Royal Oak, MI, USA
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13
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McEvoy CR, Fox SB, Prall OWJ. Emerging entities in NUTM1-rearranged neoplasms. Genes Chromosomes Cancer 2020; 59:375-385. [PMID: 32060986 DOI: 10.1002/gcc.22838] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 12/11/2022] Open
Abstract
Structural alterations of NUTM1 were originally thought to be restricted to poorly differentiated carcinomas with variable squamous differentiation originating in the midline organs of children and adolescents. Termed NUT carcinomas (NCs), they were defined by a t(15;19) chromosomal rearrangement that was found to result in a BRD4-NUTM1 gene fusion. However, the use of DNA and RNA-based next-generation sequencing has recently revealed a multitude of new NUTM1 fusion partners in a diverse array of neoplasms including sarcoma-like tumors, poromas, and acute lymphoblastic leukemias (ALLs) that we propose to call NUTM1-rearranged neoplasms (NRNs). Intriguingly, the nosology of NRNs often correlates with the functional classification of the fusion partner, suggesting different oncogenic mechanisms within each NRN division. Indeed, whereas NCs are characterized by their aggressiveness and intransigence to standard therapeutic measures, the more positive clinical outcomes seen in some sarcoma and ALL NRNs may reflect these mechanistic differences. Here we provide a broad overview of the molecular, nosological, and clinical features in these newly discovered neoplastic entities. We describe how aberrant expression of NUTM1 due to fusion with an N-terminal DNA/chromatin-binding protein can generate a potentially powerful chromatin modifier that can give rise to oncogenic transformation in numerous cellular contexts. We also conclude that classification, clinical behavior, and therapeutic options may be best defined by the NUTM1 fusion partner rather than by tumor morphology or immunohistochemical profile.
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Affiliation(s)
- Christopher R McEvoy
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Owen W J Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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14
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Neckles C, Sundara Rajan S, Caplen NJ. Fusion transcripts: Unexploited vulnerabilities in cancer? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1562. [PMID: 31407506 PMCID: PMC6916338 DOI: 10.1002/wrna.1562] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Gene fusions are an important class of mutations in several cancer types and include genomic rearrangements that fuse regulatory or coding elements from two different genes. Analysis of the genetics of cancers harboring fusion oncogenes and the proteins they encode have enhanced cancer diagnosis and in some cases patient treatment. However, the effect of the complex structure of fusion genes on the biogenesis of the resulting chimeric transcripts they express is not well studied. There are two potential RNA‐related vulnerabilities inherent to fusion‐driven cancers: (a) the processing of the fusion precursor messenger RNA (pre‐mRNA) to the mature mRNA and (b) the mature mRNA. In this study, we discuss the effects that the genetic organization of fusion oncogenes has on the generation of translatable mature RNAs and the diversity of fusion transcripts expressed in different cancer subtypes, which can fundamentally influence both tumorigenesis and treatment. We also discuss functional genomic approaches that can be utilized to identify proteins that mediate the processing of fusion pre‐mRNAs. Furthermore, we assert that an enhanced understanding of fusion transcript biogenesis and the diversity of the chimeric RNAs present in fusion‐driven cancers will increase the likelihood of successful application of RNA‐based therapies in this class of tumors. This article is categorized under:RNA Processing > RNA Editing and Modification RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Carla Neckles
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
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15
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Shiota H, Elya JE, Alekseyenko AA, Chou PM, Gorman SA, Barbash O, Becht K, Danga K, Kuroda MI, Nardi V, French CA. "Z4" Complex Member Fusions in NUT Carcinoma: Implications for a Novel Oncogenic Mechanism. Mol Cancer Res 2018; 16:1826-1833. [PMID: 30139738 DOI: 10.1158/1541-7786.mcr-18-0474] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/11/2018] [Accepted: 08/13/2018] [Indexed: 12/16/2022]
Abstract
Nuclear protein in testis (NUT) carcinoma (NC) is a rare, distinctly aggressive subtype of squamous carcinoma defined by the presence of NUT-fusion oncogenes resulting from chromosomal translocation. In most cases, the NUT gene (NUTM1) is fused to bromodomain containing 4 (BRD4) forming the BRD4-NUT oncogene. Here, a novel fusion partner to NUT was discovered using next-generation sequencing and FISH from a young patient with an undifferentiated malignant round cell tumor. Interestingly, the NUT fusion identified involved ZNF592, a zinc finger containing protein, which was previously identified as a component of the BRD4-NUT complex. In BRD4-NUT-expressing NC cells, wild-type ZNF592 and other associated "Z4" complex proteins, including ZNF532 and ZMYND8, colocalize with BRD4-NUT in characteristic nuclear foci. Furthermore, ectopic expression of BRD4-NUT in a non-NC cell line induces sequestration of Z4 factors to BRD4-NUT foci. Finally, the data demonstrate the specific dependency of NC cells on Z4 modules, ZNF532 and ZNF592. IMPLICATIONS: This study establishes the oncogenic role of Z4 factors in NC, offering potential new targeted therapeutic strategies in this incurable cancer.Visual Overview: http://mcr.aacrjournals.org/content/molcanres/16/12/1826/F1.large.jpg.
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Affiliation(s)
- Hitoshi Shiota
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Janine E Elya
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Artyom A Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Pauline M Chou
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Shelby A Gorman
- Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Olena Barbash
- Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Kelly Becht
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kristina Danga
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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16
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Brägelmann J, Dammert MA, Dietlein F, Heuckmann JM, Choidas A, Böhm S, Richters A, Basu D, Tischler V, Lorenz C, Habenberger P, Fang Z, Ortiz-Cuaran S, Leenders F, Eickhoff J, Koch U, Getlik M, Termathe M, Sallouh M, Greff Z, Varga Z, Balke-Want H, French CA, Peifer M, Reinhardt HC, Örfi L, Kéri G, Ansén S, Heukamp LC, Büttner R, Rauh D, Klebl BM, Thomas RK, Sos ML. Systematic Kinase Inhibitor Profiling Identifies CDK9 as a Synthetic Lethal Target in NUT Midline Carcinoma. Cell Rep 2018; 20:2833-2845. [PMID: 28930680 PMCID: PMC5622049 DOI: 10.1016/j.celrep.2017.08.082] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/27/2017] [Accepted: 08/24/2017] [Indexed: 12/27/2022] Open
Abstract
Kinase inhibitors represent the backbone of targeted cancer therapy, yet only a limited number of oncogenic drivers are directly druggable. By interrogating the activity of 1,505 kinase inhibitors, we found that BRD4-NUT-rearranged NUT midline carcinoma (NMC) cells are specifically killed by CDK9 inhibition (CDK9i) and depend on CDK9 and Cyclin-T1 expression. We show that CDK9i leads to robust induction of apoptosis and of markers of DNA damage response in NMC cells. While both CDK9i and bromodomain inhibition over time result in reduced Myc protein expression, only bromodomain inhibition induces cell differentiation and a p21-induced cell-cycle arrest in these cells. Finally, RNA-seq and ChIP-based analyses reveal a BRD4-NUT-specific CDK9i-induced perturbation of transcriptional elongation. Thus, our data provide a mechanistic basis for the genotype-dependent vulnerability of NMC cells to CDK9i that may be of relevance for the development of targeted therapies for NMC patients.
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Affiliation(s)
- Johannes Brägelmann
- Molecular Pathology, Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Marcel A Dammert
- Molecular Pathology, Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Felix Dietlein
- Department I of Internal Medicine and Center for Integrated Oncology, University Hospital of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | | | - Axel Choidas
- Lead Discovery Center (LDC) GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Stefanie Böhm
- Molecular Pathology, Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - André Richters
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44221 Dortmund, Germany
| | - Debjit Basu
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44221 Dortmund, Germany
| | - Verena Tischler
- Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Carina Lorenz
- Molecular Pathology, Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Peter Habenberger
- Lead Discovery Center (LDC) GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Zhizhou Fang
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44221 Dortmund, Germany
| | - Sandra Ortiz-Cuaran
- Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Frauke Leenders
- Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Jan Eickhoff
- Lead Discovery Center (LDC) GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Uwe Koch
- Lead Discovery Center (LDC) GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Matthäus Getlik
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44221 Dortmund, Germany
| | - Martin Termathe
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44221 Dortmund, Germany
| | - Muhammad Sallouh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44221 Dortmund, Germany
| | - Zoltán Greff
- Vichem Chemie Research Ltd., Herman Ottó u. 15, Budapest, Hungary
| | - Zoltán Varga
- Vichem Chemie Research Ltd., Herman Ottó u. 15, Budapest, Hungary
| | - Hyatt Balke-Want
- Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany; Department I of Internal Medicine and Center for Integrated Oncology, University Hospital of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Martin Peifer
- Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - H Christian Reinhardt
- Department I of Internal Medicine and Center for Integrated Oncology, University Hospital of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - László Örfi
- Vichem Chemie Research Ltd., Herman Ottó u. 15, Budapest, Hungary; Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes E. U.9, Budapest, Hungary
| | - György Kéri
- Vichem Chemie Research Ltd., Herman Ottó u. 15, Budapest, Hungary
| | - Sascha Ansén
- Department I of Internal Medicine and Center for Integrated Oncology, University Hospital of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Lukas C Heukamp
- Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany; Institute of Pathology, Medical Faculty, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, Medical Faculty, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44221 Dortmund, Germany
| | - Bert M Klebl
- Lead Discovery Center (LDC) GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Roman K Thomas
- Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany; Institute of Pathology, Medical Faculty, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Martin L Sos
- Molecular Pathology, Institute of Pathology, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Department of Translational Genomics, Medical Faculty, University of Cologne, Weyertal 115b, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany.
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17
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Abstract
Alterations of genes regulating epigenetic processes are frequently found as cancer drivers and may cause widespread alterations of DNA methylation, histone modification patterns, or chromatin structure that disrupt normal patterns of gene expression. Because of the inherent reversibility of epigenetic changes, inhibitors targeting these processes are promising anticancer strategies. Small molecules targeting epigenetic regulators have been developed recently, and clinical trials of these agents are under way for hematologic malignancies and solid tumors. In this review, we describe how the writers, readers, and erasers of epigenetic marks are dysregulated in cancer and summarize the development of therapies targeting these mechanisms.
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Affiliation(s)
- Richard L Bennett
- Division of Hematology & Oncology, Department of Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, Florida 32606, USA;
| | - Jonathan D Licht
- Division of Hematology & Oncology, Department of Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, Florida 32606, USA;
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18
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Stirnweiss A, Oommen J, Kotecha RS, Kees UR, Beesley AH. Molecular-genetic profiling and high-throughput in vitro drug screening in NUT midline carcinoma-an aggressive and fatal disease. Oncotarget 2017; 8:112313-112329. [PMID: 29348827 PMCID: PMC5762512 DOI: 10.18632/oncotarget.22862] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 11/26/2017] [Indexed: 12/11/2022] Open
Abstract
NUT midline carcinoma (NMC) is a rare and aggressive cancer, with survival typically less than seven months, that can arise in people of any age. Genetically, NMC is defined by the chromosomal fusion of NUTM1 with a chromatin-binding partner, typically the bromodomain-containing protein BRD4. However, little is known about other genetic aberrations in this disease. In this study, we used a unique panel of cell lines to describe the molecular-genetic features of NMC. Next-generation sequencing identified a recurring high-impact mutation in the DNA-helicase gene RECQL5 in 75% of lines studied, and biological signals from mutation-signature and network analyses consistent with a general failure in DNA-repair. A high-throughput drug screen confirmed that microtubule inhibitors, topoisomerase inhibitors and anthracyclines are highly cytotoxic in the majority of NMC lines, and that cell lines expressing the BRD4-NUTM1 (exon11:exon2) variant are an order of magnitude more responsive to bromodomain inhibitors (iBETs) on average than those with other BRD4-NUTM1 translocation variants. We also identified a highly significant correlation between iBET and aurora kinase inhibitor efficacy in this study. Integration of exome sequencing, transcriptome, and drug sensitivity profiles suggested that aberrant activity of the nuclear receptor co-activator NCOA3 may correlate with poor response to iBETs. In conclusion, our data emphasize the heterogeneity of NMC and highlights genetic aberrations that could be explored to improve therapeutic strategies. The novel finding of a recurring RECQL5 mutation, together with recent reports of chromoplexy in this disease, suggests that DNA-repair pathways are likely to play a central role in NMC tumorigenesis.
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Affiliation(s)
- Anja Stirnweiss
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia.,Drug Discovery Group, Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Joyce Oommen
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Rishi S Kotecha
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia.,Department of Haematology and Oncology, Princess Margaret Hospital for Children, Perth, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - Ursula R Kees
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Alex H Beesley
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia
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19
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Abstract
Alterations of genes regulating epigenetic processes are frequently found as cancer drivers and may cause widespread alterations of DNA methylation, histone modification patterns, or chromatin structure that disrupt normal patterns of gene expression. Because of the inherent reversibility of epigenetic changes, inhibitors targeting these processes are promising anticancer strategies. Small molecules targeting epigenetic regulators have been developed recently, and clinical trials of these agents are under way for hematologic malignancies and solid tumors. In this review, we describe how the writers, readers, and erasers of epigenetic marks are dysregulated in cancer and summarize the development of therapies targeting these mechanisms.
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Affiliation(s)
- Richard L Bennett
- Division of Hematology & Oncology, Department of Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, Florida 32606, USA;
| | - Jonathan D Licht
- Division of Hematology & Oncology, Department of Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, Florida 32606, USA;
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20
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Xu Y, Vakoc CR. Targeting Cancer Cells with BET Bromodomain Inhibitors. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026674. [PMID: 28213432 DOI: 10.1101/cshperspect.a026674] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cancer cells are often hypersensitive to the targeting of transcriptional regulators, which may reflect the deregulated gene expression programs that underlie malignant transformation. One of the most prominent transcriptional vulnerabilities in human cancer to emerge in recent years is the bromodomain and extraterminal (BET) family of proteins, which are coactivators that link acetylated transcription factors and histones to the activation of RNA polymerase II. Despite unclear mechanisms underlying the gene specificity of BET protein function, small molecules targeting these regulators preferentially suppress the transcription of cancer-promoting genes. As a consequence, BET inhibitors elicit anticancer activity in numerous malignant contexts at doses that can be tolerated by normal tissues, a finding supported by animal studies and by phase I clinical trials in human cancer patients. In this review, we will discuss the remarkable, and often perplexing, therapeutic effects of BET bromodomain inhibition in cancer.
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Affiliation(s)
- Yali Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
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21
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Uncovering BRD4 hyperphosphorylation associated with cellular transformation in NUT midline carcinoma. Proc Natl Acad Sci U S A 2017. [PMID: 28630312 DOI: 10.1073/pnas.1703071114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The epigenetic reader BRD4 plays a vital role in transcriptional regulation, cellular growth control, and cell-cycle progression. Dysregulation of BRD4 function has been implicated in the pathogenesis of a wide range of cancers. However, how BRD4 is regulated to maintain its normal function in healthy cells and how alteration of this process leads to cancer remain poorly understood. In this study, we discovered that BRD4 is hyperphosphorylated in NUT midline carcinoma and identified CDK9 as a potential kinase mediating BRD4 hyperphosphorylation. Disruption of BRD4 hyperphosphorylation using both chemical and molecular inhibitors led to the repression of BRD4 downstream oncogenes and abrogation of cellular transformation. BRD4 hyperphosphorylation is also observed in other cancers displaying enhanced BRD4 oncogenic activity. Our study revealed a mechanism that may regulate BRD4 biological function through phosphorylation, which, when dysregulated, could lead to oncogenesis. Our finding points to strategies to target the aberrant BRD4 signaling specifically for cancer intervention.
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22
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Padmanabhan B, Mathur S, Manjula R, Tripathi S. Bromodomain and extra-terminal (BET) family proteins: New therapeutic targets in major diseases. J Biosci 2017; 41:295-311. [PMID: 27240990 DOI: 10.1007/s12038-016-9600-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The bromodomains and extra-terminal domain (BET) family proteins recognize acetylated chromatin through their bromodomains (BDs) and help in regulating gene expression. BDs are chromatin 'readers': by interacting with acetylated lysines on the histone tails, they recruit chromatin-regulating proteins on the promoter region to regulate gene expression and repression. Extensive efforts have been employed by scientific communities worldwide to identify and develop potential inhibitors of BET family BDs to regulate protein expression by inhibiting acetylated histone (H3/H4) interactions. Several small molecule inhibitors have been reported, which not only have high affinity but also have high specificity to BET BDs. These developments make BET family proteins an important therapeutic targets for major diseases such as cancer, neurological disorders, obesity and inflammation. Here, we review and discuss the structural biology of BET family BDs and their applications in major diseases.
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Affiliation(s)
- Balasundaram Padmanabhan
- Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore 560 029, India
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Taniguchi Y. The Bromodomain and Extra-Terminal Domain (BET) Family: Functional Anatomy of BET Paralogous Proteins. Int J Mol Sci 2016; 17:ijms17111849. [PMID: 27827996 PMCID: PMC5133849 DOI: 10.3390/ijms17111849] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/31/2016] [Accepted: 11/02/2016] [Indexed: 12/31/2022] Open
Abstract
The Bromodomain and Extra-Terminal Domain (BET) family of proteins is characterized by the presence of two tandem bromodomains and an extra-terminal domain. The mammalian BET family of proteins comprises BRD2, BRD3, BRD4, and BRDT, which are encoded by paralogous genes that may have been generated by repeated duplication of an ancestral gene during evolution. Bromodomains that can specifically bind acetylated lysine residues in histones serve as chromatin-targeting modules that decipher the histone acetylation code. BET proteins play a crucial role in regulating gene transcription through epigenetic interactions between bromodomains and acetylated histones during cellular proliferation and differentiation processes. On the other hand, BET proteins have been reported to mediate latent viral infection in host cells and be involved in oncogenesis. Human BRD4 is involved in multiple processes of the DNA virus life cycle, including viral replication, genome maintenance, and gene transcription through interaction with viral proteins. Aberrant BRD4 expression contributes to carcinogenesis by mediating hyperacetylation of the chromatin containing the cell proliferation-promoting genes. BET bromodomain blockade using small-molecule inhibitors gives rise to selective repression of the transcriptional network driven by c-MYC These inhibitors are expected to be potential therapeutic drugs for a wide range of cancers. This review presents an overview of the basic roles of BET proteins and highlights the pathological functions of BET and the recent developments in cancer therapy targeting BET proteins in animal models.
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Affiliation(s)
- Yasushi Taniguchi
- Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa 259-1193, Japan.
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Abstract
BET proteins have recently become recognized for their role in a broad range of cancers and are defined by the presence of two acetyl-histone reading bromodomains and an ET domain. This family of proteins includes BRD2, BRD3, BRD4, and BRDT. BRD4 is the most-studied BET protein in cancer, and normally serves as an epigenetic reader that links active chromatin marks to transcriptional elongation through activation of RNA polymerase II. The role of BRD3 and BRD4 first became known in cancer as mutant oncoproteins fused to the p300-recruiting NUT protein in a rare aggressive subtype of squamous cell cancer known as NUT midline carcinoma (NMC). BET inhibitors are acetyl-histone mimetics that specifically bind BET bromodomains, competitively inhibiting its engagement with chromatin. The antineoplastic effects of BET inhibitors were first demonstrated in NMC and have since been shown to be effective at inhibiting the growth of many different cancers, particularly acute leukemia. BET inhibitors have also been instrumental as tool compounds that have demonstrated the key role of BRD4 in driving NMC and non-NMC cancer growth. Many clinical trials enrolling patients with hematologic and solid tumors are ongoing, with encouraging preliminary findings. BET proteins BRD2, BRD3, and BRD4 are expressed in nearly all cells of the body, so there are concerns of toxicity with BET inhibitors, as well as the development of resistance. Toxicity and resistance may be overcome by combining BET inhibitors with other targeted inhibitors, or through the use of novel BET inhibitor derivatives.
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Affiliation(s)
- C A French
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.
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Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, French CA. The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. Genes Dev 2015. [PMID: 26220994 PMCID: PMC4526735 DOI: 10.1101/gad.267583.115] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
NUT midline carcinoma (NMC), a subtype of squamous cell cancer, is one of the most aggressive human solid malignancies known. NMC is driven by the creation of a translocation oncoprotein, BRD4-NUT, which blocks differentiation and drives growth of NMC cells. BRD4-NUT forms distinctive nuclear foci in patient tumors, which we found correlate with ∼100 unprecedented, hyperacetylated expanses of chromatin that reach up to 2 Mb in size. These "megadomains" appear to be the result of aberrant, feed-forward loops of acetylation and binding of acetylated histones that drive transcription of underlying DNA in NMC patient cells and naïve cells induced to express BRD4-NUT. Megadomain locations are typically cell lineage-specific; however, the cMYC and TP63 regions are targeted in all NMCs tested and play functional roles in tumor growth. Megadomains appear to originate from select pre-existing enhancers that progressively broaden but are ultimately delimited by topologically associating domain (TAD) boundaries. Therefore, our findings establish a basis for understanding the powerful role played by large-scale chromatin organization in normal and aberrant lineage-specific gene transcription.
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Affiliation(s)
- Artyom A Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Erica M Walsh
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xin Wang
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Adlai R Grayson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter T Hsi
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA; Hematology/Oncology Program, Children's Hospital, Boston, Massachusetts 02115, USA; Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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Harms A, Herpel E, Pfarr N, Penzel R, Heussel CP, Herth FJF, Dienemann H, Weichert W, Warth A. NUT carcinoma of the thorax: Case report and review of the literature. Lung Cancer 2015; 90:484-91. [PMID: 26490121 DOI: 10.1016/j.lungcan.2015.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/14/2015] [Accepted: 10/03/2015] [Indexed: 12/22/2022]
Abstract
NUT (nuclear protein in testis) carcinomas are exceedingly rare neoplasms with specific molecular alterations and often follow a devastating course. Thus, a precise early diagnosis is of utmost importance. Known from the sinonasal region for years, the new 2015 WHO classification now also recognizes the existence of this entity in the thorax, specifically the lungs and the mediastinum. However, yet available data on this entity are sparse. Here, we report on a 31 years old female patient with an aggressively growing tumor localized in the median line that was initially sampled by endobronchial ultrasound-guided transbronchial biopsies. Pathological assessment of the biopsy specimens revealed a NUT carcinoma with typical morphological characteristics and an uncommon NUT translocation variant with a NSD3-NUT fusion. Diagnosis was further confirmed in the subsequent resection specimen. We describe specific clinical, histomorphological, and molecular characteristics of this tumor and provide a comprehensive review of the current literature on these rare neoplasms.
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Affiliation(s)
- Alexander Harms
- Institute of Pathology, University Hospital Heidelberg, Germany
| | - Esther Herpel
- Institute of Pathology, University Hospital Heidelberg, Germany
| | - Nicole Pfarr
- Institute of Pathology, University Hospital Heidelberg, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Germany
| | - Claus-Peter Heussel
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at Heidelberg University, Germany; Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Germany
| | - Felix J F Herth
- Department of Pneumology and Respiratory Critical Care Medicine, Thoraxklinik at Heidelberg University, Germany
| | - Hendrik Dienemann
- Department of Thoracic Surgery, Thoraxklinik at Heidelberg University, Germany
| | - Wilko Weichert
- Institute of Pathology, University Hospital Heidelberg, Germany; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Germany.
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Raza A, Cao H, Conrad R, Cobb C, Castelino-Prabhu S, Mirshahidi S, Shiraz P, Mirshahidi HR. Nuclear protein in testis midline carcinoma with unusual elevation of α-fetoprotein and synaptophysin positivity: a case report and review of the literature. Expert Rev Anticancer Ther 2015; 15:1199-213. [DOI: 10.1586/14737140.2015.1082909] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Chaidos A, Caputo V, Karadimitris A. Inhibition of bromodomain and extra-terminal proteins (BET) as a potential therapeutic approach in haematological malignancies: emerging preclinical and clinical evidence. Ther Adv Hematol 2015; 6:128-41. [PMID: 26137204 DOI: 10.1177/2040620715576662] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Post-translational modifications of the nucleosomal histone proteins orchestrate chromatin organization and gene expression in normal and cancer cells. Among them, the acetylation of N-terminal histone tails represents the fundamental epigenetic mark of open structure chromatin and active gene transcription. The bromodomain and extra-terminal (BET) proteins are epigenetic readers which utilize tandem bromodomains (BRD) modules to recognize and dock themselves on the acetylated lysine tails. The BET proteins act as scaffolds for the recruitment of transcription factors and chromatin organizers required in transcription initiation and elongation. The recent discovery of small molecules capable of blocking their lysine-binding pocket is the first paradigm of successful pharmacological inhibition of epigenetic readers. JQ1 is a prototype benzodiazepine molecule and a specific BET inhibitor with antineoplastic activity both in solid tumours and haematological malignancies. The quinolone I-BET151 and the suitable for clinical development I-BET762 benzodiazepine were introduced in parallel with JQ1 and have also shown potent antitumour activity in preclinical studies. I-BET762 is currently being tested in early phase clinical trials, along with a rapidly growing list of other BET inhibitors. Unlike older epigenetic therapies, the study of BET inhibitors has offered substantial, context-specific, mechanistic insights of their antitumour activity, which will facilitate optimal therapeutic targeting in future. Here, we review the development of this novel class of epigenetic drugs, the biology of BET protein inhibition, the emerging evidence from preclinical work and early phase clinical studies and we discuss their potential role in the treatment of haematological malignancies.
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Affiliation(s)
- Aristeidis Chaidos
- Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Valentina Caputo
- Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Anastasios Karadimitris
- Centre for Haematology, Department of Medicine, Imperial College London, 4th Floor Commonwealth Building, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
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Solomon LW, Magliocca KR, Cohen C, Müller S. Retrospective analysis of nuclear protein in testis (NUT) midline carcinoma in the upper aerodigestive tract and mediastinum. Oral Surg Oral Med Oral Pathol Oral Radiol 2015; 119:213-20. [DOI: 10.1016/j.oooo.2014.09.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 11/30/2022]
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Wang R, You J. Mechanistic analysis of the role of bromodomain-containing protein 4 (BRD4) in BRD4-NUT oncoprotein-induced transcriptional activation. J Biol Chem 2014; 290:2744-58. [PMID: 25512383 DOI: 10.1074/jbc.m114.600759] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NUT midline carcinoma (NMC) is a rare but highly aggressive cancer typically caused by the translocation t(15;19), which results in the formation of the BRD4-NUT fusion oncoprotein. Previous studies have demonstrated that fusion of the NUT protein with the double bromodomains of BRD4 may significantly alter the cellular gene expression profile to contribute to NMC tumorigenesis. However, the mechanistic details of this BRD4-NUT function remain poorly understood. In this study, we examined the NUT function in transcriptional regulation by targeting it to a LacO transgene array integrated in U2OS 2-6-3 cells, which allow us to visualize how NUT alters the in situ gene transcription dynamic. Using this system, we demonstrated that the NUT protein tethered to the LacO locus recruits p300/CREB-binding protein (CBP), induces histone hyperacetylation, and enriches BRD4 to the transgene array chromatin foci. We also discovered that, in BRD4-NUT expressed in NMC cells, the NUT moiety of the fusion protein anchored to chromatin by the double bromodomains also stimulates histone hyperacetylation, which causes BRD4 to bind tighter to chromatin. Consequently, multiple BRD4-interacting factors are recruited to the NUT-associated chromatin locus to activate in situ transgene expression. This gene transcription function was repressed by either expression of a dominant negative inhibitor of the p300-NUT interaction or treatment with (+)-JQ1, which dissociates BRD4 from the LacO chromatin locus. Our data support a model in which BRD4-NUT-stimulated histone hyperacetylation recruits additional BRD4 and interacting partners to support transcriptional activation, which underlies the BRD4-NUT oncogenic mechanism in NMC.
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Affiliation(s)
- Ranran Wang
- From the Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6076
| | - Jianxin You
- From the Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6076
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31
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Liu W, Stein P, Cheng X, Yang W, Shao NY, Morrisey EE, Schultz RM, You J. BRD4 regulates Nanog expression in mouse embryonic stem cells and preimplantation embryos. Cell Death Differ 2014; 21:1950-60. [PMID: 25146928 DOI: 10.1038/cdd.2014.124] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/10/2014] [Accepted: 07/13/2014] [Indexed: 01/06/2023] Open
Abstract
Bromodomain-containing protein 4 (BRD4) is an important epigenetic reader implicated in the pathogenesis of a number of different cancers and other diseases. Brd4-null mouse embryos die shortly after implantation and are compromised in their ability to maintain the inner cell mass, which gives rise to embryonic stem cells (ESCs). Here we report that BRD4 regulates expression of the pluripotency factor Nanog in mouse ESCs and preimplantation embryos, as well as in human ESCs and embryonic cancer stem cells. Inhibition of BRD4 function using a chemical inhibitor, small interfering RNAs, or a dominant-negative approach suppresses Nanog expression, and abolishes the self-renewal ability of ESCs. We also find that BRD4 associates with BRG1 (brahma-related gene 1, aka Smarca4 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4)), a key regulator of ESC self-renewal and pluripotency, in the Nanog regulatory regions to regulate Nanog expression. Our study identifies Nanog as a novel BRD4 target gene, providing new insights for the biological function of BRD4 in stem cells and mouse embryos. Knowledge gained from these non-cancerous systems will facilitate future investigations of how Brd4 dysfunction leads to cancers.
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Affiliation(s)
- W Liu
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - P Stein
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - X Cheng
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - W Yang
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - N-Y Shao
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - E E Morrisey
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - R M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - J You
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
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French CA, Rahman S, Walsh EM, Kühnle S, Grayson AR, Lemieux ME, Grunfeld N, Rubin BP, Antonescu CR, Zhang S, Venkatramani R, Dal Cin P, Howley PM. NSD3-NUT fusion oncoprotein in NUT midline carcinoma: implications for a novel oncogenic mechanism. Cancer Discov 2014; 4:928-41. [PMID: 24875858 DOI: 10.1158/2159-8290.cd-14-0014] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED NUT midline carcinoma (NMC) is an aggressive subtype of squamous cell carcinoma that typically harbors BRD4/3-NUT fusion oncoproteins that block differentiation and maintain tumor growth. In 20% of cases, NUT is fused to uncharacterized non-BRD gene(s). We established a new patient-derived NMC cell line (1221) and demonstrated that it harbors a novel NSD3-NUT fusion oncogene. We find that NSD3-NUT is both necessary and sufficient for the blockade of differentiation and maintenance of proliferation in NMC cells. NSD3-NUT binds to BRD4, and BRD bromodomain inhibitors induce differentiation and arrest proliferation of 1221 cells. We find further that NSD3 is required for the blockade of differentiation in BRD4-NUT-expressing NMCs. These findings identify NSD3 as a novel critical oncogenic component and potential therapeutic target in NMC. SIGNIFICANCE The existence of a family of fusion oncogenes in squamous cell carcinoma is unprecedented, and should lead to key insights into aberrant differentiation in NMC and possibly other squamous cell carcinomas. The involvement of the NSD3 methyltransferase as a component of the NUT fusion protein oncogenic complex identifies a new potential therapeutic target.
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Affiliation(s)
| | - Shaila Rahman
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Erica M Walsh
- Department of Pathology, Brigham and Women's Hospital
| | - Simone Kühnle
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | | | | | - Noam Grunfeld
- Department of Pathology, Brigham and Women's Hospital
| | - Brian P Rubin
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Department of Molecular Genetics, Cleveland Clinic, and Lerner Research Institute, Cleveland, Ohio
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Songlin Zhang
- Department of Pathology & Laboratory Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Rajkumar Venkatramani
- Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California; and
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital
| | - Peter M Howley
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
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Wang R, Liu W, Helfer CM, Bradner JE, Hornick JL, Janicki SM, French CA, You J. Activation of SOX2 expression by BRD4-NUT oncogenic fusion drives neoplastic transformation in NUT midline carcinoma. Cancer Res 2014; 74:3332-43. [PMID: 24736545 DOI: 10.1158/0008-5472.can-13-2658] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BRD4 is implicated in the pathogenesis of a number of different cancers. It is also the target of translocation t(15;19) that accounts for the highly aggressive NUT midline carcinoma (NMC). We discovered that t(15;19) NMC cells display the ability to grow into stem cell-like spheres and express an exceptionally high level of the stem cell marker, SOX2. The BRD4-NUT fusion oncogene resulting from t(15;19) translocation is required for the abnormal activation of SOX2, which drives the stem cell-like proliferation and cellular transformation in NMC cells. SOX2 knockdown phenocopies the effects of BRD4-NUT inhibition, whereas ectopic SOX2 expression rescues the phenotype. The BRD4-NUT-induced abnormal SOX2 activation was observed in multiple NMC cell lines as well as in NMC primary tumors. We further demonstrate that BRD4-NUT oncoprotein recruits p300 to stimulate transcription activation and that inhibition of p300 represses SOX2 transcription in NMC cells. These studies identify this stem cell marker as a novel BRD4-NUT target that supports the highly aggressive transforming activity of t(15;19) carcinomas. Our study provides new mechanistic insights for understanding how alteration of BRD4 function by BRD4-NUT oncogene leads to the highly malignant NMC carcinoma. Because abnormal stem cell self-renewal is frequently observed during tumor formation and metastasis, the aberrant stem cell-like proliferation associated with BRD4 dysregulation observed in NMC carcinoma may have implications for studying the oncogenic mechanism of other BRD4-associated tumors.
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Affiliation(s)
- Ranran Wang
- Authors' Affiliations: Department of Microbiology, University of Pennsylvania Perelman School of Medicine; and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania; Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 510D; and Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Wei Liu
- Authors' Affiliations: Department of Microbiology, University of Pennsylvania Perelman School of Medicine; and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania; Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 510D; and Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Christine M Helfer
- Authors' Affiliations: Department of Microbiology, University of Pennsylvania Perelman School of Medicine; and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania; Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 510D; and Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - James E Bradner
- Authors' Affiliations: Department of Microbiology, University of Pennsylvania Perelman School of Medicine; and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania; Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 510D; and Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Jason L Hornick
- Authors' Affiliations: Department of Microbiology, University of Pennsylvania Perelman School of Medicine; and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania; Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 510D; and Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Susan M Janicki
- Authors' Affiliations: Department of Microbiology, University of Pennsylvania Perelman School of Medicine; and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania; Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 510D; and Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Christopher A French
- Authors' Affiliations: Department of Microbiology, University of Pennsylvania Perelman School of Medicine; and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania; Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 510D; and Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Jianxin You
- Authors' Affiliations: Department of Microbiology, University of Pennsylvania Perelman School of Medicine; and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania; Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 510D; and Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
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Rodriguez RM, Suarez-Alvarez B, Salvanés R, Huidobro C, Toraño EG, Garcia-Perez JL, Lopez-Larrea C, Fernandez AF, Bueno C, Menendez P, Fraga MF. Role of BRD4 in hematopoietic differentiation of embryonic stem cells. Epigenetics 2014; 9:566-78. [PMID: 24445267 DOI: 10.4161/epi.27711] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The bromodomain and extra terminal (BET) protein family member BRD4 is a transcriptional regulator, critical for cell cycle progression and cellular viability. Here, we show that BRD4 plays an important role in embryonic stem cell (ESC) regulation. During differentiation of ESCs, BRD4 expression is upregulated and its gene promoter becomes demethylated. Disruption of BRD4 expression in ESCs did not induce spontaneous differentiation but severely diminished hematoendothelial potential. Although BRD4 regulates c-Myc expression, our data show that the role of BRD4 in hematopoietic commitment is not exclusively mediated by c-Myc. Our results indicate that BRD4 is epigenetically regulated during hematopoietic differentiation ESCs in the context of a still unknown signaling pathway.
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Affiliation(s)
- Ramon M Rodriguez
- Cancer Epigenetics Laboratory; Instituto Universitario de Oncología del Principado de Asturias (IUOPA); HUCA; Universidad de Oviedo; Oviedo, Spain; Department of Immunology; Hospital Universitario Central de Asturias; Oviedo, Spain
| | | | - Ruben Salvanés
- Department of Immunology; Hospital Universitario Central de Asturias; Oviedo, Spain
| | - Covadonga Huidobro
- Cancer Epigenetics Laboratory; Instituto Universitario de Oncología del Principado de Asturias (IUOPA); HUCA; Universidad de Oviedo; Oviedo, Spain; MRC Human Genetics Unit; Institute of Genetics and Molecular Medicine; University of Edinburgh; Western General Hospital; Edinburgh, UK
| | - Estela G Toraño
- Cancer Epigenetics Laboratory; Instituto Universitario de Oncología del Principado de Asturias (IUOPA); HUCA; Universidad de Oviedo; Oviedo, Spain
| | - Jose L Garcia-Perez
- Department of Human DNA Variability; Pfizer-University of Granada and Andalusian Government Center for Genomics and Oncology (GENYO); Granada, Spain
| | - Carlos Lopez-Larrea
- Department of Immunology; Hospital Universitario Central de Asturias; Oviedo, Spain; Fundacion Renal "Íñigo Álvarez de Toledo"; Madrid, Spain
| | - Agustin F Fernandez
- Cancer Epigenetics Laboratory; Instituto Universitario de Oncología del Principado de Asturias (IUOPA); HUCA; Universidad de Oviedo; Oviedo, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute; Barcelona, Spain; Centre for Genomics and Oncological Research (GENYO); Pfizer/University of Granada/Andalusian Government; Granada, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute; Barcelona, Spain; Instituciò Catalana de Reserca i Estudis Avançats (ICREA); Barcelona, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory; Instituto Universitario de Oncología del Principado de Asturias (IUOPA); HUCA; Universidad de Oviedo; Oviedo, Spain; Department of Immunology and Oncology; Centro Nacional de Biotecnología/CNB-CSIC; Cantoblanco; Madrid, Spain
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Helfer CM, Wang R, You J. Analysis of the papillomavirus E2 and bromodomain protein Brd4 interaction using bimolecular fluorescence complementation. PLoS One 2013; 8:e77994. [PMID: 24205059 PMCID: PMC3808292 DOI: 10.1371/journal.pone.0077994] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/14/2013] [Indexed: 11/19/2022] Open
Abstract
The human papillomavirus (HPV) vaccines effectively protect against new infections of up to four HPV subtypes. However, these vaccines are not protective against many other clinically relevant HPV subtypes and are ineffective at treating established HPV infections. There is therefore a significant need for antiviral treatments for persistent HPV infections. A promising anti-HPV drug target is the interaction between the HPV E2 protein and cellular bromodomain-containing protein 4 (Brd4) since this protein complex mediates several processes important for the viral life cycle including viral genome maintenance, replication, and transcription. Using bimolecular fluorescence complementation (BiFC) technology, we demonstrate the E2 and Brd4 interaction on both interphase chromatin and mitotic chromosomes throughout mitosis. The E2-Brd4 BiFC was significantly diminished by mutating the Brd4 binding sites in E2 or by a dominant negative inhibitor of the E2-Brd4 interaction, demonstrating the potential of BiFC for identifying inhibitors of this important virus-host interaction. Importantly, when Brd4 was released from chromatin using the bromodomain inhibitor JQ1(+), the E2-Brd4 interacting complex relocated into foci that no longer associate with mitotic chromosomes, pointing to JQ1(+) as a promising antiviral inhibitor of HPV genome maintenance during HPV persistent infection.
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Affiliation(s)
- Christine M. Helfer
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Ranran Wang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jianxin You
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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36
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McBride AA, Jang MK. Current understanding of the role of the Brd4 protein in the papillomavirus lifecycle. Viruses 2013; 5:1374-94. [PMID: 23722886 PMCID: PMC3717712 DOI: 10.3390/v5061374] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/21/2013] [Accepted: 05/21/2013] [Indexed: 12/19/2022] Open
Abstract
The Brd4 protein is an epigenetic reader that is central to regulation of cellular transcription and mitotic bookmarking. The transcription and replication proteins of many viruses interact with Brd4. We describe the multiple roles of Brd4 in the papillomavirus lifecycle.
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Affiliation(s)
- Alison A McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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37
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MYC, a downstream target of BRD-NUT, is necessary and sufficient for the blockade of differentiation in NUT midline carcinoma. Oncogene 2013; 33:1736-1742. [PMID: 23604113 DOI: 10.1038/onc.2013.126] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 02/21/2013] [Accepted: 02/25/2013] [Indexed: 11/08/2022]
Abstract
NUT midline carcinoma (NMC) is an aggressive type of squamous cell carcinoma that is defined by the presence of BRD-NUT fusion oncogenes, which encode chimeric proteins that block differentiation and maintain tumor growth. BRD-NUT oncoproteins contain two bromodomains whose binding to acetylated histones is required for the blockade of differentiation in NMC, but the mechanisms by which BRD-NUT act remain uncertain. Here, we provide evidence that MYC is a key downstream target of BRD4-NUT. Expression profiling of NMCs shows that the set of genes whose expression is maintained by BRD4-NUT is highly enriched for MYC upregulated genes, and MYC and BRD4-NUT protein expression is strongly correlated in primary NMCs. More directly, we find that BRD4-NUT associates with the MYC promoter and is required to maintain MYC expression in NMC cell lines. Moreover, both siRNA knockdown of MYC and a dominant-negative form of MYC, omomyc, induce differentiation of NMC cells. Conversely, differentiation of NMC cells induced by knockdown of BRD4-NUT is abrogated by enforced expression of MYC. Together, these findings suggest that MYC is a downstream target of BRD4-NUT that is required for maintenance of NMC cells in an undifferentiated, proliferative state. Our findings support a model in which dysregulation of MYC by BRD-NUT fusion proteins has a central role in the pathogenesis of NMC.
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38
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Vu LP, Luciani L, Nimer SD. Histone-modifying enzymes: their role in the pathogenesis of acute leukemia and their therapeutic potential. Int J Hematol 2013; 97:198-209. [PMID: 23288492 DOI: 10.1007/s12185-012-1247-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 12/05/2012] [Indexed: 11/30/2022]
Abstract
Histone-modifying enzymes have recently been shown to play a central role in the regulation of both normal and malignant hematopoiesis. Post-translational modifications of histones and non-histone proteins underlies a regulatory complexity affecting numerous processes including transcriptional regulation, RNA processing and DNA damage response. Insights into the functions of these enzymes as well as their role in the epigenetic alterations found in leukemia will guide the development of novel therapeutic approaches. This review discusses examples of the proteins that have been implicated in the pathogenesis of leukemia, that may serve as potential therapeutic targets.
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Affiliation(s)
- Ly P Vu
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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39
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Wang X, Li J, Schowalter RM, Jiao J, Buck CB, You J. Bromodomain protein Brd4 plays a key role in Merkel cell polyomavirus DNA replication. PLoS Pathog 2012; 8:e1003021. [PMID: 23144621 PMCID: PMC3493480 DOI: 10.1371/journal.ppat.1003021] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/24/2012] [Indexed: 12/15/2022] Open
Abstract
Merkel cell polyomavirus (MCV or MCPyV) is the first human polyomavirus to be definitively linked to cancer. The mechanisms of MCV-induced oncogenesis and much of MCV biology are largely unexplored. In this study, we demonstrate that bromodomain protein 4 (Brd4) interacts with MCV large T antigen (LT) and plays a critical role in viral DNA replication. Brd4 knockdown inhibits MCV replication, which can be rescued by recombinant Brd4. Brd4 colocalizes with the MCV LT/replication origin complex in the nucleus and recruits replication factor C (RFC) to the viral replication sites. A dominant negative inhibitor of the Brd4-MCV LT interaction can dissociate Brd4 and RFC from the viral replication complex and abrogate MCV replication. Furthermore, obstructing the physiologic interaction between Brd4 and host chromatin with the chemical compound JQ1(+) leads to enhanced MCV DNA replication, demonstrating that the role of Brd4 in MCV replication is distinct from its role in chromatin-associated transcriptional regulation. Our findings demonstrate mechanistic details of the MCV replication machinery; providing novel insight to elucidate the life cycle of this newly discovered oncogenic DNA virus. MCV is a novel human polyomavirus that has recently been discovered in Merkel cell carcinoma (MCC), a rare but highly aggressive skin cancer. Several independent studies have confirmed that MCV is present in ∼80% of MCC tumors. However, very little is known about how the interaction between MCV and its human hosts contributes to the virus-induced cancers. Many aspects of the infectious life cycle of MCV are largely unexplored. In this study, we demonstrate that the MCV-encoded large T antigen can bind to host protein Brd4, which in turn serves as a scaffold that functionally recruits cellular DNA replication factors for replication of MCV viral DNA in host cells. This study is the first report to demonstrate mechanistic details of MCV's recruitment of the host cell DNA replication machinery; providing novel insight to elucidate the life cycle of this newly discovered oncogenic DNA virus. Importantly, our work demonstrates that blocking the Brd4 and MCV LT interaction can prevent MCV from replicating in host cells. This study identifies the Brd4-MCV LT interaction as an important target for potential development of effective therapeutic strategies to treat MCV infection.
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Affiliation(s)
- Xin Wang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jing Li
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Rachel M. Schowalter
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jing Jiao
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Christopher B. Buck
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jianxin You
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Novel BRD4-NUT fusion isoforms increase the pathogenic complexity in NUT midline carcinoma. Oncogene 2012; 32:4664-74. [PMID: 23128391 DOI: 10.1038/onc.2012.487] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 09/04/2012] [Accepted: 09/05/2012] [Indexed: 01/07/2023]
Abstract
Nuclear protein in testis (NUT)-midline carcinoma (NMC) is a rare, aggressive disease typically presenting with a single t(15;19) translocation that results in the generation of a bromodomain-containing protein 4 (BRD4)-NUT fusion. PER-624 is a cell line generated from an NMC patient with an unusually complex karyotype that gave no initial indication of the involvement of the NUT locus. Analysis of PER-624 next-generation transcriptome sequencing (RNA-Seq) using the algorithm FusionFinder identified a novel transcript in which Exon 15 of BRD4 was fused to Exon 2 of NUT, therefore differing from all published NMC fusion transcripts. The three additional exons contained in the PER-624 fusion encode a series of polyproline repeats, with one predicted to form a helix. In the NMC cell line PER-403, we identified the 'standard' NMC fusion and two novel isoforms. Knockdown by small interfering RNA in either cell line resulted in decreased proliferation, increased cell size and expression of cytokeratins consistent with epithelial differentiation. These data demonstrate that the novel BRD4-NUT fusion in PER-624 encodes a functional protein that is central to the oncogenic mechanism in these cells. Genomic PCR indicated that in both PER-624 and PER-403, the translocation fuses an intron of BRD4 to a region upstream of the NUT coding sequence. Thus, the generation of BRD4-NUT fusion transcripts through post-translocation RNA-splicing appears to be a common feature of these carcinomas that has not previously been appreciated, with the mechanism facilitating the expression of alternative isoforms of the fusion. Finally, ectopic expression of wild-type NUT, a protein normally restricted to the testis, could be demonstrated in PER-403, indicating additional pathways for aberrant cell signaling in NMC. This study contributes to our understanding of the genetic diversity of NMC, an important step towards finding therapeutic targets for a disease that is refractory to current treatments.
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Abstract
NUT midline carcinomas (NMCs) comprise a group of highly aggressive tumors that have been reported primarily in the head, neck, and mediastinum of younger individuals. These tumors overexpress the nuclear protein in the testis (NUT), most commonly due to a chromosomal translocation that fuses the NUT gene on chromosome 15 with the BRD4 gene on chromosome 19. Although the earliest recognized cases were described in the thymus or mediastinum, an extensive survey for NMCs among malignant thymic or other mediastinal neoplasms has not been reported. We examined NUT expression in 114 cases of poorly differentiated carcinomas or unclassified mediastinal malignancies using a clinically validated NUT-specific monoclonal antibody. Four of 114 (3.5%) cases showed nuclear NUT expression. A NUT translocation was confirmed by fluorescence in situ hybridization in 3 of these cases. These tumors arose in 2 men and 2 women with a median age of 50 years (range, 28 to 68 y). Three of the tumors were originally diagnosed as undifferentiated epithelioid or round cell malignant neoplasms; 1 tumor contained focal squamous differentiation and was originally diagnosed as a poorly differentiated squamous carcinoma of probable thymic origin. We find that the incidence of NMC within the mediastinum, particularly among undifferentiated tumors, is similar to that reported at other anatomic sites. NMC should be considered in the differential diagnosis of any poorly differentiated epithelioid mediastinal tumor, regardless of age.
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Wang R, Li Q, Helfer CM, Jiao J, You J. Bromodomain protein Brd4 associated with acetylated chromatin is important for maintenance of higher-order chromatin structure. J Biol Chem 2012; 287:10738-52. [PMID: 22334664 DOI: 10.1074/jbc.m111.323493] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Chromatin structure organization is crucial for regulating many fundamental cellular processes. However, the molecular mechanism that regulates the assembly of higher-order chromatin structure remains poorly understood. In this study, we demonstrate that Brd4 (bromodomain-containing protein 4) protein participates in the maintenance of the higher-order chromatin structure. Brd4, a member of the BET family of proteins, has been shown to play important roles in cellular growth control, cell cycle progression, and cancer development. We apply in situ single cell chromatin imaging and micrococcal nuclease (MNase) assay to show that Brd4 depletion leads to a large scale chromatin unfolding. A dominant-negative inhibitor encoding the double bromodomains (BDI/II) of Brd4 can competitively dissociate endogenous Brd4 from chromatin to trigger severely fragmented chromatin morphology. Mechanistic studies using Brd4 truncation mutants reveal that the Brd4 C-terminal domain is crucial for maintaining normal chromatin structure. Using bimolecular fluorescence complementation technology, we demonstrate that Brd4 molecules interact intermolecularly on chromatin and that replacing Brd4 molecules by BDI/II causes abnormal nucleosome aggregation and chromatin fragmentation. These studies establish a novel structural role of Brd4 in supporting the higher chromatin architecture.
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Affiliation(s)
- Ranran Wang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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