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Hamilton GA, Ruiz PD, Ye K, Gamble MJ. Acetylation of histone H2B on lysine 120 regulates BRD4 binding to intergenic enhancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.07.637147. [PMID: 39975207 PMCID: PMC11839021 DOI: 10.1101/2025.02.07.637147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
BRD4 is a bromodomain-containing transcriptional co-regulator that plays important roles in driving transcription by binding to histone acetyl-lysines at enhancers and promoters while recruiting additional transcriptional cofactors. While the mechanisms by which BRD4 regulates transcription have been explored, the critical acetylations primarily responsible for targeting it to chromatin remain unclear. Through a machine learning approach, we determined that distinct sets of histone acetylations dominate the prediction of chromatin accessibility and BRD4 binding in distinct chromatin contexts (e.g. intergenic enhancers, gene body enhancers and promoters). Using human fibroblasts engineered to predominantly express specific histones with lysine-to-arginine mutations, we demonstrate that one such acetylation, H2BK120ac, is required to recruit BRD4 specifically to intergenic enhancers, while not affecting chromatin accessibility. Loss of H2BK120ac did not affect BRD4 binding to either promoters or gene body enhancers, demonstrating that the rules governing BRD4 recruitment to regulatory regions depends on the specific genomic context. Highlighting the importance of H2BK120ac in directing BRD4 recruitment, we found that expression of the H2BK120R mutant significantly reduces the phenotypes driven by BRD4-NUT, an oncogenic fusion protein that drives NUT midline carcinoma. This work demonstrates the critical nature that genomic context plays in BRD4 recruitment to distinct classes of regulatory elements, and suggests that intergenic and gene body enhancers represent classes of functional distinct elements.
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2
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Lu X, Zhu M, Pei X, Ma J, Wang R, Wang Y, Chen S, Yan Y, Zhu Y. Super-enhancers in hepatocellular carcinoma: regulatory mechanism and therapeutic targets. Cancer Cell Int 2025; 25:7. [PMID: 39773719 PMCID: PMC11706108 DOI: 10.1186/s12935-024-03599-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 12/05/2024] [Indexed: 01/11/2025] Open
Abstract
Super-enhancers (SEs) represent a distinct category of cis-regulatory elements notable for their robust transcriptional activation capabilities. In tumor cells, SEs intricately regulate the expression of oncogenes and pivotal cancer-associated signaling pathways, offering significant potential for cancer treatment. However, few studies have systematically discussed the crucial role of SEs in hepatocellular carcinoma (HCC), which is one of the most common liver cancers with late-stage diagnosis and limited treatment methods for advanced disease. Herein, we first summarize the identification methods and the intricate processes of formation and organization of super-enhancers. Subsequently, we delve into the roles and molecular mechanisms of SEs within the framework of HCC. Finally, we discuss the inhibitors targeting the key SE-components and their potential effects on the treatment of HCC. In conclusion, this review meticulously encapsulates the distinctive characteristics of SEs and underscores their pivotal roles in the context of hepatocellular carcinoma, presenting a novel perspective on the potential of super-enhancers as emerging therapeutic targets for HCC.
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Affiliation(s)
- Xuejin Lu
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Meizi Zhu
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Xingyue Pei
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Jinhu Ma
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rui Wang
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Yi Wang
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Shuwen Chen
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Yan Yan
- Laboratory Animal Research Center, College of Basic Medical Science, Anhui Medical University, Hefei, China.
| | - Yaling Zhu
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China.
- Laboratory Animal Research Center, College of Basic Medical Science, Anhui Medical University, Hefei, China.
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3
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Maji S, Waseem M, Sharma MK, Singh M, Singh A, Dwivedi N, Thakur P, Cooper DG, Bisht NC, Fassler JS, Subbarao N, Khurana JP, Bhavesh NS, Thakur JK. MediatorWeb: a protein-protein interaction network database for the RNA polymerase II Mediator complex. FEBS J 2024; 291:3938-3960. [PMID: 38975839 DOI: 10.1111/febs.17225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 04/24/2024] [Accepted: 06/28/2024] [Indexed: 07/09/2024]
Abstract
The protein-protein interaction (PPI) network of the Mediator complex is very tightly regulated and depends on different developmental and environmental cues. Here, we present an interactive platform for comparative analysis of the Mediator subunits from humans, baker's yeast Saccharomyces cerevisiae, and model plant Arabidopsis thaliana in a user-friendly web-interface database called MediatorWeb. MediatorWeb provides an interface to visualize and analyze the PPI network of Mediator subunits. The database facilitates downloading the untargeted and unweighted network of Mediator complex, its submodules, and individual Mediator subunits to better visualize the importance of individual Mediator subunits or their submodules. Further, MediatorWeb offers network visualization of the Mediator complex and interacting proteins that are functionally annotated. This feature provides clues to understand functions of Mediator subunits in different processes. In an additional tab, MediatorWeb provides quick access to secondary and tertiary structures, as well as residue-level contact information for Mediator subunits in each of the three model organisms. Another useful feature of MediatorWeb is detection of interologs based on orthologous analyses, which can provide clues to understand the functions of Mediator complex in less explored kingdoms. Thus, MediatorWeb and its features can help the user to understand the role of Mediator complex and its subunits in the transcription regulation of gene expression.
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Grants
- BT/PR40146/BTIS/137/4/2020 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR40169/BTIS/137/71/2023 Department of Biotechnology, Ministry of Science and Technology, India
- BT/HRD/MK-YRFP/50/27/2021 Department of Biotechnology, Ministry of Science and Technology, India
- BT/HRD/MK-YRFP/50/26/2021 Department of Biotechnology, Ministry of Science and Technology, India
- SERB, Government of India
- ICMR
- Council of Scientific and Industrial Research, India
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Affiliation(s)
- Sourobh Maji
- Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mohd Waseem
- National Institute of Plant Genome Research, New Delhi, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Maninder Singh
- National Institute of Plant Genome Research, New Delhi, India
| | - Anamika Singh
- Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nidhi Dwivedi
- National Institute of Plant Genome Research, New Delhi, India
| | - Pallabi Thakur
- National Institute of Plant Genome Research, New Delhi, India
| | - David G Cooper
- Department of Pharmaceutical Sciences, Butler University, Indianapolis, IN, USA
| | - Naveen C Bisht
- National Institute of Plant Genome Research, New Delhi, India
| | | | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jitendra P Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Jitendra Kumar Thakur
- Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- National Institute of Plant Genome Research, New Delhi, India
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4
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Trzaskoma P, Jung S, Pękowska A, Bohrer CH, Wang X, Naz F, Dell’Orso S, Dubois WD, Olivera A, Vartak SV, Zhao Y, Nayak S, Overmiller A, Morasso MI, Sartorelli V, Larson DR, Chow CC, Casellas R, O’Shea JJ. 3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network. SCIENCE ADVANCES 2024; 10:eadl4893. [PMID: 39121214 PMCID: PMC11313860 DOI: 10.1126/sciadv.adl4893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 07/08/2024] [Indexed: 08/11/2024]
Abstract
Discontinuous transcription is evolutionarily conserved and a fundamental feature of gene regulation; yet, the exact mechanisms underlying transcriptional bursting are unresolved. Analyses of bursting transcriptome-wide have focused on the role of cis-regulatory elements, but other factors that regulate this process remain elusive. We applied mathematical modeling to single-cell RNA sequencing data to infer bursting dynamics transcriptome-wide under multiple conditions to identify possible molecular mechanisms. We found that Mediator complex subunit 26 (MED26) primarily regulates frequency, MYC regulates burst size, while cohesin and Bromodomain-containing protein 4 (BRD4) can modulate both. Despite comparable effects on RNA levels among these perturbations, acute depletion of MED26 had the most profound impact on the entire gene regulatory network, acting downstream of chromatin spatial architecture and without affecting TATA box-binding protein (TBP) recruitment. These results indicate that later steps in the initiation of transcriptional bursts are primary nodes for integrating gene networks in single cells.
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Affiliation(s)
- Pawel Trzaskoma
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - SeolKyoung Jung
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aleksandra Pękowska
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | | | - Xiang Wang
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Faiza Naz
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Stefania Dell’Orso
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wendy D. Dubois
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ana Olivera
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Supriya V. Vartak
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yongbing Zhao
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Subhashree Nayak
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Overmiller
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Maria I. Morasso
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vittorio Sartorelli
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel R. Larson
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carson C. Chow
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rafael Casellas
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John J. O’Shea
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
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5
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Rosenthal ZC, Fass DM, Payne NC, She A, Patnaik D, Hennig KM, Tesla R, Werthmann GC, Guhl C, Reis SA, Wang X, Chen Y, Placzek M, Williams NS, Hooker J, Herz J, Mazitschek R, Haggarty SJ. Epigenetic modulation through BET bromodomain inhibitors as a novel therapeutic strategy for progranulin-deficient frontotemporal dementia. Sci Rep 2024; 14:9064. [PMID: 38643236 PMCID: PMC11032351 DOI: 10.1038/s41598-024-59110-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
Frontotemporal dementia (FTD) is a debilitating neurodegenerative disorder with currently no disease-modifying treatment options available. Mutations in GRN are one of the most common genetic causes of FTD, near ubiquitously resulting in progranulin (PGRN) haploinsufficiency. Small molecules that can restore PGRN protein to healthy levels in individuals bearing a heterozygous GRN mutation may thus have therapeutic value. Here, we show that epigenetic modulation through bromodomain and extra-terminal domain (BET) inhibitors (BETi) potently enhance PGRN protein levels, both intracellularly and secreted forms, in human central nervous system (CNS)-relevant cell types, including in microglia-like cells. In terms of potential for disease modification, we show BETi treatment effectively restores PGRN levels in neural cells with a GRN mutation known to cause PGRN haploinsufficiency and FTD. We demonstrate that BETi can rapidly and durably enhance PGRN in neural progenitor cells (NPCs) in a manner dependent upon BET protein expression, suggesting a gain-of-function mechanism. We further describe a CNS-optimized BETi chemotype that potently engages endogenous BRD4 and enhances PGRN expression in neuronal cells. Our results reveal a new epigenetic target for treating PGRN-deficient forms of FTD and provide mechanistic insight to aid in translating this discovery into therapeutics.
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Affiliation(s)
- Zachary C Rosenthal
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Daniel M Fass
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - N Connor Payne
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Angela She
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Debasis Patnaik
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Krista M Hennig
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Rachel Tesla
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Translational Neurodegeneration Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gordon C Werthmann
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Translational Neurodegeneration Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Charlotte Guhl
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Surya A Reis
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Xiaoyu Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yueting Chen
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Placzek
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
| | - Noelle S Williams
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jacob Hooker
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
| | - Joachim Herz
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Translational Neurodegeneration Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.
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6
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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7
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Divakaran A, Harki DA, Pomerantz WC. Recent progress and structural analyses of domain-selective BET inhibitors. Med Res Rev 2023; 43:972-1018. [PMID: 36971240 PMCID: PMC10520981 DOI: 10.1002/med.21942] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 12/21/2022] [Accepted: 02/26/2023] [Indexed: 03/29/2023]
Abstract
Epigenetic mechanisms for controlling gene expression through heritable modifications to DNA, RNA, and proteins, are essential processes in maintaining cellular homeostasis. As a result of their central role in human diseases, the proteins responsible for adding, removing, or recognizing epigenetic modifications have emerged as viable drug targets. In the case of lysine-ε-N-acetylation (Kac ), bromodomains serve as recognition modules ("readers") of this activating epigenetic mark and competition of the bromodomain-Kac interaction with small-molecule inhibitors is an attractive strategy to control aberrant bromodomain-mediated gene expression. The bromodomain and extra-terminal (BET) family proteins contain eight similar bromodomains. These BET bromodomains are among the more commonly studied bromodomain classes with numerous pan-BET inhibitors showing promising anticancer and anti-inflammatory efficacy. However, these results have yet to translate into Food and Drug Administration-approved drugs, in part due to a high degree of on-target toxicities associated with pan-BET inhibition. Improved selectivity within the BET-family has been proposed to alleviate these concerns. In this review, we analyze the reported BET-domain selective inhibitors from a structural perspective. We highlight three essential characteristics of the reported molecules in generating domain selectivity, binding affinity, and mimicking Kac molecular recognition. In several cases, we provide insight into the design of molecules with improved specificity for individual BET-bromodomains. This review provides a perspective on the current state of the field as this exciting class of inhibitors continue to be evaluated in the clinic.
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Affiliation(s)
- Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN55455, United States
| | - William C.K. Pomerantz
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN55455, United States
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8
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Pal S, Biswas D. Promoter-proximal regulation of gene transcription: Key factors involved and emerging role of general transcription factors in assisting productive elongation. Gene 2023:147571. [PMID: 37331491 DOI: 10.1016/j.gene.2023.147571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
The pausing of RNA polymerase II (Pol II) at the promoter-proximal sites is a key rate-limiting step in gene expression. Cells have dedicated a specific set of proteins that sequentially establish pause and then release the Pol II from promoter-proximal sites. A well-controlled pausing and subsequent release of Pol II is crucial for thefine tuning of expression of genes including signal-responsive and developmentally-regulated ones. The release of paused Pol II broadly involves its transition from initiation to elongation. In this review article, we will discuss the phenomenon of Pol II pausing, the underlying mechanism, and also the role of different known factors, with an emphasis on general transcription factors, involved in this overall regulation. We will further discuss some recent findings suggesting a possible role (underexplored) of initiation factors in assisting the transition of transcriptionally-engaged paused Pol II into productive elongation.
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Affiliation(s)
- Sujay Pal
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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9
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Martella N, Pensabene D, Varone M, Colardo M, Petraroia M, Sergio W, La Rosa P, Moreno S, Segatto M. Bromodomain and Extra-Terminal Proteins in Brain Physiology and Pathology: BET-ing on Epigenetic Regulation. Biomedicines 2023; 11:biomedicines11030750. [PMID: 36979729 PMCID: PMC10045827 DOI: 10.3390/biomedicines11030750] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
BET proteins function as histone code readers of acetylated lysins that determine the positive regulation in transcription of genes involved in cell cycle progression, differentiation, inflammation, and many other pathways. In recent years, thanks to the development of BET inhibitors, interest in this protein family has risen for its relevance in brain development and function. For example, experimental evidence has shown that BET modulation affects neuronal activity and the expression of genes involved in learning and memory. In addition, BET inhibition strongly suppresses molecular pathways related to neuroinflammation. These observations suggest that BET modulation may play a critical role in the onset and during the development of diverse neurodegenerative and neuropsychiatric disorders, such as Alzheimer’s disease, fragile X syndrome, and Rett syndrome. In this review article, we summarize the most recent evidence regarding the involvement of BET proteins in brain physiology and pathology, as well as their pharmacological potential as targets for therapeutic purposes.
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Affiliation(s)
- Noemi Martella
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Daniele Pensabene
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 64 via del Fosso di Fiorano, 00179 Rome, Italy
| | - Michela Varone
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Mayra Colardo
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Michele Petraroia
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - William Sergio
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, via dei Marsi 78, 00185 Rome, Italy
| | - Sandra Moreno
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 64 via del Fosso di Fiorano, 00179 Rome, Italy
| | - Marco Segatto
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
- Correspondence:
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10
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Role of RUNX3 in Restriction Point Regulation. Cells 2023; 12:cells12050708. [PMID: 36899846 PMCID: PMC10000377 DOI: 10.3390/cells12050708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 03/02/2023] Open
Abstract
A cell cycle is a series of events that takes place in a cell as it grows and divides. At the G1 phase of cell cycle, cells monitor their cumulative exposure to specific signals and make the critical decision to pass through the restriction (R)-point. The R-point decision-making machinery is fundamental to normal differentiation, apoptosis, and G1-S transition. Deregulation of this machinery is markedly associated with tumorigenesis. Therefore, identification of the molecular mechanisms that govern the R-point decision is one of the fundamental issues in tumor biology. RUNX3 is one of the genes frequently inactivated in tumors by epigenetic alterations. In particular, RUNX3 is downregulated in most K-RAS-activated human and mouse lung adenocarcinomas (ADCs). Targeted inactivation of Runx3 in the mouse lung induces adenomas (ADs), and markedly shortens the latency of ADC formation induced by oncogenic K-Ras. RUNX3 participates in the transient formation of R-point-associated activator (RPA-RX3-AC) complexes, which measure the duration of RAS signals and thereby protect cells against oncogenic RAS. This review focuses on the molecular mechanism by which the R-point participates in oncogenic surveillance.
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11
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Eischer N, Arnold M, Mayer A. Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1734. [PMID: 35491403 DOI: 10.1002/wrna.1734] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 01/31/2023]
Abstract
Transcription by RNA polymerase II (Pol II) gives rise to all nuclear protein-coding and a large set of non-coding RNAs, and is strictly regulated and coordinated with RNA processing. Bromodomain and extraterminal (BET) family proteins including BRD2, BRD3, and BRD4 have been implicated in the regulation of Pol II transcription in mammalian cells. However, only recent technological advances have allowed the analysis of direct functions of individual BET proteins with high precision in cells. These studies shed new light on the molecular mechanisms of transcription control by BET proteins challenging previous longstanding views. The most studied BET protein, BRD4, emerges as a master regulator of transcription elongation with roles also in coupling nascent transcription with RNA processing. In contrast, BRD2 is globally required for the formation of transcriptional boundaries to restrict enhancer activity to nearby genes. Although these recent findings suggest non-redundant functions of BRD4 and BRD2 in Pol II transcription, more research is needed for further clarification. Little is known about the roles of BRD3. Here, we illuminate experimental work that has initially linked BET proteins to Pol II transcription in mammalian cells, outline main methodological breakthroughs that have strongly advanced the understanding of BET protein functions, and discuss emerging roles of individual BET proteins in transcription and transcription-coupled RNA processing. Finally, we propose an updated model for the function of BRD4 in transcription and co-transcriptional RNA maturation. This article is categorized under: RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Nicole Eischer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mirjam Arnold
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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12
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Richter WF, Nayak S, Iwasa J, Taatjes DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022; 23:732-749. [PMID: 35725906 PMCID: PMC9207880 DOI: 10.1038/s41580-022-00498-3] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
Abstract
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer-promoter interactions, which reconciles contradictory data regarding whether enhancer-promoter communication is direct or indirect. We conclude with a discussion of Mediator's potential as a therapeutic target and of future research directions.
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Affiliation(s)
- William F Richter
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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13
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Abstract
Transcription elongation by RNA polymerase II (Pol II) has emerged as a regulatory hub in gene expression. A key control point occurs during early transcription elongation when Pol II pauses in the promoter-proximal region at the majority of genes in mammalian cells and at a large set of genes in Drosophila. An increasing number of trans-acting factors have been linked to promoter-proximal pausing. Some factors help to establish the pause, whereas others are required for the release of Pol II into productive elongation. A dysfunction of this elongation control point leads to aberrant gene expression and can contribute to disease development. The BET bromodomain protein BRD4 has been implicated in elongation control. However, only recently direct BRD4-specific functions in Pol II transcription elongation have been uncovered. This mainly became possible with technological advances that allow selective and rapid ablation of BRD4 in cells along with the availability of approaches that capture the immediate consequences on nascent transcription. This review sheds light on the experimental breakthroughs that led to the emerging view of BRD4 as a general regulator of transcription elongation.
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Affiliation(s)
- Elisabeth Altendorfer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Yelizaveta Mochalova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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14
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Agrawal R, Sharma M, Dwivedi N, Maji S, Thakur P, Junaid A, Fajkus J, Laxmi A, Thakur JK. MEDIATOR SUBUNIT17 integrates jasmonate and auxin signaling pathways to regulate thermomorphogenesis. PLANT PHYSIOLOGY 2022; 189:2259-2280. [PMID: 35567489 PMCID: PMC9342970 DOI: 10.1093/plphys/kiac220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/20/2022] [Indexed: 05/16/2023]
Abstract
Plant adjustment to environmental changes involves complex crosstalk between extrinsic and intrinsic cues. In the past two decades, extensive research has elucidated the key roles of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and the phytohormone auxin in thermomorphogenesis. In this study, we identified a previously unexplored role of jasmonate (JA) signaling components, the Mediator complex, and their integration with auxin signaling during thermomorphogenesis in Arabidopsis (Arabidopsis thaliana). Warm temperature induces expression of JA signaling genes including MYC2, but, surprisingly, this transcriptional activation is not JA dependent. Warm temperature also promotes accumulation of the JA signaling receptor CORONATINE INSENSITIVE1 (COI1) and degradation of the JA signaling repressor JASMONATE-ZIM-DOMAIN PROTEIN9, which probably leads to de-repression of MYC2, enabling it to contribute to the expression of MEDIATOR SUBUNIT17 (MED17). In response to warm temperature, MED17 occupies the promoters of thermosensory genes including PIF4, YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE19 (IAA19), and IAA29. Moreover, MED17 facilitates enrichment of H3K4me3 on the promoters of PIF4, YUC8, IAA19, and IAA29 genes. Interestingly, both occupancy of MED17 and enrichment of H3K4me3 on these thermomorphogenesis-related promoters are dependent on PIF4 (or PIFs). Altered accumulation of COI1 under warm temperature in the med17 mutant suggests the possibility of a feedback mechanism. Overall, this study reveals the role of the Mediator complex as an integrator of JA and auxin signaling pathways during thermomorphogenesis.
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Affiliation(s)
- Rekha Agrawal
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Mohan Sharma
- Signalling Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Nidhi Dwivedi
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Sourobh Maji
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Pallabi Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Alim Junaid
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ashverya Laxmi
- Signalling Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
- Plant Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
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15
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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16
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BRD4-directed super-enhancer organization of transcription repression programs links to chemotherapeutic efficacy in breast cancer. Proc Natl Acad Sci U S A 2022; 119:2109133119. [PMID: 35105803 PMCID: PMC8832982 DOI: 10.1073/pnas.2109133119] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 12/11/2022] Open
Abstract
BRD4 is well known for its role in super-enhancer organization and transcription activation of several prominent oncogenes including c-MYC and BCL2 As such, BRD4 inhibitors are being pursued as promising therapeutics for cancer treatment. However, drug resistance also occurs for BRD4-targeted therapies. Here, we report that BRD4 unexpectedly interacts with the LSD1/NuRD complex and colocalizes with this repressive complex on super-enhancers. Integrative genomic and epigenomic analyses indicate that the BRD4/LSD1/NuRD complex restricts the hyperactivation of a cluster of genes that are functionally linked to drug resistance. Intriguingly, treatment of breast cancer cells with a small-molecule inhibitor of BRD4, JQ1, results in no immediate activation of the drug-resistant genes, but long-time treatment or destabilization of LSD1 by PELI1 decommissions the BRD4/LSD1/NuRD complex, leading to resistance to JQ1 as well as to a broad spectrum of therapeutic compounds. Consistently, PELI1 is up-regulated in breast carcinomas, its level is negatively correlated with that of LSD1, and the expression level of the BRD4/LSD1/NuRD complex-restricted genes is strongly correlated with a worse overall survival of breast cancer patients. Together, our study uncovers a functional duality of BRD4 in super-enhancer organization of transcription activation and repression linking to oncogenesis and chemoresistance, respectively, supporting the pursuit of a combined targeting of BRD4 and PELI1 in effective treatment of breast cancer.
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17
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Naxerova K, Di Stefano B, Makofske JL, Watson EV, de Kort MA, Martin TD, Dezfulian M, Ricken D, Wooten EC, Kuroda MI, Hochedlinger K, Elledge SJ. Integrated loss- and gain-of-function screens define a core network governing human embryonic stem cell behavior. Genes Dev 2021; 35:1527-1547. [PMID: 34711655 PMCID: PMC8559676 DOI: 10.1101/gad.349048.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
In this Resource/Methodology, Naxerova et al. describe an integrated genome-scale loss- and gain-of-function screening approach to identify genetic networks governing embryonic stem cell proliferation and differentiation into the three germ layers. They identify a deep link between pluripotency maintenance and survival by showing that genetic alterations that cause pluripotency dissolution simultaneously increase apoptosis resistance, and their results show the power of integrated multilayer genetic screening for the robust mapping of complex genetic networks. Understanding the genetic control of human embryonic stem cell function is foundational for developmental biology and regenerative medicine. Here we describe an integrated genome-scale loss- and gain-of-function screening approach to identify genetic networks governing embryonic stem cell proliferation and differentiation into the three germ layers. We identified a deep link between pluripotency maintenance and survival by showing that genetic alterations that cause pluripotency dissolution simultaneously increase apoptosis resistance. We discovered that the chromatin-modifying complex SAGA and in particular its subunit TADA2B are central regulators of pluripotency, survival, growth, and lineage specification. Joint analysis of all screens revealed that genetic alterations that broadly inhibit differentiation across multiple germ layers drive proliferation and survival under pluripotency-maintaining conditions and coincide with known cancer drivers. Our results show the power of integrated multilayer genetic screening for the robust mapping of complex genetic networks.
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Affiliation(s)
- Kamila Naxerova
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Center for Systems Biology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Jessica L Makofske
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Emma V Watson
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Marit A de Kort
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Timothy D Martin
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mohammed Dezfulian
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dominik Ricken
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Eric C Wooten
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mitzi I Kuroda
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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18
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BET Proteins as Attractive Targets for Cancer Therapeutics. Int J Mol Sci 2021; 22:ijms222011102. [PMID: 34681760 PMCID: PMC8538173 DOI: 10.3390/ijms222011102] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022] Open
Abstract
Transcriptional dysregulation is a hallmark of cancer and can be an essential driver of cancer initiation and progression. Loss of transcriptional control can cause cancer cells to become dependent on certain regulators of gene expression. Bromodomain and extraterminal domain (BET) proteins are epigenetic readers that regulate the expression of multiple genes involved in carcinogenesis. BET inhibitors (BETis) disrupt BET protein binding to acetylated lysine residues of chromatin and suppress the transcription of various genes, including oncogenic transcription factors. Phase I and II clinical trials demonstrated BETis’ potential as anticancer drugs against solid tumours and haematological malignancies; however, their clinical success was limited as monotherapies. Emerging treatment-associated toxicities, drug resistance and a lack of predictive biomarkers limited BETis’ clinical progress. The preclinical evaluation demonstrated that BETis synergised with different classes of compounds, including DNA repair inhibitors, thus supporting further clinical development of BETis. The combination of BET and PARP inhibitors triggered synthetic lethality in cells with proficient homologous recombination. Mechanistic studies revealed that BETis targeted multiple essential homologous recombination pathway proteins, including RAD51, BRCA1 and CtIP. The exact mechanism of BETis’ anticancer action remains poorly understood; nevertheless, these agents provide a novel approach to epigenome and transcriptome anticancer therapy.
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19
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Bhardwaj R, Thakur JK, Kumar S. MedProDB: A database of Mediator proteins. Comput Struct Biotechnol J 2021; 19:4165-4176. [PMID: 34527190 PMCID: PMC8342855 DOI: 10.1016/j.csbj.2021.07.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/08/2021] [Accepted: 07/24/2021] [Indexed: 12/03/2022] Open
Abstract
Mediator complex is a key component of transcriptional regulation in eukaryotes. Identification of Mediator subunits was done by using computational approaches. Different physicochemical properties, and functions of Mediators were discussed. We have developed first database of Mediator proteins e.g. MedProDB. MedProDB contains different types of search and browse options, and various tools.
In the last three decades, the multi-subunit Mediator complex has emerged as the key component of transcriptional regulation of eukaryotic gene expression. Although there were initial hiccups, recent advancements in bioinformatics tools contributed significantly to in-silico prediction and characterization of Mediator subunits from several organisms belonging to different eukaryotic kingdoms. In this study, we have developed the first database of Mediator proteins named MedProDB with 33,971 Mediator protein entries. Out of those, 12531, 11545, and 9895 sequences belong to metazoans, plants, and fungi, respectively. Apart from the core information consisting of sequence, length, position, organism, molecular weight, and taxonomic lineage, additional information of each Mediator sequence like aromaticity, hydropathy, instability index, isoelectric point, functions, interactions, repeat regions, diseases, sequence alignment to Mediator subunit family, Intrinsically Disordered Regions (IDRs), Post-translation modifications (PTMs), and Molecular Recognition Features (MoRFs) may be of high utility to the users. Furthermore, different types of search and browse options with four different tools namely BLAST, Smith-Waterman Align, IUPred, and MoRF-Chibi_Light are provided at MedProDB to perform different types of analysis. Being a critical component of the transcriptional machinery and regulating almost all the aspects of transcription, it generated lots of interest in structural and functional studies of Mediator functioning. So, we think that the MedProDB database will be very useful for researchers studying the process of transcription. This database is freely available at www.nipgr.ac.in/MedProDB.
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Affiliation(s)
- Rohan Bhardwaj
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.,Plant Mediator Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra Kumar Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.,Plant Transcription Regulation, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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20
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21
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Boyson SP, Gao C, Quinn K, Boyd J, Paculova H, Frietze S, Glass KC. Functional Roles of Bromodomain Proteins in Cancer. Cancers (Basel) 2021; 13:3606. [PMID: 34298819 PMCID: PMC8303718 DOI: 10.3390/cancers13143606] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.
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Affiliation(s)
- Samuel P. Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Kathleen Quinn
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Joseph Boyd
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
- University of Vermont Cancer Center, Burlington, VT 05405, USA
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- University of Vermont Cancer Center, Burlington, VT 05405, USA
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22
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Ijaz T, Burke MA. BET Protein-Mediated Transcriptional Regulation in Heart Failure. Int J Mol Sci 2021; 22:6059. [PMID: 34199719 PMCID: PMC8199980 DOI: 10.3390/ijms22116059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
Heart failure is a complex disease process with underlying aberrations in neurohormonal systems that promote dysregulated cellular signaling and gene transcription. Over the past 10 years, the advent of small-molecule inhibitors that target transcriptional machinery has demonstrated the importance of the bromodomain and extraterminal (BET) family of epigenetic reader proteins in regulating gene transcription in multiple mouse models of cardiomyopathy. BETs bind to acetylated histone tails and transcription factors to integrate disparate stress signaling networks into a defined gene expression program. Under myocardial stress, BRD4, a BET family member, is recruited to superenhancers and promoter regions of inflammatory and profibrotic genes to promote transcription elongation. Whole-transcriptome analysis of BET-dependent gene networks suggests a major role of nuclear-factor kappa b and transforming growth factor-beta in the development of cardiac fibrosis and systolic dysfunction. Recent investigations also suggest a prominent role of BRD4 in maintaining cardiomyocyte mitochondrial respiration under basal conditions. In this review, we summarize the data from preclinical heart failure studies that explore the role of BET-regulated transcriptional mechanisms and delve into landmark studies that define BET bromodomain-independent processes involved in cardiac homeostasis.
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Affiliation(s)
| | - Michael A. Burke
- Division of Cardiology, Department of Internal Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA;
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23
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Jiang J, Yang G, Xin Y, Wang Z, Yan W, Chen Z, Tang X, Xia J. Overexpression of OsMed16 Inhibits the Growth of Rice and Causes Spontaneous Cell Death. Genes (Basel) 2021; 12:genes12050656. [PMID: 33925652 PMCID: PMC8145620 DOI: 10.3390/genes12050656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 11/16/2022] Open
Abstract
The Mediator complex transduces information from the DNA-bound transcription factors to the RNA polymerase II transcriptional machinery. Research on plant Mediator subunits has primarily been performed in Arabidopsis, while very few of them have been functionally characterized in rice. In this study, the rice Mediator subunit 16, OsMed16, was examined. OsMed16 encodes a putative protein of 1301 amino acids, which is longer than the version previously reported. It was expressed in various rice organs and localized to the nucleus. The knockout of OsMed16 resulted in rice seedling lethality. Its overexpression led to the retardation of rice growth, low yield, and spontaneous cell death in the leaf blade and sheath. RNA sequencing suggested that the overexpression of OsMed16 altered the expression of a large number of genes. Among them, the upregulation of some defense-related genes was verified. OsMed16 can regulate the expression of a wealth of genes, and alterations in its expression have a profound impact on plant growth, development, and defense responses in rice.
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Affiliation(s)
- Jie Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (J.J.); (G.Y.); (Y.X.); (Z.W.)
| | - Guangzhe Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (J.J.); (G.Y.); (Y.X.); (Z.W.)
| | - Yafeng Xin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (J.J.); (G.Y.); (Y.X.); (Z.W.)
| | - Zhigang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (J.J.); (G.Y.); (Y.X.); (Z.W.)
| | - Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China;
- Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China;
| | - Zhufeng Chen
- Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China;
- Shenzhen Agricultural Technology Promotion Center, Shenzhen 518055, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China;
- Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China;
- Correspondence: (X.T.); (J.X.)
| | - Jixing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (J.J.); (G.Y.); (Y.X.); (Z.W.)
- Correspondence: (X.T.); (J.X.)
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24
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Guo J, Wei L, Chen SS, Cai XW, Su YN, Li L, Chen S, He XJ. The CBP/p300 histone acetyltransferases function as plant-specific MEDIATOR subunits in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:755-771. [PMID: 33325122 DOI: 10.1111/jipb.13052] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 05/06/2023]
Abstract
In eukaryotes, MEDIATOR is a conserved multi-subunit complex that links transcription factors and RNA polymerase II and that thereby facilitates transcriptional initiation. Although the composition of MEDIATOR has been well studied in yeast and mammals, relatively little is known about the composition of MEDIATOR in plants. By affinity purification followed by mass spectrometry, we identified 28 conserved MEDIATOR subunits in Arabidopsis thaliana, including putative MEDIATOR subunits that were not previously validated. Our results indicated that MED34, MED35, MED36, and MED37 are not Arabidopsis MEDIATOR subunits, as previously proposed. Our results also revealed that two homologous CBP/p300 histone acetyltransferases, HAC1 and HAC5 (HAC1/5) are in fact plant-specific MEDIATOR subunits. The MEDIATOR subunits MED8 and MED25 (MED8/25) are partially responsible for the association of MEDIATOR with HAC1/5, MED8/25 and HAC1/5 co-regulate gene expression and thereby affect flowering time and floral development. Our in vitro observations indicated that MED8 and HAC1 form liquid-like droplets by phase separation, and our in vivo observations indicated that these droplets co-localize in the nuclear bodies at a subset of nuclei. The formation of liquid-like droplets is required for MED8 to interact with RNA polymerase II. In summary, we have identified all of the components of Arabidopsis MEDIATOR and revealed the mechanism underlying the link of histone acetylation and transcriptional regulation.
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Affiliation(s)
- Jing Guo
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College, Beijing, 100730, China
| | - Long Wei
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Shan-Shan Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College, Beijing, 100730, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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25
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Crump NT, Ballabio E, Godfrey L, Thorne R, Repapi E, Kerry J, Tapia M, Hua P, Lagerholm C, Filippakopoulos P, Davies JOJ, Milne TA. BET inhibition disrupts transcription but retains enhancer-promoter contact. Nat Commun 2021; 12:223. [PMID: 33431820 PMCID: PMC7801379 DOI: 10.1038/s41467-020-20400-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
Enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes in higher eukaryotes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. Bromodomain and Extra-Terminal domain (BET) and Mediator proteins have been shown capable of forming phase condensates and are thought to be essential for super-enhancer function. Here, we show that targeting of cells with inhibitors of BET proteins or pharmacological degradation of BET protein Bromodomain-containing protein 4 (BRD4) has a strong impact on transcription but very little impact on enhancer-promoter interactions. Dissolving phase condensates reduces BRD4 and Mediator binding at enhancers and can also strongly affect gene transcription, without disrupting enhancer-promoter interactions. These results suggest that activation of transcription and maintenance of enhancer-promoter interactions are separable events. Our findings further indicate that enhancer-promoter interactions are not dependent on high levels of BRD4 and Mediator, and are likely maintained by a complex set of factors including additional activator complexes and, at some sites, CTCF and cohesin.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Erica Ballabio
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ross Thorne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Emmanouela Repapi
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jon Kerry
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Marta Tapia
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peng Hua
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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26
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Alamer E, Zhong C, Hajnik R, Soong L, Hu H. Modulation of BRD4 in HIV epigenetic regulation: implications for finding an HIV cure. Retrovirology 2021; 18:3. [PMID: 33413475 PMCID: PMC7792063 DOI: 10.1186/s12977-020-00547-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/30/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022] Open
Abstract
Following reverse transcription, HIV viral DNA is integrated into host cell genomes and establishes a stable latent infection, which has posed a major obstacle for obtaining a cure for HIV. HIV proviral transcription is regulated in cellular reservoirs by complex host epigenetic and transcriptional machineries. The Bromodomain (BD) and Extra-Terminal Domain (ET) protein, BRD4, is an important epigenetic reader that interacts with acetyl-histones and a variety of chromatin and transcriptional regulators to control gene expression, including HIV. Modulation of BRD4 by a pan BET inhibitor (JQ1) has been shown to activate HIV transcription. Recent studies by my group and others indicate that the function of BRD4 is versatile and its effects on HIV transcription may depend on the partner proteins or pathways engaged by BRD4. Our studies have reported a novel class of small-molecule modulators that are distinct from JQ1 but induce HIV transcriptional suppression through BRD4. Herein, we reviewed recent research on the modulation of BRD4 in HIV epigenetic regulation and discussed their potential implications for finding an HIV cure.
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Affiliation(s)
- Edrous Alamer
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), MRB 4.142A, 301 University Blvd, Galveston, TX, 77555, USA.,Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.,Medical Research Center, Jazan University, Jazan, 45142, Saudi Arabia
| | - Chaojie Zhong
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), MRB 4.142A, 301 University Blvd, Galveston, TX, 77555, USA
| | - Renee Hajnik
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), MRB 4.142A, 301 University Blvd, Galveston, TX, 77555, USA
| | - Lynn Soong
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), MRB 4.142A, 301 University Blvd, Galveston, TX, 77555, USA.,Institute for Human Infections and Immunity, Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Haitao Hu
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), MRB 4.142A, 301 University Blvd, Galveston, TX, 77555, USA. .,Institute for Human Infections and Immunity, Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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27
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Jones K, Zhang Y, Kong Y, Farah E, Wang R, Li C, Wang X, Zhang Z, Wang J, Mao F, Liu X, Liu J. Epigenetics in prostate cancer treatment. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2021; 5:341-356. [PMID: 35372800 PMCID: PMC8974353 DOI: 10.20517/jtgg.2021.19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Prostate cancer (PCa) is the most commonly diagnosed malignancy among men, and the progression of this disease results in fewer treatment options available to clinical patients. It highlights the vital necessity for discovering novel therapeutic approaches and expanding the current understanding of molecular mechanisms. Epigenetic alternations such as DNA methylation models and histone modifications have been associated as key drivers in the development and advancement of PCa. Several studies have been conducted and demonstrated that targeting these epigenetic enzymes or regulatory proteins has been strongly associated with the regulation of cancer cell growth. Due to the success rate of these therapeutic routes in pre-clinical settings, many drugs have now advanced to clinical testing, where efficacy will be measured. This review will discuss the role of epigenetic modifications in PCa development and its function in the progression of the disease to resistant forms and introduce therapeutic strategies that have demonstrated successful results as PCa treatment.
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Affiliation(s)
- Katelyn Jones
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Yanquan Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Yifan Kong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Elia Farah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ruixin Wang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Chaohao Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Xinyi Wang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - ZhuangZhuang Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Jianlin Wang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Fengyi Mao
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Jinghui Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
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28
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Song Y, Hu G, Jia J, Yao M, Wang X, Lu W, Hutchins AP, Chen J, Ozato K, Yao H. DNA Damage Induces Dynamic Associations of BRD4/P-TEFb With Chromatin and Modulates Gene Transcription in a BRD4-Dependent and -Independent Manner. Front Mol Biosci 2020; 7:618088. [PMID: 33344510 PMCID: PMC7746802 DOI: 10.3389/fmolb.2020.618088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
The bromodomain-containing protein BRD4 has been thought to transmit epigenetic information across cell divisions by binding to both mitotic chromosomes and interphase chromatin. UV-released BRD4 mediates the recruitment of active P-TEFb to the promoter, which enhances transcriptional elongation. However, the dynamic associations between BRD4 and P-TEFb and BRD4-mediated gene regulation after UV stress are largely unknown. In this study, we found that BRD4 dissociates from chromatin within 30 min after UV treatment and thereafter recruits chromatin. However, P-TEFb binds tightly to chromatin right after UV treatment, suggesting that no interactions occur between BRD4 and P-TEFb within 30 min after UV stress. BRD4 knockdown changes the distribution of P-TEFb among nuclear soluble and chromatin and downregulates the elongation activity of RNA polymerase II. Inhibition of JNK kinase but not other MAP kinases impedes the interactions between BRD4 and P-TEFb. RNA-seq and ChIP assays indicate that BRD4 both positively and negatively regulates gene transcription in cells treated with UV stress. These results reveal previously unrecognized dynamics of BRD4 and P-TEFb after UV stress and regulation of gene transcription by BRD4 acting as either activator or repressor in a context-dependent manner.
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Affiliation(s)
- Yawei Song
- School of Life Sciences, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Gongcheng Hu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jinping Jia
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Mingze Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiaoshan Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Wenliang Lu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, MD, United States
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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29
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Belorusova AY, Bourguet M, Hessmann S, Chalhoub S, Kieffer B, Cianférani S, Rochel N. Molecular determinants of MED1 interaction with the DNA bound VDR-RXR heterodimer. Nucleic Acids Res 2020; 48:11199-11213. [PMID: 32990725 PMCID: PMC7641746 DOI: 10.1093/nar/gkaa775] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/24/2020] [Accepted: 09/08/2020] [Indexed: 12/26/2022] Open
Abstract
The MED1 subunit of the Mediator complex is an essential coactivator of nuclear receptor-mediated transcriptional activation. While structural requirements for ligand-dependent binding of classical coactivator motifs of MED1 to numerous nuclear receptor ligand-binding domains have been fully elucidated, the recognition of the full-length or truncated coactivator by full nuclear receptor complexes remain unknown. Here we present structural details of the interaction between a large part of MED1 comprising its structured N-terminal and the flexible receptor-interacting domains and the mutual heterodimer of the vitamin D receptor (VDR) and the retinoid X receptor (RXR) bound to their cognate DNA response element. Using a combination of structural and biophysical methods we show that the ligand-dependent interaction between VDR and the second coactivator motif of MED1 is crucial for complex formation and we identify additional, previously unseen, interaction details. In particular, we identified RXR regions involved in the interaction with the structured N-terminal domain of MED1, as well as VDR regions outside the classical coactivator binding cleft affected by coactivator recruitment. These findings highlight important roles of each receptor within the heterodimer in selective recognition of MED1 and contribute to our understanding of the nuclear receptor-coregulator complexes.
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Affiliation(s)
- Anna Y Belorusova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Maxime Bourguet
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Sandra Chalhoub
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bruno Kieffer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
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30
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Kim YH, Lazar MA. Transcriptional Control of Circadian Rhythms and Metabolism: A Matter of Time and Space. Endocr Rev 2020; 41:5835826. [PMID: 32392281 PMCID: PMC7334005 DOI: 10.1210/endrev/bnaa014] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023]
Abstract
All biological processes, living organisms, and ecosystems have evolved with the Sun that confers a 24-hour periodicity to life on Earth. Circadian rhythms arose from evolutionary needs to maximize daily organismal fitness by enabling organisms to mount anticipatory and adaptive responses to recurrent light-dark cycles and associated environmental changes. The clock is a conserved feature in nearly all forms of life, ranging from prokaryotes to virtually every cell of multicellular eukaryotes. The mammalian clock comprises transcription factors interlocked in negative feedback loops, which generate circadian expression of genes that coordinate rhythmic physiology. In this review, we highlight previous and recent studies that have advanced our understanding of the transcriptional architecture of the mammalian clock, with a specific focus on epigenetic mechanisms, transcriptomics, and 3-dimensional chromatin architecture. In addition, we discuss reciprocal ways in which the clock and metabolism regulate each other to generate metabolic rhythms. We also highlight implications of circadian biology in human health, ranging from genetic and environment disruptions of the clock to novel therapeutic opportunities for circadian medicine. Finally, we explore remaining fundamental questions and future challenges to advancing the field forward.
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Affiliation(s)
- Yong Hoon Kim
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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31
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Spriano F, Stathis A, Bertoni F. Targeting BET bromodomain proteins in cancer: The example of lymphomas. Pharmacol Ther 2020; 215:107631. [PMID: 32693114 DOI: 10.1016/j.pharmthera.2020.107631] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022]
Abstract
The Bromo- and Extra-Terminal domain (BET) family proteins act as "readers" of acetylated histones and they are important transcription regulators. BRD2, BRD3, BRD4 and BRDT, part of the BET family, are important in different tumors, where upregulation or translocation often occurs. The potential of targeting BET proteins as anti-cancer treatment originated with data obtained with a first series of compounds, and there are now several data supporting BET inhibition in both solid tumors and hematological malignancies. Despite very positive preclinical data in different tumor types, the clinical results have been so far moderate. Using lymphoma as an example to review the data produced in the laboratory and in the context of the early clinical trials, we discuss the modalities to make BET targeting more efficient both generating novel generation of compounds and by exploring the combination with small molecules affecting various signaling pathways, BCL2, or DNA damage response signaling, but also with additional epigenetic agents and with immunotherapy. We also discuss the mechanisms of resistance and the toxicity profiles so far reported.
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Affiliation(s)
- Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Anastasios Stathis
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland; Faculty of Biomedical Sciences, USI, Lugano, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland; Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.
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32
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Selective Mediator dependence of cell-type-specifying transcription. Nat Genet 2020; 52:719-727. [PMID: 32483291 PMCID: PMC7610447 DOI: 10.1038/s41588-020-0635-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/24/2020] [Indexed: 12/15/2022]
Abstract
The Mediator complex directs signals from DNA-binding transcription factors to RNA polymerase (Pol) II. Despite this pivotal position, mechanistic understanding of Mediator in human cells remains incomplete. Here, we quantified Mediator-controlled Pol II kinetics by coupling rapid subunit degradation with orthogonal experimental readouts. Consistent with a model of condensate-driven transcription initiation, large clusters of hypo-phosphorylated Pol II rapidly disassembled upon Mediator degradation. This was accompanied by a selective and pronounced disruption of cell type-specifying transcriptional circuits, whose constituent genes featured exceptionally high rates of Pol II turnover. Notably, transcriptional output of most other genes was largely unaffected by acute Mediator ablation. Maintenance of transcriptional activity at these genes was linked to an unexpected, CDK9-dependent compensatory feedback loop that elevated Pol II pause release rates genome-wide. Collectively, our work positions human Mediator as a globally acting coactivator that selectively safeguards the functionality of cell type-specifying transcriptional networks.
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33
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Basu S, Mackowiak SD, Niskanen H, Knezevic D, Asimi V, Grosswendt S, Geertsema H, Ali S, Jerković I, Ewers H, Mundlos S, Meissner A, Ibrahim DM, Hnisz D. Unblending of Transcriptional Condensates in Human Repeat Expansion Disease. Cell 2020; 181:1062-1079.e30. [PMID: 32386547 PMCID: PMC7261253 DOI: 10.1016/j.cell.2020.04.018] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/16/2020] [Accepted: 04/13/2020] [Indexed: 11/27/2022]
Abstract
Expansions of amino acid repeats occur in >20 inherited human disorders, and many occur in intrinsically disordered regions (IDRs) of transcription factors (TFs). Such diseases are associated with protein aggregation, but the contribution of aggregates to pathology has been controversial. Here, we report that alanine repeat expansions in the HOXD13 TF, which cause hereditary synpolydactyly in humans, alter its phase separation capacity and its capacity to co-condense with transcriptional co-activators. HOXD13 repeat expansions perturb the composition of HOXD13-containing condensates in vitro and in vivo and alter the transcriptional program in a cell-specific manner in a mouse model of synpolydactyly. Disease-associated repeat expansions in other TFs (HOXA13, RUNX2, and TBP) were similarly found to alter their phase separation. These results suggest that unblending of transcriptional condensates may underlie human pathologies. We present a molecular classification of TF IDRs, which provides a framework to dissect TF function in diseases associated with transcriptional dysregulation.
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Affiliation(s)
- Shaon Basu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Henri Niskanen
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Dora Knezevic
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Vahid Asimi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefanie Grosswendt
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Hylkje Geertsema
- Institute for Chemistry and Biochemistry, Free University Berlin, 14195 Berlin, Germany
| | - Salaheddine Ali
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, 10178 Berlin, Germany
| | - Ivana Jerković
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Free University Berlin, 14195 Berlin, Germany
| | - Stefan Mundlos
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, 10178 Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Daniel M Ibrahim
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, 10178 Berlin, Germany
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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Wang X, Cairns MJ, Yan J. Super-enhancers in transcriptional regulation and genome organization. Nucleic Acids Res 2020; 47:11481-11496. [PMID: 31724731 PMCID: PMC7145697 DOI: 10.1093/nar/gkz1038] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/19/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
Gene expression is precisely controlled in a stage and cell-type-specific manner, largely through the interaction between cis-regulatory elements and their associated trans-acting factors. Where these components aggregate in promoters and enhancers, they are able to cooperate to modulate chromatin structure and support the engagement in long-range 3D superstructures that shape the dynamics of a cell's genomic architecture. Recently, the term 'super-enhancer' has been introduced to describe a hyper-active regulatory domain comprising a complex array of sequence elements that work together to control the key gene networks involved in cell identity. Here, we survey the unique characteristics of super-enhancers compared to other enhancer types and summarize the recent advances in our understanding of their biological role in gene regulation. In particular, we discuss their capacity to attract the formation of phase-separated condensates, and capacity to generate three-dimensional genome structures that precisely activate their target genes. We also propose a multi-stage transition model to explain the evolutionary pressure driving the development of super-enhancers in complex organisms, and highlight the potential for involvement in tumorigenesis. Finally, we discuss more broadly the role of super-enhancers in human health disorders and related potential in therapeutic interventions.
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Affiliation(s)
- Xi Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education / School of Life Sciences, Northwest University, Xi'an 710069, China.,Division of Theoretical Systems Biology, Germany Cancer Research Center, Heidelberg 69115, Germany.,School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.,Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW 2308, Australia; and Hunter Medical Research Institute
| | - Jian Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education / School of Life Sciences, Northwest University, Xi'an 710069, China.,Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong S.A.R., China
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Abstract
Epigenetic mechanisms involve the placing (writing) or removal (erasing) of histone modifications that allow heterochromatin to transition to the open, activated euchromatin state necessary for transcription. A third, less studied epigenetic pathway involves the reading of these specific histone marks once placed. The BETs (bromodomain and extraterminal-containing protein family), which includes BRD2, BRD3, and BRD4 and the testis-restricted BRDT, are epigenetic reader proteins that bind to specific acetylated lysine residues on histone tails where they facilitate the assembly of transcription complexes including transcription factors and transcriptional machinery like RNA Polymerase II. As reviewed here, considerable recent data establishes BETs as novel determinants of induced transcriptional programs in vascular cells, like endothelial cells and vascular smooth muscle cells, cardiac myocytes and inflammatory cells, like monocyte/macrophages, cellular settings where these epigenetic reader proteins couple proximal stimuli to chromatin, acting at super-enhancer regulatory regions to direct gene expression. BET inhibition, including the use of specific chemical BET inhibitors like JQ-1, has many reported effects in vivo in the cardiovascular setting, like decreasing atherosclerosis, angiogenesis, intimal hyperplasia, pulmonary arterial hypertension, and cardiac hypertrophy. At the same time, data in endothelial cells, adipocytes, and elsewhere suggest BETs also help regulate gene expression under basal conditions. Studies in the cardiovascular setting have highlighted BET action as a means of controlling gene expression in differentiation, cell identity, and cell state transitions, whether physiological or pathological, adaptive, or maladaptive. While distinct BET inhibitors are being pursued as therapies in oncology, a large prospective clinical cardiovascular outcome study investigating the BET inhibitor RVX-208 (now called apabetalone) has already been completed. Independent of this specific agent and this one trial or the numerous unanswered questions that remain, BETs have emerged as novel epigenetic players involved in the execution of coordinated transcriptional programs in cardiovascular health and disease.
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Affiliation(s)
- Patricia Cristine Borck
- From the Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (P.C.B., J.P.)
| | - Lian-Wang Guo
- Davis Heart and Lung Institute, Wexner Medical Center, Ohio State University, Columbus (L.-W.G.)
| | - Jorge Plutzky
- From the Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (P.C.B., J.P.)
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36
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Olp MD, Sprague DJ, Goetz CJ, Kathman SG, Wynia-Smith SL, Shishodia S, Summers SB, Xu Z, Statsyuk AV, Smith BC. Covalent-Fragment Screening of BRD4 Identifies a Ligandable Site Orthogonal to the Acetyl-Lysine Binding Sites. ACS Chem Biol 2020; 15:1036-1049. [PMID: 32149490 DOI: 10.1021/acschembio.0c00058] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BRD4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to nonhomologous cysteine residues within the C-terminal BRD4 bromodomain (BRD4-BD2), we performed a midthroughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify BRD4. Subsequent mass spectrometry, NMR, and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to BRD4 among human bromodomains. This site is orthogonal to the BRD4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays nor an acetylated histone peptide in AlphaScreen assays. Finally, we tethered our top-performing covalent fragment to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace BRD4 from chromatin.
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Affiliation(s)
- Michael D. Olp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Daniel J. Sprague
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Christopher J. Goetz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Stefan G. Kathman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Sarah L. Wynia-Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Shifali Shishodia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Steven B. Summers
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Ziyang Xu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexander V. Statsyuk
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- College of Pharmacy, University of Houston, Houston, Texas 77004, United States
| | - Brian C. Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
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Trivedi A, Mehrotra A, Baum CE, Lewis B, Basuroy T, Blomquist T, Trumbly R, Filipp FV, Setaluri V, de la Serna IL. Bromodomain and extra-terminal domain (BET) proteins regulate melanocyte differentiation. Epigenetics Chromatin 2020; 13:14. [PMID: 32151278 PMCID: PMC7063807 DOI: 10.1186/s13072-020-00333-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/19/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Pharmacologic inhibition of bromodomain and extra-terminal (BET) proteins is currently being explored as a new therapeutic approach in cancer. Some studies have also implicated BET proteins as regulators of cell identity and differentiation through their interactions with lineage-specific factors. However, the role of BET proteins has not yet been investigated in melanocyte differentiation. Melanocyte inducing transcription factor (MITF) is the master regulator of melanocyte differentiation, essential for pigmentation and melanocyte survival. In this study, we tested the hypothesis that BET proteins regulate melanocyte differentiation through interactions with MITF. RESULTS Here we show that chemical inhibition of BET proteins prevents differentiation of unpigmented melanoblasts into pigmented melanocytes and results in de-pigmentation of differentiated melanocytes. BET inhibition also slowed cell growth, without causing cell death, increasing the number of cells in G1. Transcriptional profiling revealed that BET inhibition resulted in decreased expression of pigment-specific genes, including many MITF targets. The expression of pigment-specific genes was also down-regulated in melanoma cells, but to a lesser extent. We found that RNAi depletion of the BET family members, bromodomain-containing protein 4 (BRD4) and bromodomain-containing protein 2 (BRD2) inhibited expression of two melanin synthesis enzymes, TYR and TYRP1. Both BRD4 and BRD2 were detected on melanocyte promoters surrounding MITF-binding sites, were associated with open chromatin structure, and promoted MITF binding to these sites. Furthermore, BRD4 and BRD2 physically interacted with MITF. CONCLUSION These findings indicate a requirement for BET proteins in the regulation of pigmentation and melanocyte differentiation. We identified changes in pigmentation specific gene expression that occur upon BET inhibition in melanoblasts, melanocytes, and melanoma cells.
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Affiliation(s)
- Archit Trivedi
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| | - Aanchal Mehrotra
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
- Present Address: Department of Genome Sciences, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195 USA
| | - Caitlin E. Baum
- Department of Pathology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| | - Brandon Lewis
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| | - Tupa Basuroy
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
- Present Address: Cancer Center Division, Massachusetts General Hospital Harvard Medical School, 149 Thirteenth Street, 7th Floor, Charlestown, MA 02129 USA
| | - Thomas Blomquist
- Department of Pathology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| | - Robert Trumbly
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| | - Fabian V. Filipp
- Cancer Systems Biology, Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, München, 85764 Germany
- School of Life Sciences Weihenstephan, Technical University München, Maximus-von-Imhof-Forum 3, Freising, 85354 Germany
| | - Vijayasaradhi Setaluri
- Department of Dermatology, University of Wisconsin-Madison, The School of Medicine and Public Health, 1 S. Park Street, Madison, WI 53715 USA
| | - Ivana L. de la Serna
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
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Abstract
During aging, deterioration in cardiac structure and function leads to increased susceptibility to heart failure. The need for interventions to combat this age-related cardiac decline is becoming increasingly urgent as the elderly population continues to grow. Our understanding of cardiac aging, and aging in general, is limited. However, recent studies of age-related decline and its prevention through interventions like exercise have revealed novel pathological and cardioprotective pathways. In this review, we summarize recent findings concerning the molecular mechanisms of age-related heart failure and highlight exercise as a valuable experimental platform for the discovery of much-needed novel therapeutic targets in this chronic disease.
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Affiliation(s)
- Haobo Li
- From the Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston (H.L., M.H.H., J.R., L.E.T., J.D.R., A.R.)
| | - Margaret H Hastings
- From the Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston (H.L., M.H.H., J.R., L.E.T., J.D.R., A.R.)
| | - James Rhee
- From the Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston (H.L., M.H.H., J.R., L.E.T., J.D.R., A.R.).,Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston (J.R.)
| | - Lena E Trager
- From the Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston (H.L., M.H.H., J.R., L.E.T., J.D.R., A.R.)
| | - Jason D Roh
- From the Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston (H.L., M.H.H., J.R., L.E.T., J.D.R., A.R.)
| | - Anthony Rosenzweig
- From the Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston (H.L., M.H.H., J.R., L.E.T., J.D.R., A.R.)
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Jiang G, Deng W, Liu Y, Wang C. General mechanism of JQ1 in inhibiting various types of cancer. Mol Med Rep 2020; 21:1021-1034. [PMID: 31922235 PMCID: PMC7003028 DOI: 10.3892/mmr.2020.10927] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/04/2019] [Indexed: 01/21/2023] Open
Abstract
Bromodomain-containing 4 (BRD4) is a histone modification reader and transcriptional regulator that has been reported to interact with acetylated lysine histone motifs transcription factors (TFs), transcription co-activators and RNA polymerase II. The selective small molecule inhibitor JQ1, which binds competitively to bromodomains, has been reported to exhibit anti-proliferative effects in various types of cancer. Previous studies on the mechanism of action of JQ1 mostly focused on a specific tumor type or disease; however, the general mechanism through which JQ1 affects various tumors remains to be determined. In the present study, chromatin immunoprecipitation sequencing data for BRD4 and its expression profiles in six cancer cell lines were integrated and analyzed systematically. The results indicated that BRD4 binds to enhancers with histone H3 acetylated at lysine 27 (H3K27Ac) and mediator complex subunit 1 in a cell type-specific manner, as well as binds to promoter regions with the oncogenic TFs MYC and E2F1 in a cell type-common manner. The cell type-common sites across the six cell types investigated were found to be functionally important for tumorigenesis, whereas the cell type-specific sites were functionally enriched with the cell identity, all of which were sensitive to JQ1 treatment. Furthermore, a core set of JQ1-regulated BRD4 binding genes were obtained, which were significantly inhibited by JQ1 in various cancer cell lines and contributed to hallmarks of cancer. These results implied a common mechanism underlying the therapeutic effects of JQ1 and suggested its potential suitability as an anti-cancer drug targeting BRD4-mediated transcriptional regulation.
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Affiliation(s)
- Guojuan Jiang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, P.R. China
| | - Wanglong Deng
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, P.R. China
| | - Yang Liu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, P.R. China
| | - Chengde Wang
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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40
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Reyes-Garau D, Ribeiro ML, Roué G. Pharmacological Targeting of BET Bromodomain Proteins in Acute Myeloid Leukemia and Malignant Lymphomas: From Molecular Characterization to Clinical Applications. Cancers (Basel) 2019; 11:cancers11101483. [PMID: 31581671 PMCID: PMC6826405 DOI: 10.3390/cancers11101483] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/16/2022] Open
Abstract
Alterations in protein-protein and DNA-protein interactions and abnormal chromatin remodeling are a major cause of uncontrolled gene transcription and constitutive activation of critical signaling pathways in cancer cells. Multiple epigenetic regulators are known to be deregulated in several hematologic neoplasms, by somatic mutation, amplification, or deletion, allowing the identification of specific epigenetic signatures, but at the same time providing new therapeutic opportunities. While these vulnerabilities have been traditionally addressed by hypomethylating agents or histone deacetylase inhibitors, pharmacological targeting of bromodomain-containing proteins has recently emerged as a promising approach in a number of lymphoid and myeloid malignancies. Indeed, preclinical and clinical studies highlight the relevance of targeting the bromodomain and extra-terminal (BET) family as an efficient strategy of target transcription irrespective of the presence of epigenetic mutations. Here we will summarize the main advances achieved in the last decade regarding the preclinical and clinical evaluation of BET bromodomain inhibitors in hematologic cancers, either as monotherapies or in combinations with standard and/or experimental agents. A mention will finally be given to the new concept of the protein degrader, and the perspective it holds for the design of bromodomain-based therapies.
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Affiliation(s)
- Diana Reyes-Garau
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, 08035 Barcelona, Spain.
| | - Marcelo L Ribeiro
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, 08035 Barcelona, Spain.
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University Medical School, Braganca Paulista, São Paulo 12916-900, Brazil.
| | - Gaël Roué
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, 08035 Barcelona, Spain.
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41
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The Cornelia de Lange Syndrome-associated factor NIPBL interacts with BRD4 ET domain for transcription control of a common set of genes. Cell Death Dis 2019; 10:548. [PMID: 31320616 PMCID: PMC6639259 DOI: 10.1038/s41419-019-1792-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/17/2019] [Accepted: 07/02/2019] [Indexed: 01/19/2023]
Abstract
Mutations in NIPBL are the major cause of Cornelia de Lange Syndrome (CdLS). NIPBL is the cohesin-loading factor and has recently been associated with the BET (bromodomains and extra-terminal (ET) domain) proteins BRD2 and BRD4. Related to this, a CdLS-like phenotype has been described associated to BRD4 mutations. Here, we show direct interaction of NIPBL with different BET members in yeast, and selective interaction with BRD4 in cells, being the ET domain involved in the interaction. To understand the relationship between NIPBL and BET proteins, we have performed RNA-Seq expression analysis following depletion of the different proteins. Results indicate that genes regulated by NIPBL largely overlap with those regulated by BRD4 but not with those regulated by BRD2. ChIP-Seq analysis indicates preferential NIPBL occupancy at promoters, and knockdown experiments show mutual stabilization of NIPBL and BRD4 on co-regulated promoters. Moreover, human fibroblasts from CdLS probands with mutations in NIPBL show reduced BRD4 at co-occupied promoters. Functional analysis in vivo, using mutants of Drosophila melanogaster, confirmed the genetic interaction between Nipped-B and fs(1)h, the orthologs of human NIPBL and BRD4, respectively. Thus, we provide evidence for NIPBL and BRD4 cooperation in transcriptional regulation, which should contribute to explain the recently observed CdLS-like phenotype associated with BRD4 mutations.
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42
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Jia Y, Chng WJ, Zhou J. Super-enhancers: critical roles and therapeutic targets in hematologic malignancies. J Hematol Oncol 2019; 12:77. [PMID: 31311566 PMCID: PMC6636097 DOI: 10.1186/s13045-019-0757-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022] Open
Abstract
Super-enhancers (SEs) in a broad range of human cell types are large clusters of enhancers with aberrant high levels of transcription factor binding, which are central to drive expression of genes in controlling cell identity and stimulating oncogenic transcription. Cancer cells acquire super-enhancers at oncogene and cancerous phenotype relies on these abnormal transcription propelled by SEs. Furthermore, specific inhibitors targeting SEs assembly and activation have offered potential targets for treating various tumors including hematological malignancies. Here, we first review the identification, functional significance of SEs. Next, we summarize recent findings of SEs and SE-driven gene regulation in normal hematopoiesis and hematologic malignancies. The importance and various modes of SE-mediated MYC oncogene amplification are illustrated. Finally, we highlight the progress of SEs as selective therapeutic targets in basic research and clinical trials. Some open questions regarding functional significance and future directions of targeting SEs in the clinic will be discussed too.
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Affiliation(s)
- Yunlu Jia
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599 Republic of Singapore
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016 Zhejiang China
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599 Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Republic of Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228 Republic of Singapore
| | - Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599 Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Republic of Singapore
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43
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Bromodomain inhibitor JQ1 reversibly blocks IFN-γ production. Sci Rep 2019; 9:10280. [PMID: 31311960 PMCID: PMC6635431 DOI: 10.1038/s41598-019-46516-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/29/2019] [Indexed: 02/07/2023] Open
Abstract
As a class, ‘BET’ inhibitors disrupt binding of bromodomain and extra-terminal motif (BET) proteins, BRD2, BRD3, BRD4 and BRDT, to acetylated histones preventing recruitment of RNA polymerase 2 to enhancers and promoters, especially super-enhancers, to inhibit gene transcription. As such, BET inhibitors may be useful therapeutics for treatment of cancer and inflammatory disease. For example, the small molecule BET inhibitor, JQ1, selectively represses MYC, an important oncogene regulated by a super-enhancer. IFN-γ, a critical cytokine for both innate and adaptive immune responses, is also regulated by a super-enhancer. Here, we show that JQ1 represses IFN-γ expression in TH1 polarized PBMC cultures, CD4+ memory T cells, and NK cells. JQ1 treatment does not reduce activating chromatin marks at the IFNG locus, but displaces RNA polymerase II from the locus. Further, IFN-γ expression recovers in polarized TH1 cultures following removal of JQ1. Our results show that JQ1 abrogates IFN-γ expression, but repression is reversible. Thus, BET inhibitors may disrupt the normal functions of the innate and adaptive immune response.
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44
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Quevedo M, Meert L, Dekker MR, Dekkers DHW, Brandsma JH, van den Berg DLC, Ozgür Z, van IJcken WFJ, Demmers J, Fornerod M, Poot RA. Mediator complex interaction partners organize the transcriptional network that defines neural stem cells. Nat Commun 2019; 10:2669. [PMID: 31209209 PMCID: PMC6573065 DOI: 10.1038/s41467-019-10502-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/10/2019] [Indexed: 01/13/2023] Open
Abstract
The Mediator complex regulates transcription by connecting enhancers to promoters. High Mediator binding density defines super enhancers, which regulate cell-identity genes and oncogenes. Protein interactions of Mediator may explain its role in these processes but have not been identified comprehensively. Here, we purify Mediator from neural stem cells (NSCs) and identify 75 protein-protein interaction partners. We identify super enhancers in NSCs and show that Mediator-interacting chromatin modifiers colocalize with Mediator at enhancers and super enhancers. Transcription factor families with high affinity for Mediator dominate enhancers and super enhancers and can explain genome-wide Mediator localization. We identify E-box transcription factor Tcf4 as a key regulator of NSCs. Tcf4 interacts with Mediator, colocalizes with Mediator at super enhancers and regulates neurogenic transcription factor genes with super enhancers and broad H3K4me3 domains. Our data suggest that high binding-affinity for Mediator is an important organizing feature in the transcriptional network that determines NSC identity. The Mediator complex regulates transcription by connecting enhancers to promoters. Here, the authors purify Mediator from neural stem cells (NSCs), identify 75 novel protein-protein interaction partners and characterize the Mediator-interacting network that regulates transcription and establishes NSC identity.
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Affiliation(s)
- Marti Quevedo
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Lize Meert
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Mike R Dekker
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Dick H W Dekkers
- Center for Proteomics, Erasmus MC, 3015 CN, Rotterdam, Netherlands
| | - Johannes H Brandsma
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | | | - Zeliha Ozgür
- Center for Biomics, Erasmus MC, 3015 CN, Rotterdam, Netherlands
| | | | - Jeroen Demmers
- Center for Proteomics, Erasmus MC, 3015 CN, Rotterdam, Netherlands
| | - Maarten Fornerod
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands.
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45
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Abstract
Recurrent chromosomal rearrangements leading to the generation of oncogenic fusion proteins are a common feature of many cancers. These aberrations are particularly prevalent in sarcomas and haematopoietic malignancies and frequently involve genes required for chromatin regulation and transcriptional control. In many cases, these fusion proteins are thought to be the primary driver of cancer development, altering chromatin dynamics to initiate oncogenic gene expression programmes. In recent years, mechanistic insights into the underlying molecular functions of a number of these oncogenic fusion proteins have been discovered. These insights have allowed the design of mechanistically anchored therapeutic approaches promising substantial treatment advances. In this Review, we discuss how our understanding of fusion protein function is informing therapeutic innovations and illuminating mechanisms of chromatin and transcriptional regulation in cancer and normal cells.
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Affiliation(s)
- Gerard L Brien
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
- Department of Pediatric Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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Ma J, Chen H, Yang J, Yu Z, Huang P, Yang H, Zheng B, Liu R, Li Q, Hu G, Chen Z. Binding pocket-based design, synthesis and biological evaluation of novel selective BRD4-BD1 inhibitors. Bioorg Med Chem 2019; 27:1871-1881. [DOI: 10.1016/j.bmc.2019.03.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 01/09/2023]
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Napolitano M, Venturelli M, Molinaro E, Toss A. NUT midline carcinoma of the head and neck: current perspectives. Onco Targets Ther 2019; 12:3235-3244. [PMID: 31118674 PMCID: PMC6501778 DOI: 10.2147/ott.s173056] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/12/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract: NUT midline carcinoma (NMC) is a rare and aggressive subtype of squamous carcinoma that typically arises from midline supradiaphragmatic structures, frequently from the head and neck area. NMC is genetically driven by a chromosomal rearrangement involving the NUT gene, which forms oncoproteins considered major pathogenic drivers of cellular transformation. Diagnosis of NMC has been made remarkably easier with the availability of a commercial antibody against NUT, and can be established through positive nuclear immunohistochemical staining. Although NMC remains an underrecognized malignancy, in recent years there has appeared to be increasing awareness of disease and frequency of diagnosis in adults. To date, a standard treatment for head and neck NMC has not been established and a multimodal approach with systemic chemotherapy, surgery and radiation therapy is currently adopted in clinical practice. Recently, BET inhibitors and histone deacetylase inhibitors have emerged as two promising classes of targeted agents, currently investigated in clinical trials for adults with head and neck NMC. At the same time, combination approaches and novel targeted agents, such as next-generation BET inhibitors and CDK9 inhibitors, have shown preclinical activity. The present review explores the clinical pathological characteristics of NMC of the head and neck and presents the current state of the art on diagnosis, prognosis, and treatment of this rare but lethal disease.
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Affiliation(s)
- M Napolitano
- Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy
| | - M Venturelli
- Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy
| | - E Molinaro
- Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy
| | - A Toss
- Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy
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Huijbregts L, Petersen MBK, Berthault C, Hansson M, Aiello V, Rachdi L, Grapin-Botton A, Honore C, Scharfmann R. Bromodomain and Extra Terminal Protein Inhibitors Promote Pancreatic Endocrine Cell Fate. Diabetes 2019; 68:761-773. [PMID: 30655386 DOI: 10.2337/db18-0224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 01/07/2019] [Indexed: 11/13/2022]
Abstract
Bromodomain and extraterminal (BET) proteins are epigenetic readers that interact with acetylated lysines of histone tails. Recent studies have demonstrated their role in cancer progression because they recruit key components of the transcriptional machinery to modulate gene expression. However, their role during embryonic development of the pancreas has never been studied. Using mouse embryonic pancreatic explants and human induced pluripotent stem cells (hiPSCs), we show that BET protein inhibition with I-BET151 or JQ1 enhances the number of neurogenin3 (NEUROG3) endocrine progenitors. In mouse explants, BET protein inhibition further led to increased expression of β-cell markers but in the meantime, strongly downregulated Ins1 expression. Similarly, although acinar markers, such as Cpa1 and CelA, were upregulated, Amy expression was repressed. In hiPSCs, BET inhibitors strongly repressed C-peptide and glucagon during endocrine differentiation. Explants and hiPSCs were then pulsed with BET inhibitors to increase NEUROG3 expression and further chased without inhibitors. Endocrine development was enhanced in explants with higher expression of insulin and maturation markers, such as UCN3 and MAFA. In hiPSCs, the outcome was different because C-peptide expression remained lower than in controls, but ghrelin expression was increased. Altogether, by using two independent models of pancreatic development, we show that BET proteins regulate multiple aspects of pancreatic development.
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Affiliation(s)
- Lukas Huijbregts
- INSERM U1016, Institut Cochin, Université Paris Descartes, Paris, France
| | - Maja Borup Kjær Petersen
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Claire Berthault
- INSERM U1016, Institut Cochin, Université Paris Descartes, Paris, France
| | | | - Virginie Aiello
- INSERM U1016, Institut Cochin, Université Paris Descartes, Paris, France
| | - Latif Rachdi
- INSERM U1016, Institut Cochin, Université Paris Descartes, Paris, France
| | - Anne Grapin-Botton
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Christian Honore
- Department of Stem Cell Biology, Novo Nordisk A/S, Måløv, Denmark
| | - Raphael Scharfmann
- INSERM U1016, Institut Cochin, Université Paris Descartes, Paris, France
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Design, synthesis and biological evaluation of novel indole derivatives as potential HDAC/BRD4 dual inhibitors and anti-leukemia agents. Bioorg Chem 2019; 84:410-417. [DOI: 10.1016/j.bioorg.2018.12.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/03/2018] [Accepted: 12/10/2018] [Indexed: 12/12/2022]
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Abstract
PURPOSE OF REVIEW Increasing evidence suggests that epigenome plays a central role in cancer development making it a promising target for anticancer treatments. Here, we review two new classes of epigenome-targeting agents: the bromodomain and extraterminal domain proteins (BET) inhibitors and the enhancer of zeste homolog (EZH2) inhibitors. RECENT FINDINGS Clinical research evaluating BET and EZH2 inhibitors is still at an early stage; however, both classes of drugs have demonstrated activity among different hematologic malignancies and solid tumors. Several studies on BETi and EZH2i are ongoing to better define their potential role in cancer treatment, which patients are most likely to benefit and if the association with other drugs can improve their efficacy.
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