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Qiao XP, Wang XT, Wang S, Mu HX, Wang QS, Chen SW. Discovery of indole-2-one derivatives as BRD4 (BD1) selective inhibitors. Bioorg Med Chem 2024; 106:117752. [PMID: 38749341 DOI: 10.1016/j.bmc.2024.117752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
Bromodomain protein 4 (BRD4) is a member of the BET family, and its overexpression is closely associated with the development of many tumors. Inhibition of BRD4 shows great therapeutic potential in anti-tumor, and pan-BRD4 inhibitors show adverse effects of dose limiting toxicity and thrombocytopenia in clinical trials. To improve clinical effects and reduce side effects, more efforts have focused on seeking selective inhibitors of BD1 or BD2. Herein, a series of indole-2-one derivatives were designed and synthesized through docking-guided optimization to find BRD4-BD1 selective inhibitors, and their BRD4 inhibitory and antiproliferation activities were evaluated. Among them, compound 21r had potent BRD4 inhibitory activity (the IC50 values of 41 nM and 313 nM in BD1 and BD2 domain), excellent anti-proliferation (the IC50 values of 4.64 ± 0.30 µM, 0.78 ± 0.03 µM, 5.57 ± 1.03 µM against HL-60, MV-4-11 and HT-29 cells), and displayed low toxicity against normal cell GES-1 cells. Further studies revealed that 21r inhibited proliferation by decreasing the expression of proto-oncogene c-Myc, blocking cell cycle in G0/G1 phase, and inducing apoptosis in MV-4-11 cells in a dose-dependent manner. All the results showed that compound 21r was a potent BRD4 inhibitor with BD1 selectivity, which had potential in treatment of leukemia.
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Affiliation(s)
- Xue-Peng Qiao
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Xue-Ting Wang
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Shuai Wang
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Hong-Xia Mu
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Qing-Shan Wang
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China
| | - Shi-Wu Chen
- School of Pharmacy & Collaborative Innovation Center for Northwestern Chinese Medicine, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
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2
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Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024; 21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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3
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Kisaka JK, Rauch D, Griffith M, Kyei GB. A macrophage-cell model of HIV latency reveals the unusual importance of the bromodomain axis. Virol J 2024; 21:80. [PMID: 38581045 PMCID: PMC10996205 DOI: 10.1186/s12985-024-02343-9] [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: 01/10/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Although macrophages are now recognized as an essential part of the HIV latent reservoir, whether and how viral latency is established and reactivated in these cell types is poorly understood. To understand the fundamental mechanisms of viral latency in macrophages, there is an urgent need to develop latency models amenable to genetic manipulations and screening for appropriate latency-reversing agents (LRAs). Given that differentiated THP-1 cells resemble monocyte-derived macrophages in HIV replication mechanisms, we set out to establish a macrophage cell model for HIV latency using THP-1 cells. METHODS We created single-cell clones of THP-1 cells infected with a single copy of the dual-labeled HIVGKO in which a codon switched eGFP (csGFP) is under the control of the HIV-1 5' LTR promoter, and a monomeric Kusabira orange 2 (mKO2) under the control of cellular elongation factor one alpha promoter (EF1α). Latently infected cells are csGFP-, mKO2+, while cells with actively replicating HIV (or reactivated virus) are csGFP+,mKO2+. After sorting for latently infected cells, each of the THP-1 clones with unique integration sites for HIV was differentiated into macrophage-like cells with phorbol 12-myristate 13-acetate (PMA) and treated with established LRAs to stimulate HIV reactivation. Monocyte-derived macrophages (MDMs) harboring single copies of HIVGKO were used to confirm our findings. RESULTS We obtained clones of THP-1 cells with latently infected HIV with unique integration sites. When the differentiated THP-1 or primary MDMs cells were treated with various LRAs, the bromodomain inhibitors JQ1 and I-BET151 were the most potent compounds. Knockdown of BRD4, the target of JQ1, resulted in increased reactivation, thus confirming the pharmacological effect. The DYRK1A inhibitor Harmine and lipopolysaccharide (LPS) also showed significant reactivation across all three MDM donors. Remarkably, LRAs like PMA/ionomycin, bryostatin-1, and histone deacetylase inhibitors known to potently reactivate latent HIV in CD4 + T cells showed little activity in macrophages. CONCLUSIONS Our results indicate that this model could be used to screen for appropriate LRAs for macrophages and show that HIV latency and reactivation mechanisms in macrophages may be distinct from those of CD4 + T cells.
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Affiliation(s)
- Javan K Kisaka
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Daniel Rauch
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO, 63108, USA
| | - George B Kyei
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
- Department of Virology, College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.
- Medical and Scientific Research Center, University of Ghana Medical Center, Accra, Ghana.
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4
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Amir N, Taube R. Role of long noncoding RNA in regulating HIV infection-a comprehensive review. mBio 2024; 15:e0192523. [PMID: 38179937 PMCID: PMC10865847 DOI: 10.1128/mbio.01925-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
A complete cure against human immunodeficiency virus (HIV) infection remains out of reach, as the virus persists in stable cell reservoirs that are resistant to antiretroviral therapy. The key to eliminating these reservoirs lies in deciphering the processes that govern viral gene expression and latency. However, while we comprehensively understand how host proteins influence HIV gene expression and viral latency, the emerging role of long noncoding RNAs (lncRNAs) in the context of T cell activation, HIV gene expression, and viral latency remain unexplored. This review dives into the evolving significance of lncRNAs and their impact on HIV gene expression and viral latency. We provide an overview of the current knowledge regarding how lncRNAs regulate HIV gene expression, categorizing them as either activators or inhibitors of viral gene expression and infectivity. Furthermore, we offer insights into the potential therapeutic applications of lncRNAs in combatting HIV. A deeper understanding of how lncRNAs modulate HIV gene transcription holds promise for developing novel RNA-based therapies to complement existing treatment strategies to eradicate HIV reservoirs.
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Affiliation(s)
- Noa Amir
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Negev, Israel
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Negev, Israel
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5
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Sun M, Clayton N, Alam S, Asmussen N, Wong A, Kim JH, Luong G, Mokhtari S, Pellei D, Carrico CK, Schwartz Z, Boyan BD, Giannobile WV, Sahingur SE, Lin Z. Selective BET inhibitor RVX-208 ameliorates periodontal inflammation and bone loss. J Clin Periodontol 2023; 50:1658-1669. [PMID: 37855275 DOI: 10.1111/jcpe.13887] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 09/06/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023]
Abstract
AIM To determine the effects of RVX-208, a selective bromodomain and extra-terminal domain (BET) inhibitor targeting bromodomain 2 (BD2), on periodontal inflammation and bone loss. MATERIALS AND METHODS Macrophage-like cells (RAW264.7) and human gingival epithelial cells were challenged by Porphyromonas gingivalis (Pg) with or without RVX-208. Inflammatory gene expression and cytokine production were measured by reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. RAW264.7 cells were induced to osteoclast differentiation. After RVX-208 treatment, osteoclast differentiation was evaluated by histology, tartrate-resistant-acid-phosphatase (TRAP) activity and the expression of osteoclast-specific genes. The effect of RVX-208 on osteoclast transcriptome was studied by RNA sequencing. Periodontitis was induced in rats by ligature and local RVX-208 treatment was administered every other day. Alveolar bone loss was measured by micro-computed tomography. RESULTS RVX-208 inhibited inflammatory gene expression and cytokine production in Pg-infected cells. Osteoclast differentiation was inhibited by RVX-208, as evidenced by reduced osteoclast number, TRAP activity and osteoclast-specific gene expression. RVX-208 displayed a more selective and less profound suppressive impact on transcriptome compared with pan-BET inhibitor, JQ1. RVX-208 administration prevented the alveolar bone loss in vivo. CONCLUSIONS RVX-208 regulated both upstream (inflammatory cytokine production) and downstream (osteoclast differentiation) events that lead to periodontal tissue destruction, suggesting that it may be a promising 'epi-drug' for the prevention of periodontitis.
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Affiliation(s)
- Mingxu Sun
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, USA
- Jianbo Dental Clinic, Qingdao, People's Republic of China
| | - Nicholas Clayton
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Sheikh Alam
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Niels Asmussen
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Andrew Wong
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jin Ha Kim
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Gary Luong
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Sasan Mokhtari
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - David Pellei
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Caroline K Carrico
- Department of Dental Public Health and Policy, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Zvi Schwartz
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Barbara D Boyan
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, USA
| | - William V Giannobile
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Sinem Esra Sahingur
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zhao Lin
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, USA
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Sun J, Gui Y, Zhou S, Zheng XL. Unlocking the secrets of aging: Epigenetic reader BRD4 as the target to combatting aging-related diseases. J Adv Res 2023:S2090-1232(23)00329-6. [PMID: 37956861 DOI: 10.1016/j.jare.2023.11.006] [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: 09/23/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Aging, a complex and profound journey, leads us through a labyrinth of physiological and pathological transformations, rendering us increasingly susceptible to aging-related diseases. Emerging investigations have unveiled the function of bromodomain containing protein 4 (BRD4) in manipulating the aging process and driving the emergence and progression of aging-related diseases. AIM OF REVIEW This review aims to offer a comprehensive outline of BRD4's functions involved in the aging process, and potential mechanisms through which BRD4 governs the initiation and progression of various aging-related diseases. KEY SCIENTIFIC CONCEPTS OF REVIEW BRD4 has a fundamental role in regulating the cell cycle, apoptosis, cellular senescence, the senescence-associated secretory phenotype (SASP), senolysis, autophagy, and mitochondrial function, which are involved in the aging process. Several studies have indicated that BRD4 governs the initiation and progression of various aging-related diseases, including Alzheimer's disease, ischemic cerebrovascular diseases, hypertension, atherosclerosis, heart failure, aging-related pulmonary fibrosis, and intervertebral disc degeneration (IVDD). Thus, the evidence from this review supports that BRD4 could be a promising target for managing various aging-related diseases, while further investigation is warranted to gain a thorough understanding of BRD4's role in these diseases.
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Affiliation(s)
- Jiaxing Sun
- Departments of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, AB, Canada; Department of Cardiology, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Yu Gui
- Departments of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Shenghua Zhou
- Department of Cardiology, the Second Xiangya Hospital of Central South University, Changsha, China.
| | - Xi-Long Zheng
- Departments of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, AB, Canada.
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7
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Schmitt A, Grimm M, Kreienkamp N, Junge H, Labisch J, Schuhknecht L, Schönfeld C, Görsch E, Tibello A, Menck K, Bleckmann A, Lengerke C, Rosenbauer F, Grau M, Zampieri M, Schulze-Osthoff K, Klener P, Dolnikova A, Lenz G, Hailfinger S. BRD4 inhibition sensitizes diffuse large B-cell lymphoma cells to ferroptosis. Blood 2023; 142:1143-1155. [PMID: 37294920 DOI: 10.1182/blood.2022019274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/11/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL), the most common form of non-Hodgkin lymphoma, is characterized by an aggressive clinical course. In approximately one-third of patients with DLBCL, first-line multiagent immunochemotherapy fails to produce a durable response. Molecular heterogeneity and apoptosis resistance pose major therapeutic challenges in DLBCL treatment. To circumvent apoptosis resistance, the induction of ferroptosis might represent a promising strategy for lymphoma therapy. In this study, a compound library, targeting epigenetic modulators, was screened to identify ferroptosis-sensitizing drugs. Strikingly, bromodomain and extra-terminal domain (BET) inhibitors sensitized cells of the germinal center B-cell-like (GCB) subtype of DLBCL to ferroptosis induction and the combination of BET inhibitors with ferroptosis inducers, such as dimethyl fumarate or RSL3, synergized in the killing of DLBCL cells in vitro and in vivo. On the molecular level, the BET protein BRD4 was found to be an essential regulator of ferroptosis suppressor protein 1 expression and thus to protect GCB-DLBCL cells from ferroptosis. Collectively, we identified and characterized BRD4 as an important player in ferroptosis suppression in GCB-DLBCL and provide a rationale for the combination of BET inhibitors with ferroptosis-inducing agents as a novel therapeutic approach for DLBCL treatment.
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Affiliation(s)
- Anja Schmitt
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Melanie Grimm
- Department of Molecular Medicine, Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Nina Kreienkamp
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Hannah Junge
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Jan Labisch
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | | | - Caroline Schönfeld
- Department of Molecular Medicine, Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Elsa Görsch
- Department for Internal Medicine, Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Alessia Tibello
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Münster, Münster, Germany
| | - Kerstin Menck
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Annalen Bleckmann
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Claudia Lengerke
- Department for Internal Medicine, Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Münster, Münster, Germany
| | - Michael Grau
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Mattia Zampieri
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Klaus Schulze-Osthoff
- Department of Molecular Medicine, Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (Deutsches Konsortium für Translationale Krebsforschung) and German Cancer Research Center (Deutsches Krebsforschungszentrum), Heidelberg, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Pavel Klener
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University Prague, Prague, Czech Republic
- First Department of Medicine, Hematology, University General Hospital and First Faculty of Medicine, Charles University Prague, Prague, Czech Republic
| | - Alexandra Dolnikova
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University Prague, Prague, Czech Republic
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Stephan Hailfinger
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
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8
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Das ND, Chang JC, Hon CC, Kelly ST, Ito S, Lizio M, Kaczkowski B, Watanabe H, Katsushima K, Natsume A, Koseki H, Kondo Y, Minoda A, Umehara T. Defining super-enhancers by highly ranked histone H4 multi-acetylation levels identifies transcription factors associated with glioblastoma stem-like properties. BMC Genomics 2023; 24:574. [PMID: 37759202 PMCID: PMC10523799 DOI: 10.1186/s12864-023-09659-w] [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: 07/26/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Super-enhancers (SEs), which activate genes involved in cell-type specificity, have mainly been defined as genomic regions with top-ranked enrichment(s) of histone H3 with acetylated K27 (H3K27ac) and/or transcription coactivator(s) including a bromodomain and extra-terminal domain (BET) family protein, BRD4. However, BRD4 preferentially binds to multi-acetylated histone H4, typically with acetylated K5 and K8 (H4K5acK8ac), leading us to hypothesize that SEs should be defined by high H4K5acK8ac enrichment at least as well as by that of H3K27ac. RESULTS Here, we conducted genome-wide profiling of H4K5acK8ac and H3K27ac, BRD4 binding, and the transcriptome by using a BET inhibitor, JQ1, in three human glial cell lines. When SEs were defined as having the top ranks for H4K5acK8ac or H3K27ac signal, 43% of H4K5acK8ac-ranked SEs were distinct from H3K27ac-ranked SEs in a glioblastoma stem-like cell (GSC) line. CRISPR-Cas9-mediated deletion of the H4K5acK8ac-preferred SEs associated with MYCN and NFIC decreased the stem-like properties in GSCs. CONCLUSIONS Collectively, our data highlights H4K5acK8ac's utility for identifying genes regulating cell-type specificity.
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Affiliation(s)
- Nando D Das
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Jen-Chien Chang
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Chung-Chau Hon
- Laboratory for Genome Information Analysis, RIKEN IMS, Yokohama, Japan
| | - S Thomas Kelly
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Shinsuke Ito
- Laboratory of Developmental Genetics, RIKEN IMS, Yokohama, Japan
| | - Marina Lizio
- Laboratory for Genome Information Analysis, RIKEN IMS, Yokohama, Japan
| | - Bogumil Kaczkowski
- Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN IMS, Yokohama, Japan
| | - Hisami Watanabe
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Keisuke Katsushima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsushi Natsume
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN IMS, Yokohama, Japan
- Immune Regulation, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Aki Minoda
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
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9
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Gajjela BK, Zhou MM. Bromodomain inhibitors and therapeutic applications. Curr Opin Chem Biol 2023; 75:102323. [PMID: 37207401 PMCID: PMC10524616 DOI: 10.1016/j.cbpa.2023.102323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023]
Abstract
The bromodomain acts to recognize acetylated lysine in histones and transcription proteins and plays a fundamental role in chromatin-based cellular processes including gene transcription and chromatin remodeling. Many bromodomain proteins, particularly the bromodomain and extra terminal domain (BET) protein BRD4 have been implicated in cancers and inflammatory disorders and recognized as attractive drug targets. Although clinical studies of many BET bromodomain inhibitors have made substantial progress toward harnessing the therapeutic potential of targeting the bromodomain proteins, the development of this new class of epigenetic drugs is met with challenges, especially on-target dose-limiting toxicity. In this review, we highlight the current development of new-generation small molecule inhibitors for the BET and non-BET bromodomain proteins and discuss the research strategies used to target different bromodomain proteins for a wide array of human diseases including cancers and inflammatory disorders.
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Affiliation(s)
- Bharath Kumar Gajjela
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States.
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10
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Camara MB, Sobeh AM, Eichhorn CD. Progress in 7SK ribonucleoprotein structural biology. Front Mol Biosci 2023; 10:1154622. [PMID: 37051324 PMCID: PMC10083321 DOI: 10.3389/fmolb.2023.1154622] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
The 7SK ribonucleoprotein (RNP) is a dynamic and multifunctional regulator of RNA Polymerase II (RNAPII) transcription in metazoa. Comprised of the non-coding 7SK RNA, core proteins, and numerous accessory proteins, the most well-known 7SK RNP function is the sequestration and inactivation of the positive transcription elongation factor b (P-TEFb). More recently, 7SK RNP has been shown to regulate RNAPII transcription through P-TEFb-independent pathways. Due to its fundamental role in cellular function, dysregulation has been linked with human diseases including cancers, heart disease, developmental disorders, and viral infection. Significant advances in 7SK RNP structural biology have improved our understanding of 7SK RNP assembly and function. Here, we review progress in understanding the structural basis of 7SK RNA folding, biogenesis, and RNP assembly.
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Affiliation(s)
- Momodou B. Camara
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
| | - Amr M. Sobeh
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
| | - Catherine D. Eichhorn
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
- Nebraska Center for Integrated Biomolecular Communication, Lincoln, NE, United States
- *Correspondence: Catherine D. Eichhorn,
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11
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Zhao L, Wang Y, Jaganathan A, Sun Y, Ma N, Li N, Han X, Sun X, Yi H, Fu S, Han F, Li X, Xiao K, Walsh MJ, Zeng L, Zhou M, Cheung KL. BRD4-PRC2 represses transcription of T-helper 2-specific negative regulators during T-cell differentiation. EMBO J 2023; 42:e111473. [PMID: 36719036 PMCID: PMC10015369 DOI: 10.15252/embj.2022111473] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 12/26/2022] [Accepted: 01/11/2023] [Indexed: 02/01/2023] Open
Abstract
BRD4 is a well-recognized transcriptional activator, but how it regulates gene transcriptional repression in a cell type-specific manner has remained elusive. In this study, we report that BRD4 works with Polycomb repressive complex 2 (PRC2) to repress transcriptional expression of the T-helper 2 (Th2)-negative regulators Foxp3 and E3-ubiqutin ligase Fbxw7 during lineage-specific differentiation of Th2 cells from mouse primary naïve CD4+ T cells. Brd4 binds to the lysine-acetylated-EED subunit of the PRC2 complex via its second bromodomain (BD2) to facilitate histone H3 lysine 27 trimethylation (H3K27me3) at target gene loci and thereby transcriptional repression. We found that Foxp3 represses transcription of Th2-specific transcription factor Gata3, while Fbxw7 promotes its ubiquitination-directed protein degradation. BRD4-mediated repression of Foxp3 and Fbxw7 in turn promotes BRD4- and Gata3-mediated transcriptional activation of Th2 cytokines including Il4, Il5, and Il13. Chemical inhibition of the BRD4 BD2 induces transcriptional de-repression of Foxp3 and Fbxw7, and thus transcriptional downregulation of Il4, Il5, and Il13, resulting in inhibition of Th2 cell lineage differentiation. Our study presents a previously unappreciated mechanism of BRD4's role in orchestrating a Th2-specific transcriptional program that coordinates gene repression and activation, and safeguards cell lineage differentiation.
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Affiliation(s)
- Li Zhao
- Institute of Epigenetic Medicine, First Hospital of Jilin UniversityChangchunChina
| | - Yiqi Wang
- Institute of Epigenetic Medicine, First Hospital of Jilin UniversityChangchunChina
| | - Anbalagan Jaganathan
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Yifei Sun
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Ning Ma
- Institute of Epigenetic Medicine, First Hospital of Jilin UniversityChangchunChina
| | - Ning Li
- The Institute of Genetics and Cytology, Northeast Normal UniversityChangchunChina
| | - Xinye Han
- Institute of Epigenetic Medicine, First Hospital of Jilin UniversityChangchunChina
| | - Xueying Sun
- Institute of Epigenetic Medicine, First Hospital of Jilin UniversityChangchunChina
| | - Huanfa Yi
- Institute of Epigenetic Medicine, First Hospital of Jilin UniversityChangchunChina
| | - Shibo Fu
- Institute of Epigenetic Medicine, First Hospital of Jilin UniversityChangchunChina
| | - Fangbin Han
- Institute of Epigenetic Medicine, First Hospital of Jilin UniversityChangchunChina
| | - Xue Li
- Department of ChemistryMichigan State UniversityEast LansingMIUSA
| | - Kunhong Xiao
- Center for Proteomics & Artificial Intelligence and Center for Clinical Mass SpectrometryAllegheny Health Network Cancer InstitutePittsburghPAUSA
- Department of Pharmacology and Chemical Biology, School of MedicineUniversity of PittsburghPittsburghPAUSA
| | - Martin J Walsh
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Lei Zeng
- Institute of Epigenetic Medicine, First Hospital of Jilin UniversityChangchunChina
| | - Ming‐Ming Zhou
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Ka Lung Cheung
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
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12
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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: 0] [Impact Index Per Article: 0] [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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13
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Akcan TS, Vilov S, Heinig M. Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures. Nucleic Acids Res 2023; 51:1608-1624. [PMID: 36727445 PMCID: PMC9976927 DOI: 10.1093/nar/gkac1272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/09/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023] Open
Abstract
Promoter-proximal Polymerase II (Pol II) pausing is a key rate-limiting step for gene expression. DNA and RNA-binding trans-acting factors regulating the extent of pausing have been identified. However, we lack a quantitative model of how interactions of these factors determine pausing, therefore the relative importance of implicated factors is unknown. Moreover, previously unknown regulators might exist. Here we address this gap with a machine learning model that accurately predicts the extent of promoter-proximal Pol II pausing from large-scale genome and transcriptome binding maps and gene annotation and sequence composition features. We demonstrate high accuracy and generalizability of the model by validation on an independent cell line which reveals the model's cell line agnostic character. Model interpretation in light of prior knowledge about molecular functions of regulatory factors confirms the interconnection of pausing with other RNA processing steps. Harnessing underlying feature contributions, we assess the relative importance of each factor, quantify their predictive effects and systematically identify previously unknown regulators of pausing. We additionally identify 16 previously unknown 7SK ncRNA interacting RNA-binding proteins predictive of pausing. Our work provides a framework to further our understanding of the regulation of the critical early steps in transcriptional elongation.
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Affiliation(s)
- Toray S Akcan
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, Munich, Germany
| | - Sergey Vilov
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich, 10785 Berlin, Germany
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14
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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: 1] [Impact Index Per Article: 1.0] [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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15
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Chen IP, Ott M. Viral Hijacking of BET Proteins. Viruses 2022; 14:v14102274. [PMID: 36298829 PMCID: PMC9609653 DOI: 10.3390/v14102274] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/29/2022] Open
Abstract
Proteins of the bromodomain and exterminal domain (BET) family mediate critical host functions such as cell proliferation, transcriptional regulation, and the innate immune response, which makes them preferred targets for viruses. These multidomain proteins are best known as transcriptional effectors able to read acetylated histone and non-histone proteins through their tandem bromodomains. They also contain other short motif-binding domains such as the extraterminal domain, which recognizes transcriptional regulatory proteins. Here, we describe how different viruses have evolved to hijack or disrupt host BET protein function through direct interactions with BET family members to support their own propagation. The network of virus-BET interactions emerges as highly intricate, which may complicate the use of small-molecule BET inhibitors-currently in clinical development for the treatment of cancer and cardiovascular diseases-to treat viral infections.
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Affiliation(s)
- Irene P. Chen
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Correspondence:
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16
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Wernersson S, Bobby R, Flavell L, Milbradt AG, Holdgate GA, Embrey KJ, Akke M. Bromodomain Interactions with Acetylated Histone 4 Peptides in the BRD4 Tandem Domain: Effects on Domain Dynamics and Internal Flexibility. Biochemistry 2022; 61:2303-2318. [PMID: 36215732 PMCID: PMC9631989 DOI: 10.1021/acs.biochem.2c00226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The bromodomain and extra-terminal (BET) protein BRD4
regulates
gene expression via recruitment of transcriptional regulatory complexes
to acetylated chromatin. Like other BET proteins, BRD4 contains two
bromodomains, BD1 and BD2, that can interact cooperatively with target
proteins and designed ligands, with important implications for drug
discovery. Here, we used nuclear magnetic resonance (NMR) spectroscopy
to study the dynamics and interactions of the isolated bromodomains,
as well as the tandem construct including both domains and the intervening
linker, and investigated the effects of binding a tetra-acetylated
peptide corresponding to the tail of histone 4. The peptide affinity
is lower for both domains in the tandem construct than for the isolated
domains. Using 15N spin relaxation, we determined the global
rotational correlation times and residue-specific order parameters
for BD1 and BD2. Isolated BD1 is monomeric in the apo state but apparently
dimerizes upon binding the tetra-acetylated peptide. Isolated BD2
partially dimerizes in both the apo and peptide-bound states. The
backbone order parameters reveal marked differences between BD1 and
BD2, primarily in the acetyl-lysine binding site where the ZA loop
is more flexible in BD2. Peptide binding reduces the order parameters
of the ZA loop in BD1 and the ZA and BC loops in BD2. The AB loop,
located distally from the binding site, shows variable dynamics that
reflect the different dimerization propensities of the domains. These
results provide a basis for understanding target recognition by BRD4.
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Affiliation(s)
- Sven Wernersson
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Romel Bobby
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Liz Flavell
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge Science Park, CambridgeCB4 0WG, U.K
| | - Alexander G Milbradt
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Geoffrey A Holdgate
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Kevin J Embrey
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
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17
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Tanemoto F, Nangaku M, Mimura I. Epigenetic memory contributing to the pathogenesis of AKI-to-CKD transition. Front Mol Biosci 2022; 9:1003227. [PMID: 36213117 PMCID: PMC9532834 DOI: 10.3389/fmolb.2022.1003227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Epigenetic memory, which refers to the ability of cells to retain and transmit epigenetic marks to their daughter cells, maintains unique gene expression patterns. Establishing programmed epigenetic memory at each stage of development is required for cell differentiation. Moreover, accumulating evidence shows that epigenetic memory acquired in response to environmental stimuli may be associated with diverse diseases. In the field of kidney diseases, the “memory” of acute kidney injury (AKI) leads to progression to chronic kidney disease (CKD); epidemiological studies show that patients who recover from AKI are at high risk of developing CKD. The underlying pathological processes include nephron loss, maladaptive epithelial repair, inflammation, and endothelial injury with vascular rarefaction. Further, epigenetic alterations may contribute as well to the pathophysiology of this AKI-to-CKD transition. Epigenetic changes induced by AKI, which can be recorded in cells, exert long-term effects as epigenetic memory. Considering the latest findings on the molecular basis of epigenetic memory and the pathophysiology of AKI-to-CKD transition, we propose here that epigenetic memory contributing to AKI-to-CKD transition can be classified according to the presence or absence of persistent changes in the associated regulation of gene expression, which we designate “driving” memory and “priming” memory, respectively. “Driving” memory, which persistently alters the regulation of gene expression, may contribute to disease progression by activating fibrogenic genes or inhibiting renoprotective genes. This process may be involved in generating the proinflammatory and profibrotic phenotypes of maladaptively repaired tubular cells after kidney injury. “Priming” memory is stored in seemingly successfully repaired tubular cells in the absence of detectable persistent phenotypic changes, which may enhance a subsequent transcriptional response to the second stimulus. This type of memory may contribute to AKI-to-CKD transition through the cumulative effects of enhanced expression of profibrotic genes required for wound repair after recurrent AKI. Further understanding of epigenetic memory will identify therapeutic targets of future epigenetic intervention to prevent AKI-to-CKD transition.
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18
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Liu Z, Lin D, Zhou Y, Zhang L, Yang C, Guo B, Xia F, Li Y, Chen D, Wang C, Chen Z, Leng C, Xiao Z. Exploring synthetic lethal network for the precision treatment of clear cell renal cell carcinoma. Sci Rep 2022; 12:13222. [PMID: 35918352 PMCID: PMC9345903 DOI: 10.1038/s41598-022-16657-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022] Open
Abstract
The emerging targeted therapies have revolutionized the treatment of advanced clear cell renal cell carcinoma (ccRCC) over the past 15 years. Nevertheless, lack of personalized treatment limits the development of effective clinical guidelines and improvement of patient prognosis. In this study, large-scale genomic profiles from ccRCC cohorts were explored for integrative analysis. A credible method was developed to identify synthetic lethality (SL) pairs and a list of 72 candidate pairs was determined, which might be utilized to selectively eliminate tumors with genetic aberrations using SL partners of specific mutations. Further analysis identified BRD4 and PRKDC as novel medical targets for patients with BAP1 mutations. After mapping these target genes to the comprehensive drug datasets, two agents (BI-2536 and PI-103) were found to have considerable therapeutic potentials in the BAP1 mutant tumors. Overall, our findings provided insight into the overview of ccRCC mutation patterns and offered novel opportunities for improving individualized cancer treatment.
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Affiliation(s)
- Zhicheng Liu
- Department of Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Dongxu Lin
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yi Zhou
- Department of Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Linmeng Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Chen Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Bin Guo
- Department of Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Feng Xia
- Department of Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yan Li
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Danyang Chen
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Cun Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Zhong Chen
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Chao Leng
- Department of Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Zhenyu Xiao
- Department of Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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19
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French CA, Cheng ML, Hanna GJ, DuBois SG, Chau NG, Hann CL, Storck S, Salgia R, Trucco M, Tseng J, Stathis A, Piekarz R, Lauer UM, Massard C, Bennett K, Coker S, Tontsch-Grunt U, Sos ML, Liao S, Wu CJ, Polyak K, Piha-Paul SA, Shapiro GI. Report of the First International Symposium on NUT Carcinoma. Clin Cancer Res 2022; 28:2493-2505. [PMID: 35417004 PMCID: PMC9197941 DOI: 10.1158/1078-0432.ccr-22-0591] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 04/08/2022] [Indexed: 12/15/2022]
Abstract
NUT carcinoma is a rare, aggressive cancer defined by rearrangements of the NUTM1 gene. No routinely effective treatments of NUT carcinoma exist, despite harboring a targetable oncoprotein, most commonly BRD4-NUT. The vast majority of cases are fatal. Poor awareness of the disease is a major obstacle to progress in the treatment of NUT carcinoma. While the incidence likely exceeds that of Ewing sarcoma, and BRD4-NUT heralded the bromodomain and extra-terminal domain (BET) inhibitor class of selective epigenetic modulators, NUT carcinoma is incorrectly perceived as "impossibly rare," and therefore receives comparatively little private or governmental funding or prioritization by pharma. To raise awareness, propagate scientific knowledge, and initiate a consensus on standard and targeted treatment of NUT carcinoma, we held the First International Symposium on NUT Carcinoma on March 3, 2021. This virtual event had more than eighty attendees from the Americas, Europe, Asia, and Australia. Patients with NUT carcinoma and family members were represented and shared perspectives. Broadly, the four areas discussed by experts in the field included (1) the biology of NUT carcinoma; (2) standard approaches to the treatment of NUT carcinoma; (3) results of clinical trials using BET inhibitors; and (4) future directions, including novel BET bromodomain inhibitors, combinatorial approaches, and immunotherapy. It was concluded that standard chemotherapeutic approaches and first-generation BET bromodomain inhibitors, the latter complicated by a narrow therapeutic window, are only modestly effective in a minority of cases. Nonetheless, emerging second-generation targeted inhibitors, novel rational synergistic combinations, and the incorporation of immuno-oncology approaches hold promise to improve the prognosis of this disease.
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Affiliation(s)
| | | | | | - Steven G. DuBois
- Dana-Farber Cancer Institute, Boston, MA, USA,Boston Children’s Hospital, Boston, MA, USA
| | - Nicole G. Chau
- British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, Canada
| | | | - Simone Storck
- Swabian Children’s Cancer Center, Paediatric and Adolescent Medicine, University Medical Center Augsburg, Augsburg, Germany
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA
| | | | | | - Anastasios Stathis
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland and Faculty of Biomedical Sciences, Universita della Svizzera Italiana, Lugano, Switzerland
| | - Richard Piekarz
- Investigational Drug Branch, Cancer Therapy Evaluation Program (CTEP), Bethesda, MD
| | | | - Christophe Massard
- Gustave Roussy-Molecular Radiotherapy INSERM U1030, Faculty of Medicine Kremlin-Bicêtre and Paris-Saclay University , France
| | | | - Shodeinde Coker
- Bristol-Myers Squibb Company, Lawrenceville, New Jersey, USA
| | | | - Martin L. Sos
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Molecular Pathology University of Cologne, Cologne, Germany and Department of Translational Genomics and Center for Molecular Medicine Cologne, Cologne, Germany
| | - Sida Liao
- TScan Therapeutics, Waltham, MA, USA
| | | | | | - Sarina A. Piha-Paul
- Department of Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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20
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Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Khalid MM, Taha TY, Tabata T, Hayashi JM, Soveg FW, Carlson-Stevermer J, Gupta M, Zhang MY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, Krogan N, Fujimori DG, Ott M. Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2. Cell Rep 2022; 40:111088. [PMID: 35839775 PMCID: PMC9234021 DOI: 10.1016/j.celrep.2022.111088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/27/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
Inhibitors of bromodomain and extraterminal domain (BET) proteins are possible anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prophylactics as they downregulate angiotensin-converting enzyme 2 (ACE2). Here we show that BET proteins should not be inactivated therapeutically because they are critical antiviral factors at the post-entry level. Depletion of BRD3 or BRD4 in cells overexpressing ACE2 exacerbates SARS-CoV-2 infection; the same is observed when cells with endogenous ACE2 expression are treated with BET inhibitors during infection and not before. Viral replication and mortality are also enhanced in BET inhibitor-treated mice overexpressing ACE2. BET inactivation suppresses interferon production induced by SARS-CoV-2, a process phenocopied by the envelope (E) protein previously identified as a possible “histone mimetic.” E protein, in an acetylated form, directly binds the second bromodomain of BRD4. Our data support a model where SARS-CoV-2 E protein evolved to antagonize interferon responses via BET protein inhibition; this neutralization should not be further enhanced with BET inhibitor treatment.
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Affiliation(s)
- Irene P Chen
- Gladstone Institutes, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA
| | - James E Longbotham
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sarah McMahon
- Gladstone Institutes, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Mir M Khalid
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Taha Y Taha
- Gladstone Institutes, San Francisco, CA 94158, USA
| | | | | | | | | | - Meghna Gupta
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Meng Yao Zhang
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Victor L Lam
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yang Li
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zanlin Yu
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erron W Titus
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Amy Diallo
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer Oki
- Synthego Corporation, 3696 Haven Avenue, Suite A, Menlo Park, CA 94063, USA
| | - Kevin Holden
- Synthego Corporation, 3696 Haven Avenue, Suite A, Menlo Park, CA 94063, USA
| | - Nevan Krogan
- Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danica Galonić Fujimori
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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21
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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: 0] [Impact Index Per Article: 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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22
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Kaiser C, Bradu A, Gamble N, Caldwell JA, Koh AS. AIRE in context: Leveraging chromatin plasticity to trigger ectopic gene expression. Immunol Rev 2022; 305:59-76. [PMID: 34545959 PMCID: PMC9250823 DOI: 10.1111/imr.13026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022]
Abstract
The emergence of antigen receptor diversity in clonotypic lymphocytes drove the evolution of a novel gene, Aire, that enabled the adaptive immune system to discriminate foreign invaders from self-constituents. AIRE functions in the epithelial cells of the thymus to express genes highly restricted to alternative cell lineages. This somatic plasticity facilitates the selection of a balanced repertoire of T cells that protects the host from harmful self-reactive clones, yet maintains a wide range of affinities for virtually any foreign antigen. Here, we review the latest understanding of AIRE's molecular actions with a focus on its interplay with chromatin. We argue that AIRE is a multi-valent chromatin effector that acts late in the transcription cycle to modulate the activity of previously poised non-coding regulatory elements of tissue-specific genes. We postulate a role for chromatin instability-caused in part by ATP-dependent chromatin remodeling-that variably sets the scope of the accessible landscape on which AIRE can act. We highlight AIRE's intrinsic repressive function and its relevance in providing feedback control. We synthesize these recent advances into a putative model for the mechanistic modes by which AIRE triggers ectopic transcription for immune repertoire selection.
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Affiliation(s)
- Caroline Kaiser
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Alexandra Bradu
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Noah Gamble
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Jason A. Caldwell
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Andrew S. Koh
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
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23
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Jones-Tabah J, Martin RD, Chen JJ, Tanny JC, Clarke PBS, Hébert TE. A role for BET proteins in regulating basal, dopamine-induced and cAMP/PKA-dependent transcription in rat striatal neurons. Cell Signal 2021; 91:110226. [PMID: 34974082 DOI: 10.1016/j.cellsig.2021.110226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/01/2023]
Abstract
The activity of striatal medium-spiny projection neurons is regulated by D1 and D2 dopamine receptors. The D1 receptor (D1R) is a Gαs/olf-coupled GPCR which activates a cAMP/PKA/DARPP-32 signalling cascade that increases excitability and facilitates plasticity, partly through the regulation of transcription. Upon activation via D1R, PKA can translocate to the nucleus to regulate transcription through the phosphorylation of various targets. One candidate effector of PKA-dependent transcriptional regulation is the BET protein Brd4. It is known that when Brd4 is activated by phosphorylation, it binds more readily to acetylated histones at promoters and enhancers; moreover, in non-neuronal cells, PKA signalling has been shown to increase recruitment of Brd4 to chromatin. However, it is unknown whether BET proteins, or Brd4 specifically, are involved in transcriptional activation by cAMP/PKA in neurons. Here, we demonstrate that in adult rats, inhibition of BET proteins with the bromodomain inhibitor JQ1 suppressed the expression of ~25% of D1R-upregulated genes, while also increasing the expression of a subset of immediate-early genes. We further found that cAMP/PKA signalling promotes Brd4 recruitment to dopamine-induced genes in striatal neurons, and that knockdown of Brd4 attenuates D1R-induced gene expression. Finally, we report that JQ1 treatment downregulated expression of many GPCRs and also impaired ERK1/2 signalling in striatal neurons. Our findings identify the BET protein family, and Brd4 in particular, as novel regulators of basal and D1R-dependent transcription in rat striatal neurons, and delineate complex bi-directional effects of bromodomain inhibitors on neuronal transcription.
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Affiliation(s)
- Jace Jones-Tabah
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Jennifer J Chen
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Paul B S Clarke
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada.
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada.
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24
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Zhou K, Zhuang S, Liu F, Chen Y, Li Y, Wang S, Li Y, Wen H, Lin X, Wang J, Huang Y, He C, Xu N, Li Z, Xu L, Zhang Z, Chen LF, Chen R, Liu M. Disrupting the Cdk9/Cyclin T1 heterodimer of 7SK snRNP for the Brd4 and AFF1/4 guided reconstitution of active P-TEFb. Nucleic Acids Res 2021; 50:750-762. [PMID: 34935961 PMCID: PMC8789079 DOI: 10.1093/nar/gkab1228] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/23/2021] [Accepted: 12/10/2021] [Indexed: 01/16/2023] Open
Abstract
P-TEFb modulates RNA polymerase II elongation through alternative interaction with negative and positive regulation factors. While inactive P-TEFbs are mainly sequestered in the 7SK snRNP complex in a chromatin-free state, most of its active forms are in complex with its recruitment factors, Brd4 and SEC, in a chromatin-associated state. Thus, switching from inactive 7SK snRNP to active P-TEFb (Brd4/P-TEFb or SEC/P-TEFb) is essential for global gene expression. Although it has been shown that cellular signaling stimulates the disruption of 7SK snRNP, releasing dephosphorylated and catalytically inactive P-TEFb, little is known about how the inactive released P-TEFb is reactivated. Here, we show that the Cdk9/CycT1 heterodimer released from 7SK snRNP is completely dissociated into monomers in response to stress. Brd4 or SEC then recruits monomerized Cdk9 and CycT1 to reassemble the core P-TEFb. Meanwhile, the binding of monomeric dephosphorylated Cdk9 to either Brd4 or SEC induces the autophosphorylation of T186 of Cdk9. Finally, the same mechanism is employed during nocodazole released entry into early G1 phase of cell cycle. Therefore, our studies demonstrate a novel mechanism by which Cdk9 and CycT1 monomers are reassembled on chromatin to form active P-TEFb by its interaction with Brd4 or SEC to regulate transcription.
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Affiliation(s)
- Kai Zhou
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Songkuan Zhuang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Fulong Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Yanheng Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - You Li
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
| | - Shihui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Yuxuan Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Huixin Wen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Xiaohua Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Jie Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Yue Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Cailing He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Nan Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Zongshu Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Lang Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Zixuan Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Lin-Feng Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruichuan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Min Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
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25
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Progress in the development of domain selective inhibitors of the bromo and extra terminal domain family (BET) proteins. Eur J Med Chem 2021; 226:113853. [PMID: 34547507 DOI: 10.1016/j.ejmech.2021.113853] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/04/2021] [Accepted: 09/11/2021] [Indexed: 12/13/2022]
Abstract
Dysfunction of the bromo and extra terminal domain (BET) family proteins is associated with many human diseases, therefore the BET family proteins have been considered as promising targets for drug development. Numerous small molecular compounds targeting the N-terminal two tandem bromodomains BD1 and BD2 of the BET family proteins have been reported, and a number of them have been advanced into clinical trials. Most of the BET inhibitors entered clinical trials are pan-BET inhibitors which show poor selectivity among BET members and bind to the BD1 and BD2 of the BET family proteins with comparable binding affinities. In order to elucidate the distinct functions of BD1s and BD2s, many BD1 and BD2 selective BET inhibitors have also been developed. In this review, we summarized the recent progress in the development of BD1 and BD2 selective BET inhibitors, and provided the perspectives for future studies of BET inhibitors.
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26
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Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Carlson-Stevermer J, Gupta M, Zhang MY, Soveg FW, Hayashi JM, Taha TY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, Krogan N, Galonić Fujimori D, Ott M. Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34816261 DOI: 10.1101/2021.11.14.468537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Inhibitors of Bromodomain and Extra-terminal domain (BET) proteins are possible anti-SARS-CoV-2 prophylactics as they downregulate angiotensin-converting enzyme 2 (ACE2). Here, we show that BET proteins should not be inactivated therapeutically as they are critical antiviral factors at the post-entry level. Knockouts of BRD3 or BRD4 in cells overexpressing ACE2 exacerbate SARS-CoV-2 infection; the same is observed when cells with endogenous ACE2 expression are treated with BET inhibitors during infection, and not before. Viral replication and mortality are also enhanced in BET inhibitor-treated mice overexpressing ACE2. BET inactivation suppresses interferon production induced by SARS-CoV-2, a process phenocopied by the envelope (E) protein previously identified as a possible "histone mimetic." E protein, in an acetylated form, directly binds the second bromodomain of BRD4. Our data support a model where SARS-CoV-2 E protein evolved to antagonize interferon responses via BET protein inhibition; this neutralization should not be further enhanced with BET inhibitor treatment.
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27
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Liang Y, Tian J, Wu T. BRD4 in physiology and pathology: ''BET'' on its partners. Bioessays 2021; 43:e2100180. [PMID: 34697817 DOI: 10.1002/bies.202100180] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 12/20/2022]
Abstract
Bromodomain-containing 4 (BRD4), a member of Bromo and Extra-Terminal (BET) family, recognizes acetylated histones and is of importance in transcription, replication, and DNA repair. It also binds non-histone proteins, DNA and RNA, contributing to development, tissue growth, and various physiological processes. Additionally, BRD4 has been implicated in driving diverse diseases, ranging from cancer, viral infection, inflammation to neurological disorders. Inhibiting its functions with BET inhibitors (BETis) suppresses the progression of several types of cancer, creating an impetus for translating these chemicals to the clinic. The diverse roles of BRD4 are largely dependent on its interaction partners in different contexts. In this review we discuss the molecular mechanisms of BRD4 with its interacting partners in physiology and pathology. Current development of BETis is also summarized. Further understanding the functions of BRD4 and its partners will facilitate resolving the liabilities of present BETis and accelerate their clinical translation.
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Affiliation(s)
- Yin Liang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Jieyi Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Tao Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
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28
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Cheung KL, Kim C, Zhou MM. The Functions of BET Proteins in Gene Transcription of Biology and Diseases. Front Mol Biosci 2021; 8:728777. [PMID: 34540900 PMCID: PMC8446420 DOI: 10.3389/fmolb.2021.728777] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/31/2021] [Indexed: 12/25/2022] Open
Abstract
The BET (bromodomain and extra-terminal domain) family proteins, consisting of BRD2, BRD3, BRD4, and testis-specific BRDT, are widely acknowledged as major transcriptional regulators in biology. They are characterized by two tandem bromodomains (BDs) that bind to lysine-acetylated histones and transcription factors, recruit transcription factors and coactivators to target gene sites, and activate RNA polymerase II machinery for transcriptional elongation. Pharmacological inhibition of BET proteins with BD inhibitors has been shown as a promising therapeutic strategy for the treatment of many human diseases including cancer and inflammatory disorders. The recent advances in bromodomain protein biology have further uncovered the complex and versatile functions of BET proteins in the regulation of gene expression in chromatin. In this review article, we highlight our current understanding of BET proteins' functions in mediating protein-protein interactions required for chromatin-templated gene transcription and splicing, chromatin remodeling, DNA replication, and DNA damage repair. We further discuss context-dependent activator vs. repressor functions of individual BET proteins, isoforms, and bromodomains that may be harnessed for future development of BET bromodomain inhibitors as emerging epigenetic therapies for cancer and inflammatory disorders.
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29
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Halder TG, Soldi R, Sharma S. Bromodomain and extraterminal domain protein bromodomain inhibitor based cancer therapeutics. Curr Opin Oncol 2021; 33:526-531. [PMID: 34280171 DOI: 10.1097/cco.0000000000000763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE OF REVIEW Bromodomain and extraterminal domain (BET) proteins are evolutionarily conserved, multifunctional super-regulators that specifically recognize acetyl-lysine on histones and other proteins controlling gene transcription. Several studies show that small molecules targeting these regulators preferentially suppress the transcription of cancer-promoting genes. Consequently, several BET inhibitors reached clinical trials and are in various stages for different kind of malignancies. In this review, we provide a concise summary of the molecular basis and preliminary clinical outcomes of BET inhibitors as anticancer therapeutics. RECENT FINDINGS Results from early clinical trials with BET inhibitors confirmed their antitumor potential in both hematologic and solid tumours, but the evidence does not support the application of BET inhibitors as a monotherapy for cancer treatment. Treatment-emergent toxicities such as thrombocytopenia and gastrointestinal disorders are also reported. Preclinical data suggest that BET inhibitors may have a promising future in combination with other anticancer agents. SUMMARY Despite of various challenges, BET inhibitors have high potential in combinatorial therapy and the future development of next-generation inhibitors could be promising. Further studies are needed to determine the predictive biomarkers for therapeutic response, which would translate into the long-term success of BET inhibitors as personalized medicines in cancer treatment.
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Affiliation(s)
- Tithi Ghosh Halder
- Applied Cancer Research and Drug Discovery, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
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30
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A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3'-processing and termination. Mol Cell 2021; 81:3589-3603.e13. [PMID: 34324863 DOI: 10.1016/j.molcel.2021.06.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/14/2021] [Accepted: 06/22/2021] [Indexed: 12/15/2022]
Abstract
Transcription elongation has emerged as a regulatory hub in gene expression of metazoans. A major control point occurs during early elongation before RNA polymerase II (Pol II) is released into productive elongation. Prior research has linked BRD4 with transcription elongation. Here, we use rapid BET protein and BRD4-selective degradation along with quantitative genome-wide approaches to investigate direct functions of BRD4 in Pol II transcription regulation. Notably, as an immediate consequence of acute BRD4 loss, promoter-proximal pause release is impaired, and transcriptionally engaged Pol II past this checkpoint undergoes readthrough transcription. An integrated proteome-wide analysis uncovers elongation and 3'-RNA processing factors as core BRD4 interactors. BRD4 ablation disrupts the recruitment of general 3'-RNA processing factors at the 5'-control region, which correlates with RNA cleavage and termination defects. These studies, performed in human cells, reveal a BRD4-mediated checkpoint and begin to establish a molecular link between 5'-elongation control and 3'-RNA processing.
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31
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Gao M, Wang J, Rousseaux S, Tan M, Pan L, Peng L, Wang S, Xu W, Ren J, Liu Y, Spinck M, Barral S, Wang T, Chuffart F, Bourova-Flin E, Puthier D, Curtet S, Bargier L, Cheng Z, Neumann H, Li J, Zhao Y, Mi JQ, Khochbin S. Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution. Cell Rep 2021; 36:109460. [PMID: 34320364 DOI: 10.1016/j.celrep.2021.109460] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/11/2021] [Accepted: 07/08/2021] [Indexed: 01/04/2023] Open
Abstract
In addition to acetylation, histones are modified by a series of competing longer-chain acylations. Most of these acylation marks are enriched and co-exist with acetylation on active gene regulatory elements. Their seemingly redundant functions hinder our understanding of histone acylations' specific roles. Here, by using an acute lymphoblastic leukemia (ALL) cell model and blasts from individuals with B-precusor ALL (B-ALL), we demonstrate a role of mitochondrial activity in controlling the histone acylation/acetylation ratio, especially at histone H4 lysine 5 (H4K5). An increase in the ratio of non-acetyl acylations (crotonylation or butyrylation) over acetylation on H4K5 weakens bromodomain containing protein 4 (BRD4) bromodomain-dependent chromatin interaction and enhances BRD4 nuclear mobility and availability for binding transcription start site regions of active genes. Our data suggest that the metabolism-driven control of the histone acetylation/longer-chain acylation(s) ratio could be a common mechanism regulating the bromodomain factors' functional genomic distribution.
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Affiliation(s)
- Mengqing Gao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China; CNRS UMR 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, 38706 La Tronche, France; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Jin Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Sophie Rousseaux
- CNRS UMR 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, 38706 La Tronche, France; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Minjia Tan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, 201203 Shanghai, China
| | - Lulu Pan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, 201203 Shanghai, China
| | - Lijun Peng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Sisi Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Wenqian Xu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Jiayi Ren
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Yuanfang Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China
| | - Martin Spinck
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Sophie Barral
- CNRS UMR 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, 38706 La Tronche, France; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Tao Wang
- CNRS UMR 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, 38706 La Tronche, France; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Florent Chuffart
- CNRS UMR 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, 38706 La Tronche, France; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Ekaterina Bourova-Flin
- CNRS UMR 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, 38706 La Tronche, France; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Denis Puthier
- Aix Marseille Université, INSERM, TAGC, TGML, 13288 Marseille, France
| | - Sandrine Curtet
- CNRS UMR 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, 38706 La Tronche, France; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China
| | - Lisa Bargier
- Aix Marseille Université, INSERM, TAGC, TGML, 13288 Marseille, France
| | - Zhongyi Cheng
- Jingjie PTM Biolab (Hangzhou), 310018 Hangzhou, China
| | - Heinz Neumann
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Jian Li
- Clinical Research Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jian-Qing Mi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China.
| | - Saadi Khochbin
- CNRS UMR 5309/INSERM U1209/Université Grenoble-Alpes/Institute for Advanced Biosciences, 38706 La Tronche, France; Pôle Franco-Chinois de Recherche en Sciences du Vivant et Génomique, 200025 Shanghai, China.
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CDK9 keeps RNA polymerase II on track. Cell Mol Life Sci 2021; 78:5543-5567. [PMID: 34146121 PMCID: PMC8257543 DOI: 10.1007/s00018-021-03878-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/26/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9), the kinase component of positive transcription elongation factor b (P-TEFb), is essential for transcription of most protein-coding genes by RNA polymerase II (RNAPII). By releasing promoter-proximally paused RNAPII into gene bodies, CDK9 controls the entry of RNAPII into productive elongation and is, therefore, critical for efficient synthesis of full-length messenger (m)RNAs. In recent years, new players involved in P-TEFb-dependent processes have been identified and an important function of CDK9 in coordinating elongation with transcription initiation and termination has been unveiled. As the regulatory functions of CDK9 in gene expression continue to expand, a number of human pathologies, including cancers, have been associated with aberrant CDK9 activity, underscoring the need to properly regulate CDK9. Here, I provide an overview of CDK9 function and regulation, with an emphasis on CDK9 dysregulation in human diseases.
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Salahong T, Schwartz C, Sungthong R. Are BET Inhibitors yet Promising Latency-Reversing Agents for HIV-1 Reactivation in AIDS Therapy? Viruses 2021; 13:v13061026. [PMID: 34072421 PMCID: PMC8228869 DOI: 10.3390/v13061026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/26/2022] Open
Abstract
AIDS first emerged decades ago; however, its cure, i.e., eliminating all virus sources, is still unachievable. A critical burden of AIDS therapy is the evasive nature of HIV-1 in face of host immune responses, the so-called "latency." Recently, a promising approach, the "Shock and Kill" strategy, was proposed to eliminate latently HIV-1-infected cell reservoirs. The "Shock and Kill" concept involves two crucial steps: HIV-1 reactivation from its latency stage using a latency-reversing agent (LRA) followed by host immune responses to destroy HIV-1-infected cells in combination with reinforced antiretroviral therapy to kill the progeny virus. Hence, a key challenge is to search for optimal LRAs. Looking at epigenetics of HIV-1 infection, researchers proved that some bromodomains and extra-terminal motif protein inhibitors (BETis) are able to reactivate HIV-1 from latency. However, to date, only a few BETis have shown HIV-1-reactivating functions, and none of them have yet been approved for clinical trial. In this review, we aim to demonstrate the epigenetic roles of BETis in HIV-1 infection and HIV-1-related immune responses. Possible future applications of BETis and their HIV-1-reactivating properties are summarized and discussed.
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Affiliation(s)
- Thanarat Salahong
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Christian Schwartz
- Research Unit 7292, DHPI, IUT Louis Pasteur, University of Strasbourg, 67300 Schiltigheim, France
- Correspondence: (C.S.); (R.S.)
| | - Rungroch Sungthong
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
- Laboratory of Hydrology and Geochemistry of Strasbourg, University of Strasbourg, UMR 7517 CNRS/EOST, 67084 Strasbourg CEDEX, France
- Correspondence: (C.S.); (R.S.)
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Design, synthesis, biological evaluation, and molecular docking of 1,7-dibenzyl-substituted theophylline derivatives as novel BRD4-BD1-selective inhibitors. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02737-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Epigenetic Effects of Benzene in Hematologic Neoplasms: The Altered Gene Expression. Cancers (Basel) 2021; 13:cancers13102392. [PMID: 34069279 PMCID: PMC8156840 DOI: 10.3390/cancers13102392] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Benzene is produced by diverse petroleum transformation processes and it is widely employed in industry despite its oncogenic effects. In fact, occupational exposure to benzene may cause hematopoietic malignancy. The leukemogenic action of benzene is particularly complex. Possible processes of onset of hematological malignancies have been recognized as a genotoxic action and the provocation of immunosuppression. However, benzene can induce modifications that do not involve alterations in the DNA sequence, the so-called epigenetics changes. Acquired epigenetic modification may also induce leukemogenesis, as benzene may alter nuclear receptors, and cause changes at the protein level, thereby modifying the function of regulatory proteins, including oncoproteins and tumor suppressor proteins. Abstract Benzene carcinogenic ability has been reported, and chronic exposure to benzene can be one of the risk elements for solid cancers and hematological neoplasms. Benzene is acknowledged as a myelotoxin, and it is able to augment the risk for the onset of acute myeloid leukemia, myelodysplastic syndromes, aplastic anemia, and lymphomas. Possible mechanisms of benzene initiation of hematological tumors have been identified, as a genotoxic effect, an action on oxidative stress and inflammation and the provocation of immunosuppression. However, it is becoming evident that genetic alterations and the other causes are insufficient to fully justify several phenomena that influence the onset of hematologic malignancies. Acquired epigenetic alterations may participate with benzene leukemogenesis, as benzene may affect nuclear receptors, and provoke post-translational alterations at the protein level, thereby touching the function of regulatory proteins, comprising oncoproteins and tumor suppressor proteins. DNA hypomethylation correlates with stimulation of oncogenes, while the hypermethylation of CpG islands in promoter regions of specific tumor suppressor genes inhibits their transcription and stimulates the onset of tumors. The discovery of the systems of epigenetic induction of benzene-caused hematological tumors has allowed the possibility to operate with pharmacological interventions able of stopping or overturning the negative effects of benzene.
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Anshabo AT, Milne R, Wang S, Albrecht H. CDK9: A Comprehensive Review of Its Biology, and Its Role as a Potential Target for Anti-Cancer Agents. Front Oncol 2021; 11:678559. [PMID: 34041038 PMCID: PMC8143439 DOI: 10.3389/fonc.2021.678559] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/16/2021] [Indexed: 12/25/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are proteins pivotal to a wide range of cellular functions, most importantly cell division and transcription, and their dysregulations have been implicated as prominent drivers of tumorigenesis. Besides the well-established role of cell cycle CDKs in cancer, the involvement of transcriptional CDKs has been confirmed more recently. Most cancers overtly employ CDKs that serve as key regulators of transcription (e.g., CDK9) for a continuous production of short-lived gene products that maintain their survival. As such, dysregulation of the CDK9 pathway has been observed in various hematological and solid malignancies, making it a valuable anticancer target. This therapeutic potential has been utilized for the discovery of CDK9 inhibitors, some of which have entered human clinical trials. This review provides a comprehensive discussion on the structure and biology of CDK9, its role in solid and hematological cancers, and an updated review of the available inhibitors currently being investigated in preclinical and clinical settings.
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Affiliation(s)
- Abel Tesfaye Anshabo
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Robert Milne
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Shudong Wang
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Hugo Albrecht
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
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37
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Edwards DS, Maganti R, Tanksley JP, Luo J, Park JJH, Balkanska-Sinclair E, Ling J, Floyd SR. BRD4 Prevents R-Loop Formation and Transcription-Replication Conflicts by Ensuring Efficient Transcription Elongation. Cell Rep 2021; 32:108166. [PMID: 32966794 PMCID: PMC7507985 DOI: 10.1016/j.celrep.2020.108166] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/13/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022] Open
Abstract
Effective spatio-temporal control of transcription and replication during S-phase is paramount to maintaining genomic integrity and cell survival. Dysregulation of these systems can lead to conflicts between the transcription and replication machinery, causing DNA damage and cell death. BRD4 allows efficient transcriptional elongation by stimulating phosphorylation of RNA polymerase II (RNAPII). We report that bromodomain and extra-terminal domain (BET) protein loss of function (LOF) causes RNAPII pausing on the chromatin and DNA damage affecting cells in S-phase. This persistent RNAPII-dependent pausing leads to an accumulation of RNA:DNA hybrids (R-loops) at sites of BRD4 occupancy, leading to transcription-replication conflicts (TRCs), DNA damage, and cell death. Finally, our data show that the BRD4 C-terminal domain, which interacts with P-TEFb, is required to prevent R-loop formation and DNA damage caused by BET protein LOF.
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Affiliation(s)
- Drake S Edwards
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Jarred P Tanksley
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jie Luo
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | - James J H Park
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | - Scott R Floyd
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27710, USA.
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Mandal R, Becker S, Strebhardt K. Targeting CDK9 for Anti-Cancer Therapeutics. Cancers (Basel) 2021; 13:2181. [PMID: 34062779 PMCID: PMC8124690 DOI: 10.3390/cancers13092181] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/23/2022] Open
Abstract
Cyclin Dependent Kinase 9 (CDK9) is one of the most important transcription regulatory members of the CDK family. In conjunction with its main cyclin partner-Cyclin T1, it forms the Positive Transcription Elongation Factor b (P-TEFb) whose primary function in eukaryotic cells is to mediate the positive transcription elongation of nascent mRNA strands, by phosphorylating the S2 residues of the YSPTSPS tandem repeats at the C-terminus domain (CTD) of RNA Polymerase II (RNAP II). To aid in this process, P-TEFb also simultaneously phosphorylates and inactivates a number of negative transcription regulators like 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) Sensitivity-Inducing Factor (DSIF) and Negative Elongation Factor (NELF). Significantly enhanced activity of CDK9 is observed in multiple cancer types, which is universally associated with significantly shortened Overall Survival (OS) of the patients. In these cancer types, CDK9 regulates a plethora of cellular functions including proliferation, survival, cell cycle regulation, DNA damage repair and metastasis. Due to the extremely critical role of CDK9 in cancer cells, inhibiting its functions has been the subject of intense research, resulting the development of multiple, increasingly specific small-molecule inhibitors, some of which are presently in clinical trials. The search for newer generation CDK9 inhibitors with higher specificity and lower potential toxicities and suitable combination therapies continues. In fact, the Phase I clinical trials of the latest, highly specific CDK9 inhibitor BAY1251152, against different solid tumors have shown good anti-tumor and on-target activities and pharmacokinetics, combined with manageable safety profile while the phase I and II clinical trials of another inhibitor AT-7519 have been undertaken or are undergoing. To enhance the effectiveness and target diversity and reduce potential drug-resistance, the future of CDK9 inhibition would likely involve combining CDK9 inhibitors with inhibitors like those against BRD4, SEC, MYC, MCL-1 and HSP90.
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Affiliation(s)
- Ranadip Mandal
- Department of Gynecology and Obstetrics, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; (R.M.); (S.B.)
| | - Sven Becker
- Department of Gynecology and Obstetrics, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; (R.M.); (S.B.)
| | - Klaus Strebhardt
- Department of Gynecology and Obstetrics, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; (R.M.); (S.B.)
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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Her YR, Wang L, Chepelev I, Manterola M, Berkovits B, Cui K, Zhao K, Wolgemuth DJ. Genome-wide chromatin occupancy of BRDT and gene expression analysis suggest transcriptional partners and specific epigenetic landscapes that regulate gene expression during spermatogenesis. Mol Reprod Dev 2021; 88:141-157. [PMID: 33469999 DOI: 10.1002/mrd.23449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/13/2020] [Accepted: 12/27/2020] [Indexed: 11/09/2022]
Abstract
BRDT, a member of the BET family of double bromodomain-containing proteins, is essential for spermatogenesis in the mouse and has been postulated to be a key regulator of transcription in meiotic and post-meiotic cells. To understand the function of BRDT in these processes, we first characterized the genome-wide distribution of the BRDT binding sites, in particular within gene units, by ChIP-Seq analysis of enriched fractions of pachytene spermatocytes and round spermatids. In both cell types, BRDT binding sites were mainly located in promoters, first exons, and introns of genes. BRDT binding sites in promoters overlapped with several histone modifications and histone variants associated with active transcription, and were enriched for consensus sequences for specific transcription factors, including MYB, RFX, ETS, and ELF1 in pachytene spermatocytes, and JunD, c-Jun, CRE, and RFX in round spermatids. Subsequent integration of the ChIP-seq data with available transcriptome data revealed that stage-specific gene expression programs are associated with BRDT binding to their gene promoters, with most of the BDRT-bound genes being upregulated. Gene Ontology analysis further identified unique sets of genes enriched in diverse biological processes essential for meiosis and spermiogenesis between the two cell types, suggesting distinct developmentally stage-specific functions for BRDT. Taken together, our data suggest that BRDT cooperates with different transcription factors at distinctive chromatin regions within gene units to regulate diverse downstream target genes that function in male meiosis and spermiogenesis.
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Affiliation(s)
- Yoon Ra Her
- Department of Genetics & Development, Columbia University Medical Center, New York, New York, USA
| | - Li Wang
- Department of Genetics & Development, Columbia University Medical Center, New York, New York, USA
| | - Iouri Chepelev
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Marcia Manterola
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Binyamin Berkovits
- Department of Genetics & Development, Columbia University Medical Center, New York, New York, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Debra J Wolgemuth
- Department of Genetics & Development, Columbia University Medical Center, New York, New York, USA.,Department Obstetrics & Gynecology, Columbia University Medical Center, New York, New York, USA.,Institute of Human Nutrition, Columbia University Medical Center, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
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40
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Design, synthesis and biological evaluation of indole-2-one derivatives as potent BRD4 inhibitors. Eur J Med Chem 2020; 208:112780. [PMID: 32883643 DOI: 10.1016/j.ejmech.2020.112780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/16/2020] [Accepted: 08/19/2020] [Indexed: 11/23/2022]
Abstract
Bromodomain protein 4 (BRD4) plays a crucial role in transcriptional regulation and is considered to be a viable drug target for cancer treatment. Herein, we designed and synthesized a series of indole-2-one derivatives through scaffold hopping drug design. Most of the compounds showed potent BRD4 inhibitory activities and anti-proliferation activities in cancer cell lines. Especially, compound 12j exhibited excellent BRD4 inhibitory activities (BD1 IC50 = 19 nM, BD2 IC50 = 28 nM) and anti-proliferation potency with IC50 values of 4.75 μM and 1.35 μM in HT-29 and HL-60 cells, respectively. Additionally, docking studies showed that the hydrophobic pocket next to KAc region and WPF shelf were critical to the activity of the compound. Compound 12j could arrest the cell-cycle progression of HT-29 cells into the G1 phase and reduce the expression of c-Myc. Moreover, compound 12j exhibited favorable oral pharmacokinetic properties. All the results demonstrated that compound 12j was a potent BRD4 inhibitor and had merely potential for colon cancer treatment.
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41
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Kim SY, Zhang X, Schiattarella GG, Altamirano F, Ramos TAR, French KM, Jiang N, Szweda PA, Evers BM, May HI, Luo X, Li H, Szweda LI, Maracaja-Coutinho V, Lavandero S, Gillette TG, Hill JA. Epigenetic Reader BRD4 (Bromodomain-Containing Protein 4) Governs Nucleus-Encoded Mitochondrial Transcriptome to Regulate Cardiac Function. Circulation 2020; 142:2356-2370. [PMID: 33113340 PMCID: PMC7736324 DOI: 10.1161/circulationaha.120.047239] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 10/23/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND BET (bromodomain and extraterminal) epigenetic reader proteins, in particular BRD4 (bromodomain-containing protein 4), have emerged as potential therapeutic targets in a number of pathological conditions, including cancer and cardiovascular disease. Small-molecule BET protein inhibitors such as JQ1 have demonstrated efficacy in reversing cardiac hypertrophy and heart failure in preclinical models. Yet, genetic studies elucidating the biology of BET proteins in the heart have not been conducted to validate pharmacological findings and to unveil potential pharmacological side effects. METHODS By engineering a cardiomyocyte-specific BRD4 knockout mouse, we investigated the role of BRD4 in cardiac pathophysiology. We performed functional, transcriptomic, and mitochondrial analyses to evaluate BRD4 function in developing and mature hearts. RESULTS Unlike pharmacological inhibition, loss of BRD4 protein triggered progressive declines in myocardial function, culminating in dilated cardiomyopathy. Transcriptome analysis of BRD4 knockout mouse heart tissue identified early and specific disruption of genes essential to mitochondrial energy production and homeostasis. Functional analysis of isolated mitochondria from these hearts confirmed that BRD4 ablation triggered significant changes in mitochondrial electron transport chain protein expression and activity. Computational analysis identified candidate transcription factors participating in the BRD4-regulated transcriptome. In particular, estrogen-related receptor α, a key nuclear receptor in metabolic gene regulation, was enriched in promoters of BRD4-regulated mitochondrial genes. CONCLUSIONS In aggregate, we describe a previously unrecognized role for BRD4 in regulating cardiomyocyte mitochondrial homeostasis, observing that its function is indispensable to the maintenance of normal cardiac function.
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MESH Headings
- Animals
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/metabolism
- Cardiomyopathy, Dilated/pathology
- Cardiomyopathy, Dilated/physiopathology
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Cell Nucleus/pathology
- Electron Transport Chain Complex Proteins/genetics
- Electron Transport Chain Complex Proteins/metabolism
- Energy Metabolism/genetics
- Epigenesis, Genetic
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Gene Expression Profiling
- Heart Failure/genetics
- Heart Failure/metabolism
- Heart Failure/pathology
- Heart Failure/physiopathology
- Mice, Knockout
- Mitochondria, Heart/genetics
- Mitochondria, Heart/metabolism
- Mitochondria, Heart/pathology
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcriptome
- Ventricular Dysfunction, Left/genetics
- Ventricular Dysfunction, Left/metabolism
- Ventricular Dysfunction, Left/pathology
- Ventricular Dysfunction, Left/physiopathology
- Ventricular Function, Left/genetics
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Affiliation(s)
- Soo Young Kim
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
| | - Xin Zhang
- Institute of Model Animal, Wuhan University, Wuhan, China
| | - Gabriele G. Schiattarella
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
| | - Francisco Altamirano
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX
| | - Thais A. R. Ramos
- Advanced Center for Chronic Disease, Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, University of Chile, Santiago, Chile
- Bioinformatics Multidisciplinary Environment, Digital Metropolis Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Kristin M. French
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
| | - Nan Jiang
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
| | - Pamela A. Szweda
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
| | - Bret M. Evers
- Department of Pathology, University of Texas Southwestern, Dallas, TX, USA
| | - Herman I. May
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
| | - Xiang Luo
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
| | - Hongliang Li
- Institute of Model Animal, Wuhan University, Wuhan, China
| | - Luke I. Szweda
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
| | - Vinicius Maracaja-Coutinho
- Advanced Center for Chronic Disease, Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, University of Chile, Santiago, Chile
- Bioinformatics Multidisciplinary Environment, Digital Metropolis Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Sergio Lavandero
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
- Advanced Center for Chronic Disease, Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, University of Chile, Santiago, Chile
| | - Thomas G. Gillette
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
| | - Joseph A. Hill
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
- Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, USA
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42
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Noncoding RNAs Set the Stage for RNA Polymerase II Transcription. Trends Genet 2020; 37:279-291. [PMID: 33046273 DOI: 10.1016/j.tig.2020.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/24/2022]
Abstract
Effective synthesis of mammalian messenger (m)RNAs depends on many factors that together direct RNA polymerase II (pol II) through the different stages of the transcription cycle and ensure efficient cotranscriptional processing of mRNAs. In addition to the many proteins involved in transcription initiation, elongation, and termination, several noncoding (nc)RNAs also function as global transcriptional regulators. Understanding the mode of action of these non-protein regulators has been an intense area of research in recent years. Here, we describe how these ncRNAs influence key regulatory steps of the transcription process, to affect large numbers of genes. Through direct association with pol II or by modulating the activity of transcription or RNA processing factors, these regulatory RNAs perform critical roles in gene expression.
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43
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Lam FC, Kong YW, Huang Q, Vu Han TL, Maffa AD, Kasper EM, Yaffe MB. BRD4 prevents the accumulation of R-loops and protects against transcription-replication collision events and DNA damage. Nat Commun 2020; 11:4083. [PMID: 32796829 PMCID: PMC7428008 DOI: 10.1038/s41467-020-17503-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Proper chromatin function and maintenance of genomic stability depends on spatiotemporal coordination between the transcription and replication machinery. Loss of this coordination can lead to DNA damage from increased transcription-replication collision events. We report that deregulated transcription following BRD4 loss in cancer cells leads to the accumulation of RNA:DNA hybrids (R-loops) and collisions with the replication machinery causing replication stress and DNA damage. Whole genome BRD4 and γH2AX ChIP-Seq with R-loop IP qPCR reveals that BRD4 inhibition leads to accumulation of R-loops and DNA damage at a subset of known BDR4, JMJD6, and CHD4 co-regulated genes. Interference with BRD4 function causes transcriptional downregulation of the DNA damage response protein TopBP1, resulting in failure to activate the ATR-Chk1 pathway despite increased replication stress, leading to apoptotic cell death in S-phase and mitotic catastrophe. These findings demonstrate that inhibition of BRD4 induces transcription-replication conflicts, DNA damage, and cell death in oncogenic cells.
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Affiliation(s)
- Fred C Lam
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA.
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA.
- Faculty of Health Sciences, Division of Neurosurgery, Hamilton General Hospital, McMaster University, 237 Barton St E, Hamilton, ON, L8L 2X2, Canada.
| | - Yi Wen Kong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA
| | - Qiuying Huang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA
| | - Tu-Lan Vu Han
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA
| | - Amanda D Maffa
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA
| | - Ekkehard M Kasper
- Faculty of Health Sciences, Division of Neurosurgery, Hamilton General Hospital, McMaster University, 237 Barton St E, Hamilton, ON, L8L 2X2, Canada
| | - Michael B Yaffe
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA.
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA.
- Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Beth Israel Deaconess Medical Center, Department of Surgery, Harvard Medical School, Boston, MA, 02215, USA.
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44
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Zhang J, Chen P, Zhu P, Zheng P, Wang T, Wang L, Xu C, Zhou J, Zhang H. Development of small-molecule BRD4 degraders based on pyrrolopyridone derivative. Bioorg Chem 2020; 99:103817. [DOI: 10.1016/j.bioorg.2020.103817] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/30/2022]
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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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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: 26] [Impact Index Per Article: 6.5] [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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Mota de Sá P, Richard AJ, Stephens JM. Bromodomain and Extraterminal Inhibition by JQ1 Produces Divergent Transcriptional Regulation of Suppressors of Cytokine Signaling Genes in Adipocytes. Endocrinology 2020; 161:5686880. [PMID: 31875887 PMCID: PMC7007879 DOI: 10.1210/endocr/bqz034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/18/2019] [Indexed: 12/27/2022]
Abstract
The Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway has cell-specific functions. Suppressors of cytokine signaling (SOCS) proteins are negative-feedback regulators of JAK-STAT signaling. STAT5 plays a significant role in adipocyte development and function, and bromodomain and extraterminal (BET) proteins may be involved in STAT5 transcriptional activity. We treated 3T3-L1 adipocytes with the BET inhibitor JQ1 and observed that growth hormone (GH)-induced expression of 2 STAT5 target genes from the SOCS family, Socs3 and Cish, were inversely regulated (increased and decreased, respectively) by BET inhibition. Chromatin immunoprecipitation analyses revealed that changes in STAT5 binding did not correlate with gene expression changes. GH promoted the recruitment of the BET protein BRD2 to the Cish, but not Socs3, promoter. JQ1 treatment ablated this effect as well as the GH-induced binding of ribonucleic acid polymerase II (RNA Pol II) to the Cish transcription start site. BRD2 knockdown also suppressed GH induction of Cish, further supporting the role of BRD2 in Cish transcriptional activation. In contrast, JQ1 increased the binding of activated Pol II to the Socs3 coding region, suggesting enhanced messenger RNA (mRNA) elongation. Our finding that JQ1 transiently reduced the interaction between the positive transcription elongation factor (P-TEFb) and its inhibitor hexamethylene bis-acetamide inducible 1 (HEXIM1) is consistent with a previously described off-target effect of JQ1, whereby P-TEFb becomes more available to be recruited by genes that do not depend on BET proteins for activating transcription. These results demonstrate substantially different transcriptional regulation of Socs3 and Cish and suggest distinct roles in adipocytes for these 2 closely related proteins.
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Affiliation(s)
- Paula Mota de Sá
- Adipocyte Biology Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Allison J Richard
- Adipocyte Biology Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana
| | - Jacqueline M Stephens
- Adipocyte Biology Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
- Correspondence: Jacqueline Stephens, Adipocyte Biology Laboratory, Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, Louisiana 70803. E-mail:
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H.S. Richter G, Hensel T, Schmidt O, Saratov V, von Heyking K, Becker-Dettling F, Prexler C, Yen HY, Steiger K, Fulda S, Dirksen U, Weichert W, Wang S, Burdach S, Schäfer BW. Combined Inhibition of Epigenetic Readers and Transcription Initiation Targets the EWS-ETS Transcriptional Program in Ewing Sarcoma. Cancers (Basel) 2020; 12:cancers12020304. [PMID: 32012890 PMCID: PMC7072515 DOI: 10.3390/cancers12020304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Previously, we used inhibitors blocking BET bromodomain binding proteins (BRDs) in Ewing sarcoma (EwS) and observed that long term treatment resulted in the development of resistance. Here, we analyze the possible interaction of BRD4 with cyclin-dependent kinase (CDK) 9. Methods: Co-immunoprecipitation experiments (CoIP) to characterize BRD4 interaction and functional consequences of inhibiting transcriptional elongation were assessed using drugs targeting of BRD4 or CDK9, either alone or in combination. Results: CoIP revealed an interaction of BRD4 with EWS-FLI1 and CDK9 in EwS. Treatment of EwS cells with CDKI-73, a specific CDK9 inhibitor (CDK9i), induced a rapid downregulation of EWS-FLI1 expression and block of contact-dependent growth. CDKI-73 induced apoptosis in EwS, as depicted by cleavage of Caspase 7 (CASP7), PARP and increased CASP3 activity, similar to JQ1. Microarray analysis following CDKI-73 treatment uncovered a transcriptional program that was only partially comparable to BRD inhibition. Strikingly, combined treatment of EwS with BRD- and CDK9-inhibitors re-sensitized cells, and was overall more effective than individual drugs not only in vitro but also in a preclinical mouse model in vivo. Conclusion: Treatment with BRD inhibitors in combination with CDK9i offers a new treatment option that significantly blocks the pathognomonic EWS-ETS transcriptional program and malignant phenotype of EwS.
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Affiliation(s)
- Günther H.S. Richter
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
- Division of Oncology and Hematology, Department of Pediatrics, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
- Correspondence:
| | - Tim Hensel
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
| | - Oxana Schmidt
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
| | - Vadim Saratov
- Department of Oncology and Children’s Research Center, University Children’s Hospital, 8032 Zurich, Switzerland; (V.S.); (B.W.S.)
| | - Kristina von Heyking
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
| | - Fiona Becker-Dettling
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
| | - Carolin Prexler
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
| | - Hsi-Yu Yen
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
- Institute of Pathology, Technical University of Munich and Comparative Experimental Pathology (CEP), Technical University of Munich, 81675 Munich, Germany;
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich and Comparative Experimental Pathology (CEP), Technical University of Munich, 81675 Munich, Germany;
| | - Simone Fulda
- Institute for Experimental Cancer Research in Paediatrics, Goethe-University Frankfurt, 60528 Frankfurt/Main, Germany;
| | - Uta Dirksen
- Pediatrics III, West German Cancer Centre, University Hospital of Essen, 45147 Essen, Germany;
- German Cancer Research Center (DKFZ), partner site Essen, 45147 Essen, Germany
| | - Wilko Weichert
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
- Institute of Pathology, Technical University of Munich and Comparative Experimental Pathology (CEP), Technical University of Munich, 81675 Munich, Germany;
| | - Shudong Wang
- Centre for Drug Discovery and Development and School of Pharmacy and Medical Sciences, University of South Australia Cancer Research Institute, Adelaide, South Australia 5001, Australia;
| | - Stefan Burdach
- Children’s Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, 80804 München, Germany; (T.H.); (O.S.); (K.v.H.); (F.B.-D.); (C.P.); (S.B.)
- German Cancer Research Center (DKFZ), partner site Munich, 81377 Munich, Germany; (H.-Y.Y.); (W.W.)
| | - Beat W. Schäfer
- Department of Oncology and Children’s Research Center, University Children’s Hospital, 8032 Zurich, Switzerland; (V.S.); (B.W.S.)
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Chen JY, Lim DH, Fu XD. Mechanistic Dissection of RNA-Binding Proteins in Regulated Gene Expression at Chromatin Levels. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:55-66. [PMID: 31900328 PMCID: PMC7332398 DOI: 10.1101/sqb.2019.84.039222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Eukaryotic genomes are known to prevalently transcribe diverse classes of RNAs, virtually all of which, including nascent RNAs from protein-coding genes, are now recognized to have regulatory functions in gene expression, suggesting that RNAs are both the products and the regulators of gene expression. Their functions must enlist specific RNA-binding proteins (RBPs) to execute their regulatory activities, and recent evidence suggests that nearly all biochemically defined chromatin regions in the human genome, whether defined for gene activation or silencing, have the involvement of specific RBPs. Interestingly, the boundary between RNA- and DNA-binding proteins is also melting, as many DNA-binding proteins traditionally studied in the context of transcription are able to bind RNAs, some of which may simultaneously bind both DNA and RNA to facilitate network interactions in three-dimensional (3D) genome. In this review, we focus on RBPs that function at chromatin levels, with particular emphasis on their mechanisms of action in regulated gene expression, which is intended to facilitate future functional and mechanistic dissection of chromatin-associated RBPs.
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Affiliation(s)
- Jia-Yu Chen
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Do-Hwan Lim
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, California 92093, USA
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50
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Bowry A, Piberger AL, Rojas P, Saponaro M, Petermann E. BET Inhibition Induces HEXIM1- and RAD51-Dependent Conflicts between Transcription and Replication. Cell Rep 2019; 25:2061-2069.e4. [PMID: 30463005 PMCID: PMC6280123 DOI: 10.1016/j.celrep.2018.10.079] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/27/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022] Open
Abstract
BET bromodomain proteins are required for oncogenic transcription activities, and BET inhibitors have been rapidly advanced into clinical trials. Understanding the effects of BET inhibition on processes such as DNA replication will be important for future clinical applications. Here, we show that BET inhibition, and specifically inhibition of BRD4, causes replication stress through a rapid overall increase in RNA synthesis. We provide evidence that BET inhibition acts by releasing P-TEFb from its inhibitor HEXIM1, promoting interference between transcription and replication. Unusually, these transcription-replication conflicts do not activate the ATM/ATR-dependent DNA damage response but recruit the homologous recombination factor RAD51. Both HEXIM1 and RAD51 promote BET inhibitor-induced fork slowing but also prevent a DNA damage response. Our data suggest that BET inhibitors slow replication through concerted action of transcription and recombination machineries and shed light on the importance of replication stress in the action of this class of experimental cancer drugs.
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Affiliation(s)
- Akhil Bowry
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ann Liza Piberger
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Patricia Rojas
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Marco Saponaro
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Eva Petermann
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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