1
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Panichnantakul P, Aguilar LC, Daynard E, Guest M, Peters C, Vogel J, Oeffinger M. Protein UFMylation regulates early events during ribosomal DNA-damage response. Cell Rep 2024; 43:114738. [PMID: 39277864 DOI: 10.1016/j.celrep.2024.114738] [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: 02/25/2024] [Revised: 07/03/2024] [Accepted: 08/23/2024] [Indexed: 09/17/2024] Open
Abstract
The highly repetitive and transcriptionally active ribosomal DNA (rDNA) genes are exceedingly susceptible to genotoxic stress. Induction of DNA double-strand breaks (DSBs) in rDNA repeats is associated with ataxia-telangiectasia-mutated (ATM)-dependent rDNA silencing and nucleolar reorganization where rDNA is segregated into nucleolar caps. However, the regulatory events underlying this response remain elusive. Here, we identify protein UFMylation as essential for rDNA-damage response in human cells. We further show the only ubiquitin-fold modifier 1 (UFM1)-E3 ligase UFL1 and its binding partner DDRGK1 localize to nucleolar caps upon rDNA damage and that UFL1 loss impairs ATM activation and rDNA transcriptional silencing, leading to reduced rDNA segregation. Moreover, analysis of nuclear and nucleolar UFMylation targets in response to DSB induction further identifies key DNA-repair factors including ATM, in addition to chromatin and actin network regulators. Taken together, our data provide evidence of an essential role for UFMylation in orchestrating rDNA DSB repair.
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Affiliation(s)
- Pudchalaluck Panichnantakul
- Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Lisbeth C Aguilar
- Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Evan Daynard
- Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Mackenzie Guest
- Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Colten Peters
- Department of Biology, Faculty of Medicine, McGill University, Montréal, QC H3A 1B1, Canada
| | - Jackie Vogel
- Department of Biology, Faculty of Medicine, McGill University, Montréal, QC H3A 1B1, Canada
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal, Center for Genetic and Neurological Diseases, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H4A 3J1, Canada; Département de biochimie et médicine moléculaire, Faculté de Médicine, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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2
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Zhang S, Roeder RG. Resistance of estrogen receptor function to BET bromodomain inhibition is mediated by transcriptional coactivator cooperativity. Nat Struct Mol Biol 2024:10.1038/s41594-024-01384-6. [PMID: 39251822 DOI: 10.1038/s41594-024-01384-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 08/01/2024] [Indexed: 09/11/2024]
Abstract
The bromodomain and extraterminal domain (BET) family of proteins are critical chromatin readers that bind to acetylated histones through their bromodomains to activate transcription. Here, we reveal that bromodomain inhibition fails to repress oncogenic targets of estrogen receptor because of an intrinsic transcriptional mechanism. While bromodomains are necessary for the transcription of many genes, bromodomain-containing protein 4 (BRD4) binds to estrogen receptor binding sites and activates transcription of critical oncogenes such as MYC, independently of its bromodomains. BRD4 associates with the Mediator complex and disruption of Mediator reduces BRD4's enhancer occupancy. Profiling changes of the post-initiation RNA polymerase II (Pol II)-associated factors revealed that BET proteins regulate interactions between Pol II and elongation factors SPT5, SPT6 and the polymerase-associated factor 1 complex, which associate with BET proteins independently of their bromodomains and mediate their transcription elongation effect. Our findings highlight the importance of bromodomain-independent functions and interactions of BET proteins in the development of future therapeutic strategies.
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Affiliation(s)
- Sicong Zhang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA.
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3
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Tarakhovsky A, Zhang T, Marina R, Veugelen S, Mander P, Prinjha R, Schaefer A, Adelman K. The signaling cascade of induction and maintenance of ES cell diapause. RESEARCH SQUARE 2024:rs.3.rs-4946357. [PMID: 39281867 PMCID: PMC11398561 DOI: 10.21203/rs.3.rs-4946357/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
Nutrient deficiency during pregnancy in numerous animal species can induce the state of embryonic diapause. Diapause is characterized by changes in protein and gene expression that minimize the organism's reliance on external energy sources and ensure survival. Remarkably, the systematic changes associated with diapause appear to spare the gene expression program that supports embryonic cells' maintenance in the pluripotent state. The phenomenon of the differentiation "freeze" during diapause can be reproduced in vitro . Mimicking nutrient deficiency by pharmacological inhibition of mTOR induces the diapause-like state in ES cells without affecting ES cell pluripotency. We discovered a connection between mTOR signaling and the chromatin-bound bromodomain and extra-terminal (BET) transcriptional regulator BRD4, showing a key role of BET-protein in the induction of diapause-like state in ES cells. mTOR inhibition rapidly and negatively impacts BRD4 binding to chromatin, which is associated with changes in gene expression that can contribute to diapause. Conversely, pharmacological inhibition of BET-protein circumvents the diapause dependence on mTOR inhibition and causes the diapause-like state. BET-repressed diapause-like ES cells retain the undifferentiated pluripotent state, which is associated with upregulation of a functionally linked group of genes encoding negative regulators of MAP kinase (MAPK) signaling and inactivation of MAP kinase. The transcriptional switch-off of MAP kinase following chronic BET inhibition imitates the transcriptional de-repression of MAP kinase negative regulators in response to mTOR inhibition. Mechanistically, suppression of mTOR or BET-protein leads to a profound decline in Capicua transcriptional repressor (CIC) at promoters of key negative regulators of MAP kinase. The discovered mTOR-BRD4 axis in the induction of diapause and the rapid transcriptional shut-off of differentiation program is likely to play a major role in the maintenance of embryonic diapause in vivo , as well as in controlling of the undifferentiated state of various types of stem cells during diapause-like metabolic dormancy.
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4
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Wang Y, Wang Y, Xu Y, Tocci D, Wang C. Development and Evaluation of [ 11C]I-58: A Novel PET Radiotracer Targeting BRD4 BD2 for Advanced Epigenetic Imaging. ACS OMEGA 2024; 9:36177-36184. [PMID: 39220497 PMCID: PMC11360046 DOI: 10.1021/acsomega.4c01495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 09/04/2024]
Abstract
The paired bromodomains (BD1 and BD2), located in the bromodomain and extra-terminal (BET) family proteins, perform specific functions in gene transcriptional control and expression. Targeting specific bromodomains with inhibitors holds promise for achieving therapeutic benefits with reduced side effects. However, the comprehension of this target related to the disease is still restricted. Positron emission tomography (PET) imaging is a powerful tool that provides a valuable avenue for exploring the BD2 bromodomain. This investigation introduces a novel radioligand, [11C]I-58, for PET targeting the BET BD2 domain. The synthesis of compound I-58, along with its radiosynthetic process for C11 labeling, is detailed, and the suitability of [11C]I-58 for PET imaging of the BD2 bromodomain is evaluated. Initial PET study findings in mice indicate that [11C]I-58 exhibits suitable biodistribution in peripheral organs and tissues. Additionally, in vitro autoradiography studies and blocking experiments provide compelling evidence supporting the specific binding of [11C]I-58 to the BD2 bromodomain. These results establish [11C]I-58 as a promising instrument for the PET imaging of the BD2 bromodomain. This research not only holds the potential to pave the path for developing PET radioligands precisely targeting the BD2 bromodomain but also adds to a more profound comprehension of the biological mechanisms linked to the BD bromodomain.
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Affiliation(s)
- Yanli Wang
- Department
of Radiology Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts 02129, United States
| | - Yongle Wang
- Department
of Radiology Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts 02129, United States
- School
of Pharmacy, Minzu University of China, Beijing 100081, China
| | - Yulong Xu
- Department
of Radiology Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts 02129, United States
| | - Darcy Tocci
- Department
of Radiology Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts 02129, United States
| | - Changning Wang
- Department
of Radiology Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts 02129, United States
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5
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Bhushan V, Nita-Lazar A. Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology. J Proteome Res 2024; 23:2700-2722. [PMID: 38451675 PMCID: PMC11296931 DOI: 10.1021/acs.jproteome.3c00839] [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: 03/08/2024]
Abstract
The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.
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Affiliation(s)
- Vanya Bhushan
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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6
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Zhang S, Roeder RG. Resistance of estrogen receptor function to BET bromodomain inhibition is mediated by transcriptional coactivator cooperativity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.25.605008. [PMID: 39211208 PMCID: PMC11361192 DOI: 10.1101/2024.07.25.605008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The Bromodomain and Extra-Terminal Domain (BET) family of proteins are critical chromatin readers that bind to acetylated histones through their bromodomains to activate transcription. Here, we reveal that bromodomain inhibition fails to repress oncogenic targets of estrogen receptor due to an intrinsic transcriptional mechanism. While bromodomains are necessary for the transcription of many genes, BRD4 binds to estrogen receptor binding sites and activates transcription of critical oncogenes independently of its bromodomains. BRD4 associates with the Mediator complex and disruption of Mediator complex reduces BRD4's enhancer occupancy. Profiling changes in the post-initiation RNA polymerase II (Pol II)-associated factors revealed that BET proteins regulate interactions between Pol II and elongation factors SPT5, SPT6, and PAF1 complex, which associate with BET proteins independently of their bromodomains and mediate their transcription elongation effect. Our findings highlight the importance of bromodomain-independent functions and interactions of BET proteins in the development of future therapeutic strategies.
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7
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Mondal A, Singh B, Felkner RH, De Falco A, Swapna G, Montelione GT, Roth MJ, Perez A. A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries. Angew Chem Int Ed Engl 2024; 63:e202405767. [PMID: 38588243 DOI: 10.1002/anie.202405767] [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: 03/26/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
Identifying the interactome for a protein of interest is challenging due to the large number of possible binders. High-throughput experimental approaches narrow down possible binding partners but often include false positives. Furthermore, they provide no information about what the binding region is (e.g., the binding epitope). We introduce a novel computational pipeline based on an AlphaFold2 (AF) Competitive Binding Assay (AF-CBA) to identify proteins that bind a target of interest from a pull-down experiment and the binding epitope. Our focus is on proteins that bind the Extraterminal (ET) domain of Bromo and Extraterminal domain (BET) proteins, but we also introduce nine additional systems to show transferability to other peptide-protein systems. We describe a series of limitations to the methodology based on intrinsic deficiencies of AF and AF-CBA to help users identify scenarios where the approach will be most useful. Given the method's speed and accuracy, we anticipate its broad applicability to identify binding epitope regions among potential partners, setting the stage for experimental verification.
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Affiliation(s)
- Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL, USA
| | - Bhumika Singh
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL, USA
| | - Roland H Felkner
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854, USA
| | - Anna De Falco
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Gvt Swapna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Monica J Roth
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854, USA
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL, USA
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8
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Hashimoto M, Masuda T, Nakano Y, Tobo T, Saito H, Koike K, Takahashi J, Abe T, Ando Y, Ozato Y, Hosoda K, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Hata T, Uemura M, Eguchi H, Doki Y, Mori M, Mimori K. Tumor suppressive role of the epigenetic master regulator BRD3 in colorectal cancer. Cancer Sci 2024; 115:1866-1880. [PMID: 38494600 PMCID: PMC11145117 DOI: 10.1111/cas.16129] [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] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 03/19/2024] Open
Abstract
Bromodomain and extraterminal domain (BET) family proteins are epigenetic master regulators of gene expression via recognition of acetylated histones and recruitment of transcription factors and co-activators to chromatin. Hence, BET family proteins have emerged as promising therapeutic targets in cancer. In this study, we examined the functional role of bromodomain containing 3 (BRD3), a BET family protein, in colorectal cancer (CRC). In vitro and vivo analyses using BRD3-knockdown or BRD3-overexpressing CRC cells showed that BRD3 suppressed tumor growth and cell cycle G1/S transition and induced p21 expression. Clinical analysis of CRC datasets from our hospital or The Cancer Genome Atlas revealed that BET family genes, including BRD3, were overexpressed in tumor tissues. In immunohistochemical analyses, BRD3 was observed mainly in the nucleus of CRC cells. According to single-cell RNA sequencing in untreated CRC tissues, BRD3 was highly expressed in malignant epithelial cells, and cell cycle checkpoint-related pathways were enriched in the epithelial cells with high BRD3 expression. Spatial transcriptomic and single-cell RNA sequencing analyses of CRC tissues showed that BRD3 expression was positively associated with high p21 expression. Furthermore, overexpression of BRD3 combined with knockdown of, a driver gene in the BRD family, showed strong inhibition of CRC cells in vitro. In conclusion, we demonstrated a novel tumor suppressive role of BRD3 that inhibits tumor growth by cell cycle inhibition in part via induction of p21 expression. BRD3 activation might be a novel therapeutic approach for CRC.
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Affiliation(s)
- Masahiro Hashimoto
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Takaaki Masuda
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Yusuke Nakano
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Taro Tobo
- Department of PathologyKyushu University Beppu HospitalBeppuJapan
| | - Hideyuki Saito
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Kensuke Koike
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | | | - Tadashi Abe
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Yuki Ando
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Yuki Ozato
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Kiyotaka Hosoda
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Satoshi Higuchi
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | | | - Takeo Toshima
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Yusuke Yonemura
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Tsuyoshi Hata
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Mamoru Uemura
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Hidetoshi Eguchi
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Yuichiro Doki
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Masaki Mori
- Tokai University School of MedicineIseharaJapan
| | - Koshi Mimori
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
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9
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Qiang Y, Fan J, Xie C, Yan L, Song X, Zhang N, Lin Y, Xiong J, Zhang W, Liu Y, Wei L, Li Y, Chen S, Liang K, Li F. KDM5C-Mediated Recruitment of BRD4 to Chromatin Regulates Enhancer Activation and BET Inhibitor Sensitivity. Cancer Res 2024; 84:1252-1269. [PMID: 38285760 DOI: 10.1158/0008-5472.can-23-2888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/05/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
The BET family member BRD4 is a bromodomain-containing protein that plays a vital role in driving oncogene expression. Given their pivotal role in regulating oncogenic networks in various cancer types, BET inhibitors (BETi) have been developed, but the clinical application has been impeded by dose-limiting toxicity and resistance. Understanding the mechanisms of BRD4 activity and identifying predictive biomarkers could facilitate the successful clinical use of BETis. Herein, we show that KDM5C and BRD4 cooperate to sustain tumor cell growth. Mechanistically, KDM5C interacted with BRD4 and stimulated BRD4 enhancer recruitment. Moreover, binding of the BRD4 C-terminus to KDM5C stimulated the H3K4 demethylase activity of KDM5C. The abundance of both KDM5C-associated BRD4 and H3K4me1/3 determined the transcriptional activation of many oncogenes. Notably, depletion or pharmacologic degradation of KDM5C dramatically reduced BRD4 chromatin enrichment and significantly increased BETi efficacy across multiple cancer types in both tumor cell lines and patient-derived organoid models. Furthermore, targeting KDM5C in combination with BETi suppressed tumor growth in vivo in a xenograft mouse model. Collectively, this work reveals a KDM5C-mediated mechanism by which BRD4 regulates transcription, providing a rationale for incorporating BETi into combination therapies with KDM5C inhibitors to enhance treatment efficacy. SIGNIFICANCE BRD4 is recruited to enhancers in a bromodomain-independent manner by binding KDM5C and stimulates KDM5C H3K4 demethylase activity, leading to synergistic effects of BET and KDM5C inhibitor combinations in cancer.
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Affiliation(s)
- Yulong Qiang
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Jiachen Fan
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Chuanshuai Xie
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Leilei Yan
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Xiaofei Song
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Nan Zhang
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Yan Lin
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Jie Xiong
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wei Zhang
- Department of Gynaecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Lei Wei
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yu Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Shizhen Chen
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Kaiwei Liang
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Feng Li
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
- Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, China
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10
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Schreiber KJ, Kadijk E, Youn JY. Exploring Options for Proximity-Dependent Biotinylation Experiments: Comparative Analysis of Labeling Enzymes and Affinity Purification Resins. J Proteome Res 2024; 23:1531-1543. [PMID: 38507741 PMCID: PMC11002925 DOI: 10.1021/acs.jproteome.3c00908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Proximity-dependent biotinylation (PDB) techniques provide information about the molecular neighborhood of a protein of interest, yielding insights into its function and localization. Here, we assessed how different labeling enzymes and streptavidin resins influence PDB results. We compared the high-confidence interactors of the DNA/RNA-binding protein transactive response DNA-binding protein 43 kDa (TDP-43) identified using either miniTurbo (biotin ligase) or APEX2 (peroxidase) enzymes. We also evaluated two commercial affinity resins for purification of biotinylated proteins: conventional streptavidin sepharose versus a new trypsin-resistant streptavidin conjugated to magnetic resin, which significantly reduces the level of contamination by streptavidin peptides following on-bead trypsin digestion. Downstream analyses involved liquid chromatography coupled to mass spectrometry in data-dependent acquisition mode, database searching, and statistical analysis of high-confidence interactors using SAINTexpress. The APEX2-TDP-43 experiment identified more interactors than miniTurbo-TDP-43, although miniTurbo provided greater overlap with previously documented TDP-43 interactors. Purifications on sepharose resin yielded more interactors than magnetic resin in small-scale experiments using a range of magnetic resin volumes. We suggest that resin-specific background protein binding profiles and different lysate-to-resin ratios cumulatively affect the distributions of prey protein abundance in experimental and control samples, which impact statistical confidence scores. Overall, we highlight key experimental variables to consider for the empirical optimization of PDB experiments.
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Affiliation(s)
- Karl J. Schreiber
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Eileigh Kadijk
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ji-Young Youn
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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11
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Yan L, Tan S, Wang H, Yuan H, Liu X, Chen Y, de Thé H, Zhu J, Zhou J. Znf687 recruits Brd4-Smrt complex to regulate gfi1aa during neutrophil development. Leukemia 2024; 38:851-864. [PMID: 38326409 DOI: 10.1038/s41375-024-02165-2] [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: 06/28/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024]
Abstract
Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well-coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia, neutrophilia, and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage-preferential transcription factor, whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically, Znf687 functions as a negative regulator of gfi1aa, a pivotal modulator in terminal granulopoiesis, to regulate neutrophil maturation. Moreover, we found BRD4, an important epigenetic regulator, directly interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator, Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. In addition, the ZNF687-BRD4-SMRT-GFI1 transcriptional regulatory network is evolutionary conserved in higher vertebrate. Overall, our work indicates Znf687 and Brd4 are two novel master regulators in promoting terminal granulopoiesis.
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Affiliation(s)
- Lin Yan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuiyi Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haihong Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Yuan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohui Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hugues de Thé
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France
| | - Jun Zhu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France.
| | - Jun Zhou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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12
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Manji J, Pipella J, Brawerman G, Thompson PJ. Exploring Transcriptional Regulation of Beta Cell SASP by Brd4-Associated Proteins and Cell Cycle Control Protein p21. EPIGENOMES 2024; 8:10. [PMID: 38534794 DOI: 10.3390/epigenomes8010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/14/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Type 1 diabetes (T1D) is a metabolic disease resulting from progressive autoimmune destruction of insulin-producing pancreatic beta cells. Although the majority of beta cells are lost in T1D, a small subset undergoes senescence, a stress response involving growth arrest, DNA damage response, and activation of a senescence-associated secretory phenotype (SASP). SASP in beta cells of the nonobese diabetic (NOD) mouse model of T1D and primary human islets is regulated at the level of transcription by bromodomain extra-terminal (BET) proteins, but the mechanisms remain unclear. To explore how SASP is transcriptionally regulated in beta cells, we used the NOD beta cell line NIT-1 to model beta cell SASP and identified binding partners of BET protein Brd4 and explored the role of the cyclin-dependent kinase inhibitor p21. Brd4 interacted with a variety of proteins in senescent NIT-1 cells including subunits of the Ino80 chromatin remodeling complex, which was expressed in beta cells during T1D progression in NOD mice and in human beta cells of control, autoantibody-positive, and T1D donors as determined from single-cell RNA-seq data. RNAi knockdown of p21 during senescence in NIT-1 cells did not significantly impact viability or SASP. Taken together, these results suggest that Brd4 interacts with several protein partners during senescence in NIT-1 cells, some of which may play roles in SASP gene activation and that p21 is dispensable for the SASP in this beta cell model.
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Affiliation(s)
- Jasmine Manji
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Department of Physiology & Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Jasmine Pipella
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Department of Physiology & Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Gabriel Brawerman
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Department of Physiology & Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Peter J Thompson
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Department of Physiology & Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
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13
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Binet R, Lambert JP, Tomkova M, Tischfield S, Baggiolini A, Picaud S, Sarkar S, Louphrasitthiphol P, Dias D, Carreira S, Humphrey TC, Fillipakopoulos P, White R, Goding CR. DNA damage remodels the MITF interactome to increase melanoma genomic instability. Genes Dev 2024; 38:70-94. [PMID: 38316520 PMCID: PMC10903946 DOI: 10.1101/gad.350740.123] [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: 04/21/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024]
Abstract
Since genome instability can drive cancer initiation and progression, cells have evolved highly effective and ubiquitous DNA damage response (DDR) programs. However, some cells (for example, in skin) are normally exposed to high levels of DNA-damaging agents. Whether such high-risk cells possess lineage-specific mechanisms that tailor DNA repair to the tissue remains largely unknown. Using melanoma as a model, we show here that the microphthalmia-associated transcription factor MITF, a lineage addition oncogene that coordinates many aspects of melanocyte and melanoma biology, plays a nontranscriptional role in shaping the DDR. On exposure to DNA-damaging agents, MITF is phosphorylated at S325, and its interactome is dramatically remodeled; most transcription cofactors dissociate, and instead MITF interacts with the MRE11-RAD50-NBS1 (MRN) complex. Consequently, cells with high MITF levels accumulate stalled replication forks and display defects in homologous recombination-mediated repair associated with impaired MRN recruitment to DNA damage. In agreement with this, high MITF levels are associated with increased single-nucleotide and copy number variant burdens in melanoma. Significantly, the SUMOylation-defective MITF-E318K melanoma predisposition mutation recapitulates the effects of DNA-PKcs-phosphorylated MITF. Our data suggest that a nontranscriptional function of a lineage-restricted transcription factor contributes to a tissue-specialized modulation of the DDR that can impact cancer initiation.
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Affiliation(s)
- Romuald Binet
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Université Laval, Québec City, Québec G1V 4G2, Canada
- Endocrinology-Nephrology Axis, CHU de Québec-Université Laval Research Center, Québec City, Québec G1V 4G2, Canada
| | - Marketa Tomkova
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, USA
| | - Samuel Tischfield
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Arianna Baggiolini
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Sovan Sarkar
- Cancer Research UK, Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Diogo Dias
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Suzanne Carreira
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Timothy C Humphrey
- Cancer Research UK, Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Panagis Fillipakopoulos
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Richard White
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom;
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14
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Mondal A, Singh B, Felkner RH, De Falco A, Swapna GVT, Montelione GT, Roth MJ, Perez A. Sifting Through the Noise: A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576374. [PMID: 38328039 PMCID: PMC10849530 DOI: 10.1101/2024.01.20.576374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Identifying the interactome for a protein of interest is challenging due to the large number of possible binders. High-throughput experimental approaches narrow down possible binding partners, but often include false positives. Furthermore, they provide no information about what the binding region is (e.g. the binding epitope). We introduce a novel computational pipeline based on an AlphaFold2 (AF) Competition Assay (AF-CBA) to identify proteins that bind a target of interest from a pull-down experiment, along with the binding epitope. Our focus is on proteins that bind the Extraterminal (ET) domain of Bromo and Extraterminal domain (BET) proteins, but we also introduce nine additional systems to show transferability to other peptide-protein systems. We describe a series of limitations to the methodology based on intrinsic deficiencies to AF and AF-CBA, to help users identify scenarios where the approach will be most useful. Given the speed and accuracy of the methodology, we expect it to be generally applicable to facilitate target selection for experimental verification starting from high-throughput protein libraries.
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Affiliation(s)
- Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL
| | - Bhumika Singh
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL
| | - Roland H. Felkner
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854
| | - Anna De Falco
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - GVT Swapna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Monica J. Roth
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL
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15
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Iazzi M, St-Germain J, Acharya S, Raught B, Gupta GD. Proximity Mapping of Ciliary Proteins by BioID. Methods Mol Biol 2024; 2725:181-198. [PMID: 37856025 DOI: 10.1007/978-1-0716-3507-0_11] [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] [Indexed: 10/20/2023]
Abstract
The primary cilium is a highly conserved microtubule-based organelle present in most vertebrate cell types. Mutations in ciliary protein genes can lead to dysfunctional or absent cilia and are the cause of a large group of heterogeneous diseases known as ciliopathies. ARL13B is a member of the ARF family of regulatory GTPases and is highly enriched on the ciliary membrane. The absence of ARL13B disrupts cilia architecture and mutations have been linked to several diseases; yet there remain major gaps in our understanding of the role that ARL13B plays in primary cilia function. Here, we demonstrate how in cellulo proximity-dependent biotinylation (BioID) can be used to generate a comprehensive protein proximity map of ciliary proteins by performing BioID on N- and C-terminally BirA*-tagged ARL13B. This method can theoretically provide insight into any cilia protein, identifying key interactors that play a critical role in ciliary biology.
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Affiliation(s)
- Melissa Iazzi
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Saujanya Acharya
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
| | - Gagan D Gupta
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada.
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16
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Liu G, Zhang S, Lin R, Cao X, Yuan L. Anti-tumor target screening of sea cucumber saponin Frondoside A: a bioinformatics and molecular docking analysis. Front Oncol 2023; 13:1307838. [PMID: 38144520 PMCID: PMC10739435 DOI: 10.3389/fonc.2023.1307838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Cancer remains the leading cause of death worldwide. In spite of significant advances in targeted and immunotherapeutic approaches, clinical outcomes for cancer remain poor. The aim of the present study was to investigate the potential mechanisms and therapeutic targets of Frondoside A for the treatment of liver, pancreatic, and bladder cancers. The data presented in our study demonstrated that Frondoside A reduced the viability and migration of HepG2, Panc02, and UM-UC-3 cancer cell in vitro. Moreover, we utilized the GEO database to screen and identify for differentially expressed genes (DEGs) in liver, pancreatic, and bladder cancers, which resulted in the identification of 714, 357, and 101 DEGs, respectively. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation were performed using the Metascape database for DEGs that were significantly associated with cancer development. The protein-protein interaction (PPI) networks of the identified DEGs in liver, pancreatic, and bladder cancers were analyzed using Cytoscape 3.9.0 software, and subsequently identified potential key genes that were associated with these networks. Subsequently, their prognostic values were assessed by gene expression level analysis and Kaplan-Meier survival analysis (GEPIA). Furthermore, we utilized TIMER 2.0 to investigate the correlation between the expression of the identified key gene and cancer immune infiltration. Finally, molecular docking simulations were performed to assess the affinity of Frondoside A and key genes. Our results showed a significant correlation between these DEGs and cancer progression. Combined, these analyses revealed that Frondoside A involves in the regulation of multiple pathways, such as drug metabolism, cell cycle in liver cancer by inhibiting the expression of CDK1, TOP2A, CDC20, and KIF20A, and regulates protein digestion and absorption, receptor interaction in pancreatic cancer by down-regulation of ASPM, TOP2A, DLGAP5, TPX2, KIF23, MELK, LAMA3, and ANLN. While in bladder cancer, Frondoside A regulates muscle contraction, complement and coagulation cascade by increase FLNC expression. In conclusion, the present study offers valuable insights into the molecular mechanism underlying the anticancer effects of Frondoside A, and suggests that Frondoside A can be used as a functional food supplement or further developed as a natural anti-cancer drug.
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Affiliation(s)
- Guangchun Liu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Shenglin Zhang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ruoyan Lin
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xudong Cao
- Deparment of Chemical and Biological Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Lihong Yuan
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
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17
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Pascual‐Reguant L, Serra‐Camprubí Q, Datta D, Cianferoni D, Kourtis S, Gañez‐Zapater A, Cannatá C, Espinar L, Querol J, García‐López L, Musa‐Afaneh S, Guirola M, Gkanogiannis A, Miró Canturri A, Guzman M, Rodríguez O, Herencia‐Ropero A, Arribas J, Serra V, Serrano L, Tian TV, Peiró S, Sdelci S. Interactions between BRD4S, LOXL2, and MED1 drive cell cycle transcription in triple-negative breast cancer. EMBO Mol Med 2023; 15:e18459. [PMID: 37937685 PMCID: PMC10701626 DOI: 10.15252/emmm.202318459] [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: 08/03/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/09/2023] Open
Abstract
Triple-negative breast cancer (TNBC) often develops resistance to single-agent treatment, which can be circumvented using targeted combinatorial approaches. Here, we demonstrate that the simultaneous inhibition of LOXL2 and BRD4 synergistically limits TNBC proliferation in vitro and in vivo. Mechanistically, LOXL2 interacts in the nucleus with the short isoform of BRD4 (BRD4S), MED1, and the cell cycle transcriptional regulator B-MyB. These interactions sustain the formation of BRD4 and MED1 nuclear transcriptional foci and control cell cycle progression at the gene expression level. The pharmacological co-inhibition of LOXL2 and BRD4 reduces BRD4 nuclear foci, BRD4-MED1 colocalization, and the transcription of cell cycle genes, thus suppressing TNBC cell proliferation. Targeting the interaction between BRD4S and LOXL2 could be a starting point for the development of new anticancer strategies for the treatment of TNBC.
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Affiliation(s)
- Laura Pascual‐Reguant
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | | | - Debayan Datta
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Damiano Cianferoni
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Savvas Kourtis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Antoni Gañez‐Zapater
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Chiara Cannatá
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Lorena Espinar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Laura García‐López
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sara Musa‐Afaneh
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Guirola
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Anestis Gkanogiannis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Andrea Miró Canturri
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
| | - Marta Guzman
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Olga Rodríguez
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | | | - Joaquin Arribas
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- Centro de Investigación Biomédica en Red de CáncerMonforte de LemosMadridSpain
- Department of Biochemistry and Molecular BiologyUniversitat Autónoma de BarcelonaBellaterraSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
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18
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Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A biotin targeting chimera (BioTAC) system to map small molecule interactomes in situ. Nat Commun 2023; 14:8016. [PMID: 38049406 PMCID: PMC10695998 DOI: 10.1038/s41467-023-43507-5] [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: 03/30/2023] [Accepted: 11/12/2023] [Indexed: 12/06/2023] Open
Abstract
Understanding how small molecules bind to specific protein complexes in living cells is critical to understanding their mechanism-of-action. Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules would provide advantages over target-focused approaches, including the ability to detect previously unknown ligand targets and complexes. However, there are few current methods for unbiased profiling of small molecule interactomes. To address this, we envisioned a technology that would combine the sensitivity and live-cell compatibility of proximity labelling coupled to mass spectrometry, with the specificity and unbiased nature of chemoproteomics. In this manuscript, we describe the BioTAC system, a small-molecule guided proximity labelling platform that can rapidly identify both direct and complexed small molecule binding proteins. We benchmark the system against µMap, photoaffinity labelling, affinity purification coupled to mass spectrometry and proximity labelling coupled to mass spectrometry datasets. We also apply the BioTAC system to provide interactome maps of Trametinib and analogues. The BioTAC system overcomes a limitation of current approaches and supports identification of both inhibitor bound and molecular glue bound complexes.
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Affiliation(s)
- Andrew J Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gillian E Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bridget T Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth J Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Justin G English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
| | - Fleur M Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
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19
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Low JKK, Patel K, Jones N, Solomon P, Norman A, Maxwell JWC, Pachl P, Matthews JM, Payne RJ, Passioura T, Suga H, Walport LJ, Mackay JP. mRNA display reveals a class of high-affinity bromodomain-binding motifs that are not found in the human proteome. J Biol Chem 2023; 299:105482. [PMID: 37992806 PMCID: PMC10758951 DOI: 10.1016/j.jbc.2023.105482] [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: 05/22/2023] [Revised: 11/01/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023] Open
Abstract
Bromodomains (BDs) regulate gene expression by recognizing protein motifs containing acetyllysine. Although originally characterized as histone-binding proteins, it has since become clear that these domains interact with other acetylated proteins, perhaps most prominently transcription factors. The likely transient nature and low stoichiometry of such modifications, however, has made it challenging to fully define the interactome of any given BD. To begin to address this knowledge gap in an unbiased manner, we carried out mRNA display screens against a BD-the N-terminal BD of BRD3-using peptide libraries that contained either one or two acetyllysine residues. We discovered peptides with very strong consensus sequences and with affinities that are significantly higher than typical BD-peptide interactions. X-ray crystal structures also revealed modes of binding that have not been seen with natural ligands. Intriguingly, however, our sequences are not found in the human proteome, perhaps suggesting that strong binders to BDs might have been selected against during evolution.
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Affiliation(s)
- Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Karishma Patel
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Natasha Jones
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Paul Solomon
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Alexander Norman
- School of Chemistry, University of Sydney, New South Wales, Australia
| | | | - Petr Pachl
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, University of Sydney, New South Wales, Australia
| | - Toby Passioura
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia; Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Louise J Walport
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, United Kingdom; Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom.
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia.
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20
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Zhang C, Shafaq-Zadah M, Pawling J, Hesketh GG, Dransart E, Pacholczyk K, Longo J, Gingras AC, Penn LZ, Johannes L, Dennis JW. SLC3A2 N-glycosylation and Golgi remodeling regulate SLC7A amino acid exchangers and stress mitigation. J Biol Chem 2023; 299:105416. [PMID: 37918808 PMCID: PMC10698284 DOI: 10.1016/j.jbc.2023.105416] [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: 08/30/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
Proteostasis requires oxidative metabolism (ATP) and mitigation of the associated damage by glutathione, in an increasingly dysfunctional relationship with aging. SLC3A2 (4F2hc, CD98) plays a role as a disulfide-linked adaptor to the SLC7A5 and SLC7A11 exchangers which import essential amino acids and cystine while exporting Gln and Glu, respectively. The positions of N-glycosylation sites on SLC3A2 have evolved with the emergence of primates, presumably in synchrony with metabolism. Herein, we report that each of the four sites in SLC3A2 has distinct profiles of Golgi-modified N-glycans. N-glycans at the primate-derived site N381 stabilized SLC3A2 in the galectin-3 lattice against coated-pit endocytosis, while N365, the site nearest the membrane promoted glycolipid-galectin-3 (GL-Lect)-driven endocytosis. Our results indicate that surface retention and endocytosis are precisely balanced by the number, position, and remodeling of N-glycans on SLC3A2. Furthermore, proteomics and functional assays revealed an N-glycan-dependent clustering of the SLC3A2∗SLC7A5 heterodimer with amino-acid/Na+ symporters (SLC1A4, SLC1A5) that balances branched-chain amino acids and Gln levels, at the expense of ATP to maintain the Na+/K+ gradient. In replete conditions, SLC3A2 interactions require Golgi-modified N-glycans at N365D and N381D, whereas reducing N-glycosylation in the endoplasmic reticulum by fluvastatin treatment promoted the recruitment of CD44 and transporters needed to mitigate stress. Thus, SLC3A2 N-glycosylation and Golgi remodeling of the N-glycans have distinct roles in amino acids import for growth, maintenance, and metabolic stresses.
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Affiliation(s)
- Cunjie Zhang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto Ontario, Canada
| | - Massiullah Shafaq-Zadah
- Cellular and Chemical Biology Unit, Institut Curie, INSERM U1143, CNRS UMR3666, PSL Research University, Paris, France
| | - Judy Pawling
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto Ontario, Canada
| | - Geoffrey G Hesketh
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto Ontario, Canada
| | - Estelle Dransart
- Cellular and Chemical Biology Unit, Institut Curie, INSERM U1143, CNRS UMR3666, PSL Research University, Paris, France
| | - Karina Pacholczyk
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto Ontario, Canada
| | - Joseph Longo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ludger Johannes
- Cellular and Chemical Biology Unit, Institut Curie, INSERM U1143, CNRS UMR3666, PSL Research University, Paris, France
| | - James W Dennis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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21
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Wahi A, Manchanda N, Jain P, Jadhav HR. Targeting the epigenetic reader "BET" as a therapeutic strategy for cancer. Bioorg Chem 2023; 140:106833. [PMID: 37683545 DOI: 10.1016/j.bioorg.2023.106833] [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: 07/04/2023] [Revised: 08/22/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
Bromodomain and extraterminal (BET) proteins have the ability to bind to acetylated lysine residues present in both histones and non-histone proteins. This binding is facilitated by the presence of tandem bromodomains. The regulatory role of BET proteins extends to chromatin dynamics, cellular processes, and disease progression. The BET family comprises of BRD 2, 3, 4 and BRDT. The BET proteins are a class of epigenetic readers that regulate the transcriptional activity of a multitude of genes that are involved in the pathogenesis of cancer. Thus, targeting BET proteins has been identified as a potentially efficacious approach for the treatment of cancer. BET inhibitors (BETis) are known to interfere with the binding of BET proteins to acetylated lysine residues of chromatin, thereby leading to the suppression of transcription of several genes, including oncogenic transcription factors. Here in this review, we focus on role of Bromodomain and extra C-terminal (BET) proteins in cancer progression. Furthermore, numerous small-molecule inhibitors with pan-BET activity have been documented, with certain compounds currently undergoing clinical assessment. However, it is apparent that the clinical effectiveness of the present BET inhibitors is restricted, prompting the exploration of novel technologies to enhance their clinical outcomes and mitigate undesired adverse effects. Thus, strategies like development of selective BET-BD1, & BD2 inhibitors, dual and acting BET are also presented in this review and attempts to cover the chemistry needed for proper establishment of designed molecules into BRD have been made. Moreover, the review attempts to summarize the details of research till date and proposes a space for future development of BET inhibitor with diminished side effects. It can be concluded that discovery of isoform selective BET inhibitors can be a way forward in order to develop BET inhibitors with negligible side effects.
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Affiliation(s)
- Abhishek Wahi
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Govt. of NCT of Delhi, Delhi, New Delhi 110017, India
| | - Namish Manchanda
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Govt. of NCT of Delhi, Delhi, New Delhi 110017, India
| | - Priti Jain
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Govt. of NCT of Delhi, Delhi, New Delhi 110017, India.
| | - Hemant R Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani-Pilani Campus, Vidya Vihar Pilani, Rajasthan 333031, India
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22
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El-Kalyoubi S, El-Sebaey SA, Elfeky SM, AL-Ghulikah HA, El-Zoghbi MS. Novel Aminopyrimidine-2,4-diones, 2-Thiopyrimidine-4-ones, and 6-Arylpteridines as Dual-Target Inhibitors of BRD4/PLK1: Design, Synthesis, Cytotoxicity, and Computational Studies. Pharmaceuticals (Basel) 2023; 16:1303. [PMID: 37765111 PMCID: PMC10535864 DOI: 10.3390/ph16091303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Structural-based drug design and solvent-free synthesis were combined to obtain three novel series of 5-arylethylidene-aminopyrimidine-2,4-diones (4, 5a-c, 6a,b), 5-arylethylidene-amino-2-thiopyrimidine-4-ones (7,8), and 6-arylpteridines (9,10) as dual BRD4 and PLK1 inhibitors. MTT assays of synthesized compounds against breast (MDA-MB-231), colorectal (HT-29), and renal (U-937) cancer cells showed excellent-to-good cytotoxic activity, compared to Methotrexate; MDA-MB-231 were the most sensitive cancer cells. The most active compounds were tested against normal Vero cells. Compounds 4 and 7 significantly inhibited BRD4 and PLK1, with IC50 values of 0.029, 0.042 µM, and 0.094, 0.02 µM, respectively, which are nearly comparable to volasertib (IC50 = 0.017 and 0.025 µM). Compound 7 triggered apoptosis and halted cell growth at the G2/M phase, similarly to volasertib. It also upregulated the BAX and caspase-3 markers while downregulating the Bcl-2 gene. Finally, active compounds fitted the volasertib binding site at BRD4 and PLK1 and showed ideal drug-like properties and pharmacokinetics, making them promising anticancer candidates.
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Affiliation(s)
- Samar El-Kalyoubi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Port Said University, Port Said 42511, Egypt
| | - Samiha A. El-Sebaey
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Youssef Abbas Street, Cairo 11754, Egypt
| | - Sherin M. Elfeky
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 355516, Egypt;
| | - Hanan A. AL-Ghulikah
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Mona S. El-Zoghbi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Menoufia University, Menoufia, Gamal Abd Al-Nasir Street, Shibin-Elkom 32511, Egypt;
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23
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Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A Biotin Targeting Chimera (BioTAC) System to Map Small Molecule Interactomes in situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554211. [PMID: 37662262 PMCID: PMC10473607 DOI: 10.1101/2023.08.21.554211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules provide advantages over target-focused approaches, including the ability to detect previously unknown targets, and the inclusion of chemical off-compete controls leading to high-confidence identifications. We describe the BioTAC system, a small-molecule guided proximity labelling platform, to rapidly identify both direct and complexed small molecule binding proteins. The BioTAC system overcomes a limitation of current approaches, and supports identification of both inhibitor bound and molecular glue bound complexes.
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Affiliation(s)
- Andrew J. Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Gillian E. Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Bridget T. Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth J. Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Justin G. English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Fleur M. Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
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24
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Mumby S, Perros F, Grynblat J, Manaud G, Papi A, Casolari P, Caramori G, Humbert M, John Wort S, Adcock IM. Differential responses of pulmonary vascular cells from PAH patients and controls to TNFα and the effect of the BET inhibitor JQ1. Respir Res 2023; 24:193. [PMID: 37516840 PMCID: PMC10386603 DOI: 10.1186/s12931-023-02499-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) encompasses a group of diseases characterized by raised pulmonary vascular resistance, resulting from vascular remodelling and inflammation. Bromodomain and extra-terminal (BET) proteins are required for the expression of a subset of NF-κB-induced inflammatory genes which can be inhibited by the BET mimic JQ1+. We hypothesised that JQ+ would supress TNFα-driven inflammatory responses in human pulmonary vascular cells from PAH patients. METHODS Immunohistochemical staining of human peripheral lung tissue (N = 14 PAH and N = 12 non-PAH) was performed for the BET proteins BRD2 and 4. Human pulmonary microvascular endothelial cells (HPMEC) and pulmonary artery smooth muscle cells (HPASMC) from PAH patients (N = 4) and non-PAH controls (N = 4) were stimulated with TNFα in presence or absence of JQ1+ or its inactive isomer JQ1-. IL-6 and -8 mRNA was measured by RT-qPCR and protein levels by ELISA. Chromatin immunoprecipitation analysis was performed using EZ-ChIP™ and NF-κB p65 activation determined using a TransAm kit. MTT assay was used to measure cell viability. RESULTS Nuclear staining of BRD2 and BRD4 was significantly (p < 0.0001) increased in the lung vascular endothelial and smooth muscle cells from PAH patients compared to controls with normal lung function. TNFα-driven IL-6 release from both HPMECs and HPASMCs was greater in PAH cells than control cells. Levels of CXCL8/IL-8 protein release was higher in PAH HPASMCs than in control cells with similar release observed in HPMECs. TNFα-induced recruitment of activated NF-κB p65 to the IL-6 and CXCL8/IL-8 promoters were similar in both cell types and between subject groups. JQ1+ suppressed TNFα-induced IL-6 and CXCL8/IL-8 release and mRNA expression to a comparable extent in control and PAH HPMECs and HPASMCs. JQ1 had a greater efficacy on IL-6 release in HPMEC and on CXCL8/IL-8 release in HPASMC. CONCLUSION BET inhibition decreases TNFα driven inflammation in primary pulmonary vascular cells. The anti-inflammatory actions of JQ1 suggests distinct cell-specific regulatory control of these genes. BET proteins could be a target for future therapies for PAH.
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Affiliation(s)
- Sharon Mumby
- Respiratory Science, NHLI, Imperial College London, London, UK.
| | - Frederic Perros
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon1, Pierre-Bénite, France
| | - Julien Grynblat
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
| | - Gregoire Manaud
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
| | - Alberto Papi
- Interdepartmental Study Center for Inflammatory and Smoke-Related Airway Diseases, Cardiorespiratory and Internal Medicine Section, University of Ferrara, Ferrara, Italy
| | - Paolo Casolari
- Interdepartmental Study Center for Inflammatory and Smoke-Related Airway Diseases, Cardiorespiratory and Internal Medicine Section, University of Ferrara, Ferrara, Italy
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e Delle Immagini Morfologiche e Funzionali (BIOMORF), Università Degli Studi di Messina, Messina, Italy
| | - Marc Humbert
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
- Department of Respiratory and Intensive Care Medicine, AP-HP, Hôpital Bicêtre, Pulmonary Hypertension National Referral Center, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - S John Wort
- Respiratory Science, NHLI, Imperial College London, London, UK
- National Pulmonary Hypertension Service, Royal Brompton Hospital, London, UK
| | - Ian M Adcock
- Respiratory Science, NHLI, Imperial College London, London, UK
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25
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Kim JH, Pandit N, Yoo M, Park TH, Choi JU, Park CH, Jung KY, Lee BI. Crystal structure of [1,2,4]triazolo[4,3-b]pyridazine derivatives as BRD4 bromodomain inhibitors and structure-activity relationship study. Sci Rep 2023; 13:10805. [PMID: 37402749 DOI: 10.1038/s41598-023-37527-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023] Open
Abstract
BRD4 contains two tandem bromodomains (BD1 and BD2) that recognize acetylated lysine for epigenetic reading, and these bromodomains are promising therapeutic targets for treating various diseases, including cancers. BRD4 is a well-studied target, and many chemical scaffolds for inhibitors have been developed. Research on the development of BRD4 inhibitors against various diseases is actively being conducted. Herein, we propose a series of [1,2,4]triazolo[4,3-b]pyridazine derivatives as bromodomain inhibitors with micromolar IC50 values. We characterized the binding modes by determining the crystal structures of BD1 in complex with four selected inhibitors. Compounds containing [1,2,4] triazolo[4,3-b]pyridazine derivatives offer promising starting molecules for designing potent BRD4 BD inhibitors.
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Affiliation(s)
- Jung-Hoon Kim
- Research Institute, National Cancer Center, Goyang, Gyeonggi, 10408, Republic of Korea
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Gyeonggi, 10408, Republic of Korea
| | - Navin Pandit
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Miyoun Yoo
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Tae Hyun Park
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Ji U Choi
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, 34113, Republic of Korea
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Chi Hoon Park
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.
| | - Kwan-Young Jung
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.
| | - Byung Il Lee
- Research Institute, National Cancer Center, Goyang, Gyeonggi, 10408, Republic of Korea.
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Gyeonggi, 10408, Republic of Korea.
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26
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Divakaran A, Harki DA, Pomerantz WC. Recent progress and structural analyses of domain-selective BET inhibitors. Med Res Rev 2023; 43:972-1018. [PMID: 36971240 PMCID: PMC10520981 DOI: 10.1002/med.21942] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 12/21/2022] [Accepted: 02/26/2023] [Indexed: 03/29/2023]
Abstract
Epigenetic mechanisms for controlling gene expression through heritable modifications to DNA, RNA, and proteins, are essential processes in maintaining cellular homeostasis. As a result of their central role in human diseases, the proteins responsible for adding, removing, or recognizing epigenetic modifications have emerged as viable drug targets. In the case of lysine-ε-N-acetylation (Kac ), bromodomains serve as recognition modules ("readers") of this activating epigenetic mark and competition of the bromodomain-Kac interaction with small-molecule inhibitors is an attractive strategy to control aberrant bromodomain-mediated gene expression. The bromodomain and extra-terminal (BET) family proteins contain eight similar bromodomains. These BET bromodomains are among the more commonly studied bromodomain classes with numerous pan-BET inhibitors showing promising anticancer and anti-inflammatory efficacy. However, these results have yet to translate into Food and Drug Administration-approved drugs, in part due to a high degree of on-target toxicities associated with pan-BET inhibition. Improved selectivity within the BET-family has been proposed to alleviate these concerns. In this review, we analyze the reported BET-domain selective inhibitors from a structural perspective. We highlight three essential characteristics of the reported molecules in generating domain selectivity, binding affinity, and mimicking Kac molecular recognition. In several cases, we provide insight into the design of molecules with improved specificity for individual BET-bromodomains. This review provides a perspective on the current state of the field as this exciting class of inhibitors continue to be evaluated in the clinic.
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Affiliation(s)
- Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN55455, United States
| | - William C.K. Pomerantz
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN55455, United States
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27
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Li M, Liu M, Han W, Wang Z, Han D, Patalano S, Macoska JA, Balk SP, He HH, Corey E, Gao S, Cai C. LSD1 Inhibition Disrupts Super-Enhancer-Driven Oncogenic Transcriptional Programs in Castration-Resistant Prostate Cancer. Cancer Res 2023; 83:1684-1698. [PMID: 36877164 PMCID: PMC10192194 DOI: 10.1158/0008-5472.can-22-2433] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/18/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
The lysine demethylase LSD1 (also called KDM1A) plays important roles in promoting multiple malignancies including both hematologic cancers and solid tumors. LSD1 targets histone and nonhistone proteins and can function as a transcriptional corepressor or coactivator. LSD1 has been reported to act as a coactivator of androgen receptor (AR) in prostate cancer and to regulate the AR cistrome via demethylation of its pioneer factor FOXA1. A deeper understanding of the key oncogenic programs targeted by LSD1 could help stratify prostate cancer patients for treatment with LSD1 inhibitors, which are currently under clinical investigation. In this study, we performed transcriptomic profiling in an array of castration-resistant prostate cancer (CRPC) xenograft models that are sensitive to LSD1 inhibitor treatment. Impaired tumor growth by LSD1 inhibition was attributed to significantly decreased MYC signaling, and MYC was found to be a consistent target of LSD1. Moreover, LSD1 formed a network with BRD4 and FOXA1 and was enriched at super-enhancer regions exhibiting liquid-liquid phase separation. Combining LSD1 inhibitors with BET inhibitors exhibited strong synergy in disrupting the activities of multiple drivers in CRPC, thereby inducing significant growth repression of tumors. Importantly, the combination treatment showed superior effects than either inhibitor alone in disrupting a subset of newly identified CRPC-specific super-enhancers. These results provide mechanistic and therapeutic insights for cotargeting two key epigenetic factors and could be rapidly translated in the clinic for CRPC patients. SIGNIFICANCE LSD1 drives prostate cancer progression by activating super-enhancer-mediated oncogenic programs, which can be targeted with the combination of LSD1 and BRD4 inhibitors to suppress the growth of CRPC.
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Affiliation(s)
- Muqing Li
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
| | - Mingyu Liu
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
| | - Wanting Han
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Washington 98109, USA
| | - Zifeng Wang
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
| | - Dong Han
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
| | - Susan Patalano
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
| | - Jill A. Macoska
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
| | - Steven P. Balk
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Housheng Hansen He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G1L7, Canada
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, M5G1L7, Canada
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington 98195, USA
| | - Shuai Gao
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, New York 10595, USA
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
| | - Changmeng Cai
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
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28
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Li Y, Wang L, Zhang N, Xu Y. CircKCNQ5 controls proliferation, migration, invasion, apoptosis, and glycolysis of multiple myeloma cells by modulating miR-335-5p/BRD4 axis. Histol Histopathol 2023; 38:525-536. [PMID: 35535987 DOI: 10.14670/hh-18-466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) are key players in tumorigenesis progression. However, the role and molecular mechanisms of circKCNQ5 in multiple myeloma (MM) progression remain unclear. METHODS The quantitative real-time polymerase chain reaction was used for examining circKCNQ5, miR-335-5p, and Bromodomain-containing protein 4 (BRD4) levels. The proliferation ability of MM cells was determined by Cell Counting Kit-8 and colony-forming assays. The migration and invasion were analyzed by transwell assay. Flow cytometry was used to assess cell apoptosis. The lactate production, glucose consumption, and ATP/ADP ratios were determined by commercialized kits. The protein levels were quantified by western blot analysis. The interactions between circKCNQ5 and miR-335-5p, along with miR-335-5p and BRD4 were analyzed by dual-luciferase reporter and RNA immunoprecipitation assays. RESULTS The overexpression of circKCNQ5 was confirmed in MM tissues and cells. Importantly, knockdown of circKCNQ5 suppressed proliferation, migration, invasion, and glycolysis while it increased apoptosis of MM cells in vitro. Interestingly, the downregulation of miR-335-5p was able to rescue the circKCNQ5 inhibition-induced effects on MM cells. MiR-335-5p interacted with circKCNQ5, and was able to target BRD4 in MM cells. MiR-335-5p upregulation inhibited malignant phenotypes of MM cells depending on BRD4. CONCLUSION CircKCNQ5 was found to stimulate MM progression through competitively sponging to miR-335-5p.
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Affiliation(s)
- Yan Li
- Department of Hematology, Tianjin Fourth Central Hospital, The Fourth Central Hospital Affiliated to Nankai University, The Fourth Central Clinical College, Tianjin Medical University, Tianjin City, China.
| | - Liang Wang
- Department of Hematology, Tianjin Fourth Central Hospital, The Fourth Central Hospital Affiliated to Nankai University, The Fourth Central Clinical College, Tianjin Medical University, Tianjin City, China
| | - Nan Zhang
- Department of Hematology, Tianjin Fourth Central Hospital, The Fourth Central Hospital Affiliated to Nankai University, The Fourth Central Clinical College, Tianjin Medical University, Tianjin City, China
| | - Yan Xu
- Department of Hematology, Tianjin Fourth Central Hospital, The Fourth Central Hospital Affiliated to Nankai University, The Fourth Central Clinical College, Tianjin Medical University, Tianjin City, China
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29
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Binet R, Lambert JP, Tomkova M, Tischfield S, Baggiolini A, Picaud S, Sarkar S, Louphrasitthiphol P, Dias D, Carreira S, Humphrey T, Fillipakopoulos P, White R, Goding CR. DNA damage-induced interaction between a lineage addiction oncogenic transcription factor and the MRN complex shapes a tissue-specific DNA Damage Response and cancer predisposition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537819. [PMID: 37131595 PMCID: PMC10153263 DOI: 10.1101/2023.04.21.537819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Since genome instability can drive cancer initiation and progression, cells have evolved highly effective and ubiquitous DNA Damage Response (DDR) programs. However, some cells, in skin for example, are normally exposed to high levels of DNA damaging agents. Whether such high-risk cells possess lineage-specific mechanisms that tailor DNA repair to the tissue remains largely unknown. Here we show, using melanoma as a model, that the microphthalmia-associated transcription factor MITF, a lineage addition oncogene that coordinates many aspects of melanocyte and melanoma biology, plays a non-transcriptional role in shaping the DDR. On exposure to DNA damaging agents, MITF is phosphorylated by ATM/DNA-PKcs, and unexpectedly its interactome is dramatically remodelled; most transcription (co)factors dissociate, and instead MITF interacts with the MRE11-RAD50-NBS1 (MRN) complex. Consequently, cells with high MITF levels accumulate stalled replication forks, and display defects in homologous recombination-mediated repair associated with impaired MRN recruitment to DNA damage. In agreement, high MITF levels are associated with increased SNV burden in melanoma. Significantly, the SUMOylation-defective MITF-E318K melanoma predisposition mutation recapitulates the effects of ATM/DNA-PKcs-phosphorylated MITF. Our data suggest that a non-transcriptional function of a lineage-restricted transcription factor contributes to a tissue-specialised modulation of the DDR that can impact cancer initiation.
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Affiliation(s)
- Romuald Binet
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center and Big Data Research Center, Université Laval, Quebec, Canada; Endocrinology – Nephrology Axis, CHU de Québec – Université Laval Research Center, Quebec City, QC, Canada, G1V 4G2
| | - Marketa Tomkova
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Department of Biochemistry and Molecular Medicine, University of California, Davis, USA
| | - Samuel Tischfield
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Arianna Baggiolini
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Sovan Sarkar
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Diogo Dias
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Suzanne Carreira
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Timothy Humphrey
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Panagis Fillipakopoulos
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Richard White
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
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30
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Regulation of Cell Plasticity by Bromodomain and Extraterminal Domain (BET) Proteins: A New Perspective in Glioblastoma Therapy. Int J Mol Sci 2023; 24:ijms24065665. [PMID: 36982740 PMCID: PMC10055343 DOI: 10.3390/ijms24065665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
BET proteins are a family of multifunctional epigenetic readers, mainly involved in transcriptional regulation through chromatin modelling. Transcriptome handling ability of BET proteins suggests a key role in the modulation of cell plasticity, both in fate decision and in lineage commitment during embryonic development and in pathogenic conditions, including cancerogenesis. Glioblastoma is the most aggressive form of glioma, characterized by a very poor prognosis despite the application of a multimodal therapy. Recently, new insights are emerging about the glioblastoma cellular origin, leading to the hypothesis that several putative mechanisms occur during gliomagenesis. Interestingly, epigenome dysregulation associated with loss of cellular identity and functions are emerging as crucial features of glioblastoma pathogenesis. Therefore, the emerging roles of BET protein in glioblastoma onco-biology and the compelling demand for more effective therapeutic strategies suggest that BET family members could be promising targets for translational breakthroughs in glioblastoma treatment. Primarily, “Reprogramming Therapy”, which is aimed at reverting the malignant phenotype, is now considered a promising strategy for GBM therapy.
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31
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Agrahari AK, Srivastava M, Singh M, Asthana S. SARS-CoV-2 envelope protein attain K ac mediated dynamical interaction network to adopt 'histone mimic' at BRD4 interface. J Biomol Struct Dyn 2023; 41:15305-15319. [PMID: 36907648 DOI: 10.1080/07391102.2023.2188430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/27/2023] [Indexed: 03/13/2023]
Abstract
Interface mimicry, achieved by recognition of host-pathogen interactions, is the basis by which pathogen proteins can hijack the host machinery. The envelope (E) protein of SARS-CoV-2 is reported to mimic the histones at the BRD4 surface via establishing the structural mimicry; however, the underlying mechanism of E protein mimicking the histones is still elusive. To explore the mimics at dynamic and structural residual network level an extensive docking, and MD simulations were carried out in a comparative manner between complexes of H3-, H4-, E-, and apo-BRD4. We identified that E peptide is able to attain an 'interaction network mimicry', as its acetylated lysine (Kac) achieves orientation and residual fingerprint similar to histones, including water-mediated interactions for both the Kac positions. We identified Y59 of E, playing an anchor role to escort lysine positioning inside the binding site. Furthermore, the binding site analysis confirms that E peptide needs a higher volume, similar to the H4-BRD4 where both the lysine's (Kac5 and Kac8) can accommodate nicely, however, the position of Kac8 is mimicked by two additional water molecules other than four water-mediated bridging's, strengthening the possibility that E peptide could hijack host BRD4 surface. These molecular insights seem pivotal for mechanistic understanding and BRD4-specific therapeutic intervention. KEY POINTSMolecular mimicry is reported in hijacking and then outcompeting the host counterparts so that pathogens can rewire their cellular function by overcoming the host defense mechanism.The molecular recognition process is the basis of molecular mimicry. The E peptide of SARS-CoV-2 is reported to mimic host histone at the BRD4 surface by utilizing its C-terminally placed acetylated lysine (Kac63) to mimic the N-terminally placed acetylated lysine Kac5GGKac8 histone (H4) by interaction network mimicry identified through microsecond molecular dynamics (MD) simulations and post-processing extensive analysis.There are two steps to mimic: firstly, tyrosine residues help E to anchor at the BRD4 surface to position Kac and increase the volume of the pocket. Secondary, after positioning of Kac, a common durable interaction network N140:Kac5; Kac5:W1; W1:Y97; W1:W2; W2:W3; W3:W4; W4:P82 is established between Kac5, with key residues P82, Y97, N140, and four water molecules through water mediate bridge. Furthermore, the second acetylated lysine Kac8 position and its interaction as polar contact with Kac5 were also mimicked by E peptide through interaction network P82:W5; W5:Kac63; W5:W6; W6:Kac63.The binding event at BRD4/BD1 seems an induced-fit mechanism as a bigger binding site volume was identified at H4-BRD4 on which E peptide attains its better stability than H3-BRD4.We identified the tyrosine residue Y59 of E that acts like an anchor on the BRD4 surface to position Kac inside the pocket and attain the interaction network by using aromatic residues of the BRD4 surface.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| | - Mrityunjay Singh
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Haryana, India
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32
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Mohammed Ismail W, Mazzone A, Ghiraldini FG, Kaur J, Bains M, Munankarmy A, Bagwell MS, Safgren SL, Moore-Weiss J, Buciuc M, Shimp L, Leach KA, Duarte LF, Nagi CS, Carcamo S, Chung CY, Hasson D, Dadgar N, Zhong J, Lee JH, Couch FJ, Revzin A, Ordog T, Bernstein E, Gaspar-Maia A. MacroH2A histone variants modulate enhancer activity to repress oncogenic programs and cellular reprogramming. Commun Biol 2023; 6:215. [PMID: 36823213 PMCID: PMC9950461 DOI: 10.1038/s42003-023-04571-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Considerable efforts have been made to characterize active enhancer elements, which can be annotated by accessible chromatin and H3 lysine 27 acetylation (H3K27ac). However, apart from poised enhancers that are observed in early stages of development and putative silencers, the functional significance of cis-regulatory elements lacking H3K27ac is poorly understood. Here we show that macroH2A histone variants mark a subset of enhancers in normal and cancer cells, which we coined 'macro-Bound Enhancers', that modulate enhancer activity. We find macroH2A variants localized at enhancer elements that are devoid of H3K27ac in a cell type-specific manner, indicating a role for macroH2A at inactive enhancers to maintain cell identity. In following, reactivation of macro-bound enhancers is associated with oncogenic programs in breast cancer and their repressive role is correlated with the activity of macroH2A2 as a negative regulator of BRD4 chromatin occupancy. Finally, through single cell epigenomic profiling of normal mammary stem cells derived from mice, we show that macroH2A deficiency facilitates increased activity of transcription factors associated with stem cell activity.
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Affiliation(s)
- Wazim Mohammed Ismail
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Amelia Mazzone
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Flavia G Ghiraldini
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jagneet Kaur
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Manvir Bains
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Amik Munankarmy
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Monique S Bagwell
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Stephanie L Safgren
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - John Moore-Weiss
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Marina Buciuc
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Lynzie Shimp
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Kelsey A Leach
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Luis F Duarte
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chandandeep S Nagi
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Saul Carcamo
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chi-Yeh Chung
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Neda Dadgar
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Jian Zhong
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Jeong-Heon Lee
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Fergus J Couch
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Tamas Ordog
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandre Gaspar-Maia
- Division of Experimental Pathology, Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
- Center for Individualized Medicine, Epigenomics program, Mayo Clinic, Rochester, MN, USA.
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Zerio CJ, Sivinski J, Wijeratne EMK, Xu YM, Ngo DT, Ambrose AJ, Villa-Celis L, Ghadirian N, Clarkson MW, Zhang DD, Horton NC, Gunatilaka AAL, Fromme R, Chapman E. Physachenolide C is a Potent, Selective BET Inhibitor. J Med Chem 2023; 66:913-933. [PMID: 36577036 DOI: 10.1021/acs.jmedchem.2c01770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A pulldown using a biotinylated natural product of interest in the 17β-hydroxywithanolide (17-BHW) class, physachenolide C (PCC), identified the bromodomain and extra-terminal domain (BET) family of proteins (BRD2, BRD3, and BRD4), readers of acetyl-lysine modifications and regulators of gene transcription, as potential cellular targets. BROMOscan bromodomain profiling and biochemical assays support PCC as a BET inhibitor with increased selectivity for bromodomain (BD)-1 of BRD3 and BRD4, and X-ray crystallography and NMR studies uncovered specific contacts that underlie the potency and selectivity of PCC toward BRD3-BD1 over BRD3-BD2. PCC also displays characteristics of a molecular glue, facilitating proteasome-mediated degradation of BRD3 and BRD4. Finally, PCC is more potent than other withanolide analogues and gold-standard pan-BET inhibitor (+)-JQ1 in cytotoxicity assays across five prostate cancer (PC) cell lines regardless of androgen receptor (AR)-signaling status.
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Affiliation(s)
- Christopher J Zerio
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Jared Sivinski
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - E M Kithsiri Wijeratne
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Ya-Ming Xu
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Duc T Ngo
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Andrew J Ambrose
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Luis Villa-Celis
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Niloofar Ghadirian
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721, United States
| | - Michael W Clarkson
- Department of Chemistry and Biochemistry, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85719, United States
| | - Donna D Zhang
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721, United States
| | - A A Leslie Gunatilaka
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Raimund Fromme
- School of Molecular Sciences, Biodesign Institute, Arizona State University, 1001 S. McAllister Avenue, Tempe, Arizona 85287, United States
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
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34
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Agbo L, Loehr J, Kougnassoukou Tchara PE, Lambert JP. Characterization of the Functional Interplay between the BRD7 and BRD9 Homologues in mSWI/SNF Complexes. J Proteome Res 2023; 22:78-90. [PMID: 36484504 DOI: 10.1021/acs.jproteome.2c00464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bromodomains (BRDs) are a family of evolutionarily conserved domains that are the main readers of acetylated lysine (Kac) residues on proteins. Recently, numerous BRD-containing proteins have been proven essential for transcriptional regulation in numerous contexts. This is exemplified by the multi-subunit mSWI/SNF chromatin remodeling complexes, which incorporate up to 10 BRDs within five distinct subunits, allowing for extensive integration of Kac signaling to inform transcriptional regulation. As dysregulated transcription promotes oncogenesis, we sought to characterize how BRD-containing subunits contribute molecularly to mSWI/SNF functions. By combining genome editing, functional proteomics, and cellular biology, we found that loss of any single BRD-containing mSWI/SNF subunit altered but did not fully disrupt the various mSWI/SNF complexes. In addition, we report that the downregulation of BRD7 is common in invasive lobular carcinoma and modulates the interactome of its homologue, BRD9. We show that these alterations exacerbate sensitivities to inhibitors targeting epigenetic regulators─notably, inhibitors targeting the BRDs of non-mSWI/SNF proteins. Our results highlight the interconnections between distinct mSWI/SNF complexes and their far-reaching impacts on transcriptional regulation in human health and disease. The mass spectrometry data generated have been deposited to MassIVE and ProteomeXchange and assigned the identifiers MSV000089357, MSV000089362, and PXD033572.
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Affiliation(s)
- Lynda Agbo
- Department of Molecular Medicine, Cancer Research Center and Big Data Research Center, Université Laval, Quebec, Canada; CHU de Québec - Université Laval Research Center, Quebec City, QC G1V 4G2, Canada.,Endocrinology - Nephrology Axis, CHU de Québec - Université Laval Research Center, Quebec City, QC G1V 4G2, Canada
| | - Jérémy Loehr
- Department of Molecular Medicine, Cancer Research Center and Big Data Research Center, Université Laval, Quebec, Canada; CHU de Québec - Université Laval Research Center, Quebec City, QC G1V 4G2, Canada.,Endocrinology - Nephrology Axis, CHU de Québec - Université Laval Research Center, Quebec City, QC G1V 4G2, Canada
| | - Pata-Eting Kougnassoukou Tchara
- Department of Molecular Medicine, Cancer Research Center and Big Data Research Center, Université Laval, Quebec, Canada; CHU de Québec - Université Laval Research Center, Quebec City, QC G1V 4G2, Canada.,Endocrinology - Nephrology Axis, CHU de Québec - Université Laval Research Center, Quebec City, QC G1V 4G2, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center and Big Data Research Center, Université Laval, Quebec, Canada; CHU de Québec - Université Laval Research Center, Quebec City, QC G1V 4G2, Canada.,Endocrinology - Nephrology Axis, CHU de Québec - Université Laval Research Center, Quebec City, QC G1V 4G2, Canada
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35
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Eischer N, Arnold M, Mayer A. Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1734. [PMID: 35491403 DOI: 10.1002/wrna.1734] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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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36
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Wong A, Bi C, Chi W, Hu N, Gehring C. Amino acid motifs for the identification of novel protein interactants. Comput Struct Biotechnol J 2022; 21:326-334. [PMID: 36582434 PMCID: PMC9791077 DOI: 10.1016/j.csbj.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Biological systems consist of multiple components of different physical and chemical properties that require complex and dynamic regulatory loops to function efficiently. The discovery of ever more novel interacting sites in complex proteins suggests that we are only beginning to understand how cellular and biological functions are integrated and tuned at the molecular and systems levels. Here we review recently discovered interacting sites which have been identified through rationally designed amino acid motifs diagnostic for specific molecular functions, including enzymatic activities and ligand-binding properties. We specifically discuss the nature of the latter using as examples, novel hormone recognition and gas sensing sites that occur in moonlighting protein complexes. Drawing evidence from the current literature, we discuss the potential implications at the cellular, tissue, and/or organismal levels of such non-catalytic interacting sites and provide several promising avenues for the expansion of amino acid motif searches to discover hitherto unknown protein interactants and interaction networks. We believe this knowledge will unearth unexpected functions in both new and well-characterized proteins, thus filling existing conceptual gaps or opening new avenues for applications either as drug targets or tools in pharmacology, cell biology and bio-catalysis. Beyond this, motif searches may also support the design of novel, effective and sustainable approaches to crop improvements and the development of new therapeutics.
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Affiliation(s)
- Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chuyun Bi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Ningxin Hu
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chris Gehring
- Department of Chemistry, Biology & Biotechnology, University of Perugia, Perugia 06121, Italy
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Zhai LH, Chen KF, Hao BB, Tan MJ. Proteomic characterization of post-translational modifications in drug discovery. Acta Pharmacol Sin 2022; 43:3112-3129. [PMID: 36372853 PMCID: PMC9712763 DOI: 10.1038/s41401-022-01017-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/07/2022] [Indexed: 11/15/2022] Open
Abstract
Protein post-translational modifications (PTMs), which are usually enzymatically catalyzed, are major regulators of protein activity and involved in almost all celluar processes. Dysregulation of PTMs is associated with various types of diseases. Therefore, PTM regulatory enzymes represent as an attractive and important class of targets in drug research and development. Inhibitors against kinases, methyltransferases, deacetyltransferases, ubiquitin ligases have achieved remarkable success in clinical application. Mass spectrometry-based proteomics technologies serve as a powerful approach for system-wide characterization of PTMs, which facilitates the identification of drug targets, elucidation of the mechanisms of action of drugs, and discovery of biomakers in personalized therapy. In this review, we summarize recent advances of proteomics-based studies on PTM targeting drugs and discuss how proteomics strategies facilicate drug target identification, mechanism elucidation, and new therapy development in precision medicine.
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Affiliation(s)
- Lin-Hui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China
| | - Kai-Feng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing-Bing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Min-Jia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China.
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38
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Jiang J, Zhao PL, Sigua LH, Chan A, Schönbrunn E, Qi J, Georg GI. 1,4-Dihydropyridinebutyrolactone-derived ring-opened ester and amide analogs targeting BET bromodomains. Arch Pharm (Weinheim) 2022; 355:e2200288. [PMID: 35941525 PMCID: PMC9633406 DOI: 10.1002/ardp.202200288] [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: 05/29/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 11/11/2022]
Abstract
Based on a previously reported 1,4-dihydropyridinebutyrolactone virtual screening hit, nine lactone ring-opened ester and seven amide analogs were prepared. The analogs were designed to provide interactions with residues at the entrance of the ZA loop of the testis-specific bromodomain (ZA) channel to enhance the affinity and selectivity for the bromodomain and extra-terminal (BET) subfamily of bromodomains. Compound testing by AlphaScreen showed that neither the affinity nor the selectivity of the ester and lactam analogs was improved for BRD4-1 and the first bromodomain of the testis-specific bromodomain (BRDT-1). The esters retained affinity comparable to the parent compound, whereas the affinity for the amide analogs was reduced 10-fold. A representative benzyl ester analog was found to retain high selectivity for BET bromodomains as shown by a BROMOscan. X-ray analysis of the allyl ester analog in complex with BRD4-1 and BRDT-1 revealed that the ester side chain is located next to the ZA loop and solvent exposed.
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Affiliation(s)
- Jiewei Jiang
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Pei-Liang Zhao
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Logan H. Sigua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alice Chan
- Moffitt Cancer Center, Drug Discovery Department, Tampa, FL, USA
| | - Ernst Schönbrunn
- Moffitt Cancer Center, Drug Discovery Department, Tampa, FL, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Gunda I. Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
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Bromodomain-containing protein 4 (BRD4) as an epigenetic regulator of fatty acid metabolism genes and ferroptosis. Cell Death Dis 2022; 13:912. [PMID: 36309482 PMCID: PMC9617950 DOI: 10.1038/s41419-022-05344-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/28/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Reprogramming lipid metabolism is considered a fundamental step in tumourigenesis that influences ferroptosis. However, molecular mechanisms between lipid metabolism and ferroptosis remain largely unknown. Results from the drug screening of 464 inhibitors (for 164 targets) applied to ferroptosis cells indicated that 4 inhibitors targeted bromodomain-containing protein 4 (BRD4) significantly inhibiting erastin-induced ferroptosis. Functional studies proved that the loss of BRD4 weakened oxidative catabolism in mitochondria, protecting cells from the excessive accumulation of lipid peroxides. Mechanism research revealed that the transcriptional levels of fatty acid metabolism-related genes (HADH, ACSL1 and ACAA2) participating in the β-oxidation of fatty acids (FAO) and polyunsaturated fatty acids (PUFAs) synthesis depended on the activity of super-enhancers (SEs) formed by BRD4 and HMGB2 in their promoter regions. Conclusively, this study demonstrated that BRD4 was indispensable for fatty acid metabolism based on its epigenetic regulatory mechanisms and affecting erastin-induced ferroptosis, providing a new theoretical reference for understanding the relationship between lipid metabolism and ferroptosis deeply.
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40
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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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41
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Influence of Shear Stress, Inflammation and BRD4 Inhibition on Human Endothelial Cells: A Holistic Proteomic Approach. Cells 2022; 11:cells11193086. [PMID: 36231049 PMCID: PMC9563250 DOI: 10.3390/cells11193086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Atherosclerosis is an important risk factor in the development of cardiovascular diseases. In addition to increased plasma lipid concentrations, irregular/oscillatory shear stress and inflammatory processes trigger atherosclerosis. Inhibitors of the transcription modulatory bromo- and extra-terminal domain (BET) protein family (BETi) could offer a possible therapeutic approach due to their epigenetic mechanism and anti-inflammatory properties. In this study, the influence of laminar shear stress, inflammation and BETi treatment on human endothelial cells was investigated using global protein expression profiling by ion mobility separation-enhanced data independent acquisition mass spectrometry (IMS-DIA-MS). For this purpose, primary human umbilical cord derived vascular endothelial cells were treated with TNFα to mimic inflammation and exposed to laminar shear stress in the presence or absence of the BRD4 inhibitor JQ1. IMS-DIA-MS detected over 4037 proteins expressed in endothelial cells. Inflammation, shear stress and BETi led to pronounced changes in protein expression patterns with JQ1 having the greatest effect. To our knowledge, this is the first proteomics study on primary endothelial cells, which provides an extensive database for the effects of shear stress, inflammation and BETi on the endothelial proteome.
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42
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Vann KR, Acharya A, Jang SM, Lachance C, Zandian M, Holt TA, Smith AL, Pandey K, Durden DL, El-Gamal D, Côté J, Byrareddy SN, Kutateladze TG. Binding of the SARS-CoV-2 envelope E protein to human BRD4 is essential for infection. Structure 2022; 30:1224-1232.e5. [PMID: 35716662 PMCID: PMC9212912 DOI: 10.1016/j.str.2022.05.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 10/26/2022]
Abstract
Emerging new variants of SARS-CoV-2 and inevitable acquired drug resistance call for the continued search of new pharmacological targets to fight the potentially fatal infection. Here, we describe the mechanisms by which the E protein of SARS-CoV-2 hijacks the human transcriptional regulator BRD4. We found that SARS-CoV-2 E is acetylated in vivo and co-immunoprecipitates with BRD4 in human cells. Bromodomains (BDs) of BRD4 bind to the C-terminus of the E protein, acetylated by human acetyltransferase p300, whereas the ET domain of BRD4 recognizes the unmodified motif of the E protein. Inhibitors of BRD4 BDs, JQ1 or OTX015, decrease SARS-CoV-2 infectivity in lung bronchial epithelial cells, indicating that the acetyllysine binding function of BDs is necessary for the virus fitness and that BRD4 represents a potential anti-COVID-19 target. Our findings provide insight into molecular mechanisms that contribute to SARS-CoV-2 pathogenesis and shed light on a new strategy to block SARS-CoV-2 infection.
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Affiliation(s)
- Kendra R Vann
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Suk Min Jang
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Québec City, QC G1R 3S3, Canada
| | - Catherine Lachance
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Québec City, QC G1R 3S3, Canada
| | - Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Tina A Holt
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Audrey L Smith
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Donald L Durden
- Division of Hematology and Oncology, Department of Pediatrics, Moores Cancer Center, University of California San Diego, La Jolla, CA 92130, USA
| | - Dalia El-Gamal
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Québec City, QC G1R 3S3, Canada.
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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Abstract
Transcription elongation by RNA polymerase II (Pol II) has emerged as a regulatory hub in gene expression. A key control point occurs during early transcription elongation when Pol II pauses in the promoter-proximal region at the majority of genes in mammalian cells and at a large set of genes in Drosophila. An increasing number of trans-acting factors have been linked to promoter-proximal pausing. Some factors help to establish the pause, whereas others are required for the release of Pol II into productive elongation. A dysfunction of this elongation control point leads to aberrant gene expression and can contribute to disease development. The BET bromodomain protein BRD4 has been implicated in elongation control. However, only recently direct BRD4-specific functions in Pol II transcription elongation have been uncovered. This mainly became possible with technological advances that allow selective and rapid ablation of BRD4 in cells along with the availability of approaches that capture the immediate consequences on nascent transcription. This review sheds light on the experimental breakthroughs that led to the emerging view of BRD4 as a general regulator of transcription elongation.
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Affiliation(s)
- Elisabeth Altendorfer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Yelizaveta Mochalova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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44
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Gao C, Glass KC, Frietze S. Functional networks of the human bromodomain-containing proteins. FRONTIERS IN BIOINFORMATICS 2022; 2:835892. [PMID: 36304339 PMCID: PMC9580951 DOI: 10.3389/fbinf.2022.835892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/29/2022] [Indexed: 01/22/2023] Open
Abstract
Background: Bromodomains are a structurally conserved epigenetic reader domain that bind to acetylated lysine residues in both histone and non-histone proteins. Bromodomain-containing proteins (BRD proteins) often function as scaffolding proteins in the assembly of multi-protein complexes to regulate diverse biological processes. BRD proteins have been classified based on biological and functional similarity, however the functions of many BRD proteins remains unknown. PPI network analysis is useful for revealing organizational roles, identifying functional clusters, and predicting function for BRD proteins. Results: We used available data to construct protein-protein interaction networks (PPINs) to study the properties of the human bromodomain protein family. The network properties of the BRD PPIN establishes that the BRD proteins serve as hub proteins that are enriched near the global center to form an inter-connected PPIN. We identified dense subgraphs formed by BRD proteins and find that different BRD proteins share topological similarity and functional associations. We explored the functional relationships through clustering and Hallmark pathway gene set enrichment analysis and identify potential biological roles for different BRD proteins. Conclusion: In our network analysis we confirmed that BRD proteins are conserved central nodes in the human PPI network and function as scaffolds to form distinctive functional clusters. Overall, this study provides detailed insight into the predictive functions of BRD proteins in the context of functional complexes and biological pathways.
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Affiliation(s)
- Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Karen C. Glass
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT, United States,University of Vermont Cancer Center, Burlington, VT, United States
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, United States,University of Vermont Cancer Center, Burlington, VT, United States,*Correspondence: Seth Frietze,
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45
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Chemical biology and pharmacology of histone lysine methylation inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194840. [PMID: 35753676 DOI: 10.1016/j.bbagrm.2022.194840] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 12/20/2022]
Abstract
Histone lysine methylation is a post-translational modification that plays a key role in the epigenetic regulation of a broad spectrum of biological processes. Moreover, the dysregulation of histone lysine methyltransferases (KMTs) has been implicated in the pathogenesis of several diseases particularly cancer. Due to their pathobiological importance, KMTs have garnered immense attention over the last decade as attractive therapeutic targets. These endeavors have culminated in tens of chemical probes that have been used to interrogate many aspects of histone lysine methylation. Besides, over a dozen inhibitors have been advanced to clinical trials, including the EZH2 inhibitor tazemetostat approved for the treatment of follicular lymphoma and advanced epithelioid sarcoma. In this Review, we highlight the chemical biology and pharmacology of KMT inhibitors and targeted protein degraders focusing on the clinical development of EZH1/2, DOT1L, Menin-MLL, and WDR5-MLL inhibitors. We also briefly discuss the pharmacologic targeting of other KMTs.
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46
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Banerjee SL, Lessard F, Chartier FJM, Jacquet K, Osornio-Hernandez AI, Teyssier V, Ghani K, Lavoie N, Lavoie JN, Caruso M, Laprise P, Elowe S, Lambert JP, Bisson N. EPH receptor tyrosine kinases phosphorylate the PAR-3 scaffold protein to modulate downstream signaling networks. Cell Rep 2022; 40:111031. [PMID: 35793621 DOI: 10.1016/j.celrep.2022.111031] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 11/03/2022] Open
Abstract
EPH receptors (EPHRs) constitute the largest family among receptor tyrosine kinases in humans. They are mainly involved in short-range cell-cell communication events that regulate cell adhesion, migration, and boundary formation. However, the molecular mechanisms by which EPHRs control these processes are less understood. To address this, we unravel EPHR-associated complexes under native conditions using mass-spectrometry-based BioID proximity labeling. We obtain a composite proximity network from EPHA4, -B2, -B3, and -B4 that comprises 395 proteins, most of which were not previously linked to EPHRs. We examine the contribution of several BioID-identified candidates via loss-of-function in an EPHR-dependent cell-segregation assay. We find that the signaling scaffold PAR-3 is required for cell sorting and that EPHRs directly phosphorylate PAR-3. We also delineate a signaling complex involving the C-terminal SRC kinase (CSK), whose recruitment to PAR-3 is dependent on EPHR signals. Our work describes signaling networks by which EPHRs regulate cellular phenotypes.
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Affiliation(s)
- Sara L Banerjee
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Frédéric Lessard
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - François J M Chartier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Kévin Jacquet
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
| | - Ana I Osornio-Hernandez
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Valentine Teyssier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Karim Ghani
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
| | - Noémie Lavoie
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Josée N Lavoie
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada
| | - Manuel Caruso
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada
| | - Patrick Laprise
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada
| | - Sabine Elowe
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada; Department of Pediatrics, Université Laval, Québec, QC, Canada
| | - Jean-Philippe Lambert
- Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; Department of Molecular Medicine, Université Laval, Québec, QC, Canada; Centre de recherche en données massives de l'Université Laval, Québec, QC, Canada; Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Endocrinologie-néphrologie, Québec, QC, Canada
| | - Nicolas Bisson
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, QC, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada.
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47
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Xu YY, Ren ZL, Liu XL, Zhang GM, Huang SS, Shi WH, Ye LX, Luo X, Liu SW, Li YL, Yu L. BAP1 loss augments sensitivity to BET inhibitors in cancer cells. Acta Pharmacol Sin 2022; 43:1803-1815. [PMID: 34737422 PMCID: PMC9253001 DOI: 10.1038/s41401-021-00783-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/23/2021] [Indexed: 12/13/2022] Open
Abstract
The tumor suppressor gene BAP1 encodes a widely expressed deubiquitinase for histone H2A. Both hereditary and acquired mutations are associated with multiple cancer types, including cutaneous melanoma (CM), uveal melanoma (UM), and clear cell renal cell carcinoma (ccRCC). However, there is no personalized therapy for BAP1-mutant cancers. Here, we describe an epigenetic drug library screening to identify small molecules that exert selective cytotoxicity against BAP1 knockout CM cells over their isogenic parental cells. Hit characterization reveals that BAP1 loss renders cells more vulnerable to bromodomain and extraterminal (BET) inhibitor-induced transcriptional alterations, G1/G0 cell cycle arrest and apoptosis. The association of BAP1 loss with sensitivity to BET inhibitors is observed in multiple BAP1-deficient cancer cell lines generated by gene editing or derived from patient tumors as well as immunodeficient xenograft and immunocompetent allograft murine models. We demonstrate that BAP1 deubiquitinase activity reduces sensitivity to BET inhibitors. Concordantly, ectopic expression of RING1A or RING1B (H2AK119 E3 ubiquitin ligases) enhances sensitivity to BET inhibitors. The mechanistic study shows that the BET inhibitor OTX015 exerts a more potent suppressive effect on the transcription of various proliferation-related genes, especially MYC, in BAP1 knockout cells than in their isogenic parental cells, primarily by targeting BRD4. Furthermore, ectopic expression of Myc rescues the BET inhibitor-sensitizing effect induced by BAP1 loss. Our study reveals new approaches to specifically suppress BAP1-deficient cancers, including CM, UM, and ccRCC.
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Affiliation(s)
- Yu-Yan Xu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Zhong-Lu Ren
- College of Medical Information Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, China
- Medicinal Information and Real World Engineering Technology Center of Universities, Guangzhou, 510006, China
| | - Xiao-Lian Liu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Gui-Ming Zhang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Si-Si Huang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Wen-Hui Shi
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Lin-Xuan Ye
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xin Luo
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Shu-Wen Liu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yi-Lei Li
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Le Yu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
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48
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Wang C, Xu Q, Zhang X, Day DS, Abraham BJ, Lun K, Chen L, Huang J, Ji X. BRD2 interconnects with BRD3 to facilitate Pol II transcription initiation and elongation to prime promoters for cell differentiation. Cell Mol Life Sci 2022; 79:338. [PMID: 35665862 PMCID: PMC11072765 DOI: 10.1007/s00018-022-04349-4] [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: 02/10/2022] [Revised: 04/20/2022] [Accepted: 05/04/2022] [Indexed: 11/03/2022]
Abstract
The bromodomain and extraterminal motif (BET) proteins are critical drug targets for diseases. The precise functions and relationship of BRD2 with other BET proteins remain elusive mechanistically. Here, we used acute protein degradation and quantitative genomic and proteomic approaches to investigate the primary functions of BRD2 in transcription. We report that BRD2 is required for TAF3-mediated Pol II initiation at promoters with low levels of H3K4me3 and for R-loop suppression during Pol II elongation. Single and double depletion revealed that BRD2 and BRD3 function additively, independently, or perhaps antagonistically in Pol II transcription at different promoters. Furthermore, we found that BRD2 regulates the expression of different genes during embryonic body differentiation processes by promoter priming in embryonic stem cells. Therefore, our results suggest complex interconnections between BRD2 and BRD3 at promoters to fine-tune Pol II initiation and elongation for control of cell state.
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Affiliation(s)
- Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Qiqin Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xianhong Zhang
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Daniel S Day
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, 02142, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, 02142, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kehuan Lun
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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49
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Loehr J, Kougnassoukou Tchara PE, Gonthier K, Noufi C, Linteau N, Audet-Walsh É, Lambert JP. A Nutrient-Based Cellular Model to Characterize Acetylation-Dependent Protein-Protein Interactions. Front Mol Biosci 2022; 9:831758. [PMID: 35402505 PMCID: PMC8984119 DOI: 10.3389/fmolb.2022.831758] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/25/2022] [Indexed: 11/20/2022] Open
Abstract
Cellular homeostasis requires the orderly expression of thousands of transcripts. Gene expression is regulated by numerous proteins that recognize post-translational modifications—in particular, the acetylation of lysine residues (Kac) on histones. In addition to affecting the general condensation state of the chromatin, acetylated histones act as anchor points for bromodomain (BRD)-containing adapter proteins. BRDs are the primary Kac reader domains in humans, and proteins containing them act as chromatin scaffolds that organize large networks of interactions to regulate transcription. To characterize BRD-dependent interaction networks, we established cell lines in which histone acetylation is dependent on acetate supplementation. To do this, we used genome editing to knock out ATP citrate lyase (ACLY), the enzyme responsible for converting citrate to oxaloacetate and acetyl-CoA in the cytoplasm and nucleus. In our cellular model, removing acetate from the culture medium resulted in the rapid catabolism of acetylated histones to restore the nucleocytoplasmic acetyl-CoA pool. Here we report the use of our new model in functional proteomics studies to characterize BRD-dependent interaction networks on the chromatin.
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Affiliation(s)
- Jérémy Loehr
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, QC, Canada
- CHU de Québec Research Center, Quebec, QC, Canada
| | - Pata-Eting Kougnassoukou Tchara
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, QC, Canada
- CHU de Québec Research Center, Quebec, QC, Canada
- Big Data Research Center, Université Laval, Quebec, QC, Canada
| | - Kevin Gonthier
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, QC, Canada
- CHU de Québec Research Center, Quebec, QC, Canada
| | - Chahinez Noufi
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, QC, Canada
- CHU de Québec Research Center, Quebec, QC, Canada
| | - Naomie Linteau
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, QC, Canada
- CHU de Québec Research Center, Quebec, QC, Canada
| | - Étienne Audet-Walsh
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, QC, Canada
- CHU de Québec Research Center, Quebec, QC, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, QC, Canada
- CHU de Québec Research Center, Quebec, QC, Canada
- Big Data Research Center, Université Laval, Quebec, QC, Canada
- *Correspondence: Jean-Philippe Lambert,
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50
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Alerasool N, Leng H, Lin ZY, Gingras AC, Taipale M. Identification and functional characterization of transcriptional activators in human cells. Mol Cell 2022; 82:677-695.e7. [PMID: 35016035 DOI: 10.1016/j.molcel.2021.12.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/04/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022]
Abstract
Transcription is orchestrated by thousands of transcription factors (TFs) and chromatin-associated proteins, but how these are causally connected to transcriptional activation is poorly understood. Here, we conduct an unbiased proteome-scale screen to systematically uncover human proteins that activate transcription in a natural chromatin context. By combining interaction proteomics and chemical inhibitors, we delineate the preference of these transcriptional activators for specific co-activators, highlighting how even closely related TFs can function via distinct cofactors. We also identify potent transactivation domains among the hits and use AlphaFold2 to predict and experimentally validate interaction interfaces of two activation domains with BRD4. Finally, we show that many novel activators are partners in fusion events in tumors and functionally characterize a myofibroma-associated fusion between SRF and C3orf62, a potent p300-dependent activator. Our work provides a functional catalog of potent transactivators in the human proteome and a platform for discovering transcriptional regulators at genome scale.
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Affiliation(s)
- Nader Alerasool
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - He Leng
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada.
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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