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Breindl M, Spitzer D, Gerasimaitė R, Kairys V, Schubert T, Henfling R, Schwartz U, Lukinavičius G, Manelytė L. Biochemical and cellular insights into the Baz2B protein, a non-catalytic subunit of the chromatin remodeling complex. Nucleic Acids Res 2024; 52:337-354. [PMID: 38000389 PMCID: PMC10783490 DOI: 10.1093/nar/gkad1096] [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: 02/20/2023] [Revised: 09/21/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Baz2B is a regulatory subunit of the ATP-dependent chromatin remodeling complexes BRF1 and BRF5, which control access to DNA during DNA-templated processes. Baz2B has been implicated in several diseases and also in unhealthy ageing, however limited information is available on the domains and cellular roles of Baz2B. To gain more insight into the Baz2B function, we biochemically characterized the TAM (Tip5/ARBP/MBD) domain with the auxiliary AT-hook motifs and the bromodomain (BRD). We observed alterations in histone code recognition in bromodomains carrying cancer-associated point mutations, suggesting their potential involvement in disease. Furthermore, the depletion of Baz2B in the Hap1 cell line resulted in altered cell morphology, reduced colony formation and perturbed transcriptional profiles. Despite that, super-resolution microscopy images revealed no changes in the overall chromatin structure in the absence of Baz2B. These findings provide insights into the biological function of Baz2B.
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Affiliation(s)
- Matthias Breindl
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Dominika Spitzer
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Visvaldas Kairys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | | | - Ramona Henfling
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Uwe Schwartz
- NGS Analysis Center, University of Regensburg, Regensburg DE-93053, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Laura Manelytė
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
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2
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Wernersson S, Bobby R, Flavell L, Milbradt AG, Holdgate GA, Embrey KJ, Akke M. Bromodomain Interactions with Acetylated Histone 4 Peptides in the BRD4 Tandem Domain: Effects on Domain Dynamics and Internal Flexibility. Biochemistry 2022; 61:2303-2318. [PMID: 36215732 PMCID: PMC9631989 DOI: 10.1021/acs.biochem.2c00226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The bromodomain and extra-terminal (BET) protein BRD4
regulates
gene expression via recruitment of transcriptional regulatory complexes
to acetylated chromatin. Like other BET proteins, BRD4 contains two
bromodomains, BD1 and BD2, that can interact cooperatively with target
proteins and designed ligands, with important implications for drug
discovery. Here, we used nuclear magnetic resonance (NMR) spectroscopy
to study the dynamics and interactions of the isolated bromodomains,
as well as the tandem construct including both domains and the intervening
linker, and investigated the effects of binding a tetra-acetylated
peptide corresponding to the tail of histone 4. The peptide affinity
is lower for both domains in the tandem construct than for the isolated
domains. Using 15N spin relaxation, we determined the global
rotational correlation times and residue-specific order parameters
for BD1 and BD2. Isolated BD1 is monomeric in the apo state but apparently
dimerizes upon binding the tetra-acetylated peptide. Isolated BD2
partially dimerizes in both the apo and peptide-bound states. The
backbone order parameters reveal marked differences between BD1 and
BD2, primarily in the acetyl-lysine binding site where the ZA loop
is more flexible in BD2. Peptide binding reduces the order parameters
of the ZA loop in BD1 and the ZA and BC loops in BD2. The AB loop,
located distally from the binding site, shows variable dynamics that
reflect the different dimerization propensities of the domains. These
results provide a basis for understanding target recognition by BRD4.
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Affiliation(s)
- Sven Wernersson
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Romel Bobby
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Liz Flavell
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge Science Park, CambridgeCB4 0WG, U.K
| | - Alexander G Milbradt
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Geoffrey A Holdgate
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Kevin J Embrey
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
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3
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Liang Y, Tian J, Wu T. BRD4 in physiology and pathology: ''BET'' on its partners. Bioessays 2021; 43:e2100180. [PMID: 34697817 DOI: 10.1002/bies.202100180] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 12/20/2022]
Abstract
Bromodomain-containing 4 (BRD4), a member of Bromo and Extra-Terminal (BET) family, recognizes acetylated histones and is of importance in transcription, replication, and DNA repair. It also binds non-histone proteins, DNA and RNA, contributing to development, tissue growth, and various physiological processes. Additionally, BRD4 has been implicated in driving diverse diseases, ranging from cancer, viral infection, inflammation to neurological disorders. Inhibiting its functions with BET inhibitors (BETis) suppresses the progression of several types of cancer, creating an impetus for translating these chemicals to the clinic. The diverse roles of BRD4 are largely dependent on its interaction partners in different contexts. In this review we discuss the molecular mechanisms of BRD4 with its interacting partners in physiology and pathology. Current development of BETis is also summarized. Further understanding the functions of BRD4 and its partners will facilitate resolving the liabilities of present BETis and accelerate their clinical translation.
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Affiliation(s)
- Yin Liang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Jieyi Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Tao Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
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4
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A Glimpse into the Structural Properties of the Intermediate and Transition State in the Folding of Bromodomain 2 Domain 2 by Φ Value Analysis. Int J Mol Sci 2021; 22:ijms22115953. [PMID: 34073056 PMCID: PMC8199192 DOI: 10.3390/ijms22115953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 11/23/2022] Open
Abstract
Bromodomains (BRDs) are small protein interaction modules of about 110 amino acids that selectively recognize acetylated lysine in histones and other proteins. These domains have been identified in a variety of multi-domain proteins involved in transcriptional regulation or chromatin remodeling in eukaryotic cells. BRD inhibition is considered an attractive therapeutic approach in epigenetic disorders, particularly in oncology. Here, we present a Φ value analysis to investigate the folding pathway of the second domain of BRD2 (BRD2(2)). Using an extensive mutational analysis based on 25 site-directed mutants, we provide structural information on both the intermediate and late transition state of BRD2(2). The data reveal that the C-terminal region represents part of the initial folding nucleus, while the N-terminal region of the domain consolidates its structure only later in the folding process. Furthermore, only a small number of native-like interactions have been identified, suggesting the presence of a non-compact, partially folded state with scarce native-like characteristics. Taken together, these results indicate that, in BRD2(2), a hierarchical mechanism of protein folding can be described with non-native interactions that play a significant role in folding.
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5
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Petrosino M, Novak L, Pasquo A, Chiaraluce R, Turina P, Capriotti E, Consalvi V. Analysis and Interpretation of the Impact of Missense Variants in Cancer. Int J Mol Sci 2021; 22:ijms22115416. [PMID: 34063805 PMCID: PMC8196604 DOI: 10.3390/ijms22115416] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/03/2021] [Accepted: 05/17/2021] [Indexed: 01/10/2023] Open
Abstract
Large scale genome sequencing allowed the identification of a massive number of genetic variations, whose impact on human health is still unknown. In this review we analyze, by an in silico-based strategy, the impact of missense variants on cancer-related genes, whose effect on protein stability and function was experimentally determined. We collected a set of 164 variants from 11 proteins to analyze the impact of missense mutations at structural and functional levels, and to assess the performance of state-of-the-art methods (FoldX and Meta-SNP) for predicting protein stability change and pathogenicity. The result of our analysis shows that a combination of experimental data on protein stability and in silico pathogenicity predictions allowed the identification of a subset of variants with a high probability of having a deleterious phenotypic effect, as confirmed by the significant enrichment of the subset in variants annotated in the COSMIC database as putative cancer-driving variants. Our analysis suggests that the integration of experimental and computational approaches may contribute to evaluate the risk for complex disorders and develop more effective treatment strategies.
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Affiliation(s)
- Maria Petrosino
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
| | - Leonore Novak
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
| | - Alessandra Pasquo
- ENEA CR Frascati, Diagnostics and Metrology Laboratory FSN-TECFIS-DIM, 00044 Frascati, Italy;
| | - Roberta Chiaraluce
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
| | - Paola Turina
- Dipartimento di Farmacia e Biotecnologie (FaBiT), University of Bologna, 40126 Bologna, Italy;
| | - Emidio Capriotti
- Dipartimento di Farmacia e Biotecnologie (FaBiT), University of Bologna, 40126 Bologna, Italy;
- Correspondence: (E.C.); (V.C.)
| | - Valerio Consalvi
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
- Correspondence: (E.C.); (V.C.)
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6
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Raich L, Meier K, Günther J, Christ CD, Noé F, Olsson S. Discovery of a hidden transient state in all bromodomain families. Proc Natl Acad Sci U S A 2021; 118:e2017427118. [PMID: 33468647 PMCID: PMC7848705 DOI: 10.1073/pnas.2017427118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bromodomains (BDs) are small protein modules that interact with acetylated marks in histones. These posttranslational modifications are pivotal to regulate gene expression, making BDs promising targets to treat several diseases. While the general structure of BDs is well known, their dynamical features and their interplay with other macromolecules are poorly understood, hampering the rational design of potent and selective inhibitors. Here, we combine extensive molecular dynamics simulations, Markov state modeling, and available structural data to reveal a transiently formed state that is conserved across all BD families. It involves the breaking of two backbone hydrogen bonds that anchor the ZA-loop with the αA helix, opening a cryptic pocket that partially occludes the one associated to histone binding. By analyzing more than 1,900 experimental structures, we unveil just two adopting the hidden state, explaining why it has been previously unnoticed and providing direct structural evidence for its existence. Our results suggest that this state is an allosteric regulatory switch for BDs, potentially related to a recently unveiled BD-DNA-binding mode.
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Affiliation(s)
- Lluís Raich
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Katharina Meier
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 42096 Wuppertal, Germany
| | - Judith Günther
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Clara D Christ
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany;
- Department of Chemistry, Rice University, Houston, TX 77005
| | - Simon Olsson
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany;
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Nasim MM, Chalif DJ, Demopoulos AM, Brody J, Lee-Huang R, Spitzer SG, Kolitz JE, Zhang X. Primary Low-Grade B-Cell Lymphoma of Skull With Translocation Between Immunoglobulin and Interferon Regulatory Factor 4 Genes. Int J Surg Pathol 2019; 28:330-335. [DOI: 10.1177/1066896919883013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Low-grade B-cell lymphoma with immunoglobulin ( IG) and interferon regulatory factor 4 ( IRF4) gene rearrangement is extremely rare, with only 4 cases being previously reported. In this article, we report one additional case that arises from the skull and review the literature. The patient was a 69-year-old man who presented with recurrent and disabling vertigo and was found to have a 5.0 × 1.7 cm lesion within the left posterior parietal bone. Histological examination revealed a bone lesion with diffuse lymphoid infiltrate comprising of mostly small lymphocytes with scant cytoplasm, slightly irregular nuclei and inconspicuous nucleoli, and scattered larger cells resembling prolymphocytes and paraimmunoblasts. Immunohistochemical studies showed that the neoplastic cells were positive for CD20, CD79a, PAX5, CD23, CD43, BCL-2, BCL-6, MUM-1, LEF-1, and IgM and negative for CD5, CD10, cyclinD1, SOX11, and IgD. Flow cytometric analysis identified CD5 negative and CD10 negative monoclonal B cells with lambda light chain restriction. Fluorescence in situ hybridization analysis revealed del(13q) abnormality, but was negative for IGH/BCL2, IGH/CCND1, and BIRC3/MALT1 translocations. Next-generation sequencing identified IGK-IRF4 rearrangement and BRD4 E1113 del abnormalities. Given a low clinical stage (IE) of the disease, the patient did not receive additional treatments and was free of disease at 1 year after the diagnosis.
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Affiliation(s)
- Mansoor M. Nasim
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Lake Success, NY, USA
| | - David J. Chalif
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Lake Success, NY, USA
| | - Alexis M. Demopoulos
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Lake Success, NY, USA
| | - Judith Brody
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Lake Success, NY, USA
| | - Rova Lee-Huang
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Lake Success, NY, USA
| | - Silvia G. Spitzer
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Lake Success, NY, USA
| | - Jonathan E. Kolitz
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Lake Success, NY, USA
| | - Xinmin Zhang
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Lake Success, NY, USA
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8
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Petrosino M, Pasquo A, Novak L, Toto A, Gianni S, Mantuano E, Veneziano L, Minicozzi V, Pastore A, Puglisi R, Capriotti E, Chiaraluce R, Consalvi V. Characterization of human frataxin missense variants in cancer tissues. Hum Mutat 2019; 40:1400-1413. [PMID: 31074541 PMCID: PMC6744310 DOI: 10.1002/humu.23789] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/17/2019] [Accepted: 05/06/2019] [Indexed: 12/19/2022]
Abstract
Human frataxin is an iron-binding protein involved in the mitochondrial iron-sulfur (Fe-S) clusters assembly, a process fundamental for the functional activity of mitochondrial proteins. Decreased level of frataxin expression is associated with the neurodegenerative disease Friedreich ataxia. Defective function of frataxin may cause defects in mitochondria, leading to increased tumorigenesis. Tumor-initiating cells show higher iron uptake, a decrease in iron storage and a reduced Fe-S clusters synthesis and utilization. In this study, we selected, from COSMIC database, the somatic human frataxin missense variants found in cancer tissues p.D104G, p.A107V, p.F109L, p.Y123S, p.S161I, p.W173C, p.S181F, and p.S202F to analyze the effect of the single amino acid substitutions on frataxin structure, function, and stability. The spectral properties, the thermodynamic and the kinetic stability, as well as the molecular dynamics of the frataxin missense variants found in cancer tissues point to local changes confined to the environment of the mutated residues. The global fold of the variants is not altered by the amino acid substitutions; however, some of the variants show a decreased stability and a decreased functional activity in comparison with that of the wild-type protein.
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Affiliation(s)
- Maria Petrosino
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
- Current address: IRCCS Istituto Neurologico Carlo Besta, Milano, Italia
- European Brain Research Institute-Fondazione Rita Levi Montalcini, Roma, Italia
| | - Alessandra Pasquo
- ENEA CR Frascati, Diagnostics and Metrology Laboratory,FSN-TECFIS-DIM, Frascati, Italy
| | - Leonore Novak
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Elide Mantuano
- Institute of Translational Pharmacology, CNR, Rome, Italy
| | | | - Velia Minicozzi
- INFN and Department of Physics, University of Rome Tor Vergata, Rome, Italy
| | - Annalisa Pastore
- The Wohl Institute, King’s College London, London, United Kingdom
| | - Rita Puglisi
- The Wohl Institute, King’s College London, London, United Kingdom
| | - Emidio Capriotti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Roberta Chiaraluce
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
| | - Valerio Consalvi
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”. Sapienza University of Rome, Rome, Italy
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9
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Emerging roles of and therapeutic strategies targeting BRD4 in cancer. Cell Immunol 2019; 337:48-53. [PMID: 30832981 DOI: 10.1016/j.cellimm.2019.02.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/27/2019] [Accepted: 02/02/2019] [Indexed: 12/12/2022]
Abstract
The Bromodomain and Extra-terminal (BET) family of proteins were first recognized as important epigenetic regulators in inflammatory processes; however, there is increasing evidence to support the notion that BET proteins also play a critical role in 'reading' chromatin and recruiting chromatin-regulating enzymes to control gene expression in a number of pathologic processes, including cancer. To this end, the mechanisms by which BET proteins regulate chromatin remodeling and promote tumor-associated inflammation have been heavily studied over the past decade. This article to review the biology of BET protein dysfunction in promoting tumor-associated inflammation and cancer progression and the application of small molecule inhibitors that target specific BET proteins, alone or in combination with immunomodulatory agents as a novel therapeutic strategy for cancer patients.
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10
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Mio C, Bulotta S, Russo D, Damante G. Reading Cancer: Chromatin Readers as Druggable Targets for Cancer Treatment. Cancers (Basel) 2019; 11:cancers11010061. [PMID: 30634442 PMCID: PMC6356452 DOI: 10.3390/cancers11010061] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/30/2018] [Accepted: 01/03/2019] [Indexed: 02/07/2023] Open
Abstract
The epigenetic machinery deputed to control histone post-translational modifications is frequently dysregulated in cancer cells. With epigenetics being naturally reversible, it represents a good target for therapies directed to restore normal gene expression. Since the discovery of Bromodomain and Extra Terminal (BET) inhibitors, a great effort has been spent investigating the effects of chromatin readers’ inhibition, specifically the class of proteins assigned to bind acetylated and methylated residues. So far, focused studies have been produced on epigenetic regulation, dissecting a specific class of epigenetic-related proteins or investigating epigenetic therapy in a specific tumor type. In this review, recent steps toward drug discovery on the different classes of chromatin readers have been outlined, highlighting the pros and cons of current therapeutic approaches.
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Affiliation(s)
- Catia Mio
- Department of Medical Area, University of Udine, 33100 Udine, Italy.
| | - Stefania Bulotta
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| | - Diego Russo
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| | - Giuseppe Damante
- Department of Medical Area, University of Udine, 33100 Udine, Italy.
- Medical Genetics Institute, University Hospital of Udine, 33100 Udine, Italy.
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11
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Fiorillo A, Petrosino M, Ilari A, Pasquo A, Cipollone A, Maggi M, Chiaraluce R, Consalvi V. The phosphoglycerate kinase 1 variants found in carcinoma cells display different catalytic activity and conformational stability compared to the native enzyme. PLoS One 2018; 13:e0199191. [PMID: 29995887 PMCID: PMC6040698 DOI: 10.1371/journal.pone.0199191] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/02/2018] [Indexed: 01/18/2023] Open
Abstract
Cancer cells are able to survive in difficult conditions, reprogramming their metabolism according to their requirements. Under hypoxic conditions they shift from oxidative phosphorylation to aerobic glycolysis, a behavior known as Warburg effect. In the last years, glycolytic enzymes have been identified as potential targets for alternative anticancer therapies. Recently, phosphoglycerate kinase 1 (PGK1), an ubiquitous enzyme expressed in all somatic cells that catalyzes the seventh step of glycolysis which consists of the reversible phosphotransfer reaction from 1,3-bisphosphoglycerate to ADP, has been discovered to be overexpressed in many cancer types. Moreover, several somatic variants of PGK1 have been identified in tumors. In this study we analyzed the effect of the single nucleotide variants found in cancer tissues on the PGK1 structure and function. Our results clearly show that the variants display a decreased catalytic efficiency and/or thermodynamic stability and an altered local tertiary structure, as shown by the solved X-ray structures. The changes in the catalytic properties and in the stability of the PGK1 variants, mainly due to the local changes evidenced by the X-ray structures, suggest also changes in the functional role of PGK to support the biosynthetic need of the growing and proliferating tumour cells.
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Affiliation(s)
- Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Maria Petrosino
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Andrea Ilari
- CNR-Institute of Molecular Biology and Pathology, Rome, Italy
| | - Alessandra Pasquo
- ENEA CR Frascati, Diagnostics and Metrology Laboratory, FSN-TECFIS-DIM, Frascati, Italy
| | - Alessandra Cipollone
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Maristella Maggi
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
| | - Roberta Chiaraluce
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Valerio Consalvi
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
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12
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Stirnweiss A, Oommen J, Kotecha RS, Kees UR, Beesley AH. Molecular-genetic profiling and high-throughput in vitro drug screening in NUT midline carcinoma-an aggressive and fatal disease. Oncotarget 2017; 8:112313-112329. [PMID: 29348827 PMCID: PMC5762512 DOI: 10.18632/oncotarget.22862] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 11/26/2017] [Indexed: 12/11/2022] Open
Abstract
NUT midline carcinoma (NMC) is a rare and aggressive cancer, with survival typically less than seven months, that can arise in people of any age. Genetically, NMC is defined by the chromosomal fusion of NUTM1 with a chromatin-binding partner, typically the bromodomain-containing protein BRD4. However, little is known about other genetic aberrations in this disease. In this study, we used a unique panel of cell lines to describe the molecular-genetic features of NMC. Next-generation sequencing identified a recurring high-impact mutation in the DNA-helicase gene RECQL5 in 75% of lines studied, and biological signals from mutation-signature and network analyses consistent with a general failure in DNA-repair. A high-throughput drug screen confirmed that microtubule inhibitors, topoisomerase inhibitors and anthracyclines are highly cytotoxic in the majority of NMC lines, and that cell lines expressing the BRD4-NUTM1 (exon11:exon2) variant are an order of magnitude more responsive to bromodomain inhibitors (iBETs) on average than those with other BRD4-NUTM1 translocation variants. We also identified a highly significant correlation between iBET and aurora kinase inhibitor efficacy in this study. Integration of exome sequencing, transcriptome, and drug sensitivity profiles suggested that aberrant activity of the nuclear receptor co-activator NCOA3 may correlate with poor response to iBETs. In conclusion, our data emphasize the heterogeneity of NMC and highlights genetic aberrations that could be explored to improve therapeutic strategies. The novel finding of a recurring RECQL5 mutation, together with recent reports of chromoplexy in this disease, suggests that DNA-repair pathways are likely to play a central role in NMC tumorigenesis.
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Affiliation(s)
- Anja Stirnweiss
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia.,Drug Discovery Group, Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Joyce Oommen
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Rishi S Kotecha
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia.,Department of Haematology and Oncology, Princess Margaret Hospital for Children, Perth, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - Ursula R Kees
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Alex H Beesley
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia
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Bromodomain-containing Protein 4 Activates Voltage-gated Sodium Channel 1.7 Transcription in Dorsal Root Ganglia Neurons to Mediate Thermal Hyperalgesia in Rats. Anesthesiology 2017; 127:862-877. [DOI: 10.1097/aln.0000000000001809] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Background
Bromodomain-containing protein 4 binds acetylated promoter histones and promotes transcription; however, the role of bromodomain-containing protein 4 in inflammatory hyperalgesia remains unclear.
Methods
Male Sprague–Dawley rats received hind paw injections of complete Freund’s adjuvant to induce hyperalgesia. The dorsal root ganglia were examined to detect changes in bromodomain-containing protein 4 expression and the activation of genes involved in the expression of voltage-gated sodium channel 1.7, which is a key pain-related ion channel.
Results
The intraplantar complete Freund’s adjuvant injections resulted in thermal hyperalgesia (4.0 ± 1.5 s; n = 7). The immunohistochemistry and immunoblotting results demonstrated an increase in the bromodomain-containing protein 4–expressing dorsal root ganglia neurons (3.78 ± 0.38 fold; n = 7) and bromodomain-containing protein 4 protein levels (2.62 ± 0.39 fold; n = 6). After the complete Freund’s adjuvant injection, histone H3 protein acetylation was enhanced in the voltage-gated sodium channel 1.7 promoter, and cyclin-dependent kinase 9 and phosphorylation of RNA polymerase II were recruited to this area. Furthermore, the voltage-gated sodium channel 1.7–mediated currents were enhanced in neurons of the complete Freund’s adjuvant rats (55 ± 11 vs. 19 ± 9 pA/pF; n = 4 to 6 neurons). Using bromodomain-containing protein 4–targeted antisense small interfering RNA to the complete Freund’s adjuvant–treated rats, the authors demonstrated a reduction in the expression of bromodomain-containing protein 4 (0.68 ± 0.16 fold; n = 7), a reduction in thermal hyperalgesia (7.5 ± 1.5 s; n = 7), and a reduction in the increased voltage-gated sodium channel 1.7 currents (21 ± 4 pA/pF; n = 4 to 6 neurons).
Conclusions
Complete Freund’s adjuvant triggers enhanced bromodomain-containing protein 4 expression, ultimately leading to the enhanced excitability of nociceptive neurons and thermal hyperalgesia. This effect is likely mediated by the enhanced expression of voltage-gated sodium channel 1.7.
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Petrosino M, Bonetti D, Pasquo A, Lori L, Chiaraluce R, Consalvi V, Travaglini-Allocatelli C. Unveiling the folding mechanism of the Bromodomains. Biochem Biophys Rep 2017; 11:99-104. [PMID: 28955774 PMCID: PMC5614698 DOI: 10.1016/j.bbrep.2017.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/19/2022] Open
Abstract
Bromodomains (BRDs) are small protein domains often present in large multidomain proteins involved in transcriptional regulation in eukaryotic cells. They currently represent valuable targets for the development of inhibitors of aberrant transcriptional processes in a variety of human diseases. Here we report urea-induced equilibrium unfolding experiments monitored by circular dichroism (CD) and fluorescence on two structurally similar BRDs: BRD2(2) and BRD4(1), showing that BRD4(1) is more stable than BRD2(2). Moreover, we report a description of their kinetic folding mechanism, as obtained by careful analysis of stopped-flow and temperature-jump data. The presence of a high energy intermediate for both proteins, suggested by the non-linear dependence of the folding rate on denaturant concentration in the millisec time regime, has been experimentally observed by temperature-jump experiments. Quantitative global analysis of all the rate constants obtained over a wide range of urea concentrations, allowed us to propose a common, three-state, folding mechanism for these two BRDs. Interestingly, the intermediate of BRD4(1) appears to be more stable and structurally native-like than that populated by BRD2(2). Our results underscore the role played by structural topology and sequence in determining and tuning the folding mechanism. A three-state mechanism for the folding of two representative Bromodomains is proposed. Global analyses of BRD2(2) and BRD4(1) folding kinetics highlights the presence of an on-pathway, folding intermediate. The folding intermediate of BRD4(1) is proposed to be more native-like than that of BRD2(2).
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Affiliation(s)
- Maria Petrosino
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università di Roma “Sapienza”, P.le A. Moro 5, 00185 Rome, Italy
| | - Daniela Bonetti
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università di Roma “Sapienza”, P.le A. Moro 5, 00185 Rome, Italy
| | | | - Laura Lori
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università di Roma “Sapienza”, P.le A. Moro 5, 00185 Rome, Italy
| | - Roberta Chiaraluce
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università di Roma “Sapienza”, P.le A. Moro 5, 00185 Rome, Italy
| | - Valerio Consalvi
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università di Roma “Sapienza”, P.le A. Moro 5, 00185 Rome, Italy
| | - Carlo Travaglini-Allocatelli
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università di Roma “Sapienza”, P.le A. Moro 5, 00185 Rome, Italy
- Corresponding author.
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15
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Single-Nucleotide Polymorphism of PPARγ, a Protein at the Crossroads of Physiological and Pathological Processes. Int J Mol Sci 2017; 18:ijms18020361. [PMID: 28208577 PMCID: PMC5343896 DOI: 10.3390/ijms18020361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/24/2017] [Accepted: 02/01/2017] [Indexed: 01/28/2023] Open
Abstract
Genome polymorphisms are responsible for phenotypic differences between humans and for individual susceptibility to genetic diseases and therapeutic responses. Non-synonymous single-nucleotide polymorphisms (nsSNPs) lead to protein variants with a change in the amino acid sequence that may affect the structure and/or function of the protein and may be utilized as efficient structural and functional markers of association to complex diseases. This study is focused on nsSNP variants of the ligand binding domain of PPARγ a nuclear receptor in the superfamily of ligand inducible transcription factors that play an important role in regulating lipid metabolism and in several processes ranging from cellular differentiation and development to carcinogenesis. Here we selected nine nsSNPs variants of the PPARγ ligand binding domain, V290M, R357A, R397C, F360L, P467L, Q286P, R288H, E324K, and E460K, expressed in cancer tissues and/or associated with partial lipodystrophy and insulin resistance. The effects of a single amino acid change on the thermodynamic stability of PPARγ, its spectral properties, and molecular dynamics have been investigated. The nsSNPs PPARγ variants show alteration of dynamics and tertiary contacts that impair the correct reciprocal positioning of helices 3 and 12, crucially important for PPARγ functioning.
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