1
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Arimura Y, Konishi HA, Funabiki H. MagIC-Cryo-EM: Structural determination on magnetic beads for scarce macromolecules in heterogeneous samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.21.576499. [PMID: 38328033 PMCID: PMC10849486 DOI: 10.1101/2024.01.21.576499] [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
Cryo-EM single-particle analyses typically require target macromolecule concentration at 0.05~5.0 mg/ml, which is often difficult to achieve. Here, we devise Magnetic Isolation and Concentration (MagIC)-cryo-EM, a technique enabling direct structural analysis of targets captured on magnetic beads, thereby reducing the targets' concentration requirement to < 0.0005 mg/ml. Adapting MagIC-cryo-EM to a Chromatin Immunoprecipitation protocol, we characterized structural variations of the linker histone H1.8-associated nucleosomes that were isolated from interphase and metaphase chromosomes in Xenopus egg extract. Combining Duplicated Selection To Exclude Rubbish particles (DuSTER), a particle curation method that removes low signal-to-noise ratio particles, we also resolved the 3D cryo-EM structures of H1.8-bound nucleoplasmin NPM2 isolated from interphase chromosomes and revealed distinct open and closed structural variants. Our study demonstrates the utility of MagIC-cryo-EM for structural analysis of scarce macromolecules in heterogeneous samples and provides structural insights into the cell cycle-regulation of H1.8 association to nucleosomes.
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Affiliation(s)
- Yasuhiro Arimura
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
- Current address: Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA, 98109-1024
| | - Hide A. Konishi
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
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2
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Taha MS, Ahmadian MR. Nucleophosmin: A Nucleolar Phosphoprotein Orchestrating Cellular Stress Responses. Cells 2024; 13:1266. [PMID: 39120297 PMCID: PMC11312075 DOI: 10.3390/cells13151266] [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: 07/04/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Nucleophosmin (NPM1) is a key nucleolar protein released from the nucleolus in response to stress stimuli. NPM1 functions as a stress regulator with nucleic acid and protein chaperone activities, rapidly shuttling between the nucleus and cytoplasm. NPM1 is ubiquitously expressed in tissues and can be found in the nucleolus, nucleoplasm, cytoplasm, and extracellular environment. It plays a central role in various biological processes such as ribosome biogenesis, cell cycle regulation, cell proliferation, DNA damage repair, and apoptosis. In addition, it is highly expressed in cancer cells and solid tumors, and its mutation is a major cause of acute myeloid leukemia (AML). This review focuses on NPM1's structural features, functional diversity, subcellular distribution, and role in stress modulation.
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Affiliation(s)
- Mohamed S. Taha
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Research on Children with Special Needs Department, Institute of Medical Research and Clinical Studies, National Research Centre, Cairo 12622, Egypt
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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3
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Candela-Ferre J, Diego-Martin B, Pérez-Alemany J, Gallego-Bartolomé J. Mind the gap: Epigenetic regulation of chromatin accessibility in plants. PLANT PHYSIOLOGY 2024; 194:1998-2016. [PMID: 38236303 PMCID: PMC10980423 DOI: 10.1093/plphys/kiae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/07/2023] [Accepted: 11/23/2023] [Indexed: 01/19/2024]
Abstract
Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central in regulating these processes, determining chromatin accessibility by limiting access to DNA for various proteins and acting as important signaling hubs. The association of histones with DNA in nucleosomes and the folding of chromatin into higher-order structures are strongly influenced by a variety of epigenetic marks, including DNA methylation, histone variants, and histone post-translational modifications. Additionally, a wide array of chaperones and ATP-dependent remodelers regulate various aspects of nucleosome biology, including assembly, deposition, and positioning. This review provides an overview of recent advances in our mechanistic understanding of how nucleosomes and chromatin organization are regulated by epigenetic marks and remodelers in plants. Furthermore, we present current technologies for profiling chromatin accessibility and organization.
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Affiliation(s)
- Joan Candela-Ferre
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Borja Diego-Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Jaime Pérez-Alemany
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
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4
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Florio D, Marasco D. Could Targeting NPM1c+ Misfolding Be a Promising Strategy for Combating Acute Myeloid Leukemia? Int J Mol Sci 2024; 25:811. [PMID: 38255885 PMCID: PMC10815591 DOI: 10.3390/ijms25020811] [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: 12/03/2023] [Revised: 12/30/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous group of diseases classified into various types on the basis of distinct features concerning the morphology, cytochemistry and cytogenesis of leukemic cells. Among the different subtypes, the group "AML with gene mutations" includes the variations of the gene of the multifunctional protein nucleophosmin 1 (NPM1). These mutations are the most frequent (~30-35% of AML adult patients and less in pediatric ones) and occur predominantly in the C-terminal domain (CTD) of NPM1. The most important mutation is the insertion at W288, which determines the frame shift W288Cfs12/Ffs12/Lfs*12 and leads to the addition of 2-12 amino acids, which hamper the correct folding of NPM1. This mutation leads to the loss of the nuclear localization signal (NoLS) and to aberrant cytoplasmic localization, denoted as NPM1c+. Many investigations demonstrated that interfering with the cellular location and oligomerization status of NPM1 can influence its biological functions, including the proper buildup of the nucleolus, and therapeutic strategies have been proposed to target NPM1c+, particularly the use of drugs able to re-direct NPM1 localization. Our studies unveiled a direct link between AML mutations and the neat amyloidogenic character of the CTDs of NPM1c+. Herein, with the aim of exploiting these conformational features, novel therapeutic strategies are proposed that rely on the induction of the selective self-cytotoxicity of leukemic blasts by focusing on agents such as peptides, peptoids or small molecules able to enhance amyloid aggregation and targeting selectively AML-NPM1c+ mutations.
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Affiliation(s)
| | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy;
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5
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Buzón P, Velázquez‐Cruz A, Corrales‐Guerrero L, Díaz‐Quintana A, Díaz‐Moreno I, Roos WH. The Histone Chaperones SET/TAF-1β and NPM1 Exhibit Conserved Functionality in Nucleosome Remodeling and Histone Eviction in a Cytochrome c-Dependent Manner. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301859. [PMID: 37548614 PMCID: PMC10582448 DOI: 10.1002/advs.202301859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/07/2023] [Indexed: 08/08/2023]
Abstract
Chromatin homeostasis mediates essential processes in eukaryotes, where histone chaperones have emerged as major regulatory factors during DNA replication, repair, and transcription. The dynamic nature of these processes, however, has severely impeded their characterization at the molecular level. Here, fluorescence optical tweezers are applied to follow histone chaperone dynamics in real time. The molecular action of SET/template-activating factor-Iβ and nucleophosmin 1-representing the two most common histone chaperone folds-are examined using both nucleosomes and isolated histones. It is shown that these chaperones present binding specificity for fully dismantled nucleosomes and are able to recognize and disrupt non-native histone-DNA interactions. Furthermore, the histone eviction process and its modulation by cytochrome c are scrutinized. This approach shows that despite the different structures of these chaperones, they present conserved modes of action mediating nucleosome remodeling.
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Affiliation(s)
- Pedro Buzón
- Moleculaire BiofysicaZernike InstituutRijksuniversiteit GroningenNijenborgh 4Groningen9747 AGThe Netherlands
- Present address:
Department of BiochemistryUniversity of ZurichZurich8057Switzerland
| | - Alejandro Velázquez‐Cruz
- Instituto de Investigaciones Químicas (IIQ)Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja)Universidad de Sevilla – Consejo Superior de Investigaciones Científicas (CSIC)Avda. Américo Vespucio 49Sevilla41092Spain
| | - Laura Corrales‐Guerrero
- Instituto de Investigaciones Químicas (IIQ)Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja)Universidad de Sevilla – Consejo Superior de Investigaciones Científicas (CSIC)Avda. Américo Vespucio 49Sevilla41092Spain
| | - Antonio Díaz‐Quintana
- Instituto de Investigaciones Químicas (IIQ)Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja)Universidad de Sevilla – Consejo Superior de Investigaciones Científicas (CSIC)Avda. Américo Vespucio 49Sevilla41092Spain
| | - Irene Díaz‐Moreno
- Instituto de Investigaciones Químicas (IIQ)Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja)Universidad de Sevilla – Consejo Superior de Investigaciones Científicas (CSIC)Avda. Américo Vespucio 49Sevilla41092Spain
| | - Wouter H. Roos
- Moleculaire BiofysicaZernike InstituutRijksuniversiteit GroningenNijenborgh 4Groningen9747 AGThe Netherlands
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6
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Zhao X, Li X, Sun H, Zhao X, Gao T, Shi P, Chen F, Liu L, Lu X. Dot1l cooperates with Npm1 to repress endogenous retrovirus MERVL in embryonic stem cells. Nucleic Acids Res 2023; 51:8970-8986. [PMID: 37522386 PMCID: PMC10516645 DOI: 10.1093/nar/gkad640] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/06/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023] Open
Abstract
Dot1l is a histone methyltransferase without a SET domain and is responsible for H3K79 methylation, which marks active transcription. In contradiction, Dot1l also participates in silencing gene expression. The target regions and mechanism of Dot1l in repressing transcription remain enigmatic. Here, we show that Dot1l represses endogenous retroviruses in embryonic stem cells (ESCs). Specifically, the absence of Dot1l led to the activation of MERVL, which is a marker of 2-cell-like cells. In addition, Dot1l deletion activated the 2-cell-like state and predisposed ESCs to differentiate into trophectoderm lineage. Transcriptome analysis revealed activation of 2-cell genes and meiotic genes by Dot1l deletion. Mechanistically, Dot1l interacted with and co-localized with Npm1 on MERVL, and depletion of Npm1 similarly augmented MERVL expression. The catalytic activity and AT-hook domain of Dot1l are important to suppress MERVL. Notably, Dot1l-Npm1 restricts MERVL by regulating protein level and deposition of histone H1. Furthermore, Dot1l is critical for Npm1 to efficiently interact with histone H1 and inhibit ubiquitination of H1 whereas Npm1 is essential for Dot1l to interact with MERVL. Altogether, we discover that Dot1l represses MERVL through chaperoning H1 by collaborating with Npm1. Importantly, our findings shed light on the non-canonical transcriptional repressive role of Dot1l in ESCs.
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Affiliation(s)
- Xin Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
| | - Xiaomin Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
| | - Haiyang Sun
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
| | - Xuan Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
| | - Tingting Gao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
| | - Panpan Shi
- State Key Laboratory of Medicinal Chemical Biology, College of Life Science, Nankai University, Tianjin, Tianjin 300071, China
| | - Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, College of Life Science, Nankai University, Tianjin, Tianjin 300071, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Science, Nankai University, Tianjin, Tianjin 300071, China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
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7
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Xu SX, Han YW, Guo JL, Bian XK, Hu HM, Lee SC. The binding between NPM and H2B proteins signals for the diabetes-associated centrosome amplification. Cell Biochem Funct 2022; 40:516-525. [PMID: 35678289 DOI: 10.1002/cbf.3721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/28/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022]
Abstract
Diabetes not only increases the risk for cancer but also promotes cancer metastasis. Centrosome amplification (CA) is sufficient to initiate tumorigenesis and can enhance the invasion potential of cancer cells. We have reported that diabetes can induce CA, with diabetic pathophysiological factors as the triggers, which involves the signaling of nucleophosmin (NPM). Thus, CA can serve as a candidate biological link between diabetes and cancer. In the present study, we attempted to identify the NPM binding partners and investigated whether the binding between NPM and its partner mediated the CA. We confirmed that high glucose, insulin, and palmitic acid cancer could elicit CA in the HCT16 colon cancer cells and found that the experimental treatment increased the binding between NPM and H2B, but not between p-NPM and H2B. The molecular docking analysis supported the fact that NPM and H2B could bind to each other through various amino acid residues. The treatment also increased the colocalization of NPM and H2B in the cytosol. Importantly, disruption of the NPM1-H2B complex by individual knockdown of the protein level of NPM or H2B led to the inhibition of the treatment-evoked CA. In conclusion, our results suggest that the binding between NPM and H2B proteins signals for the CA by high glucose, insulin, and palmitic acid.
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Affiliation(s)
- Si X Xu
- Department of Cell Biology, Institute of Biomedical Science, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Ya W Han
- Department of Cell Biology, Institute of Biomedical Science, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jia Li Guo
- Department of Cell Biology, Institute of Biomedical Science, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Xue K Bian
- Department of Cell Biology, Institute of Biomedical Science, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Hong M Hu
- Department of Cell Biology, Institute of Biomedical Science, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Shao C Lee
- Department of Cell Biology, Institute of Biomedical Science, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, China
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8
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Yun H, Narayan N, Vohra S, Giotopoulos G, Mupo A, Madrigal P, Sasca D, Lara-Astiaso D, Horton SJ, Agrawal-Singh S, Meduri E, Basheer F, Marando L, Gozdecka M, Dovey OM, Castillo-Venzor A, Wang X, Gallipoli P, Müller-Tidow C, Osborne CS, Vassiliou GS, Huntly BJP. Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression. Nat Genet 2021; 53:1443-1455. [PMID: 34556857 PMCID: PMC7611829 DOI: 10.1038/s41588-021-00925-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Altered transcription is a cardinal feature of acute myeloid leukemia (AML); however, exactly how mutations synergize to remodel the epigenetic landscape and rewire three-dimensional DNA topology is unknown. Here, we apply an integrated genomic approach to a murine allelic series that models the two most common mutations in AML: Flt3-ITD and Npm1c. We then deconvolute the contribution of each mutation to alterations of the epigenetic landscape and genome organization, and infer how mutations synergize in the induction of AML. Our studies demonstrate that Flt3-ITD signals to chromatin to alter the epigenetic environment and synergizes with mutations in Npm1c to alter gene expression and drive leukemia induction. These analyses also allow the identification of long-range cis-regulatory circuits, including a previously unknown superenhancer of Hoxa locus, as well as larger and more detailed gene-regulatory networks, driven by transcription factors including PU.1 and IRF8, whose importance we demonstrate through perturbation of network members.
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MESH Headings
- Animals
- Base Sequence
- Chromatin Assembly and Disassembly/genetics
- DNA, Neoplasm/chemistry
- Disease Models, Animal
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Genetic Loci
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Mice, Inbred C57BL
- Mutation/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Principal Component Analysis
- Protein Processing, Post-Translational
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic
- fms-Like Tyrosine Kinase 3/metabolism
- Mice
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Affiliation(s)
- Haiyang Yun
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nisha Narayan
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shabana Vohra
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Annalisa Mupo
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Pedro Madrigal
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Daniel Sasca
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - David Lara-Astiaso
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah J Horton
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shuchi Agrawal-Singh
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eshwar Meduri
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Faisal Basheer
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Oliver M Dovey
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | | | - Xiaonan Wang
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gallipoli
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Cameron S Osborne
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - George S Vassiliou
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Brian J P Huntly
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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9
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Hindley A, Catherwood MA, McMullin MF, Mills KI. Significance of NPM1 Gene Mutations in AML. Int J Mol Sci 2021; 22:ijms221810040. [PMID: 34576201 PMCID: PMC8467861 DOI: 10.3390/ijms221810040] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
The aim of this literature review is to examine the significance of the nucleophosmin 1 (NPM1) gene in acute myeloid leukaemia (AML). This will include analysis of the structure and normal cellular function of NPM1, the type of mutations commonly witnessed in NPM1, and the mechanism by which this influences the development and progression of AML. The importance of NPM1 mutation on prognosis and the treatment options available to patients will also be reviewed along with current guidelines recommending the rapid return of NPM1 mutational screening results and the importance of employing a suitable laboratory assay to achieve this. Finally, future developments in the field including research into new therapies targeting NPM1 mutated AML are considered.
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Affiliation(s)
- Andrew Hindley
- Clinical Haematology, Belfast City Hospital, Belfast BT9 7AB, UK;
- Correspondence:
| | | | - Mary Frances McMullin
- Centre for Medical Education, Queen’s University Belfast, Belfast BT7 1NN, UK;
- Northern Ireland and Belfast Health and Social Care Trust, Belfast BT9 7AB, UK
| | - Ken I. Mills
- Patrick G Johnston Center for Cancer Research, Queens University Belfast, Belfast BT9 7AE, UK;
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10
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Russo LC, Ferruzo PYM, Forti FL. Nucleophosmin Protein Dephosphorylation by DUSP3 Is a Fine-Tuning Regulator of p53 Signaling to Maintain Genomic Stability. Front Cell Dev Biol 2021; 9:624933. [PMID: 33777934 PMCID: PMC7991746 DOI: 10.3389/fcell.2021.624933] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/08/2021] [Indexed: 01/06/2023] Open
Abstract
The dual-specificity phosphatase 3 (DUSP3), an atypical protein tyrosine phosphatase (PTP), regulates cell cycle checkpoints and DNA repair pathways under conditions of genotoxic stress. DUSP3 interacts with the nucleophosmin protein (NPM) in the cell nucleus after UV-radiation, implying a potential role for this interaction in mechanisms of genomic stability. Here, we show a high-affinity binding between DUSP3-NPM and NPM tyrosine phosphorylation after UV stress, which is increased in DUSP3 knockdown cells. Specific antibodies designed to the four phosphorylated NPM’s tyrosines revealed that DUSP3 dephosphorylates Y29, Y67, and Y271 after UV-radiation. DUSP3 knockdown causes early nucleolus exit of NPM and ARF proteins allowing them to disrupt the HDM2-p53 interaction in the nucleoplasm after UV-stress. The anticipated p53 release from proteasome degradation increased p53-Ser15 phosphorylation, prolonged p53 half-life, and enhanced p53 transcriptional activity. The regular dephosphorylation of NPM’s tyrosines by DUSP3 balances the p53 functioning and favors the repair of UV-promoted DNA lesions needed for the maintenance of genomic stability.
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Affiliation(s)
- Lilian C Russo
- Laboratory of Biomolecular Systems Signalling, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Pault Y M Ferruzo
- Laboratory of Biomolecular Systems Signalling, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Fabio L Forti
- Laboratory of Biomolecular Systems Signalling, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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11
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Lone IN, Sengez B, Hamiche A, Dimitrov S, Alotaibi H. The Role of Histone Variants in the Epithelial-To-Mesenchymal Transition. Cells 2020; 9:cells9112499. [PMID: 33213091 PMCID: PMC7698467 DOI: 10.3390/cells9112499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 11/16/2022] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) is a physiological process activated during early embryogenesis, which continues to shape tissues and organs later on. It is also hijacked by tumor cells during metastasis. The regulation of EMT has been the focus of many research groups culminating in the last few years and resulting in an elaborate transcriptional network buildup. However, the implication of epigenetic factors in the control of EMT is still in its infancy. Recent discoveries pointed out that histone variants, which are key epigenetic players, appear to be involved in EMT control. This review summarizes the available data on histone variants' function in EMT that would contribute to a better understanding of EMT itself and EMT-related diseases.
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Affiliation(s)
- Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
| | - Burcu Sengez
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
| | - Ali Hamiche
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67400 Illkirch, France;
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé-Allée des Alpes, 38700 La Tronche, France
| | - Hani Alotaibi
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
- Correspondence: ; Tel.: +90-232-299-4100 (ext. 5071)
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12
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Abstract
Histone variants regulate chromatin accessibility and gene transcription. Given their distinct properties and functions, histone varint substitutions allow for profound alteration of nucleosomal architecture and local chromatin landscape. Skeletal myogenesis driven by the key transcription factor MyoD is characterized by precise temporal regulation of myogenic genes. Timed substitution of variants within the nucleosomes provides a powerful means to ensure sequential expression of myogenic genes. Indeed, growing evidence has shown H3.3, H2A.Z, macroH2A, and H1b to be critical for skeletal myogenesis. However, the relative importance of various histone variants and their associated chaperones in myogenesis is not fully appreciated. In this review, we summarize the role that histone variants play in altering chromatin landscape to ensure proper muscle differentiation. The temporal regulation and cross talk between histones variants and their chaperones in conjunction with other forms of epigenetic regulation could be critical to understanding myogenesis and their involvement in myopathies.
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Affiliation(s)
- Nandini Karthik
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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13
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Cela I, Di Matteo A, Federici L. Nucleophosmin in Its Interaction with Ligands. Int J Mol Sci 2020; 21:E4885. [PMID: 32664415 PMCID: PMC7402337 DOI: 10.3390/ijms21144885] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/13/2022] Open
Abstract
Nucleophosmin (NPM1) is a mainly nucleolar protein that shuttles between nucleoli, nucleoplasm and cytoplasm to fulfill its many functions. It is a chaperone of both nucleic acids and proteins and plays a role in cell cycle control, centrosome duplication, ribosome maturation and export, as well as the cellular response to a variety of stress stimuli. NPM1 is a hub protein in nucleoli where it contributes to nucleolar organization through heterotypic and homotypic interactions. Furthermore, several alterations, including overexpression, chromosomal translocations and mutations are present in solid and hematological cancers. Recently, novel germline mutations that cause dyskeratosis congenita have also been described. This review focuses on NPM1 interactions and inhibition. Indeed, the list of NPM1 binding partners is ever-growing and, in recent years, many studies contributed to clarifying the structural basis for NPM1 recognition of both nucleic acids and several proteins. Intriguingly, a number of natural and synthetic ligands that interfere with NPM1 interactions have also been reported. The possible role of NPM1 inhibitors in the treatment of multiple cancers and other pathologies is emerging as a new therapeutic strategy.
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Affiliation(s)
- Ilaria Cela
- Center for Advanced Studies and Technology (CAST), University of Chieti “G. d’Annunzio”, Via Polacchi, 66100 Chieti, Italy;
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology (IBPM) of the CNR, c/o “Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Roma, Italy;
| | - Luca Federici
- Center for Advanced Studies and Technology (CAST), University of Chieti “G. d’Annunzio”, Via Polacchi, 66100 Chieti, Italy;
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
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14
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Li F, Ng WL, Luster TA, Hu H, Sviderskiy VO, Dowling CM, Hollinshead KER, Zouitine P, Zhang H, Huang Q, Ranieri M, Wang W, Fang Z, Chen T, Deng J, Zhao K, So HC, Khodadadi-Jamayran A, Xu M, Karatza A, Pyon V, Li S, Pan Y, Labbe K, Almonte C, Poirier JT, Miller G, Possemato R, Qi J, Wong KK. Epigenetic CRISPR Screens Identify Npm1 as a Therapeutic Vulnerability in Non-Small Cell Lung Cancer. Cancer Res 2020; 80:3556-3567. [PMID: 32646968 DOI: 10.1158/0008-5472.can-19-3782] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/03/2020] [Accepted: 07/06/2020] [Indexed: 12/20/2022]
Abstract
Despite advancements in treatment options, the overall cure and survival rates for non-small cell lung cancers (NSCLC) remain low. While small-molecule inhibitors of epigenetic regulators have recently emerged as promising cancer therapeutics, their application in patients with NSCLC is limited. To exploit epigenetic regulators as novel therapeutic targets in NSCLC, we performed pooled epigenome-wide CRISPR knockout screens in vitro and in vivo and identified the histone chaperone nucleophosmin 1 (Npm1) as a potential therapeutic target. Genetic ablation of Npm1 significantly attenuated tumor progression in vitro and in vivo. Furthermore, KRAS-mutant cancer cells were more addicted to NPM1 expression. Genetic ablation of Npm1 rewired the balance of metabolism in cancer cells from predominant aerobic glycolysis to oxidative phosphorylation and reduced the population of tumor-propagating cells. Overall, our results support NPM1 as a therapeutic vulnerability in NSCLC. SIGNIFICANCE: Epigenome-wide CRISPR knockout screens identify NPM1 as a novel metabolic vulnerability and demonstrate that targeting NPM1 is a new therapeutic opportunity for patients with NSCLC.
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Affiliation(s)
- Fei Li
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Wai-Lung Ng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Troy A Luster
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hai Hu
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | | | - Catríona M Dowling
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Kate E R Hollinshead
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Paula Zouitine
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hua Zhang
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Qingyuan Huang
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Michela Ranieri
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Wei Wang
- S. Arthur Localio Laboratory, Department of Surgery, New York University School of Medicine, New York, New York
| | - Zhaoyuan Fang
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ting Chen
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Jiehui Deng
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Kai Zhao
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Hon-Cheong So
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Department of Psychiatry, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories and Genome Technology Center, Division of Advanced Research Technologies, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Mousheng Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Angeliki Karatza
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Val Pyon
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Shuai Li
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Yuanwang Pan
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Kristen Labbe
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - Christina Almonte
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - John T Poirier
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York
| | - George Miller
- S. Arthur Localio Laboratory, Department of Surgery, New York University School of Medicine, New York, New York
| | - Richard Possemato
- Department of Pathology, New York University School of Medicine, New York, New York
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York.
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15
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DeMarino C, Cowen M, Pleet ML, Pinto DO, Khatkar P, Erickson J, Docken SS, Russell N, Reichmuth B, Phan T, Kuang Y, Anderson DM, Emelianenko M, Kashanchi F. Differences in Transcriptional Dynamics Between T-cells and Macrophages as Determined by a Three-State Mathematical Model. Sci Rep 2020; 10:2227. [PMID: 32042107 PMCID: PMC7010665 DOI: 10.1038/s41598-020-59008-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/17/2020] [Indexed: 12/18/2022] Open
Abstract
HIV-1 viral transcription persists in patients despite antiretroviral treatment, potentially due to intermittent HIV-1 LTR activation. While several mathematical models have been explored in the context of LTR-protein interactions, in this work for the first time HIV-1 LTR model featuring repressed, intermediate, and activated LTR states is integrated with generation of long (env) and short (TAR) RNAs and proteins (Tat, Pr55, and p24) in T-cells and macrophages using both cell lines and infected primary cells. This type of extended modeling framework allows us to compare and contrast behavior of these two cell types. We demonstrate that they exhibit unique LTR dynamics, which ultimately results in differences in the magnitude of viral products generated. One of the distinctive features of this work is that it relies on experimental data in reaction rate computations. Two RNA transcription rates from the activated promoter states are fit by comparison of experimental data to model predictions. Fitting to the data also provides estimates for the degradation/exit rates for long and short viral RNA. Our experimentally generated data is in reasonable agreement for the T-cell as well macrophage population and gives strong evidence in support of using the proposed integrated modeling paradigm. Sensitivity analysis performed using Latin hypercube sampling method confirms robustness of the model with respect to small parameter perturbations. Finally, incorporation of a transcription inhibitor (F07#13) into the governing equations demonstrates how the model can be used to assess drug efficacy. Collectively, our model indicates transcriptional differences between latently HIV-1 infected T-cells and macrophages and provides a novel platform to study various transcriptional dynamics leading to latency or activation in numerous cell types and physiological conditions.
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MESH Headings
- Anti-HIV Agents/pharmacology
- Anti-HIV Agents/therapeutic use
- Cell Line
- Drug Resistance, Viral/drug effects
- Drug Resistance, Viral/genetics
- Drug Resistance, Viral/immunology
- Gene Expression Regulation, Viral/immunology
- HIV Infections/blood
- HIV Infections/drug therapy
- HIV Infections/immunology
- HIV Long Terminal Repeat/genetics
- HIV-1/drug effects
- HIV-1/genetics
- HIV-1/immunology
- Humans
- Macrophages/immunology
- Macrophages/virology
- Models, Genetic
- Models, Immunological
- Primary Cell Culture
- RNA, Viral/genetics
- RNA, Viral/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/virology
- Transcription, Genetic/drug effects
- Transcription, Genetic/immunology
- Virus Replication/drug effects
- Virus Replication/genetics
- Virus Replication/immunology
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Affiliation(s)
- Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Maria Cowen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Michelle L Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Daniel O Pinto
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Pooja Khatkar
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - James Erickson
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Steffen S Docken
- Department of Mathematics, University of California Davis, Davis, CA, USA
| | - Nicholas Russell
- Department of Mathematical Sciences, University of Delaware, Newark, DE, USA
| | - Blake Reichmuth
- Department of Mathematical Sciences, George Mason University, Fairfax, VA, USA
| | - Tin Phan
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA
| | - Daniel M Anderson
- Department of Mathematical Sciences, George Mason University, Fairfax, VA, USA.
| | - Maria Emelianenko
- Department of Mathematical Sciences, George Mason University, Fairfax, VA, USA.
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA.
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16
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Ducray SP, Natarajan K, Garland GD, Turner SD, Egger G. The Transcriptional Roles of ALK Fusion Proteins in Tumorigenesis. Cancers (Basel) 2019; 11:cancers11081074. [PMID: 31366041 PMCID: PMC6721376 DOI: 10.3390/cancers11081074] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/17/2019] [Accepted: 07/23/2019] [Indexed: 12/14/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a tyrosine kinase involved in neuronal and gut development. Initially discovered in T cell lymphoma, ALK is frequently affected in diverse cancers by oncogenic translocations. These translocations involve different fusion partners that facilitate multimerisation and autophosphorylation of ALK, resulting in a constitutively active tyrosine kinase with oncogenic potential. ALK fusion proteins are involved in diverse cellular signalling pathways, such as Ras/extracellular signal-regulated kinase (ERK), phosphatidylinositol 3-kinase (PI3K)/Akt and Janus protein tyrosine kinase (JAK)/STAT. Furthermore, ALK is implicated in epigenetic regulation, including DNA methylation and miRNA expression, and an interaction with nuclear proteins has been described. Through these mechanisms, ALK fusion proteins enable a transcriptional programme that drives the pathogenesis of a range of ALK-related malignancies.
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Affiliation(s)
- Stephen P Ducray
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB20QQ, UK
| | | | - Gavin D Garland
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB20QQ, UK
| | - Suzanne D Turner
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB20QQ, UK.
| | - Gerda Egger
- Department of Pathology, Medical University Vienna, 1090 Vienna, Austria.
- Ludwig Boltzmann Institute Applied Diagnostics, 1090 Vienna, Austria.
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17
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Malfatti MC, Gerratana L, Dalla E, Isola M, Damante G, Di Loreto C, Puglisi F, Tell G. APE1 and NPM1 protect cancer cells from platinum compounds cytotoxicity and their expression pattern has a prognostic value in TNBC. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:309. [PMID: 31307523 PMCID: PMC6631760 DOI: 10.1186/s13046-019-1294-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023]
Abstract
Background Triple negative breast cancer (TNBC) is a breast cancer subgroup characterized by a lack of hormone receptors’ expression and no HER2 overexpression. These molecular features both drastically reduce treatment options and confer poor prognosis. Platinum (Pt)-salts are being investigated as a new therapeutic strategy. The base excision repair (BER) pathway is important for resistance to Pt-based therapies. Overexpression of APE1, a pivotal enzyme of the BER pathway, as well as the expression of NPM1, a functional regulator of APE1, are associated with poor outcome and resistance to Pt-based therapies. Methods We evaluated the role of NPM1, APE1 and altered NPM1/APE1 interaction in the response to Pt-salts treatment in different cell lines: APE1 knockout (KO) cells, NPM1 KO cells, cell line models having an altered APE1/NPM1 interaction and HCC70 and HCC1937 TNBC cell lines, having different levels of APE1/NPM1. We evaluated the TNBC cells response to new chemotherapeutic small molecules targeting the endonuclease activity of APE1 or the APE1/NPM1 interaction, in combination with Pt-salts treatments. Expression levels’ correlation between APE1 and NPM1 and their impact on prognosis was analyzed in a cohort of TNBC patients through immunohistochemistry. Bioinformatics analysis, using TCGA datasets, was performed to predict a molecular signature of cancers based on APE1 and NPM1 expression. Results APE1 and NPM1, and their interaction as well, protect from the cytotoxicity induced by Pt-salts treatment. HCC1937 cells, having higher levels of APE1/NPM1 proteins, are more resistant to Pt-salts treatment compared to the HCC70 cells. A sensitization effect by APE1 inhibitors to Pt-compounds was observed. The association of NPM1/APE1 with cancer gene signatures highlighted alterations concerning cell-cycle dependent proteins. Conclusions APE1 and NPM1 protect cancer cells from Pt-compounds cytotoxicity, suggesting a possible improvement of the activity of Pt-based therapy for TNBC, using the NPM1 and APE1 proteins as secondary therapeutic targets. Based on positive or negative correlation with APE1 and NPM1 gene expression levels, we finally propose several TNBC gene signatures that should deserve further attention for their potential impact on TNBC precision medicine approaches. Electronic supplementary material The online version of this article (10.1186/s13046-019-1294-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy.,Department of Oncology, ASUI Udine SMM University Hospital Udine, Udine, Italy
| | - Emiliano Dalla
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy
| | - Miriam Isola
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy
| | - Giuseppe Damante
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy
| | - Carla Di Loreto
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy.,Department of Pathology, ASUI Udine SMM University Hospital Udine, Udine, Italy
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, Italy
| | - Gianluca Tell
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy.
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18
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Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. Sci Rep 2019; 9:213. [PMID: 30659199 PMCID: PMC6338737 DOI: 10.1038/s41598-018-36135-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/14/2018] [Indexed: 01/19/2023] Open
Abstract
Throughout the HIV-1 replication cycle, complex host-pathogen interactions take place in the infected cell, leading to the production of new virions. The virus modulates the host cellular machinery in order to support its life cycle, while counteracting intracellular defense mechanisms. We investigated the dynamic host response to HIV-1 infection by systematically measuring transcriptomic, proteomic, and phosphoproteomic expression changes in infected and uninfected SupT1 CD4+ T cells at five time points of the viral replication process. By means of a Gaussian mixed-effects model implemented in the new R/Bioconductor package TMixClust, we clustered host genes based on their temporal expression patterns. We identified a proteo-transcriptomic gene expression signature of 388 host genes specific for HIV-1 replication. Comprehensive functional analyses of these genes confirmed the previously described roles of some of the genes and revealed novel key virus-host interactions affecting multiple molecular processes within the host cell, including signal transduction, metabolism, cell cycle, and immune system. The results of our analysis are accessible through a freely available, dedicated and user-friendly R/Shiny application, called PEACHi2.0. This resource constitutes a catalogue of dynamic host responses to HIV-1 infection that provides a basis for a more comprehensive understanding of virus-host interactions.
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Affiliation(s)
- Monica Golumbeanu
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Sébastien Desfarges
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- InvivoGen, Toulouse, France
| | - Céline Hernandez
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Computational Systems Biology Team, Institut de Biologie de I'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, ENS, PSL Université, Paris, France
| | - Manfredo Quadroni
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sylvie Rato
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, (CA), USA
| | - Amalio Telenti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, (CA), USA.
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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19
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Brunetti L, Gundry MC, Goodell MA. New insights into the biology of acute myeloid leukemia with mutated NPM1. Int J Hematol 2019; 110:150-160. [DOI: 10.1007/s12185-018-02578-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/25/2018] [Indexed: 12/20/2022]
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20
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Sen Gupta A, Joshi G, Pawar S, Sengupta K. Nucleolin modulates compartmentalization and dynamics of histone 2B-ECFP in the nucleolus. Nucleus 2018; 9:350-367. [PMID: 29943658 PMCID: PMC6165600 DOI: 10.1080/19491034.2018.1471936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Eukaryotic cells have 2 to 3 discrete nucleoli required for ribosome synthesis. Nucleoli are phase separated nuclear sub-organelles. Here we examined the role of nuclear Lamins and nucleolar factors in modulating the compartmentalization and dynamics of histone 2B (H2B-ECFP) in the nucleolus. Live imaging and Fluorescence Recovery After Photobleaching (FRAP) of labelled H2B, showed that the depletion of Lamin B1, Fibrillarin (FBL) or Nucleostemin (GNL3), enhances H2B-ECFP mobility in the nucleolus. Furthermore, Nucleolin knockdown significantly decreases H2B-ECFP compartmentalization in the nucleolus, while H2B-ECFP residence and mobility in the nucleolus was prolonged upon Nucleolin overexpression. Co-expression of N-terminal and RNA binding domain (RBD) deletion mutants of Nucleolin or inhibiting 45S rRNA synthesis reduces the sequestration of H2B-ECFP in the nucleolus. Taken together, these studies reveal a crucial role of Nucleolin-rRNA complex in modulating the compartmentalization, stability and dynamics of H2B within the nucleolus.
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Affiliation(s)
- Ayantika Sen Gupta
- Biology, Indian Institute of Science Education and Research (IISER), Pune, India
| | - Gaurav Joshi
- Biology, Indian Institute of Science Education and Research (IISER), Pune, India
| | - Sumit Pawar
- Biology, Indian Institute of Science Education and Research (IISER), Pune, India
| | - Kundan Sengupta
- Biology, Indian Institute of Science Education and Research (IISER), Pune, India
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21
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Ne E, Palstra RJ, Mahmoudi T. Transcription: Insights From the HIV-1 Promoter. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:191-243. [DOI: 10.1016/bs.ircmb.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Assembly and remodeling of viral DNA and RNA replicons regulated by cellular molecular chaperones. Biophys Rev 2017; 10:445-452. [PMID: 29170971 DOI: 10.1007/s12551-017-0333-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/07/2017] [Indexed: 12/12/2022] Open
Abstract
A variety of cellular reactions mediated by interactions among proteins and nucleic acids requires a series of proteins called molecular chaperones. The viral genome encodes relatively few kinds of viral proteins and, therefore, host-derived cellular factors are required for virus proliferation. Here we discuss those cellular proteins known as molecular chaperones, which are essential for the assembly of functional viral DNA/RNA replicons. The function of these molecular chaperones in the cellular context is also discussed.
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23
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Krishnan S, Smits AH, Vermeulen M, Reinberg D. Phospho-H1 Decorates the Inter-chromatid Axis and Is Evicted along with Shugoshin by SET during Mitosis. Mol Cell 2017; 67:579-593.e6. [PMID: 28781233 PMCID: PMC5562512 DOI: 10.1016/j.molcel.2017.07.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 04/26/2017] [Accepted: 07/06/2017] [Indexed: 12/22/2022]
Abstract
Precise control of sister chromatid separation during mitosis is pivotal to maintaining genomic integrity. Yet, the regulatory mechanisms involved are not well understood. Remarkably, we discovered that linker histone H1 phosphorylated at S/T18 decorated the inter-chromatid axial DNA on mitotic chromosomes. Sister chromatid resolution during mitosis required the eviction of such H1S/T18ph by the chaperone SET, with this process being independent of and most likely downstream of arm-cohesin dissociation. SET also directed the disassembly of Shugoshins in a polo-like kinase 1-augmented manner, aiding centromere resolution. SET ablation compromised mitotic fidelity as evidenced by unresolved sister chromatids with marked accumulation of H1S/T18ph and centromeric Shugoshin. Thus, chaperone-assisted eviction of linker histones and Shugoshins is a fundamental step in mammalian mitotic progression. Our findings also elucidate the functional implications of the decades-old observation of mitotic linker histone phosphorylation, serving as a paradigm to explore the role of linker histones in bio-signaling processes.
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Affiliation(s)
- Swathi Krishnan
- Howard Hughes Medical Institute, New York University Langone School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA
| | - Arne H Smits
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Danny Reinberg
- Howard Hughes Medical Institute, New York University Langone School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.
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Warren C, Shechter D. Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches. J Mol Biol 2017; 429:2401-2426. [PMID: 28610839 DOI: 10.1016/j.jmb.2017.06.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 01/21/2023]
Abstract
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly 2-meter-long human genome into a roughly 10-micron-diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly and thus the fluidity of the ever-changing chromatin landscape. Histone chaperones are responsible for binding the highly basic histone proteins, shielding them from non-specific interactions, facilitating their deposition onto DNA, and aiding in their eviction from DNA. Although most histone chaperones perform these common functions, recent structural studies of many different histone chaperones reveal that there are few commonalities in their folds. Importantly, sequence-based predictions show that histone chaperones are highly enriched in intrinsically disordered regions (IDRs) and acidic stretches. In this review, we focus on the molecular mechanisms underpinning histone binding, selectivity, and regulation of these highly dynamic protein regions. We highlight new evidence suggesting that IDRs are often critical for histone chaperone function and play key roles in chromatin assembly and disassembly pathways.
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Affiliation(s)
- Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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25
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Hanley ML, Yoo TY, Sonnett M, Needleman DJ, Mitchison TJ. Chromosomal passenger complex hydrodynamics suggests chaperoning of the inactive state by nucleoplasmin/nucleophosmin. Mol Biol Cell 2017; 28:1444-1456. [PMID: 28404751 PMCID: PMC5449145 DOI: 10.1091/mbc.e16-12-0860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/27/2017] [Accepted: 04/04/2017] [Indexed: 01/30/2023] Open
Abstract
The chromosomal passenger complex (CPC) is a conserved, essential regulator of cell division. As such, significant anti-cancer drug development efforts have been focused on targeting it, most notably by inhibiting its AURKB kinase subunit. The CPC is activated by AURKB-catalyzed autophosphorylation on multiple subunits, but how this regulates CPC interactions with other mitotic proteins remains unclear. We investigated the hydrodynamic behavior of the CPC in Xenopus laevis egg cytosol using sucrose gradient sedimentation and in HeLa cells using fluorescence correlation spectroscopy. We found that autophosphorylation of the CPC decreases its sedimentation coefficient in egg cytosol and increases its diffusion coefficient in live cells, indicating a decrease in mass. Using immunoprecipitation coupled with mass spectrometry and immunoblots, we discovered that inactive, unphosphorylated CPC interacts with nucleophosmin/nucleoplasmin proteins, which are known to oligomerize into pentamers and decamers. Autophosphorylation of the CPC causes it to dissociate from nucleophosmin/nucleoplasmin. We propose that nucleophosmin/nucleoplasmin complexes serve as chaperones that negatively regulate the CPC and/or stabilize its inactive form, preventing CPC autophosphorylation and recruitment to chromatin and microtubules in mitosis.
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Affiliation(s)
- Mariah L Hanley
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701.,Department of Chemistry, Harvard University, Cambridge, MA 02138-2902
| | - Tae Yeon Yoo
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138-2902
| | - Matthew Sonnett
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701
| | - Daniel J Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138-2902.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138-2902
| | - Timothy J Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA 02114-5701
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26
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Regulation of Cellular Dynamics and Chromosomal Binding Site Preference of Linker Histones H1.0 and H1.X. Mol Cell Biol 2016; 36:2681-2696. [PMID: 27528617 DOI: 10.1128/mcb.00200-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 08/08/2016] [Indexed: 01/01/2023] Open
Abstract
Linker histones play important roles in the genomic organization of mammalian cells. Of the linker histone variants, H1.X shows the most dynamic behavior in the nucleus. Recent research has suggested that the linker histone variants H1.X and H1.0 have different chromosomal binding site preferences. However, it remains unclear how the dynamics and binding site preferences of linker histones are determined. Here, we biochemically demonstrated that the DNA/nucleosome and histone chaperone binding activities of H1.X are significantly lower than those of other linker histones. This explains why H1.X moves more rapidly than other linker histones in vivo Domain swapping between H1.0 and H1.X suggests that the globular domain (GD) and C-terminal domain (CTD) of H1.X independently contribute to the dynamic behavior of H1.X. Our results also suggest that the N-terminal domain (NTD), GD, and CTD cooperatively determine the preferential binding sites, and the contribution of each domain for this determination is different depending on the target genes. We also found that linker histones accumulate in the nucleoli when the nucleosome binding activities of the GDs are weak. Our results contribute to understanding the molecular mechanisms of dynamic behaviors, binding site selection, and localization of linker histones.
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27
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Zhang P, Branson OE, Freitas MA, Parthun MR. Identification of replication-dependent and replication-independent linker histone complexes: Tpr specifically promotes replication-dependent linker histone stability. BMC BIOCHEMISTRY 2016; 17:18. [PMID: 27716023 PMCID: PMC5045598 DOI: 10.1186/s12858-016-0074-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 09/20/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND There are 11 variants of linker histone H1 in mammalian cells. Beyond their shared abilities to stabilize and condense chromatin, the H1 variants have been found to have non-redundant functions, the mechanisms of which are not fully understood. Like core histones, there are both replication-dependent and replication-independent linker histone variants. The histone chaperones and other factors that regulate linker histone dynamics in the cell are largely unknown. In particular, it is not known whether replication-dependent and replication-independent linker histones interact with distinct or common sets of proteins. To better understand linker histone dynamics and assembly, we used chromatography and mass spectrometry approaches to identify proteins that are associated with replication-dependent and replication-independent H1 variants. We then used a variety of in vivo analyses to validate the functional relevance of identified interactions. RESULTS We identified proteins that bind to all linker histone variants and proteins that are specific for only one class of variant. The factors identified include histone chaperones, transcriptional regulators, RNA binding proteins and ribosomal proteins. The nuclear pore complex protein Tpr, which was found to associate with only replication-dependent linker histones, specifically promoted their stability. CONCLUSION Replication-dependent and replication-independent linker histone variants can interact with both common and distinct sets of proteins. Some of these factors are likely to function as histone chaperones while others may suggest novel links between linker histones and RNA metabolism. The nuclear pore complex protein Tpr specifically interacts with histone H1.1 and H1.2 but not H1x and can regulate the stability of these replication-dependent linker histones.
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Affiliation(s)
- Pei Zhang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210 USA
| | - Owen E. Branson
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210 USA
| | - Michael A. Freitas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210 USA
| | - Mark R. Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210 USA
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Box JK, Paquet N, Adams MN, Boucher D, Bolderson E, O'Byrne KJ, Richard DJ. Nucleophosmin: from structure and function to disease development. BMC Mol Biol 2016; 17:19. [PMID: 27553022 PMCID: PMC4995807 DOI: 10.1186/s12867-016-0073-9] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 08/16/2016] [Indexed: 12/11/2022] Open
Abstract
Nucleophosmin (NPM1) is a critical cellular protein that has been implicated in a number of pathways including mRNA transport, chromatin remodeling, apoptosis and genome stability. NPM1 function is a critical requirement for normal cellular biology as is underlined in cancer where NPM1 is commonly overexpressed, mutated, rearranged and sporadically deleted. Consistent with a multifunctional role within the cell, NPM1 can function not only as a proto-oncogene but also as a tumor suppressor. The aim of this review is to look at the less well-described role of NPM1 in the DNA repair pathways as well as the role of NPM1 in the regulation of apoptosis and its mutation in cancers.
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Affiliation(s)
- Joseph K Box
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Nicolas Paquet
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia.
| | - Mark N Adams
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Didier Boucher
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Emma Bolderson
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kenneth J O'Byrne
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Derek J Richard
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia.
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29
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Li M, Tucker LD, Asara JM, Cheruiyot CK, Lu H, Wu ZJ, Newstein MC, Dooner MS, Friedman J, Lally MA, Ramratnam B. Stem-loop binding protein is a multifaceted cellular regulator of HIV-1 replication. J Clin Invest 2016; 126:3117-29. [PMID: 27454292 PMCID: PMC4966322 DOI: 10.1172/jci82360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/26/2016] [Indexed: 01/12/2023] Open
Abstract
A rare subset of HIV-1-infected individuals is able to maintain plasma viral load (VL) at low levels without antiretroviral treatment. Identifying the mechanisms underlying this atypical response to infection may lead to therapeutic advances for treating HIV-1. Here, we developed a proteomic analysis to compare peripheral blood cell proteomes in 20 HIV-1-infected individuals who maintained either high or low VL with the aim of identifying host factors that impact HIV-1 replication. We determined that the levels of multiple histone proteins were markedly decreased in cohorts of individuals with high VL. This reduction was correlated with lower levels of stem-loop binding protein (SLBP), which is known to control histone metabolism. Depletion of cellular SLBP increased promoter engagement with the chromatin structures of the host gene high mobility group protein A1 (HMGA1) and viral long terminal repeat (LTR), which led to higher levels of HIV-1 genomic integration and proviral transcription. Further, we determined that TNF-α regulates expression of SLBP and observed that plasma TNF-α levels in HIV-1-infected individuals correlated directly with VL levels and inversely with cellular SLBP levels. Our findings identify SLBP as a potentially important cellular regulator of HIV-1, thereby establishing a link between histone metabolism, inflammation, and HIV-1 infection.
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Affiliation(s)
- Ming Li
- Laboratory of Retrovirology, Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Division of Infectious Diseases, Department of Medicine, The Miriam Hospital and Rhode Island Hospital, Providence, Rhode Island, USA
| | - Lynne D. Tucker
- Laboratory of Retrovirology, Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Division of Infectious Diseases, Department of Medicine, The Miriam Hospital and Rhode Island Hospital, Providence, Rhode Island, USA
| | - John M. Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, and Harvard Medical School, Boston, Massachusetts, USA
| | - Collins K. Cheruiyot
- Laboratory of Retrovirology, Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Division of Infectious Diseases, Department of Medicine, The Miriam Hospital and Rhode Island Hospital, Providence, Rhode Island, USA
| | - Huafei Lu
- Laboratory of Retrovirology, Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Division of Infectious Diseases, Department of Medicine, The Miriam Hospital and Rhode Island Hospital, Providence, Rhode Island, USA
| | - Zhijin J. Wu
- Department of Biostatistics, Brown University, Providence, Rhode Island, USA
| | - Michael C. Newstein
- Department of Medicine, Milford Regional Medical Center, and University of Massachusetts Medical School, Milford, Massachusetts, USA
| | - Mark S. Dooner
- Division of Hematology and Oncology, Department of Medicine, Rhode Island Hospital, and Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Jennifer Friedman
- Center for International Health Research, Rhode Island Hospital, Providence, Rhode Island, USA
- Department of Pediatrics, Rhode Island Hospital, and Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Michelle A. Lally
- Division of Infectious Diseases, Department of Medicine, The Miriam Hospital and Rhode Island Hospital, Providence, Rhode Island, USA
- Providence Veterans Affairs Medical Center, Providence, Rhode Island, USA
- Lifespan/Tufts/Brown Center for AIDS Research, Providence, Rhode Island, USA
| | - Bharat Ramratnam
- Laboratory of Retrovirology, Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Division of Infectious Diseases, Department of Medicine, The Miriam Hospital and Rhode Island Hospital, Providence, Rhode Island, USA
- Lifespan/Tufts/Brown Center for AIDS Research, Providence, Rhode Island, USA
- COBRE Center for Cancer Research, Rhode Island Hospital, and Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Clinical Research Center of Lifespan, Providence, Rhode Island, USA
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30
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Yue H, Fang H, Wei S, Hayes JJ, Lee TH. Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome. Biochemistry 2016; 55:2069-77. [PMID: 27010485 PMCID: PMC5436050 DOI: 10.1021/acs.biochem.5b01247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Linker histone H1 regulates chromatin structure and gene expression. Investigating the dynamics and stoichiometry of binding of H1 to DNA and the nucleosome is crucial to elucidating its functions. Because of the abundant positive charges and the strong self-affinity of H1, quantitative in vitro studies of its binding to DNA and the nucleosome have generated results that vary widely and, therefore, should be interpreted in a system specific manner. We sought to overcome this limitation by developing a specially passivated microscope slide surface to monitor binding of H1 to DNA and the nucleosome at a single-molecule level. According to our measurements, the stoichiometry of binding of H1 to DNA and the nucleosome is very heterogeneous with a wide distribution whose averages are in reasonable agreement with previously published values. Our study also revealed that H1 does not dissociate from DNA or the nucleosome on a time scale of tens of minutes. We found that histone chaperone Nap1 readily dissociates H1 from DNA and superstoichiometrically bound H1 from the nucleosome, supporting a hypothesis whereby histone chaperones contribute to the regulation of the H1 profile in chromatin.
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Affiliation(s)
- Hongjun Yue
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - He Fang
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, New York 14625, United States
| | - Sijie Wei
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jeffrey J. Hayes
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, New York 14625, United States
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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NPM1 histone chaperone is upregulated in glioblastoma to promote cell survival and maintain nucleolar shape. Sci Rep 2015; 5:16495. [PMID: 26559910 PMCID: PMC4642306 DOI: 10.1038/srep16495] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023] Open
Abstract
Glioblastoma (grade IV glioma) is the most common and aggressive adult brain tumor. A better understanding of the biology of glioblastoma cells is crucial to identify molecular targets stimulating cell death. NPM1 (nucleophosmin) is a multifunctional chaperone that plays an important role in cancer development. Herein, NPM1 was analyzed by immunohistochemistry in human astrocytic gliomas. NPM1 was detected in all tumors but with a significantly higher staining intensity in grade IV than in low grade tumors. Depletion of NPM1 had only modest effects on the viability of U251MG, U1242MG, and U343MGa Cl2:6 glioma cells, despite alterations in nucleolar morphology. Glioma cell cultures depleted of NPM1 exposed to micromolar levels of actinomycin D were more prone to cell death (apoptosis) compared to cultures retaining NPM1. We had previously found that NPM1 binds to linker histone H1.5. Here we could show that silencing of H1.5 triggered glioma cell apoptosis as evidenced by a marked increase in both the numbers of cleaved caspase-3+ cells and in the amounts of cleaved PARP. Enforced expression of NPM1 suppressed apoptosis in H1.5 depleted glioma cells. Although our studies would suggest little effectiveness of targeting NPM1 alone there could be potential using it as a combination treatment.
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Bednar J, Hamiche A, Dimitrov S. H1-nucleosome interactions and their functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:436-43. [PMID: 26477489 DOI: 10.1016/j.bbagrm.2015.10.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 01/13/2023]
Abstract
Linker histones are three domain proteins and consist of a structured (globular) domain, flanked by two likely non-structured NH2- and COOH-termini. The binding of the linker histones to the nucleosome was characterized by different methods in solution. Apparently, the globular domain interacts with the linker DNA and the nucleosome dyad, while the binding of the large and rich in lysines COOH-terminus results in "closing" the linker DNA of the nucleosome and the formation of the "stem" structure. What is the mode of binding of the linker histones within the chromatin fiber remains still elusive. Nonetheless, it is clear that linker histones are essential for both the assembly and maintenance of the condensed chromatin fiber. Interestingly, linker histones are post-translationally modified and how this affects both their binding to chromatin and functions is now beginning to emerge. In addition, linker histones are highly mobile in vivo, but not in vitro. No explanation of this finding is reported for the moment. The higher mobility of the linker histones should, however, have strong impact on their function. Linker histones plays an important role in gene expression regulation and other chromatin related process and their function is predominantly regulated by their posttranslational modifications. However, the detailed mechanism how the linker histones do function remains still not well understood despite numerous efforts. Here we will summarize and analyze the data on the linker histone binding to the nucleosome and the chromatin fiber and will discuss its functional consequences.
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Affiliation(s)
- Jan Bednar
- Université de Grenoble Alpes/CNRS, Laboratoire Interdisciplinaire de Physique, UMR 5588, 140 rue de la Physique, B.P. 87, St. Martin d'Heres, F-38402, France.
| | - Ali Hamiche
- Equipe labellisée Ligue contre le Cancer, Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UDS, CNRS, INSERM, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France
| | - Stefan Dimitrov
- INSERM/UJF, Institut Albert Bonniot, U823, Site Santé-BP 170, 38042 Grenoble Cedex 9, France
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Arnoldo L, Sgarra R, Chiefari E, Iiritano S, Arcidiacono B, Pegoraro S, Pellarin I, Brunetti A, Manfioletti G. A novel mechanism of post-translational modulation of HMGA functions by the histone chaperone nucleophosmin. Sci Rep 2015; 5:8552. [PMID: 25711412 PMCID: PMC4339810 DOI: 10.1038/srep08552] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/12/2015] [Indexed: 02/07/2023] Open
Abstract
High Mobility Group A are non-histone nuclear proteins that regulate chromatin plasticity and accessibility, playing an important role both in physiology and pathology. Their activity is controlled by transcriptional, post-transcriptional, and post-translational mechanisms. In this study we provide evidence for a novel modulatory mechanism for HMGA functions. We show that HMGAs are complexed in vivo with the histone chaperone nucleophosmin (NPM1), that this interaction requires the histone-binding domain of NPM1, and that NPM1 modulates both DNA-binding affinity and specificity of HMGAs. By focusing on two human genes whose expression is directly regulated by HMGA1, the Insulin receptor (INSR) and the Insulin-like growth factor-binding protein 1 (IGFBP1) genes, we demonstrated that occupancy of their promoters by HMGA1 was NPM1-dependent, reflecting a mechanism in which the activity of these cis-regulatory elements is directly modulated by NPM1 leading to changes in gene expression. HMGAs need short stretches of AT-rich nucleosome-free regions to bind to DNA. Therefore, many putative HMGA binding sites are present within the genome. Our findings indicate that NPM1, by exerting a chaperoning activity towards HMGAs, may act as a master regulator in the control of DNA occupancy by these proteins and hence in HMGA-mediated gene expression.
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Affiliation(s)
- Laura Arnoldo
- Department of Life Sciences, University of Trieste, Trieste, 34127, Italy
| | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, Trieste, 34127, Italy
| | - Eusebio Chiefari
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Catanzaro, 88100, Italy
| | - Stefania Iiritano
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Catanzaro, 88100, Italy
| | - Biagio Arcidiacono
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Catanzaro, 88100, Italy
| | - Silvia Pegoraro
- Department of Life Sciences, University of Trieste, Trieste, 34127, Italy
| | - Ilenia Pellarin
- Department of Life Sciences, University of Trieste, Trieste, 34127, Italy
| | - Antonio Brunetti
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Catanzaro, 88100, Italy
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Holmberg Olausson K, Nistér M, Lindström MS. Loss of nucleolar histone chaperone NPM1 triggers rearrangement of heterochromatin and synergizes with a deficiency in DNA methyltransferase DNMT3A to drive ribosomal DNA transcription. J Biol Chem 2014; 289:34601-19. [PMID: 25349213 DOI: 10.1074/jbc.m114.569244] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleoli are prominent nuclear structures assembled and organized around actively transcribed ribosomal DNA (rDNA). The nucleolus has emerged as a platform for the organization of chromatin enriched for repressive histone modifications associated with repetitive DNA. NPM1 is a nucleolar protein required for the maintenance of genome stability. However, the role of NPM1 in nucleolar chromatin dynamics and ribosome biogenesis remains unclear. We found that normal fibroblasts and cancer cells depleted of NPM1 displayed deformed nucleoli and a striking rearrangement of perinucleolar heterochromatin, as identified by immunofluorescence staining of trimethylated H3K9, trimethylated H3K27, and heterochromatin protein 1γ (HP1γ/CBX3). By co-immunoprecipitation we found NPM1 associated with HP1γ and core and linker histones. Moreover, NPM1 was required for efficient tethering of HP1γ-enriched chromatin to the nucleolus. We next tested whether the alterations in perinucleolar heterochromatin architecture correlated with a difference in the regulation of rDNA. U1242MG glioma cells depleted of NPM1 presented with altered silver staining of nucleolar organizer regions, coupled to a modest decrease in H3K9 di- and trimethylation at the rDNA promoter. rDNA transcription and cell proliferation were sustained in these cells, indicating that altered organization of heterochromatin was not secondary to inhibition of rDNA transcription. Furthermore, knockdown of DNA methyltransferase DNMT3A markedly enhanced rDNA transcription in NPM1-depleted U1242MG cells. In summary, this study highlights a function of NPM1 in the spatial organization of nucleolus-associated heterochromatin.
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Affiliation(s)
- Karl Holmberg Olausson
- From the Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Monica Nistér
- From the Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Mikael S Lindström
- From the Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Karolinska University Hospital, SE-17176 Stockholm, Sweden
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PTEN interacts with histone H1 and controls chromatin condensation. Cell Rep 2014; 8:2003-2014. [PMID: 25199838 DOI: 10.1016/j.celrep.2014.08.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 07/05/2014] [Accepted: 08/05/2014] [Indexed: 01/16/2023] Open
Abstract
Chromatin organization and dynamics are integral to global gene transcription. Histone modification influences chromatin status and gene expression. PTEN plays multiple roles in tumor suppression, development, and metabolism. Here, we report on the interplay of PTEN, histone H1, and chromatin. We show that loss of PTEN leads to dissociation of histone H1 from chromatin and decondensation of chromatin. PTEN deletion also results in elevation of histone H4 acetylation at lysine 16, an epigenetic marker for chromatin activation. We found that PTEN and histone H1 physically interact through their C-terminal domains. Disruption of the PTEN C terminus promotes the chromatin association of MOF acetyltransferase and induces H4K16 acetylation. Hyperacetylation of H4K16 impairs the association of PTEN with histone H1, which constitutes regulatory feedback that may reduce chromatin stability. Our results demonstrate that PTEN controls chromatin condensation, thus influencing gene expression. We propose that PTEN regulates global gene transcription profiling through histones and chromatin remodeling.
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Shandilya J, Senapati P, Dhanasekaran K, Bangalore SS, Kumar M, Kishore AH, Bhat A, Kodaganur GS, Kundu TK. Phosphorylation of multifunctional nucleolar protein nucleophosmin (NPM1) by aurora kinase B is critical for mitotic progression. FEBS Lett 2014; 588:2198-205. [PMID: 24857377 DOI: 10.1016/j.febslet.2014.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 04/17/2014] [Accepted: 05/08/2014] [Indexed: 01/05/2023]
Abstract
The functional association of NPM1 with Aurora kinases is well documented. Surprisingly, although NPM1 is a well characterized phosphoprotein, it is unknown whether it is a substrate of Aurora kinases. We have found that Aurora kinases A and B can phosphorylate NPM1 at a single serine residue, Ser125, in vitro and in vivo. Phosphorylated-S125-NPM1 (pS125-NPM1) localizes to the midbody region during late cytokinesis where it colocalizes with Aurora B. The overexpression of mutant (S125A) NPM1 resulted in the deregulation of centrosome duplication and mitotic defects possibly due to cytokinesis failure. These data suggest that Aurora kinase B-mediated phosphorylation of NPM1 plays a critical role during mitosis, which could have wider implications in oncogenesis.
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Affiliation(s)
- Jayasha Shandilya
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, Karnataka, India
| | - Parijat Senapati
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, Karnataka, India
| | - Karthigeyan Dhanasekaran
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, Karnataka, India
| | - Suma S Bangalore
- Confocal Facility, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, Karnataka, India
| | - Manoj Kumar
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, Karnataka, India
| | - A Hari Kishore
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, Karnataka, India
| | - Akshay Bhat
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, Karnataka, India
| | | | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, Karnataka, India.
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Poletto M, Lirussi L, Wilson DM, Tell G. Nucleophosmin modulates stability, activity, and nucleolar accumulation of base excision repair proteins. Mol Biol Cell 2014; 25:1641-52. [PMID: 24648491 PMCID: PMC4019495 DOI: 10.1091/mbc.e13-12-0717] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/19/2014] [Accepted: 03/10/2014] [Indexed: 01/25/2023] Open
Abstract
Nucleophosmin (NPM1) is a multifunctional protein that controls cell growth and genome stability via a mechanism that involves nucleolar-cytoplasmic shuttling. It is clear that NPM1 also contributes to the DNA damage response, yet its exact function is poorly understood. We recently linked NPM1 expression to the functional activation of the major abasic endonuclease in mammalian base excision repair (BER), apurinic/apyrimidinic endonuclease 1 (APE1). Here we unveil a novel role for NPM1 as a modulator of the whole BER pathway by 1) controlling BER protein levels, 2) regulating total BER capacity, and 3) modulating the nucleolar localization of several BER enzymes. We find that cell treatment with the genotoxin cisplatin leads to concurrent relocalization of NPM1 and BER components from nucleoli to the nucleoplasm, and cellular experiments targeting APE1 suggest a role for the redistribution of nucleolar BER factors in determining cisplatin toxicity. Finally, based on the use of APE1 as a representative protein of the BER pathway, our data suggest a function for BER proteins in the regulation of ribogenesis.
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Affiliation(s)
- Mattia Poletto
- Department of Medical and Biological Sciences, University of Udine, Udine 33100, Italy
| | - Lisa Lirussi
- Department of Medical and Biological Sciences, University of Udine, Udine 33100, Italy
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224
| | - Gianluca Tell
- Department of Medical and Biological Sciences, University of Udine, Udine 33100, Italy
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Towards a mechanism for histone chaperones. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1819:211-221. [PMID: 24459723 DOI: 10.1016/j.bbagrm.2011.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Histone chaperones can be broadly defined as histone-binding proteins that influence chromatin dynamics in an ATP-independent manner. Their existence reflects the importance of chromatin homeostasis and the unique and unusual biochemistry of the histone proteins. Histone supply and demand at chromatin is regulated by a network of structurally and functionally diverse histone chaperones. At the core of this network is a mechanistic variability that is only beginning to be appreciated. In this review, we highlight the challenges in determining histone chaperone mechanism and discuss possible mechanisms in the context of nucleosome thermodynamics. We discuss how histone chaperones prevent promiscuous histone interactions, and consider if this activity represents the full extent of histone chaperone function in governing chromatin dynamics. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.
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Reddy D, Bhattacharya S, Gupta S. Histone Chaperones: Functions beyond Nucleosome Deposition. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/abb.2014.56064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Hisaoka M, Nagata K, Okuwaki M. Intrinsically disordered regions of nucleophosmin/B23 regulate its RNA binding activity through their inter- and intra-molecular association. Nucleic Acids Res 2013; 42:1180-95. [PMID: 24106084 PMCID: PMC3902904 DOI: 10.1093/nar/gkt897] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Nucleophosmin (NPM1/B23) is a nucleolar protein implicated in growth-associated functions, in which the RNA binding activity of B23 plays essential roles in ribosome biogenesis. The C-terminal globular domain (CTD) of B23 has been believed to be the RNA binding domain because the splicing variant B23.2 lacking the CTD binds considerably less efficiently to RNA. However, the recognition of target RNAs by B23 remains poorly understood. Herein, we report a novel mechanism by which B23 recognizes specific RNA targets. We observed that the nucleolar retention of B23.3 lacking the basic region of B23.1 was lower than that of B23.1 because of its low RNA binding activity. Circular dichroism measurements indicated that the basic region and adjacent acidic regions of B23 are intrinsically disordered regions (IDRs). Biochemical analyses revealed that the basic IDR alone strongly binds to RNA with low specificity. The excessive RNA binding activity of the basic IDR was restrained by intra-molecular interaction with the acidic IDR of B23. Chemical cross-linking experiments and fluorescent labeling of bipartite tetracysteine-tagged proteins suggested that the inter- and intra-molecular interactions between the two IDRs contribute to the regulation of the RNA binding activity of CTD to control the cellular localization and functions of B23.
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Affiliation(s)
- Miharu Hisaoka
- Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8575, Japan
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Kumari S, Swaminathan A, Chatterjee S, Senapati P, Boopathi R, Kundu TK. Chromatin organization, epigenetics and differentiation: an evolutionary perspective. Subcell Biochem 2013; 61:3-35. [PMID: 23150244 DOI: 10.1007/978-94-007-4525-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Genome packaging is a universal phenomenon from prokaryotes to higher mammals. Genomic constituents and forces have however, travelled a long evolutionary route. Both DNA and protein elements constitute the genome and also aid in its dynamicity. With the evolution of organisms, these have experienced several structural and functional changes. These evolutionary changes were made to meet the challenging scenario of evolving organisms. This review discusses in detail the evolutionary perspective and functionality gain in the phenomena of genome organization and epigenetics.
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Affiliation(s)
- Sujata Kumari
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Post, Bangalore, 560064, India
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Liu Y, Zhang F, Zhang XF, Qi LS, Yang L, Guo H, Zhang N. Expression of nucleophosmin/NPM1 correlates with migration and invasiveness of colon cancer cells. J Biomed Sci 2012; 19:53. [PMID: 22631075 PMCID: PMC3404909 DOI: 10.1186/1423-0127-19-53] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Accepted: 05/25/2012] [Indexed: 12/23/2022] Open
Abstract
Background We aimed to examine the expression level of Nucleophosmin (NPM1) protein in colon cancer tissues and to investigate the potential role of NPM1 in the regulation of cell migration and invasiveness. Methods Immunohistochemical assay was performed to examine the expression pattern of NPM1 in 31 groups of colonic carcinoma samples, including colon tumors, adjacent normal tissues, and matched metastatic lymph nodes from the same patients. Small interfering RNA technique and exogenous expression of wild type NPM1 methods were used to further verify the function of NPM1. Results High-expression of NPM1 correlates with lymph node metastasis (P = 0.0003) and poor survival rate of human colon cancer patients (P = 0.017). SiRNA-mediated reduction of NPM1 was also shown to inhibit the migration and invasiveness of metastatic colon cancer HCT116 cell line. In addition, the exogenous expression of NPM1 in HT29 cells, a NPM1 low expression and low invasive colon cancer cell line, enhanced cell migration and invasiveness along with increased cell proliferation. Conclusions The current study uncovered the critical role of NPM1 in the regulation of colon cancer cells migration and invasion, and NPM1 may serve as a potential marker for the prognosis of colon cancer patients.
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Affiliation(s)
- Yan Liu
- Tianjin Medical University, Cancer Institute and Hospital, Research Center of Basic Medical Sciences, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin 300060, China
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Capriotti AL, Caracciolo G, Caruso G, Foglia P, Pozzi D, Samperi R, Laganà A. Differential analysis of “protein corona” profile adsorbed onto different nonviral gene delivery systems. Anal Biochem 2011; 419:180-9. [DOI: 10.1016/j.ab.2011.08.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 07/29/2011] [Accepted: 08/02/2011] [Indexed: 01/28/2023]
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Falini B, Gionfriddo I, Cecchetti F, Ballanti S, Pettirossi V, Martelli MP. Acute myeloid leukemia with mutated nucleophosmin (NPM1): any hope for a targeted therapy? Blood Rev 2011; 25:247-54. [PMID: 21724308 DOI: 10.1016/j.blre.2011.06.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Acute myeloid leukemia (AML) carrying nucleophosmin (NPM1) mutations displays distinct molecular and clinical-pathological features that led to its inclusion as provisional entity in 2008 WHO classification of myeloid neoplasms. Since NPM1 mutations behave as a founder genetic lesion in AML, they could be an attractive target for therapeutic intervention. Here, we discuss the potential for developing targeted therapies for NPM1-mutated AML with focus on: (i) interfering with the abnormal traffic of the NPM1 leukemic mutant, i.e., its cytoplasmic dislocation; (ii) disrupting the nucleolar structure/function by interfering with residual wild-type nucleophosmin and other nucleolar components acting as hub proteins; and (iii) evaluating the activity of epigenetic drugs (e.g., 5-azacytidine) or agents acting on differentiation and apoptosis. As quantitative assessment of NPM1 mutated transcript copies now provides the means to measure minimal residual disease, we also discuss the potential for intervening in NPM1-mutated AML before overt hematological relapse occurs (so-called pre-emptive therapy).
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Affiliation(s)
- Brunangelo Falini
- Institute of Hematology, Strada Sant'Andrea delle Fratte, University of Perugia, 06122 Perugia, Italy.
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