1
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Abou-Ghali M, Lallemand-Breitenbach V. PML Nuclear bodies: the cancer connection and beyond. Nucleus 2024; 15:2321265. [PMID: 38411156 PMCID: PMC10900273 DOI: 10.1080/19491034.2024.2321265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/16/2024] [Indexed: 02/28/2024] Open
Abstract
Promyelocytic leukemia (PML) nuclear bodies, membrane-less organelles in the nucleus, play a crucial role in cellular homeostasis. These dynamic structures result from the assembly of scaffolding PML proteins and various partners. Recent crystal structure analyses revealed essential self-interacting domains, while liquid-liquid phase separation contributes to their formation. PML bodies orchestrate post-translational modifications, particularly stress-induced SUMOylation, impacting target protein functions. Serving as hubs in multiple signaling pathways, they influence cellular processes like senescence. Dysregulation of PML expression contributes to diseases, including cancer, highlighting their significance. Therapeutically, PML bodies are promising targets, exemplified by successful acute promyelocytic leukemia treatment with arsenic trioxide and retinoic acid restoring PML bodies. Understanding their functions illuminates both normal and pathological cellular physiology, guiding potential therapies. This review explores recent advancements in PML body biogenesis, biochemical activity, and their evolving biological roles.
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Affiliation(s)
- Majdouline Abou-Ghali
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université 11 PSL, Paris, France
- Saint-Louis Research Institute, Paris, France
| | - Valérie Lallemand-Breitenbach
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université 11 PSL, Paris, France
- Saint-Louis Research Institute, Paris, France
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2
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León NY, Le TNU, Garvie A, Wong LH, Bagheri-Fam S, Harley VR. Y chromosome damage underlies testicular abnormalities in ATR-X syndrome. iScience 2024; 27:109629. [PMID: 38616920 PMCID: PMC11015497 DOI: 10.1016/j.isci.2024.109629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/27/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
ATR-X (alpha thalassemia, mental retardation, X-linked) syndrome features genital and testicular abnormalities including atypical genitalia and small testes with few seminiferous tubules. Our mouse model recapitulated the testicular defects when Atrx was deleted in Sertoli cells (ScAtrxKO) which displayed G2/M arrest and apoptosis. Here, we investigated the mechanisms underlying these defects. In control mice, Sertoli cells contain a single novel "GATA4 PML nuclear body (NB)" that contained the transcription factor GATA4, ATRX, DAXX, HP1α, and PH3 and co-localized with the Y chromosome short arm (Yp). ScAtrxKO mice contain single giant GATA4 PML-NBs with frequent DNA double-strand breaks (DSBs) in G2/M-arrested apoptotic Sertoli cells. HP1α and PH3 were absent from giant GATA4 PML-NBs indicating a failure in heterochromatin formation and chromosome condensation. Our data suggest that ATRX protects a Yp region from DNA damage, thereby preventing Sertoli cell death. We discuss Y chromosome damage/decondensation as a mechanism for testicular failure.
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Affiliation(s)
- Nayla Y. León
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Thanh Nha Uyen Le
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Andrew Garvie
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Lee H. Wong
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Stefan Bagheri-Fam
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Vincent R. Harley
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
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3
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Hofmann S, Luther J, Plank V, Oswald A, Mai J, Simons I, Miller J, Falcone V, Hansen-Palmus L, Hengel H, Nassal M, Protzer U, Schreiner S. Arsenic trioxide impacts hepatitis B virus core nuclear localization and efficiently interferes with HBV infection. Microbiol Spectr 2024; 12:e0378823. [PMID: 38567974 PMCID: PMC11064512 DOI: 10.1128/spectrum.03788-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/14/2024] [Indexed: 05/03/2024] Open
Abstract
The key to a curative treatment of hepatitis B virus (HBV) infection is the eradication of the intranuclear episomal covalently closed circular DNA (cccDNA), the stable persistence reservoir of HBV. Currently, established therapies can only limit HBV replication but fail to tackle the cccDNA. Thus, novel therapeutic approaches toward curative treatment are urgently needed. Recent publications indicated a strong association between the HBV core protein SUMOylation and the association with promyelocytic leukemia nuclear bodies (PML-NBs) on relaxed circular DNA to cccDNA conversion. We propose that interference with the cellular SUMOylation system and PML-NB integrity using arsenic trioxide provides a useful tool in the treatment of HBV infection. Our study showed a significant reduction in HBV-infected cells, core protein levels, HBV mRNA, and total DNA. Additionally, a reduction, albeit to a limited extent, of HBV cccDNA could be observed. Furthermore, this interference was also applied for the treatment of an established HBV infection, characterized by a stably present nuclear pool of cccDNA. Arsenic trioxide (ATO) treatment not only changed the amount of expressed HBV core protein but also induced a distinct relocalization to an extranuclear phenotype during infection. Moreover, ATO treatment resulted in the redistribution of transfected HBV core protein away from PML-NBs, a phenotype similar to that previously observed with SUMOylation-deficient HBV core. Taken together, these findings revealed the inhibition of HBV replication by ATO treatment during several steps of the viral replication cycle, including viral entry into the nucleus as well as cccDNA formation and maintenance. We propose ATO as a novel prospective treatment option for further pre-clinical and clinical studies against HBV infection. IMPORTANCE The main challenge for the achievement of a functional cure for hepatitis B virus (HBV) is the covalently closed circular DNA (cccDNA), the highly stable persistence reservoir of HBV, which is maintained by further rounds of infection with newly generated progeny viruses or by intracellular recycling of mature nucleocapsids. Eradication of the cccDNA is considered to be the holy grail for HBV curative treatment; however, current therapeutic approaches fail to directly tackle this HBV persistence reservoir. The molecular effect of arsenic trioxide (ATO) on HBV infection, protein expression, and cccDNA formation and maintenance, however, has not been characterized and understood until now. In this study, we reveal ATO treatment as a novel and innovative therapeutic approach against HBV infections, repressing viral gene expression and replication as well as the stable cccDNA pool at low micromolar concentrations by affecting the cellular function of promyelocytic leukemia nuclear bodies.
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Affiliation(s)
- Samuel Hofmann
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (Resolving Infection Susceptibility, EXC 2155), Hannover Medical School, Hannover, Germany
- Division of Pediatric Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Julius Luther
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (Resolving Infection Susceptibility, EXC 2155), Hannover Medical School, Hannover, Germany
| | - Verena Plank
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Andreas Oswald
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Mai
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (Resolving Infection Susceptibility, EXC 2155), Hannover Medical School, Hannover, Germany
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Ilka Simons
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (Resolving Infection Susceptibility, EXC 2155), Hannover Medical School, Hannover, Germany
| | - Julija Miller
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Valeria Falcone
- Institute of Virology, Medical Center – University of Freiburg, Freiburg, Germany
| | - Lea Hansen-Palmus
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Hartmut Hengel
- Institute of Virology, Medical Center – University of Freiburg, Freiburg, Germany
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Sabrina Schreiner
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (Resolving Infection Susceptibility, EXC 2155), Hannover Medical School, Hannover, Germany
- Institute of Virology, Medical Center – University of Freiburg, Freiburg, Germany
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4
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McPhee M, Lee J, Salsman J, Pinelli M, Di Cara F, Rosen K, Dellaire G, Ridgway ND. Nuclear lipid droplets in Caco2 cells originate from nascent precursors and in situ at the nuclear envelope. J Lipid Res 2024; 65:100540. [PMID: 38570093 PMCID: PMC11077042 DOI: 10.1016/j.jlr.2024.100540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
Intestinal epithelial cells convert excess fatty acids into triglyceride (TAG) for storage in cytoplasmic lipid droplets and secretion in chylomicrons. Nuclear lipid droplets (nLDs) are present in intestinal cells but their origin and relationship to cytoplasmic TAG synthesis and secretion is unknown. nLDs and related lipid-associated promyelocytic leukemia structures (LAPS) were abundant in oleate-treated Caco2 but less frequent in other human colorectal cancer cell lines and mouse intestinal organoids. nLDs and LAPS in undifferentiated oleate-treated Caco2 cells harbored the phosphatidate phosphatase Lipin1, its product diacylglycerol, and CTP:phosphocholine cytidylyltransferase (CCT)α. CCTα knockout Caco2 cells had fewer but larger nLDs, indicating a reliance on de novo PC synthesis for assembly. Differentiation of Caco2 cells caused large nLDs and LAPS to form regardless of oleate treatment or CCTα expression. nLDs and LAPS in Caco2 cells did not associate with apoCIII and apoAI and formed dependently of microsomal triglyceride transfer protein expression and activity, indicating they are not derived from endoplasmic reticulum luminal LDs precursors. Instead, undifferentiated Caco2 cells harbored a constitutive pool of nLDs and LAPS in proximity to the nuclear envelope that expanded in size and number with oleate treatment. Inhibition of TAG synthesis did affect the number of nascent nLDs and LAPS but prevented their association with promyelocytic leukemia protein, Lipin1α, and diacylglycerol, which instead accumulated on the nuclear membranes. Thus, nLD and LAPS biogenesis in Caco2 cells is not linked to lipoprotein secretion but involves biogenesis and/or expansion of nascent nLDs by de novo lipid synthesis.
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Affiliation(s)
- Michael McPhee
- Depts of Pediatrics and Biochemistry & Molecular Biology, Atlantic Research Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jonghwa Lee
- Depts of Pediatrics and Biochemistry & Molecular Biology, Atlantic Research Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jayme Salsman
- Depts of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Marinella Pinelli
- Dept of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Francesca Di Cara
- Dept of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kirill Rosen
- Depts of Pediatrics and Biochemistry & Molecular Biology, Atlantic Research Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Graham Dellaire
- Depts of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Neale D Ridgway
- Depts of Pediatrics and Biochemistry & Molecular Biology, Atlantic Research Centre, Dalhousie University, Halifax, Nova Scotia, Canada.
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5
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Foster J, McPhee M, Yue L, Dellaire G, Pelech S, Ridgway ND. Lipid- and phospho-regulation of CTP:Phosphocholine Cytidylyltransferase α association with nuclear lipid droplets. Mol Biol Cell 2024; 35:ar33. [PMID: 38170618 PMCID: PMC10916874 DOI: 10.1091/mbc.e23-09-0354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
Fatty acids stored in triacylglycerol-rich lipid droplets are assembled with a surface monolayer composed primarily of phosphatidylcholine (PC). Fatty acids stimulate PC synthesis by translocating CTP:phosphocholine cytidylyltransferase (CCT) α to the inner nuclear membrane, nuclear lipid droplets (nLD) and lipid associated promyelocytic leukemia (PML) structures (LAPS). Huh7 cells were used to identify how CCTα translocation onto these nuclear structures are regulated by fatty acids and phosphorylation of its serine-rich P-domain. Oleate treatment of Huh7 cells increased nLDs and LAPS that became progressively enriched in CCTα. In cells expressing the phosphatidic acid phosphatase Lipin1α or 1β, the expanded pool of nLDs and LAPS had a proportional increase in associated CCTα. In contrast, palmitate induced few nLDs and LAPS and inhibited the oleate-dependent translocation of CCTα without affecting total nLDs. Phospho-memetic or phospho-null mutations in the P-domain revealed that a 70% phosphorylation threshold, rather than site-specific phosphorylation, regulated CCTα association with nLDs and LAPS. In vitro candidate kinase and inhibitor studies in Huh7 cells identified cyclin-dependent kinase (CDK) 1 and 2 as putative P-domain kinases. In conclusion, CCTα translocation onto nLDs and LAPS is dependent on available surface area and fatty acid composition, as well as threshold phosphorylation of the P-domain potentially involving CDKs.
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Affiliation(s)
- Jason Foster
- Departments of Pediatrics and Biochemistry & Molecular Biology, Atlantic Research Centre, and
| | - Michael McPhee
- Departments of Pediatrics and Biochemistry & Molecular Biology, Atlantic Research Centre, and
| | - Lambert Yue
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada V6T 2B5
| | - Graham Dellaire
- Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Steven Pelech
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada V6T 2B5
- Kinexus Bioinformatics Corporation, Vancouver, BC, Canada V6P 6T3
| | - Neale D. Ridgway
- Departments of Pediatrics and Biochemistry & Molecular Biology, Atlantic Research Centre, and
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6
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Collin V, Biquand É, Tremblay V, Lavoie ÉG, Blondeau A, Gravel A, Galloy M, Lashgari A, Dessapt J, Côté J, Flamand L, Fradet-Turcotte A. The immediate-early protein 1 of human herpesvirus 6B interacts with NBS1 and inhibits ATM signaling. EMBO Rep 2024; 25:725-744. [PMID: 38177923 PMCID: PMC10897193 DOI: 10.1038/s44319-023-00035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
Viral infection often trigger an ATM serine/threonine kinase (ATM)-dependent DNA damage response in host cells that suppresses viral replication. Viruses evolved different strategies to counteract this antiviral surveillance system. Here, we report that human herpesvirus 6B (HHV-6B) infection causes genomic instability by suppressing ATM signaling in host cells. Expression of immediate-early protein 1 (IE1) phenocopies this phenotype and blocks homology-directed double-strand break repair. Mechanistically, IE1 interacts with NBS1, and inhibits ATM signaling through two distinct domains. HHV-6B seems to efficiently inhibit ATM signaling as further depletion of either NBS1 or ATM do not significantly boost viral replication in infected cells. Interestingly, viral integration of HHV-6B into the host's telomeres is not strictly dependent on NBS1, challenging current models where integration occurs through homology-directed repair. Given that spontaneous IE1 expression has been detected in cells of subjects with inherited chromosomally-integrated form of HHV-6B (iciHHV-6B), a condition associated with several health conditions, our results raise the possibility of a link between genomic instability and the development of iciHHV-6-associated diseases.
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Affiliation(s)
- Vanessa Collin
- Division of Infectious Disease and Immunity, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1V 4G2, Canada
- Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Élise Biquand
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
- INSERM, Centre d'Étude des Pathologies Respiratoires (CEPR), UMR 1100, Université de Tours, Tours, France
| | - Vincent Tremblay
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Élise G Lavoie
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Andréanne Blondeau
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Annie Gravel
- Division of Infectious Disease and Immunity, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1V 4G2, Canada
- Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Maxime Galloy
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Anahita Lashgari
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Julien Dessapt
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Jacques Côté
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Louis Flamand
- Division of Infectious Disease and Immunity, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1V 4G2, Canada.
- Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, G1V 0A6, Canada.
| | - Amélie Fradet-Turcotte
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada.
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada.
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada.
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7
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Salomoni P. Gelling Bodies: Understanding the Mechanisms Underlying Arsenic Trioxide Action. Cancer Discov 2023; 13:2505-2506. [PMID: 38084094 DOI: 10.1158/2159-8290.cd-23-1004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
SUMMARY The study by Bercier and colleagues investigates the mechanisms of action of arsenic trioxide (ATO). The authors find that ATO promotes transition of PML nuclear bodies to a gel-like state via the PML trimerization domain and a critical cysteine residue. Overall, this work sheds new light onto how PML-RARα, the oncogene of APL, is targeted by ATO for disease eradication. See related article by Bercier et al., p. 2548 (6).
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Affiliation(s)
- Paolo Salomoni
- Nuclear Function Group, German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, Bonn, Germany
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8
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SoRelle ED, Reinoso-Vizcaino NM, Dai J, Barry AP, Chan C, Luftig MA. Epstein-Barr virus evades restrictive host chromatin closure by subverting B cell activation and germinal center regulatory loci. Cell Rep 2023; 42:112958. [PMID: 37561629 PMCID: PMC10559315 DOI: 10.1016/j.celrep.2023.112958] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Chromatin accessibility fundamentally governs gene expression and biological response programs that can be manipulated by pathogens. Here we capture dynamic chromatin landscapes of individual B cells during Epstein-Barr virus (EBV) infection. EBV+ cells that exhibit arrest via antiviral sensing and proliferation-linked DNA damage experience global accessibility reduction. Proliferative EBV+ cells develop expression-linked architectures and motif accessibility profiles resembling in vivo germinal center (GC) phenotypes. Remarkably, EBV elicits dark zone (DZ), light zone (LZ), and post-GC B cell chromatin features despite BCL6 downregulation. Integration of single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), single-cell RNA sequencing (scRNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) data enables genome-wide cis-regulatory predictions implicating EBV nuclear antigens (EBNAs) in phenotype-specific control of GC B cell activation, survival, and immune evasion. Knockouts validate bioinformatically identified regulators (MEF2C and NFE2L2) of EBV-induced GC phenotypes and EBNA-associated loci that regulate gene expression (CD274/PD-L1). These data and methods can inform high-resolution investigations of EBV-host interactions, B cell fates, and virus-mediated lymphomagenesis.
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Affiliation(s)
- Elliott D SoRelle
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Nicolás M Reinoso-Vizcaino
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joanne Dai
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ashley P Barry
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA.
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9
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Rérolle D, de Thé H. The PML hub: An emerging actor of leukemia therapies. J Exp Med 2023; 220:e20221213. [PMID: 37382966 PMCID: PMC10309189 DOI: 10.1084/jem.20221213] [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: 03/28/2023] [Revised: 05/29/2023] [Accepted: 06/09/2023] [Indexed: 06/30/2023] Open
Abstract
PML assembles into nuclear domains that have attracted considerable attention from cell and cancer biologists. Upon stress, PML nuclear bodies modulate sumoylation and other post-translational modifications, providing an integrated molecular framework for the multiple roles of PML in apoptosis, senescence, or metabolism. PML is both a sensor and an effector of oxidative stress. Emerging data has demonstrated its key role in promoting therapy response in several hematological malignancies. While these membrane-less nuclear hubs can enforce efficient cancer cell clearance, their downstream pathways deserve better characterization. PML NBs are druggable and their known modulators may have broader clinical utilities than initially thought.
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Affiliation(s)
- Domitille Rérolle
- Center for Interdisciplinary Research in Biology, Collège de France, Inserm, PSL Research University, Paris, France
- Université Paris Cité, Inserm U944, CNRS, GenCellDis, Institut de Recherche Saint-Louis, Paris, France
| | - Hugues de Thé
- Center for Interdisciplinary Research in Biology, Collège de France, Inserm, PSL Research University, Paris, France
- Université Paris Cité, Inserm U944, CNRS, GenCellDis, Institut de Recherche Saint-Louis, Paris, France
- Chaire d'Oncologie Cellulaire et Moléculaire, Collège de France, Paris, France
- Service d'Hématologie Biologique, Assistance Publique-Hôpitaux de Paris, Hôpital St. Louis, Paris, France
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10
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Hofmann S, Plank V, Groitl P, Skvorc N, Hofmann K, Luther J, Ko C, Zimmerman P, Bruss V, Stadler D, Carpentier A, Rezk S, Nassal M, Protzer U, Schreiner S. SUMO Modification of Hepatitis B Virus Core Mediates Nuclear Entry, Promyelocytic Leukemia Nuclear Body Association, and Efficient Formation of Covalently Closed Circular DNA. Microbiol Spectr 2023; 11:e0044623. [PMID: 37199632 PMCID: PMC10269885 DOI: 10.1128/spectrum.00446-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Persistence of hepatitis B virus (HBV) infection is due to a nuclear covalently closed circular DNA (cccDNA), generated from the virion-borne relaxed circular DNA (rcDNA) genome in a process likely involving numerous cell factors from the host DNA damage response (DDR). The HBV core protein mediates rcDNA transport to the nucleus and likely affects stability and transcriptional activity of cccDNA. Our study aimed at investigating the role of HBV core protein and its posttranslational modification (PTM) with SUMO (small ubiquitin-like modifiers) during the establishment of cccDNA. HBV core protein SUMO PTM was analyzed in His-SUMO-overexpressing cell lines. The impact of HBV core SUMOylation on association with cellular interaction partners and on the HBV life cycle was determined using SUMOylation-deficient mutants of the HBV core protein. Here, we show that the HBV core protein is posttranslationally modified by the addition of SUMO and that this modification impacts nuclear import of rcDNA. By using SUMOylation-deficient HBV core mutants, we show that SUMO modification is a prerequisite for the association with specific promyelocytic leukemia nuclear bodies (PML-NBs) and regulates the conversion of rcDNA to cccDNA. By in vitro SUMOylation of HBV core, we obtained evidence that SUMOylation triggers nucleocapsid disassembly, providing novel insights into the nuclear import process of rcDNA. HBV core protein SUMOylation and subsequent association with PML bodies in the nucleus constitute a key step in the conversion of HBV rcDNA to cccDNA and therefore a promising target for inhibiting formation of the HBV persistence reservoir. IMPORTANCE HBV cccDNA is formed from the incomplete rcDNA involving several host DDR proteins. The exact process and the site of cccDNA formation are poorly understood. Here, we show that HBV core protein SUMO modification is a novel PTM regulating the function of HBV core. A minor specific fraction of the HBV core protein resides with PML-NBs in the nuclear matrix. SUMO modification of HBV core protein mediates its recruitment to specific PML-NBs within the host cell. Within HBV nucleocapsids, SUMOylation of HBV core induces HBV capsid disassembly and is a prerequisite for nuclear entry of HBV core. SUMO HBV core protein association with PML-NBs is crucial for efficient conversion of rcDNA to cccDNA and for the establishment of the viral persistence reservoir. HBV core protein SUMO modification and the subsequent association with PML-NBs might constitute a potential novel target in the development of drugs targeting the cccDNA.
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Affiliation(s)
- Samuel Hofmann
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Verena Plank
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
| | - Peter Groitl
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
| | - Nathalie Skvorc
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
| | - Katharina Hofmann
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Julius Luther
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Chunkyu Ko
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Peter Zimmerman
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Volker Bruss
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Daniela Stadler
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | | | - Shahinda Rezk
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Medical Research Institute, Department of Molecular and Diagnostic Microbiology, Alexandria University, Alexandria, Egypt
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research, Munich, Germany
| | - Sabrina Schreiner
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research, Munich, Germany
- Cluster of Excellence RESIST (Resolving Infection Susceptibility; EXC 2155), Hannover Medical School, Hannover, Germany
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11
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Procario MC, Sexton JZ, Halligan BS, Imperiale MJ. Single-Cell, High-Content Microscopy Analysis of BK Polyomavirus Infection. Microbiol Spectr 2023; 11:e0087323. [PMID: 37154756 PMCID: PMC10269497 DOI: 10.1128/spectrum.00873-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/08/2023] [Indexed: 05/10/2023] Open
Abstract
By adulthood, the majority of the population is persistently infected with BK polyomavirus (BKPyV). Only a subset of the population, generally transplant recipients on immunosuppressive drugs, will experience disease from BKPyV, but those who do have few treatment options and, frequently, poor outcomes, because to date there are no effective antivirals to treat or approved vaccines to prevent BKPyV. Most studies of BKPyV have been performed on bulk populations of cells, and the dynamics of infection at single-cell resolution have not been explored. As a result, much of our knowledge is based upon the assumption that all cells within a greater population are behaving the same way with respect to infection. The present study examines BKPyV infection on a single-cell level using high-content microscopy to measure and analyze the viral protein large T antigen (TAg), promyelocytic leukemia protein (PML), DNA, and nuclear morphological features. We observed significant heterogeneity among infected cells, within and across time points. We found that the levels of TAg within individual cells did not necessarily increase with time and that cells with the same TAg levels varied in other ways. Overall, high-content, single-cell microscopy is a novel approach to studying BKPyV that enables experimental insight into the heterogenous nature of the infection. IMPORTANCE BK polyomavirus (BKPyV) is a human pathogen that infects nearly everyone by adulthood and persists throughout a person's life. Only people with significant immune suppression develop disease from the virus, however. Until recently the only practical means of studying many viral infections was to infect a group of cells in the laboratory and measure the outcomes in that group. However, interpreting these bulk population experiments requires the assumption that infection influences all cells within a group similarly. This assumption has not held for multiple viruses tested so far. Our study establishes a novel single-cell microscopy assay for BKPyV infection. Using this assay, we discovered differences among individual infected cells that have not been apparent in bulk population studies. The knowledge gained in this study and the potential for future use demonstrate the power of this assay as a tool for understanding the biology of BKPyV.
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Affiliation(s)
- Megan C. Procario
- Department of Microbiology and Immunology, Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonathan Z. Sexton
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
- Center for Drug Repurposing, University of Michigan, Ann Arbor, Michigan, USA
| | - Benjamin S. Halligan
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael J. Imperiale
- Department of Microbiology and Immunology, Medical School, University of Michigan, Ann Arbor, Michigan, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
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12
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Trier I, Black EM, Joo YK, Kabeche L. ATR protects centromere identity by promoting DAXX association with PML nuclear bodies. Cell Rep 2023; 42:112495. [PMID: 37163376 DOI: 10.1016/j.celrep.2023.112495] [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: 10/03/2022] [Revised: 03/10/2023] [Accepted: 04/25/2023] [Indexed: 05/12/2023] Open
Abstract
Centromere protein A (CENP-A) defines centromere identity and nucleates kinetochore formation for mitotic chromosome segregation. Here, we show that ataxia telangiectasia and Rad3-related (ATR) kinase, a master regulator of the DNA damage response, protects CENP-A occupancy at interphase centromeres in a DNA damage-independent manner. In unperturbed cells, ATR localizes to promyelocytic leukemia nuclear bodies (PML NBs), which house the histone H3.3 chaperone DAXX (death domain-associated protein 6). We find that ATR inhibition reduces DAXX association with PML NBs, resulting in the DAXX-dependent loss of CENP-A and an aberrant increase in H3.3 at interphase centromeres. Additionally, we show that ATR-dependent phosphorylation within the C terminus of DAXX regulates CENP-A occupancy at centromeres and DAXX localization. Lastly, we demonstrate that acute ATR inhibition during interphase leads to kinetochore formation defects and an increased rate of lagging chromosomes. These findings highlight a mechanism by which ATR protects centromere identity and genome stability.
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Affiliation(s)
- Isabelle Trier
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Elizabeth M Black
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yoon Ki Joo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Lilian Kabeche
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA.
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13
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Voss PG, Wang JL. Liquid-liquid phase separation: Galectin-3 in nuclear speckles and ribonucleoprotein complexes. Exp Cell Res 2023; 427:113571. [PMID: 37003559 DOI: 10.1016/j.yexcr.2023.113571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]
Abstract
Nuclear speckles are subcellular structures originally characterized by punctate immunofluorescence staining of the monoclonal antibody SC35, which recognizes an epitope on SRRM2 (serine/arginine repetitive matrix protein 2) and Sfrs2, a member of the SR (serine/arginine-rich) family of splicing factors. Galectin-3 co-localizes with SC35 in nuclear speckles, which represent one group of nuclear bodies that include the nucleolus, Cajal bodies and gems, paraspeckles, etc. Although they appear to have well-delineated physical boundaries, these nuclear bodies are not membrane-bound structures but represent macromolecular assemblies arising from a phenomenon called liquid-liquid phase separation. There has been much recent interest in liquid phase condensation as a newly recognized mechanism by which a cell can organize and compartmentalize subcellular structures with distinct composition. The punctate/speckled staining of galectin-3 with SC3 demonstrates their co-localization in a phase-separated body in vivo, under conditions endogenous to the cell. The purpose of the present review is to summarize the studies that document three key features of galectin-3 for its localization in liquid phase condensates: (a) an intrinsically disordered domain; (b) oligomer formation for multivalent binding; and (c) association with RNA and ribonucleoprotein complexes.
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Affiliation(s)
- Patricia G Voss
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - John L Wang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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14
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Cobb AM, De Silva SA, Hayward R, Sek K, Ulferts S, Grosse R, Shanahan CM. Filamentous nuclear actin regulation of PML NBs during the DNA damage response is deregulated by prelamin A. Cell Death Dis 2022; 13:1042. [PMID: 36522328 PMCID: PMC9755150 DOI: 10.1038/s41419-022-05491-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/16/2022]
Abstract
Nuclear actin participates in a continuously expanding list of core processes within eukaryotic nuclei, including the maintenance of genomic integrity. In response to DNA damage, nuclear actin polymerises into filaments that are involved in the repair of damaged DNA through incompletely defined mechanisms. We present data to show that the formation of nuclear F-actin in response to genotoxic stress acts as a scaffold for PML NBs and that these filamentous networks are essential for PML NB fission and recruitment of microbodies to DNA lesions. Further to this, we demonstrate that the accumulation of the toxic lamin A precursor prelamin A induces mislocalisation of nuclear actin to the nuclear envelope and prevents the establishment of nucleoplasmic F-actin networks in response to stress. Consequently, PML NB dynamics and recruitment to DNA lesions is ablated, resulting in impaired DNA damage repair. Inhibition of nuclear export of formin mDia2 restores nuclear F-actin formation by augmenting polymerisation of nuclear actin in response to stress and rescues PML NB localisation to sites of DNA repair, leading to reduced levels of DNA damage.
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Affiliation(s)
- Andrew M. Cobb
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Shanelle A. De Silva
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Robert Hayward
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Karolina Sek
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Svenja Ulferts
- grid.5963.9Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Robert Grosse
- grid.5963.9Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Catherine M. Shanahan
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
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15
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Liebl MC, Hofmann TG. Regulating the p53 Tumor Suppressor Network at PML Biomolecular Condensates. Cancers (Basel) 2022; 14:4549. [PMID: 36230470 PMCID: PMC9558958 DOI: 10.3390/cancers14194549] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
By forming specific functional entities, nuclear biomolecular condensates play an important function in guiding biological processes. PML biomolecular condensates, also known as PML nuclear bodies (NBs), are macro-molecular sub-nuclear organelles involved in central biological processes, including anti-viral response and cell fate control upon genotoxic stress. PML condensate formation is stimulated upon cellular stress, and relies on protein-protein interactions establishing a PML protein meshwork capable of recruiting the tumor suppressor p53, along with numerous modifiers of p53, thus balancing p53 posttranslational modifications and activity. This stress-regulated process appears to be controlled by liquid-liquid phase separation (LLPS), which may facilitate regulated protein-unmixing of p53 and its regulators into PML nuclear condensates. In this review, we summarize and discuss the molecular mechanisms underlying PML nuclear condensate formation, and how these impact the biological function of p53 in driving the cell death and senescence responses. In addition, by using an in silico approach, we identify 299 proteins which share PML and p53 as binding partners, thus representing novel candidate proteins controlling p53 function and cell fate decision-making at the level of PML nuclear biocondensates.
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Affiliation(s)
| | - Thomas G. Hofmann
- Institute of Toxicology, University Medical Center Mainz, Johannes Gutenberg University, 55131 Mainz, Germany
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16
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Jeon P, Ham HJ, Park S, Lee JA. Regulation of Cellular Ribonucleoprotein Granules: From Assembly to Degradation via Post-translational Modification. Cells 2022; 11:cells11132063. [PMID: 35805146 PMCID: PMC9265587 DOI: 10.3390/cells11132063] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/09/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Cells possess membraneless ribonucleoprotein (RNP) granules, including stress granules, processing bodies, Cajal bodies, or paraspeckles, that play physiological or pathological roles. RNP granules contain RNA and numerous RNA-binding proteins, transiently formed through the liquid–liquid phase separation. The assembly or disassembly of numerous RNP granules is strongly controlled to maintain their homeostasis and perform their cellular functions properly. Normal RNA granules are reversibly assembled, whereas abnormal RNP granules accumulate and associate with various neurodegenerative diseases. This review summarizes current studies on the physiological or pathological roles of post-translational modifications of various cellular RNP granules and discusses the therapeutic methods in curing diseases related to abnormal RNP granules by autophagy.
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17
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Yin S, Zhang F, Lin S, Chen W, Weng K, Liu D, Wang C, He Z, Chen Y, Ma W, Huang J, Huang Y, Songyang Z. TIN2 deficiency leads to ALT-associated phenotypes and differentiation defects in embryonic stem cells. Stem Cell Reports 2022; 17:1183-1197. [PMID: 35395177 PMCID: PMC9120858 DOI: 10.1016/j.stemcr.2022.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/17/2022] Open
Abstract
Telomere integrity is critical for embryonic development, and core telomere-binding proteins, such as TIN2, are key to maintaining telomere stability. Here, we report that homozygous Tin2S341X resulted in embryonic lethality in mice and reduced expression of Tin2 in the derived mouse embryonic stem cells (mESCs). Homozygous mutant mESCs were able to self-renew and remain undifferentiated but displayed many phenotypes associated with alternative lengthening of telomeres (ALT), including excessively long and heterogeneous telomeres, increased ALT-associated promyelocytic leukemia (PML) bodies, and unstable chromosomal ends. These cells also showed upregulation of Zscan4 expression and elevated targeting of DAXX/ATRX and H3K9me3 marks on telomeres. Furthermore, the mutant mESCs were impeded in their differentiation capacity. Upon differentiation, DAXX/ATRX and PML bodies disassociated from telomeres in these cells, where elevated DNA damage was also apparent. Our results reveal differential responses to telomere dysfunction in mESCs versus differentiated cells and highlight the critical role of TIN2 in embryonic development.
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Affiliation(s)
- Shanshan Yin
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Fangyingnan Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Song Lin
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wei Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kai Weng
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Dan Liu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Chuanle Wang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zibin He
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuxi Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yan Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.
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18
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Hornofova T, Pokorna B, Hubackova SS, Uvizl A, Kosla J, Bartek J, Hodny Z, Vasicova P. Phospho-SIM and exon8b of PML protein regulate formation of doxorubicin-induced rDNA-PML compartment. DNA Repair (Amst) 2022; 114:103319. [DOI: 10.1016/j.dnarep.2022.103319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/25/2022] [Accepted: 03/10/2022] [Indexed: 12/18/2022]
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19
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McPhee MJ, Salsman J, Foster J, Thompson J, Mathavarajah S, Dellaire G, Ridgway ND. Running 'LAPS' Around nLD: Nuclear Lipid Droplet Form and Function. Front Cell Dev Biol 2022; 10:837406. [PMID: 35178392 PMCID: PMC8846306 DOI: 10.3389/fcell.2022.837406] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
The nucleus harbours numerous protein subdomains and condensates that regulate chromatin organization, gene expression and genomic stress. A novel nuclear subdomain that is formed following exposure of cells to excess fatty acids is the nuclear lipid droplet (nLD), which is composed of a neutral lipid core surrounded by a phospholipid monolayer and associated regulatory and lipid biosynthetic enzymes. While structurally resembling cytoplasmic LDs, nLDs are formed by distinct but poorly understood mechanisms that involve the emergence of lipid droplets from the lumen of the nucleoplasmic reticulum and de novo lipid synthesis. Luminal lipid droplets that emerge into the nucleoplasm do so at regions of the inner nuclear membrane that become enriched in promyelocytic leukemia (PML) protein. The resulting nLDs that retain PML on their surface are termed lipid-associated PML structures (LAPS), and are distinct from canonical PML nuclear bodies (NB) as they lack key proteins and modifications associated with these NBs. PML is a key regulator of nuclear signaling events and PML NBs are sites of gene regulation and post-translational modification of transcription factors. Therefore, the subfraction of nLDs that form LAPS could regulate lipid stress responses through their recruitment and retention of the PML protein. Both nLDs and LAPS have lipid biosynthetic enzymes on their surface suggesting they are active sites for nuclear phospholipid and triacylglycerol synthesis as well as global lipid regulation. In this review we have summarized the current understanding of nLD and LAPS biogenesis in different cell types, their structure and composition relative to other PML-associated cellular structures, and their role in coordinating a nuclear response to cellular overload of fatty acids.
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Affiliation(s)
- Michael J McPhee
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Jason Foster
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Jordan Thompson
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | | | - Graham Dellaire
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Neale D Ridgway
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
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20
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Delbarre E, Janicki SM. Modulation of H3.3 chromatin assembly by PML: A way to regulate epigenetic inheritance. Bioessays 2021; 43:e2100038. [PMID: 34423467 DOI: 10.1002/bies.202100038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Although the promyelocytic leukemia (PML) protein is renowned for regulating a wide range of cellular processes and as an essential component of PML nuclear bodies (PML-NBs), the mechanisms through which it exerts its broad physiological impact are far from fully elucidated. Here, we review recent studies supporting an emerging view that PML's pleiotropic effects derive, at least partially, from its role in regulating histone H3.3 chromatin assembly, a critical epigenetic mechanism. These studies suggest that PML maintains heterochromatin organization by restraining H3.3 incorporation. Examination of PML's contribution to H3.3 chromatin assembly in the context of the cell cycle and PML-NB assembly suggests that PML represses heterochromatic H3.3 deposition during S phase and that transcription and SUMOylation regulate PML's recruitment to heterochromatin. Elucidating PML' s contributions to H3.3-mediated epigenetic regulation will provide insight into PML's expansive influence on cellular physiology and open new avenues for studying oncogenesis linked to PML malfunction.
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Affiliation(s)
- Erwan Delbarre
- Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Susan M Janicki
- Drexel University Thomas R. Kline School of Law, Philadelphia, Pennsylvania, USA
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21
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Impacts of chromatin dynamics and compartmentalization on DNA repair. DNA Repair (Amst) 2021; 105:103162. [PMID: 34182258 DOI: 10.1016/j.dnarep.2021.103162] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 11/22/2022]
Abstract
The proper spatial organization of DNA, RNA, and proteins is critical for a variety of cellular processes. The genome is organized into numerous functional units, such as topologically associating domains (TADs), the formation of which is regulated by both proteins and RNA. In addition, a group of chromatin-bound proteins with the ability to undergo liquid-liquid phase separation (LLPS) can affect the spatial organization and compartmentalization of chromatin, RNA, and proteins by forming condensates, conferring unique properties to specific chromosomal regions. Although the regulation of DNA repair by histone modifications and chromatin accessibility is well established, the impacts of higher-order chromatin and protein organization on the DNA damage response (DDR) have not been appreciated until recently. In this review, we will focus on the movement of chromatin during the DDR, the compartmentalization of DDR proteins via LLPS, and the roles of membraneless nuclear bodies and transcription in DNA repair. With this backdrop, we will discuss the importance of the spatial organization of chromatin and proteins for the maintenance of genome integrity.
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Abstract
Cells activate their DNA damage response (DDR) in response to DNA virus infection, including adenoviruses, papillomaviruses, polyomaviruses, and herpesviruses. In this study, we found that the DDR kinase pathways activated in normal human fibroblasts by herpes simplex virus 1 (HSV-1) input genomic DNA, HSV-1 replicating DNA, and progeny DNA and in uninfected cells treated with etoposide are different. We also found using clustered regularly interspaced palindromic repeat (CRISPR)-Cas9 technology that different host gene products are required for the DDR in uninfected versus infected cells. Individual DDR components can be proviral or antiviral in that ataxia-telangiectasia mutated (ATM) and p53 promote and Mre11 restricts replication of ICP0-null HSV-1, but ICP0 expression eliminates these DDR effects. Thus, in total, these results argue that HSV-1 manipulates the host cell DDR to utilize specific components for its optimal replication while inactivating the antiviral aspects of the DDR.IMPORTANCE We investigated the relationship between the DNA damage response, a collection of vital cellular pathways that repair potentially lethal damage to the genome, and the DNA virus herpes simplex virus 1. We found that infection by the virus triggers the DNA damage response, and key proteins that mediate this response have opposing effects on the replication and production of progeny viruses. Our work provides novel insights into the relationship between DNA virus infection and the cellular response to the viral genome. We speculate that viral gene products modulate this response, providing potentially novel targets for therapeutic intervention against the virus.
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Corpet A, Kleijwegt C, Roubille S, Juillard F, Jacquet K, Texier P, Lomonte P. PML nuclear bodies and chromatin dynamics: catch me if you can! Nucleic Acids Res 2020; 48:11890-11912. [PMID: 33068409 PMCID: PMC7708061 DOI: 10.1093/nar/gkaa828] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic cells compartmentalize their internal milieu in order to achieve specific reactions in time and space. This organization in distinct compartments is essential to allow subcellular processing of regulatory signals and generate specific cellular responses. In the nucleus, genetic information is packaged in the form of chromatin, an organized and repeated nucleoprotein structure that is a source of epigenetic information. In addition, cells organize the distribution of macromolecules via various membrane-less nuclear organelles, which have gathered considerable attention in the last few years. The macromolecular multiprotein complexes known as Promyelocytic Leukemia Nuclear Bodies (PML NBs) are an archetype for nuclear membrane-less organelles. Chromatin interactions with nuclear bodies are important to regulate genome function. In this review, we will focus on the dynamic interplay between PML NBs and chromatin. We report how the structure and formation of PML NBs, which may involve phase separation mechanisms, might impact their functions in the regulation of chromatin dynamics. In particular, we will discuss how PML NBs participate in the chromatinization of viral genomes, as well as in the control of specific cellular chromatin assembly pathways which govern physiological mechanisms such as senescence or telomere maintenance.
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Affiliation(s)
- Armelle Corpet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Constance Kleijwegt
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Simon Roubille
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Franceline Juillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Karine Jacquet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Pascale Texier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Patrick Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
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Sandy Z, da Costa IC, Schmidt CK. More than Meets the ISG15: Emerging Roles in the DNA Damage Response and Beyond. Biomolecules 2020; 10:E1557. [PMID: 33203188 PMCID: PMC7698331 DOI: 10.3390/biom10111557] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
Maintenance of genome stability is a crucial priority for any organism. To meet this priority, robust signalling networks exist to facilitate error-free DNA replication and repair. These signalling cascades are subject to various regulatory post-translational modifications that range from simple additions of chemical moieties to the conjugation of ubiquitin-like proteins (UBLs). Interferon Stimulated Gene 15 (ISG15) is one such UBL. While classically thought of as a component of antiviral immunity, ISG15 has recently emerged as a regulator of genome stability, with key roles in the DNA damage response (DDR) to modulate p53 signalling and error-free DNA replication. Additional proteomic analyses and cancer-focused studies hint at wider-reaching, uncharacterised functions for ISG15 in genome stability. We review these recent discoveries and highlight future perspectives to increase our understanding of this multifaceted UBL in health and disease.
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Affiliation(s)
| | | | - Christine K. Schmidt
- Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M20 4GJ, UK; (Z.S.); (I.C.d.C.)
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25
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PML Regulates the Epidermal Differentiation Complex and Skin Morphogenesis during Mouse Embryogenesis. Genes (Basel) 2020; 11:genes11101130. [PMID: 32992884 PMCID: PMC7600374 DOI: 10.3390/genes11101130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/13/2020] [Accepted: 09/17/2020] [Indexed: 11/17/2022] Open
Abstract
The promyelocytic leukemia (PML) protein is an essential component of nuclear compartments called PML bodies. This protein participates in several cellular processes, including growth control, senescence, apoptosis, and differentiation. Previous studies have suggested that PML regulates gene expression at a subset of loci through a function in chromatin remodeling. Here we have studied global gene expression patterns in mouse embryonic skin derived from Pml depleted and wild type mouse embryos. Differential gene expression analysis at different developmental stages revealed a key role of PML in regulating genes involved in epidermal stratification. In particular, we observed dysregulation of the late cornified envelope gene cluster, which is a sub-region of the epidermal differentiation complex. In agreement with these data, PML body numbers are elevated in basal keratinocytes during embryogenesis, and we observed reduced epidermal thickness and defective hair follicle development in PML depleted mouse embryos.
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The HECT E3 Ligase E6AP/UBE3A as a Therapeutic Target in Cancer and Neurological Disorders. Cancers (Basel) 2020; 12:cancers12082108. [PMID: 32751183 PMCID: PMC7464832 DOI: 10.3390/cancers12082108] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 11/23/2022] Open
Abstract
The HECT (Homologous to the E6-AP Carboxyl Terminus)-family protein E6AP (E6-associated protein), encoded by the UBE3A gene, is a multifaceted ubiquitin ligase that controls diverse signaling pathways involved in cancer and neurological disorders. The oncogenic role of E6AP in papillomavirus-induced cancers is well known, with its action to trigger p53 degradation in complex with the E6 viral oncoprotein. However, the roles of E6AP in non-viral cancers remain poorly defined. It is well established that loss-of-function alterations of the UBE3A gene cause Angelman syndrome, a severe neurodevelopmental disorder with autosomal dominant inheritance modified by genomic imprinting on chromosome 15q. Moreover, excess dosage of the UBE3A gene markedly increases the penetrance of autism spectrum disorders, suggesting that the expression level of UBE3A must be regulated tightly within a physiologically tolerated range during brain development. In this review, current the knowledge about the substrates of E6AP-mediated ubiquitination and their functions in cancer and neurological disorders is discussed, alongside with the ongoing efforts to pharmacologically modulate this ubiquitin ligase as a promising therapeutic target.
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Li Y, Ma X, Wu W, Chen Z, Meng G. PML Nuclear Body Biogenesis, Carcinogenesis, and Targeted Therapy. Trends Cancer 2020; 6:889-906. [PMID: 32527650 DOI: 10.1016/j.trecan.2020.05.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/20/2020] [Accepted: 05/11/2020] [Indexed: 01/16/2023]
Abstract
Targeted therapy has become increasingly important in cancer therapy. For example, targeting the promyelocytic leukemia PML protein in leukemia has proved to be an effective treatment. PML is the core component of super-assembled structures called PML nuclear bodies (NBs). Although this nuclear megaDalton complex was first observed in the 1960s, the mechanism of its assembly remains poorly understood. We review recent breakthroughs in the PML field ranging from a revised assembly mechanism to PML-driven genome organization and carcinogenesis. In addition, we highlight that oncogenic oligomerization might also represent a promising target in the treatment of leukemias and solid tumors.
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Affiliation(s)
- Yuwen Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaodan Ma
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenyu Wu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Guoyu Meng
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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28
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The Viral SUMO–Targeted Ubiquitin Ligase ICP0 is Phosphorylated and Activated by Host Kinase Chk2. J Mol Biol 2020; 432:1952-1977. [DOI: 10.1016/j.jmb.2020.01.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/06/2020] [Accepted: 01/17/2020] [Indexed: 11/22/2022]
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29
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PML nuclear body biogenesis and oligomerization-driven leukemogenesis. BLOOD SCIENCE 2020; 2:7-10. [PMID: 35399865 PMCID: PMC8975047 DOI: 10.1097/bs9.0000000000000034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 10/02/2019] [Indexed: 11/26/2022] Open
Abstract
PML nuclear bodies (NBs), which are increasingly recognized as the central hub of many cellular signaling events, are superassembled spherical complexes with diameters of 0.1–2 μm. Recent studies reveal that RING tetramerization and B1-box polymerization are key factors to the overall PML NBs assembly. The productive RBCC oligomerization allows subsequent PML biogenesis steps, including the PML auto-sumoylation and partners recruitment via SUMO–SIM interactions. In promyelocytic leukemia, the oncoprotein PML/RARα (P/R) inhibits PML NBs assembly and leads to a full-fledged leukemogenesis. In this review, we review the recent progress in PML and acute promyelocytic leukemia fields, highlighting the protein oligomerization as an important direction of future targeted therapy.
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30
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Mascle XH, Gagnon C, Wahba HM, Lussier-Price M, Cappadocia L, Sakaguchi K, Omichinski JG. Acetylation of SUMO1 Alters Interactions with the SIMs of PML and Daxx in a Protein-Specific Manner. Structure 2019; 28:157-168.e5. [PMID: 31879127 DOI: 10.1016/j.str.2019.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/14/2019] [Accepted: 11/27/2019] [Indexed: 11/26/2022]
Abstract
The interactions between SUMO proteins and SUMO-interacting motif (SIM) in nuclear bodies formed by the promyelocytic leukemia (PML) protein (PML-NBs) have been shown to be modulated by either phosphorylation of the SIMs or acetylation of SUMO proteins. However, little is known about how this occurs at the atomic level. In this work, we examined the role that acetylation of SUMO1 plays on its binding to the phosphorylated SIMs (phosphoSIMs) of PML and Daxx. Our results demonstrate that SUMO1 binding to the phosphoSIM of either PML or Daxx is dramatically reduced by acetylation at either K39 or K46. However, acetylation at K37 only impacts binding to Daxx. Structures of acetylated SUMO1 variants bound to the phosphoSIMs of PML and Daxx demonstrate that there is structural plasticity in SUMO-SIM interactions. The plasticity observed in these structures provides a robust mechanism for regulating SUMO-SIM interactions in PML-NBs using signaling generated post-translational modifications.
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Affiliation(s)
- Xavier H Mascle
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Christina Gagnon
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Haytham M Wahba
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada; Department of Biochemistry, Beni-Suef University, Beni-Suef 62521, Egypt
| | - Mathieu Lussier-Price
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Laurent Cappadocia
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Kazuyasu Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - James G Omichinski
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada.
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31
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Attwood KM, Salsman J, Chung D, Mathavarajah S, Van Iderstine C, Dellaire G. PML isoform expression and DNA break location relative to PML nuclear bodies impacts the efficiency of homologous recombination. Biochem Cell Biol 2019; 98:314-326. [PMID: 31671275 DOI: 10.1139/bcb-2019-0115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Promyelocytic leukemia nuclear bodies (PML NBs) are nuclear subdomains that respond to genotoxic stress by increasing in number via changes in chromatin structure. However, the role of the PML protein and PML NBs in specific mechanisms of DNA repair has not been fully characterized. Here, we have directly examined the role of PML in homologous recombination (HR) using I-SceI extrachromosomal and chromosome-based homology-directed repair (HDR) assays, and in HDR by CRISPR/Cas9-mediated gene editing. We determined that PML loss can inhibit HR in an extrachromosomal HDR assay but had less of an effect on CRISPR/Cas9-mediated chromosomal HDR. Overexpression of PML also inhibited both CRISPR HDR and I-SceI-induced HDR using a chromosomal reporter, and in an isoform-specific manner. However, the impact of PML overexpression on the chromosomal HDR reporter was dependent on the intranuclear chromosomal positioning of the reporter. Specifically, HDR at the TAP1 gene locus, which is associated with PML NBs, was reduced compared with a locus not associated with a PML NB; yet, HDR could be reduced at the non-PML NB-associated locus by PML overexpression. Thus, both loss and overexpression of PML isoforms can inhibit HDR, and proximity of a chromosomal break to a PML NB can impact HDR efficiency.
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Affiliation(s)
- Kathleen M Attwood
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Dudley Chung
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | | | | | - Graham Dellaire
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.,Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
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32
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Imrichova T, Hubackova S, Kucerova A, Kosla J, Bartek J, Hodny Z, Vasicova P. Dynamic PML protein nucleolar associations with persistent DNA damage lesions in response to nucleolar stress and senescence-inducing stimuli. Aging (Albany NY) 2019; 11:7206-7235. [PMID: 31493766 PMCID: PMC6756913 DOI: 10.18632/aging.102248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/22/2019] [Indexed: 04/10/2023]
Abstract
Diverse stress insults trigger interactions of PML with nucleolus, however, the function of these PML nucleolar associations (PNAs) remains unclear. Here we show that during induction of DNA damage-induced senescence in human non-cancerous cells, PML accumulates at the nucleolar periphery simultaneously with inactivation of RNA polymerase I (RNAP I) and nucleolar segregation. Using time-lapse and high-resolution microscopy, we followed the genesis, structural transitions and destiny of PNAs to show that: 1) the dynamic structural changes of the PML-nucleolar interaction are tightly associated with inactivation and reactivation of RNAP I-mediated transcription, respectively; 2) the PML-nucleolar compartment develops sequentially under stress and, upon stress termination, it culminates in either of two fates: disappearance or persistence; 3) all PNAs stages can associate with DNA damage markers; 4) the persistent, commonly long-lasting PML multi-protein nucleolar structures (PML-NDS) associate with markers of DNA damage, indicating a role of PNAs in persistent DNA damage response characteristic for senescent cells. Given the emerging evidence implicating PML in homologous recombination-directed DNA repair, we propose that PNAs contribute to sequestration and faithful repair of the highly unstable ribosomal DNA repeats, a fundamental process to maintain a precise balance between DNA repair mechanisms, with implications for genomic integrity and aging.
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Affiliation(s)
- Terezie Imrichova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sona Hubackova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Present address: Institute of Biotechnology, Czech Academy of Sciences, Prague-West, Czech Republic
| | - Alena Kucerova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Kosla
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Bartek
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavla Vasicova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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33
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Gong P, Wang H, Zhang J, Fu Y, Zhu Z, Wang J, Yin Y, Wang H, Zhou Z, Yang J, Liu L, Gou M, Zeng M, Yuan J, Wang F, Pan X, Xiang R, Weissman SM, Qi F, Liu L. Telomere Maintenance-Associated PML Is a Potential Specific Therapeutic Target of Human Colorectal Cancer. Transl Oncol 2019; 12:1164-1176. [PMID: 31207547 PMCID: PMC6580093 DOI: 10.1016/j.tranon.2019.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 02/06/2023] Open
Abstract
Telomere length maintenance is essential for cell proliferation, which is particularly prominent in cancer. We validate that the primary colorectal tumors exhibit heterogeneous telomere lengths but mostly (90%) short telomeres relative to normal tissues. Intriguingly, relatively short telomeres are associated with tumor malignancy as indicated by poorly differentiated state, and these tumors contain more cancer stem-like cells (CSLCs) identified by several commonly used markers CD44, EPHB2 or LGR5. Moreover, promyelocytic leukemia (PML) and ALT-associated PML nuclear bodies (APBs) are frequently found in tumors with short telomeres and high proliferation. In contrast, distant normal tissues rarely or only minimally express PML. Inhibition of PML and APBs by an ATR inhibitor decreases proliferation of CSLCs and organoids, suggesting a potential therapeutic target to progressive colorectal tumors. Together, telomere maintenance underling tumor progression is connected with CSLCs.
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Affiliation(s)
- Peng Gong
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hua Wang
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jingsong Zhang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Yudong Fu
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zhengmao Zhu
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jinmiao Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Yu Yin
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Haiying Wang
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zhongcheng Zhou
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jiao Yang
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Linlin Liu
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Mo Gou
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ming Zeng
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jinghua Yuan
- Department of Genetics, Tianjin Medical University, Tianjin, 300070, China
| | - Feng Wang
- Department of Genetics, Tianjin Medical University, Tianjin, 300070, China
| | - Xinghua Pan
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Rong Xiang
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy
| | - Sherman M Weissman
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Feng Qi
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, 2011 Collaborative Innovation Center for Biotherapy; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, 300071, China.
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34
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Chung D, Salsman J, Dellaire G. Inhibition of neddylation induces mitotic defects and alters MKLP1 accumulation at the midbody during cytokinesis. Cell Cycle 2019; 18:1135-1153. [PMID: 31057046 PMCID: PMC6592236 DOI: 10.1080/15384101.2019.1612696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The cullin-RING E3 ubiquitin ligases (CRLs) play crucial roles in modulating the stability of proteins in the cell and are, in turn, regulated by post-translational modification by the ubiquitin-like (Ubl) protein NEDD8. This process, termed neddylation, is reversible through the action of the COP9 signalosome (CSN); a multi-subunit metalloprotease conserved among eukaryotes that plays direct or indirect roles in DNA repair, cell signaling and cell cycle regulation in part through modulating the activity of the CRLs. Previously, inhibition of CRL neddylation by MLN4924, a small molecule inhibitor of the NEDD8-activating enzyme 1 (NAE1), was shown to induce interphase cell cycle arrest and cell death. Using fixed and living cell microscopy, we re-evaluated the cell cycle effects of inhibition of neddylation by MLN4924 in both asynchronous and mitotic cell populations. Consistent with previous studies, treatment of asynchronous cells with MLN4924 increased CDT1 expression levels, induced G2 arrest and increased nuclear size. However, in synchronized cells treated in mitosis, mitotic defects were observed including lagging chromosomes and binucleated daughter cells. Consistent with neddylation and deneddylation playing a role in cytokinesis, NEDD8, as well as subunits of the CSN, could be localized at the midbody and cleavage furrow. Finally, treatment of mitotic cells with MLN4924 induced the premature accumulation of MKLP1 at the cleavage furrow, a key regulator of cytokinesis, which was concomitant with increased abscission delay and failure. Thus, these studies uncover an uncharacterized mitotic effect of MLN4924 on MKLP1 accumulation at the midbody and support a role for neddylation during cytokinesis. Abbreviations: CSN, COP9 Signalosome; MKLP1, mitotic kinesin-like protein 1; NEDD8, Neural precursor cell Expressed, Developmentally Down-regulated 8.
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Affiliation(s)
- Dudley Chung
- a Department of Pathology , Dalhousie University , Halifax , Canada
| | - Jayme Salsman
- a Department of Pathology , Dalhousie University , Halifax , Canada
| | - Graham Dellaire
- a Department of Pathology , Dalhousie University , Halifax , Canada.,b Department of Biochemistry & Molecular Biology , Dalhousie University , Halifax , Canada.,c Beatrice Hunter Cancer Research Institute , Halifax , Canada
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Vancurova M, Hanzlikova H, Knoblochova L, Kosla J, Majera D, Mistrik M, Burdova K, Hodny Z, Bartek J. PML nuclear bodies are recruited to persistent DNA damage lesions in an RNF168-53BP1 dependent manner and contribute to DNA repair. DNA Repair (Amst) 2019; 78:114-127. [PMID: 31009828 DOI: 10.1016/j.dnarep.2019.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/07/2019] [Accepted: 04/01/2019] [Indexed: 11/29/2022]
Abstract
The bulk of DNA damage caused by ionizing radiation (IR) is generally repaired within hours, yet a subset of DNA lesions may persist even for long periods of time. Such persisting IR-induced foci (pIRIF) co-associate with PML nuclear bodies (PML-NBs) and are among the characteristics of cellular senescence. Here we addressed some fundamental questions concerning the nature and determinants of this co-association, the role of PML-NBs at such sites, and the reason for the persistence of DNA damage in human primary cells. We show that the persistent DNA lesions are devoid of homologous recombination (HR) proteins BRCA1 and Rad51. Our super-resolution microscopy-based analysis showed that PML-NBs are juxtaposed to and partially overlap with the pIRIFs. Notably, depletion of 53BP1 resulted in decreased intersection between PML-NBs and pIRIFs implicating the RNF168-53BP1 pathway in their interaction. To test whether the formation and persistence of IRIFs is PML-dependent and to investigate the role of PML in the context of DNA repair and senescence, we genetically deleted PML in human hTERT-RPE-1 cells. Unexpectedly, upon high-dose IR treatment, cells displayed similar DNA damage signalling, repair dynamics and kinetics of cellular senescence regardless of the presence or absence of PML. In contrast, the PML knock-out cells showed increased sensitivity to low doses of IR and DNA-damaging agents mitomycin C, cisplatin and camptothecin that all cause DNA lesions requiring repair by HR. These results, along with enhanced sensitivity of the PML knock-out cells to DNA-PK and PARP inhibitors implicate PML as a factor contributing to HR-mediated DNA repair.
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Affiliation(s)
- Marketa Vancurova
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Hana Hanzlikova
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lucie Knoblochova
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kosla
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Dusana Majera
- Laboratory of Genome Integrity, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Martin Mistrik
- Laboratory of Genome Integrity, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Kamila Burdova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | - Jiri Bartek
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic; Laboratory of Genome Integrity, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic; Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden.
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36
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Shastrula PK, Sierra I, Deng Z, Keeney F, Hayden JE, Lieberman PM, Janicki SM. PML is recruited to heterochromatin during S phase and represses DAXX-mediated histone H3.3 chromatin assembly. J Cell Sci 2019; 132:jcs.220970. [PMID: 30796101 DOI: 10.1242/jcs.220970] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/09/2019] [Indexed: 12/18/2022] Open
Abstract
The incorporation of the histone H3 variant, H3.3, into chromatin by the H3.3-specific chaperone DAXX and the ATP-dependent chromatin remodeling factor ATRX is a critical mechanism for silencing repetitive DNA. DAXX and ATRX are also components of promyelocytic nuclear bodies (PML-NBs), which have been identified as sites of H3.3 chromatin assembly. Here, we use a transgene array that can be visualized in single living cells to investigate the mechanisms that recruit PML-NB proteins (i.e. PML, DAXX, ATRX, and SUMO-1, SUMO-2 and SUMO-3) to heterochromatin and their functions in H3.3 chromatin assembly. We show that DAXX and PML are recruited to the array through distinct SUMOylation-dependent mechanisms. Additionally, PML is recruited during S phase and its depletion increases H3.3 deposition. Since this effect is abrogated when PML and DAXX are co-depleted, it is likely that PML represses DAXX-mediated H3.3 chromatin assembly. Taken together, these results suggest that, at heterochromatin, PML-NBs coordinate H3.3 chromatin assembly with DNA replication, which has important implications for understanding how transcriptional silencing is established and maintained.
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Affiliation(s)
- Prashanth Krishna Shastrula
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.,University of the Sciences in Philadelphia, Department of Biological Sciences, 600 South 43rd Street, Philadelphia, PA 19104, USA
| | - Isabel Sierra
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Zhong Deng
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Frederick Keeney
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - James E Hayden
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Paul M Lieberman
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Susan M Janicki
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
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Nagashima R, Hibino K, Ashwin SS, Babokhov M, Fujishiro S, Imai R, Nozaki T, Tamura S, Tani T, Kimura H, Shribak M, Kanemaki MT, Sasai M, Maeshima K. Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II. J Cell Biol 2019; 218:1511-1530. [PMID: 30824489 PMCID: PMC6504897 DOI: 10.1083/jcb.201811090] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/31/2019] [Accepted: 02/07/2019] [Indexed: 01/01/2023] Open
Abstract
When a gene is activated, chromatin in the transcribed region is thought to be more open and dynamic. However, Nagashima et al. found that this is not necessarily the case—inhibition of transcription globally increases chromatin motion, revealing the existence of loose genome chromatin networks via transcriptional machinery. Although chromatin organization and dynamics play a critical role in gene transcription, how they interplay remains unclear. To approach this issue, we investigated genome-wide chromatin behavior under various transcriptional conditions in living human cells using single-nucleosome imaging. While transcription by RNA polymerase II (RNAPII) is generally thought to need more open and dynamic chromatin, surprisingly, we found that active RNAPII globally constrains chromatin movements. RNAPII inhibition or its rapid depletion released the chromatin constraints and increased chromatin dynamics. Perturbation experiments of P-TEFb clusters, which are associated with active RNAPII, had similar results. Furthermore, chromatin mobility also increased in resting G0 cells and UV-irradiated cells, which are transcriptionally less active. Our results demonstrated that chromatin is globally stabilized by loose connections through active RNAPII, which is compatible with models of classical transcription factories or liquid droplet formation of transcription-related factors. Together with our computational modeling, we propose the existence of loose chromatin domain networks for various intra-/interchromosomal contacts via active RNAPII clusters/droplets.
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Affiliation(s)
- Ryosuke Nagashima
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
| | - Kayo Hibino
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
| | - S S Ashwin
- Department of Applied Physics, Nagoya University, Nagoya, Japan.,Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan
| | - Michael Babokhov
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Shin Fujishiro
- Department of Applied Physics, Nagoya University, Nagoya, Japan.,Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan
| | - Ryosuke Imai
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
| | - Tadasu Nozaki
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Tomomi Tani
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Michael Shribak
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA
| | - Masato T Kanemaki
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan.,Molecular Cell Engineering Laboratory, National Institute of Genetics, ROIS, Mishima, Japan
| | - Masaki Sasai
- Department of Applied Physics, Nagoya University, Nagoya, Japan.,Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan .,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
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Hossain MG, Ohsaki E, Honda T, Ueda K. Importance of Promyelocytic Leukema Protein (PML) for Kaposi's Sarcoma-Associated Herpesvirus Lytic Replication. Front Microbiol 2018; 9:2324. [PMID: 30349510 PMCID: PMC6186782 DOI: 10.3389/fmicb.2018.02324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/11/2018] [Indexed: 12/14/2022] Open
Abstract
Many DNA virus replication-related proteins are associated with promyelocytic leukemia protein (PML), a component of nuclear domain 10 (ND10), which has been investigated for its potential involvement in viral replication. In the case of Kaposi’s sarcoma-associated herpesvirus (KSHV) lytic gene products, K8 (K-bZIP), ORF59, and ORF75 have been shown to colocalize with PML, but its importance in KSHV lytic replication is still unclear. In this study, we analyzed the functional influence of PML on KSHV latency and lytic replication in KSHV-infected primary effusion lymphoma (PEL) cell lines. Stable PML-knockout (BC3-PMLKO) and PML-overexpressing BC3 cells (BC3PML) were successfully generated and the latency and reactivation status were analyzed. The results demonstrated that neither KSHV latency nor the episome copy number was affected in BC3-PMLKO cells. In the reactivation phase, the expression dynamics of KSHV immediate-early or early lytic proteins such as RTA, K9 (vIRF1), K5, K3, ORF59, and K8 (K-bZIP) were comparable between wild-type, control BC3, and BC3-PMLKO cells. Interestingly, KSHV lytic replication, virion production, and expression of late genes were downregulated in BC3-PMLKO cells and upregulated in BC3PML cells, compared to those in control or wild-type BC3 cells. Moreover, exogenous PML increased the size of the PML dots and recruited additional K8 (K-bZIP) to PML-NBs as dots. Therefore, PML would function as a positive regulator for KSHV lytic DNA replication by recruiting KSHV replication factors such as 8 (K-bZIP) or ORF59 to the PML-NBs.
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Affiliation(s)
- Md Golzar Hossain
- Division of Virology, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Eriko Ohsaki
- Division of Virology, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tomoyuki Honda
- Division of Virology, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Keiji Ueda
- Division of Virology, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
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39
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Sawyer IA, Bartek J, Dundr M. Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing. Semin Cell Dev Biol 2018; 90:94-103. [PMID: 30017905 DOI: 10.1016/j.semcdb.2018.07.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/03/2018] [Indexed: 01/01/2023]
Abstract
Proteins and RNAs inside the cell nucleus are organized into distinct phases, also known as liquid-liquid phase separated (LLPS) droplet organelles or nuclear bodies. These regions exist within the spaces between chromatin-rich regions but their function is tightly linked to gene activity. They include major microscopically-observable structures such as the nucleolus, paraspeckle and Cajal body. The biochemical and assembly factors enriched inside these microenvironments regulate chromatin structure, transcription, and RNA processing, and other important cellular functions. Here, we describe published evidence that suggests nuclear bodies are bona fide LLPS droplet organelles and major regulators of the processes listed above. We also outline an updated "Supply or Sequester" model to describe nuclear body function, in which proteins or RNAs are supplied to surrounding genomic regions or sequestered away from their sites of activity. Finally, we describe recent evidence that suggests these microenvironments are both reflective and drivers of diverse pathophysiological states.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, United States; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jiri Bartek
- Danish Cancer, Society Research Center, Genome Integrity Unit, Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, United States.
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40
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Li Q, Wang J, Liao D, Ai J, Jin L, Gao Q. Degradation of DAXX by adenovirus type 12 E1B-55K circumvents chemoresistance of ovarian cancer to cisplatin. Virology 2018; 521:118-128. [PMID: 29906705 DOI: 10.1016/j.virol.2018.05.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/27/2018] [Accepted: 05/29/2018] [Indexed: 01/27/2023]
Abstract
Adenovirus E1B 55-kilodalton (E1B-55K) mediated DAXX degradation represents a potential mechanism by which E1B-55K sensitizes cancer cells to chemotherapy. Here we report the effects of E1B-55K-mediated DAXX degradation in chemoresistant ovarian cancer cells on response to chemotherapy. Cells with E1B-55K expression were more sensitive to cisplatin than cells without E1B-55K expression. In vivo C13* xenograft studies showed that the combination of cisplatin and E1B-55K was markedly more effective to slow tumor growth and to confer prolonged survival of tumor-bearing mice than either cisplatin or E1B-55K alone. Our studies show that DAXX plays an important role in cisplatin resistance in ovarian cancer, and strategies that promote DAXX degradation such as E1B-55K expression in combination with cisplatin can overcome drug resistance and improve responses to standard chemotherapy. These results also indicate that E1B-55K might be a novel agent for enhancing treatment responses for cisplatin-resistant ovarian cancer.
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Affiliation(s)
- Qiang Li
- Department of Gynecology and Obstetrics, Tongji hospital, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Junnai Wang
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, Henan Province, China
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL 32610-0235, USA
| | - Jihui Ai
- Department of Gynecology and Obstetrics, Tongji hospital, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Lei Jin
- Department of Gynecology and Obstetrics, Tongji hospital, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China.
| | - Qinglei Gao
- Department of Gynecology and Obstetrics, Tongji hospital, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China.
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41
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Hoischen C, Monajembashi S, Weisshart K, Hemmerich P. Multimodal Light Microscopy Approaches to Reveal Structural and Functional Properties of Promyelocytic Leukemia Nuclear Bodies. Front Oncol 2018; 8:125. [PMID: 29888200 PMCID: PMC5980967 DOI: 10.3389/fonc.2018.00125] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/05/2018] [Indexed: 12/11/2022] Open
Abstract
The promyelocytic leukemia (pml) gene product PML is a tumor suppressor localized mainly in the nucleus of mammalian cells. In the cell nucleus, PML seeds the formation of macromolecular multiprotein complexes, known as PML nuclear bodies (PML NBs). While PML NBs have been implicated in many cellular functions including cell cycle regulation, survival and apoptosis their role as signaling hubs along major genome maintenance pathways emerged more clearly. However, despite extensive research over the past decades, the precise biochemical function of PML in these pathways is still elusive. It remains a big challenge to unify all the different previously suggested cellular functions of PML NBs into one mechanistic model. With the advent of genetically encoded fluorescent proteins it became possible to trace protein function in living specimens. In parallel, a variety of fluorescence fluctuation microscopy (FFM) approaches have been developed which allow precise determination of the biophysical and interaction properties of cellular factors at the single molecule level in living cells. In this report, we summarize the current knowledge on PML nuclear bodies and describe several fluorescence imaging, manipulation, FFM, and super-resolution techniques suitable to analyze PML body assembly and function. These include fluorescence redistribution after photobleaching, fluorescence resonance energy transfer, fluorescence correlation spectroscopy, raster image correlation spectroscopy, ultraviolet laser microbeam-induced DNA damage, erythrocyte-mediated force application, and super-resolution microscopy approaches. Since most if not all of the microscopic equipment to perform these techniques may be available in an institutional or nearby facility, we hope to encourage more researches to exploit sophisticated imaging tools for their research in cancer biology.
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42
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Hsu KS, Kao HY. PML: Regulation and multifaceted function beyond tumor suppression. Cell Biosci 2018; 8:5. [PMID: 29416846 PMCID: PMC5785837 DOI: 10.1186/s13578-018-0204-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 01/12/2018] [Indexed: 01/15/2023] Open
Abstract
Promyelocytic leukemia protein (PML) was originally identified as a fusion partner of retinoic acid receptor alpha in acute promyelocytic leukemia patients with the (15;17) chromosomal translocation, giving rise to PML–RARα and RARα–PML fusion proteins. A body of evidence indicated that PML possesses tumor suppressing activity by regulating apoptosis, cell cycle, senescence and DNA damage responses. PML is enriched in discrete nuclear substructures in mammalian cells with 0.2–1 μm diameter in size, referred to as alternately Kremer bodies, nuclear domain 10, PML oncogenic domains or PML nuclear bodies (NBs). Dysregulation of PML NB formation results in altered transcriptional regulation, protein modification, apoptosis and cellular senescence. In addition to PML NBs, PML is also present in nucleoplasm and cytoplasmic compartments, including the endoplasmic reticulum and mitochondria-associated membranes. The role of PML in tumor suppression has been extensively studied but increasing evidence indicates that PML also plays versatile roles in stem cell renewal, metabolism, inflammatory responses, neural function, mammary development and angiogenesis. In this review, we will briefly describe the known PML regulation and function and include new findings.
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Affiliation(s)
- Kuo-Sheng Hsu
- 1Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 USA.,Present Address: Tumor Angiogenesis Section, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702 USA
| | - Hung-Ying Kao
- 1Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 USA.,The Comprehensive Cancer Center of Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH 44106 USA
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43
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Lee SI, Celik S, Logsdon BA, Lundberg SM, Martins TJ, Oehler VG, Estey EH, Miller CP, Chien S, Dai J, Saxena A, Blau CA, Becker PS. A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia. Nat Commun 2018; 9:42. [PMID: 29298978 PMCID: PMC5752671 DOI: 10.1038/s41467-017-02465-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 11/30/2017] [Indexed: 02/06/2023] Open
Abstract
Cancers that appear pathologically similar often respond differently to the same drug regimens. Methods to better match patients to drugs are in high demand. We demonstrate a promising approach to identify robust molecular markers for targeted treatment of acute myeloid leukemia (AML) by introducing: data from 30 AML patients including genome-wide gene expression profiles and in vitro sensitivity to 160 chemotherapy drugs, a computational method to identify reliable gene expression markers for drug sensitivity by incorporating multi-omic prior information relevant to each gene’s potential to drive cancer. We show that our method outperforms several state-of-the-art approaches in identifying molecular markers replicated in validation data and predicting drug sensitivity accurately. Finally, we identify SMARCA4 as a marker and driver of sensitivity to topoisomerase II inhibitors, mitoxantrone, and etoposide, in AML by showing that cell lines transduced to have high SMARCA4 expression reveal dramatically increased sensitivity to these agents. Identification of markers of drug response is essential for precision therapy. Here the authors introduce an algorithm that uses prior information about each gene’s importance in AML to identify the most predictive gene-drug associations from transcriptome and drug response data from 30 AML samples.
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Affiliation(s)
- Su-In Lee
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E Stevens Way NE, Seattle, WA, 98195, USA. .,Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA. .,Center for Cancer Innovation, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.
| | - Safiye Celik
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E Stevens Way NE, Seattle, WA, 98195, USA
| | | | - Scott M Lundberg
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E Stevens Way NE, Seattle, WA, 98195, USA
| | - Timothy J Martins
- Quellos High Throughput Screening Core, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Vivian G Oehler
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.,Division of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Elihu H Estey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.,Division of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Chris P Miller
- Division of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Sylvia Chien
- Division of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Jin Dai
- Division of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Akanksha Saxena
- Division of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - C Anthony Blau
- Center for Cancer Innovation, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.,Division of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
| | - Pamela S Becker
- Center for Cancer Innovation, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.,Division of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA
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Fernandez-Vidal A, Vignard J, Mirey G. Around and beyond 53BP1 Nuclear Bodies. Int J Mol Sci 2017; 18:ijms18122611. [PMID: 29206178 PMCID: PMC5751214 DOI: 10.3390/ijms18122611] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/27/2017] [Accepted: 12/01/2017] [Indexed: 12/17/2022] Open
Abstract
Within the nucleus, sub-nuclear domains define territories where specific functions occur. Nuclear bodies (NBs) are dynamic structures that concentrate nuclear factors and that can be observed microscopically. Recently, NBs containing the p53 binding protein 1 (53BP1), a key component of the DNA damage response, were defined. Interestingly, 53BP1 NBs are visualized during G1 phase, in daughter cells, while DNA damage was generated in mother cells and not properly processed. Unlike most NBs involved in transcriptional processes, replication has proven to be key for 53BP1 NBs, with replication stress leading to the formation of these large chromatin domains in daughter cells. In this review, we expose the composition and organization of 53BP1 NBs and focus on recent findings regarding their regulation and dynamics. We then concentrate on the importance of the replication stress, examine the relation of 53BP1 NBs with DNA damage and discuss their dysfunction.
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Affiliation(s)
- Anne Fernandez-Vidal
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027 Toulouse, France.
| | - Julien Vignard
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027 Toulouse, France.
| | - Gladys Mirey
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027 Toulouse, France.
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Hafez AY, Luftig MA. Characterization of the EBV-Induced Persistent DNA Damage Response. Viruses 2017; 9:E366. [PMID: 29194355 PMCID: PMC5744141 DOI: 10.3390/v9120366] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 12/21/2022] Open
Abstract
Epstein-Barr virus (EBV) is an oncogenic herpesvirus that is ubiquitous in the human population. Early after EBV infection in vitro, primary human B cells undergo a transient period of hyper-proliferation, which results in replicative stress and DNA damage, activation of the DNA damage response (DDR) pathway and, ultimately, senescence. In this study, we investigated DDR-mediated senescence in early arrested EBV-infected B cells and characterized the establishment of persistent DNA damage foci. We found that arrested EBV-infected B cells exhibited an increase in promyelocytic leukemia nuclear bodies (PML NBs), which predominantly localized to markers of DNA damage, as well as telomeric DNA. Furthermore, arrested EBV-infected B cells exhibited an increase in the presence of telomere dysfunction-induced foci. Importantly, we found that increasing human telomerase reverse transcriptase (hTERT) expression with danazol, a drug used to treat telomere diseases, permitted early EBV-infected B cells to overcome cellular senescence and enhanced transformation. Finally, we report that EBV-infected B cells undergoing hyper-proliferation are more sensitive than lymphoblastoid cell lines (LCLs) to inhibition of Bloom syndrome-associated helicase, which facilitates telomere replication. Together, our results describe the composition of persistent DNA damage foci in the early stages of EBV infection and define key regulators of this barrier to long-term outgrowth.
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Affiliation(s)
- Amy Y Hafez
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, NC 27710, USA.
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PML nuclear bodies, membrane-less domains acting as ROS sensors? Semin Cell Dev Biol 2017; 80:29-34. [PMID: 29157919 DOI: 10.1016/j.semcdb.2017.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/04/2017] [Accepted: 11/06/2017] [Indexed: 12/23/2022]
Abstract
PML Nuclear bodies (PML NBs) are spherical domains associated with a broad range of activities upon stress responses such as apoptosis, senescence DNA repair, epigenetic control, as well as control of oncogenesis. These bodies are considered as privileged sites for post-translational modifications, where sumoylation plays a key role. Here we summarize recent in vitro and in vivo findings on the link between PML NBs and ROS, in particular PML contributions to oxidative stress response. We discuss how it may regulate switch from cell protection against stress to cell arrest/cell death.
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Chang HR, Munkhjargal A, Kim MJ, Park SY, Jung E, Ryu JH, Yang Y, Lim JS, Kim Y. The functional roles of PML nuclear bodies in genome maintenance. Mutat Res 2017; 809:99-107. [PMID: 28521962 DOI: 10.1016/j.mrfmmm.2017.05.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/28/2017] [Accepted: 05/04/2017] [Indexed: 02/07/2023]
Abstract
In the nucleus, there are several membraneless structures called nuclear bodies. Among them, promyelocytic leukemia nuclear bodies (PML-NBs) are involved in multiple genome maintenance pathways including the DNA damage response, DNA repair, telomere homeostasis, and p53-associated apoptosis. In response to DNA damage, PML-NBs are coalesced and divided by a fission mechanism, thus increasing their number. PML-NBs also play a role in repairing DNA double-strand breaks (DSBs) by homologous recombination (HR). Clinically, the dominant negative PML-RARα fusion protein expressed in acute promyelocytic leukemia (APL) inhibits the transactivation of downstream factors and disrupts PML function, revealing the tumor suppressor role of PML-NBs. All-trans retinoic acid and arsenic trioxide treatment has been implemented for promyelocytic leukemia to target the PML-RARα fusion protein. PML-NBs are associated with various factors implicated in genome maintenance, and are found at the sites of DNA damage. Their interaction with proteins such as p53 indicates that PML-NBs may play a significant role in apoptosis and cancer. Decades of research have revealed the importance of PML-NBs in diverse cellular pathways, yet the underlying molecular mechanisms and exact functions of PML-NBs remain elusive. In this review, PML protein modifications and the functional relevance of PML-NB and its associated factors in genome maintenance will be discussed.
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Affiliation(s)
- Hae Ryung Chang
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Anudari Munkhjargal
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Myung-Jin Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Seon Young Park
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Eunyoung Jung
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Jae-Ha Ryu
- Research Center for Cell Fate Control, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Young Yang
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Jong-Seok Lim
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Yonghwan Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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Vaurijoux A, Voisin P, Freneau A, Barquinero JF, Gruel G. Transmission of persistent ionizing radiation-induced foci through cell division in human primary cells. Mutat Res 2017; 797-799:15-25. [PMID: 28340407 DOI: 10.1016/j.mrfmmm.2017.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 02/01/2017] [Accepted: 03/06/2017] [Indexed: 01/13/2023]
Abstract
Unrepaired DNA double-strand breaks (DSBs) induced by ionizing radiation are associated with lethal effects and genomic instability. After the initial breaks and chromatin destabilization, a set of post-translational modifications of histones occurs, including phosphorylation of serine 139 of histone H2AX (γH2AX), which leads to the formation of ionizing radiation-induced foci (IRIF). DSB repair results in the disappearance of most IRIF within hours after exposure, although some remain 24h after irradiation. Their relation to unrepaired DSBs is generally accepted but still controversial. This study evaluates the frequency and kinetics of persistent IRIF and analyzes their impact on cell proliferation. We observed persistent IRIF up to 7 days postirradiation, and more than 70% of cells exposed to 5Gy had at least one of these persistent IRIF 24h after exposure. Moreover we demonstrated that persistent IRIF did not block cell proliferation definitively. The frequency of IRIF was lower in daughter cells, due to asymmetric distribution of IRIF between some of them. We report a positive association between the presence of IRIF and the likelihood of DNA missegregation. Hence, the structure formed after the passage of a persistent IRI focus across the S and G2 phases may impede the correct segregation of the affected chromosome's sister chromatids. The ensuing abnormal resolution of anaphase might therefore cause the nature of IRIF in daughter-cell nuclei to differ before and after the first cell division. The resulting atypical chromosomal assembly may be lethal or result in a gene dosage imbalance and possibly enhanced genomic instability, in particular in the daughter cells.
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Affiliation(s)
- Aurelie Vaurijoux
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), Laboratoire de Dosimétrie Biologique, BP 17, 92262 Fontenay aux roses cedex, France.
| | - Pascale Voisin
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), Laboratoire de Dosimétrie Biologique, BP 17, 92262 Fontenay aux roses cedex, France
| | - Amelie Freneau
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), Laboratoire de Dosimétrie Biologique, BP 17, 92262 Fontenay aux roses cedex, France
| | | | - Gaetan Gruel
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), Laboratoire de Dosimétrie Biologique, BP 17, 92262 Fontenay aux roses cedex, France
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Lomonte P. Herpesvirus Latency: On the Importance of Positioning Oneself. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2017; 223:95-117. [PMID: 28528441 DOI: 10.1007/978-3-319-53168-7_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nucleus is composed of multiple compartments and domains, which directly or indirectly influence many cellular processes including gene expression, RNA splicing and maturation, protein post-translational modifications, and chromosome segregation. Nuclear-replicating viruses, especially herpesviruses, have co-evolved with the cell, adopting strategies to counteract and eventually hijack this hostile environment for their own benefit. This allows them to persist in the host for the entire life of an individual and to ensure their maintenance in the target species. Herpesviruses establish latency in dividing or postmitotic cells from which they can efficiently reactivate after sometimes years of a seemingly dormant state. Therefore, herpesviruses circumvent the threat of permanent silencing by reactivating their dormant genomes just enough to escape extinction, but not too much to avoid life-threatening damage to the host. In addition, herpesviruses that establish latency in dividing cells must adopt strategies to maintain their genomes in the daughter cells to avoid extinction by dilution of their genomes following multiple cell divisions. From a biochemical point of view, reactivation and maintenance of viral genomes in dividing cells occur successfully because the viral genomes interact with the nuclear architecture in a way that allows the genomes to be transmitted faithfully and to benefit from the nuclear micro-environments that allow reactivation following specific stimuli. Therefore, spatial positioning of the viral genomes within the nucleus is likely to be essential for the success of the latent infection and, beyond that, for the maintenance of herpesviruses in their respective hosts.
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Affiliation(s)
- Patrick Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5310, INSERM U-1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Assembly, Nuclear Domains, Virus, 69008, Lyon, France.
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Franek M, Kovaříková A, Bártová E, Kozubek S. Nucleolar Reorganization Upon Site-Specific Double-Strand Break Induction. J Histochem Cytochem 2016; 64:669-686. [PMID: 27680669 PMCID: PMC5084524 DOI: 10.1369/0022155416668505] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/09/2016] [Indexed: 12/20/2022] Open
Abstract
DNA damage response (DDR) in ribosomal genes and mechanisms of DNA repair in embryonic stem cells (ESCs) are less explored nuclear events. DDR in ESCs should be unique due to their high proliferation rate, expression of pluripotency factors, and specific chromatin signature. Given short population doubling time and fast progress through G1 phase, ESCs require a sustained production of rRNA, which leads to the formation of large and prominent nucleoli. Although transcription of rRNA in the nucleolus is relatively well understood, little is known about DDR in this nuclear compartment. Here, we directed formation of double-strand breaks in rRNA genes with I- PpoI endonuclease, and we studied nucleolar morphology, DDR, and chromatin modifications. We observed a pronounced formation of I- PpoI-induced nucleolar caps, positive on BRCA1, NBS1, MDC1, γH2AX, and UBF1 proteins. We showed interaction of nucleolar protein TCOF1 with HDAC1 and TCOF1 with CARM1 after DNA injury. Moreover, H3R17me2a modification mediated by CARM1 was found in I- PpoI-induced nucleolar caps. Finally, we report that heterochromatin protein 1 is not involved in DNA repair of nucleolar caps.
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Affiliation(s)
- Michal Franek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic (MF, AK, EB, SK)
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