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Lu W, Yan J, Wang C, Qin W, Han X, Qin Z, Wei Y, Xu H, Gao J, Gao C, Ye T, Tay FR, Niu L, Jiao K. Interorgan communication in neurogenic heterotopic ossification: the role of brain-derived extracellular vesicles. Bone Res 2024; 12:11. [PMID: 38383487 PMCID: PMC10881583 DOI: 10.1038/s41413-023-00310-8] [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: 05/01/2023] [Revised: 11/06/2023] [Accepted: 12/11/2023] [Indexed: 02/23/2024] Open
Abstract
Brain-derived extracellular vesicles participate in interorgan communication after traumatic brain injury by transporting pathogens to initiate secondary injury. Inflammasome-related proteins encapsulated in brain-derived extracellular vesicles can cross the blood‒brain barrier to reach distal tissues. These proteins initiate inflammatory dysfunction, such as neurogenic heterotopic ossification. This recurrent condition is highly debilitating to patients because of its relatively unknown pathogenesis and the lack of effective prophylactic intervention strategies. Accordingly, a rat model of neurogenic heterotopic ossification induced by combined traumatic brain injury and achillotenotomy was developed to address these two issues. Histological examination of the injured tendon revealed the coexistence of ectopic calcification and fibroblast pyroptosis. The relationships among brain-derived extracellular vesicles, fibroblast pyroptosis and ectopic calcification were further investigated in vitro and in vivo. Intravenous injection of the pyroptosis inhibitor Ac-YVAD-cmk reversed the development of neurogenic heterotopic ossification in vivo. The present work highlights the role of brain-derived extracellular vesicles in the pathogenesis of neurogenic heterotopic ossification and offers a potential strategy for preventing neurogenic heterotopic ossification after traumatic brain injury. Brain-derived extracellular vesicles (BEVs) are released after traumatic brain injury. These BEVs contain pathogens and participate in interorgan communication to initiate secondary injury in distal tissues. After achillotenotomy, the phagocytosis of BEVs by fibroblasts induces pyroptosis, which is a highly inflammatory form of lytic programmed cell death, in the injured tendon. Fibroblast pyroptosis leads to an increase in calcium and phosphorus concentrations and creates a microenvironment that promotes osteogenesis. Intravenous injection of the pyroptosis inhibitor Ac-YVAD-cmk suppressed fibroblast pyroptosis and effectively prevented the onset of heterotopic ossification after neuronal injury. The use of a pyroptosis inhibitor represents a potential strategy for the treatment of neurogenic heterotopic ossification.
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Affiliation(s)
- Weicheng Lu
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Jianfei Yan
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Chenyu Wang
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Wenpin Qin
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Xiaoxiao Han
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Zixuan Qin
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yu Wei
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Haoqing Xu
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Jialu Gao
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Changhe Gao
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Tao Ye
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Franklin R Tay
- The Dental College of Georgia, Augusta University, Augusta, GA, USA
| | - Lina Niu
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Kai Jiao
- Department of Stomatology, Tangdu Hospital & State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration & School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China.
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2
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Moris VC, Bruneau L, Berthe J, Heuskin AC, Penninckx S, Ritter S, Weber U, Durante M, Danchin EGJ, Hespeels B, Doninck KV. Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga. BMC Biol 2024; 22:11. [PMID: 38273318 PMCID: PMC10809525 DOI: 10.1186/s12915-023-01807-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The remarkable resistance to ionizing radiation found in anhydrobiotic organisms, such as some bacteria, tardigrades, and bdelloid rotifers has been hypothesized to be incidental to their desiccation resistance. Both stresses produce reactive oxygen species and cause damage to DNA and other macromolecules. However, this hypothesis has only been investigated in a few species. RESULTS In this study, we analyzed the transcriptomic response of the bdelloid rotifer Adineta vaga to desiccation and to low- (X-rays) and high- (Fe) LET radiation to highlight the molecular and genetic mechanisms triggered by both stresses. We identified numerous genes encoding antioxidants, but also chaperones, that are constitutively highly expressed, which may contribute to the protection of proteins against oxidative stress during desiccation and ionizing radiation. We also detected a transcriptomic response common to desiccation and ionizing radiation with the over-expression of genes mainly involved in DNA repair and protein modifications but also genes with unknown functions that were bdelloid-specific. A distinct transcriptomic response specific to rehydration was also found, with the over-expression of genes mainly encoding Late Embryogenesis Abundant proteins, specific heat shock proteins, and glucose repressive proteins. CONCLUSIONS These results suggest that the extreme resistance of bdelloid rotifers to radiation might indeed be a consequence of their capacity to resist complete desiccation. This study paves the way to functional genetic experiments on A. vaga targeting promising candidate proteins playing central roles in radiation and desiccation resistance.
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Affiliation(s)
- Victoria C Moris
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium.
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium.
| | - Lucie Bruneau
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Jérémy Berthe
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Anne-Catherine Heuskin
- Namur Research Institute for Life Sciences (NARILIS), Laboratory of Analysis By Nuclear Reactions (LARN), University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet - Université Libre de Bruxelles, 90 Rue Meylemeersch, 1070, Brussels, Belgium
| | - Sylvia Ritter
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Uli Weber
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Marco Durante
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 06903, Sophia Antipolis, France
| | - Boris Hespeels
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium
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3
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Vickridge E, Faraco CCF, Lo F, Rahimian H, Liu Z, Tehrani P, Djerir B, Ramdzan ZM, Leduy L, Maréchal A, Gingras AC, Nepveu A. The function of BCL11B in base excision repair contributes to its dual role as an oncogene and a haplo-insufficient tumor suppressor gene. Nucleic Acids Res 2024; 52:223-242. [PMID: 37956270 PMCID: PMC10783527 DOI: 10.1093/nar/gkad1037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Genetic studies in mice and human cancers established BCL11B as a haploinsufficient tumor suppressor gene. Paradoxically, BCL11B is overexpressed in some human cancers where its knockdown is synthetic lethal. We identified the BCL11B protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro DNA repair assays demonstrated that both BCL11B and a small recombinant BCL11B213-560 protein lacking transcription regulation potential can stimulate the enzymatic activities of two base excision repair (BER) enzymes: NTHL1 and Pol β. In cells, BCL11B is rapidly recruited to sites of DNA damage caused by laser microirradiation. BCL11B knockdown delays, whereas ectopic expression of BCL11B213-560 accelerates, the repair of oxidative DNA damage. Inactivation of one BCL11B allele in TK6 lymphoblastoid cells causes an increase in spontaneous and radiation-induced mutation rates. In turn, ectopic expression of BCL11B213-560 cooperates with the RAS oncogene in cell transformation by reducing DNA damage and cellular senescence. These findings indicate that BCL11B functions as a BER accessory factor, safeguarding normal cells from acquiring mutations. Paradoxically, it also enables the survival of cancer cells that would otherwise undergo senescence or apoptosis due to oxidative DNA damage resulting from the elevated production of reactive oxygen species.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Camila C F Faraco
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Fanny Lo
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Hedyeh Rahimian
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Zi Yang Liu
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Payman S Tehrani
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario Canada
| | - Billel Djerir
- Department of Biology and Cancer Research Institute, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Zubaidah M Ramdzan
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Alexandre Maréchal
- Department of Biology and Cancer Research Institute, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alain Nepveu
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Medicine, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Oncology, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
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4
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Hananya N, Ye X, Koren S, Muir T. A genetically encoded photoproximity labeling approach for mapping protein territories. Proc Natl Acad Sci U S A 2023; 120:e2219339120. [PMID: 37036999 PMCID: PMC10120045 DOI: 10.1073/pnas.2219339120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023] Open
Abstract
Studying dynamic biological processes requires approaches compatible with the lifetimes of the biochemical transactions under investigation, which can be very short. We describe a genetically encoded system that allows protein neighborhoods to be mapped using visible light. Our approach involves fusing an engineered flavoprotein to a protein of interest. Brief excitation of the fusion protein leads to the labeling of nearby proteins with cell-permeable probes. Mechanistic studies reveal different labeling pathways are operational depending on the nature of the exogenous probe that is employed. When combined with quantitative proteomics, this photoproximity labeling system generates "snapshots" of protein territories with high temporal and spatial resolution. The intrinsic fluorescence of the fusion domain permits correlated imaging and proteomics analyses, a capability that is exploited in several contexts, including defining the protein clients of the major vault protein. The technology should be broadly useful in the biomedical area.
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Affiliation(s)
- Nir Hananya
- Department of Chemistry, Princeton University, Princeton, NJ08544
| | - Xuanjia Ye
- Department of Chemistry, Princeton University, Princeton, NJ08544
| | - Shany Koren
- Department of Chemistry, Princeton University, Princeton, NJ08544
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, NJ08544
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5
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Mensah MA, Niskanen H, Magalhaes AP, Basu S, Kircher M, Sczakiel HL, Reiter AMV, Elsner J, Meinecke P, Biskup S, Chung BHY, Dombrowsky G, Eckmann-Scholz C, Hitz MP, Hoischen A, Holterhus PM, Hülsemann W, Kahrizi K, Kalscheuer VM, Kan A, Krumbiegel M, Kurth I, Leubner J, Longardt AC, Moritz JD, Najmabadi H, Skipalova K, Snijders Blok L, Tzschach A, Wiedersberg E, Zenker M, Garcia-Cabau C, Buschow R, Salvatella X, Kraushar ML, Mundlos S, Caliebe A, Spielmann M, Horn D, Hnisz D. Aberrant phase separation and nucleolar dysfunction in rare genetic diseases. Nature 2023; 614:564-571. [PMID: 36755093 PMCID: PMC9931588 DOI: 10.1038/s41586-022-05682-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/22/2022] [Indexed: 02/10/2023]
Abstract
Thousands of genetic variants in protein-coding genes have been linked to disease. However, the functional impact of most variants is unknown as they occur within intrinsically disordered protein regions that have poorly defined functions1-3. Intrinsically disordered regions can mediate phase separation and the formation of biomolecular condensates, such as the nucleolus4,5. This suggests that mutations in disordered proteins may alter condensate properties and function6-8. Here we show that a subset of disease-associated variants in disordered regions alter phase separation, cause mispartitioning into the nucleolus and disrupt nucleolar function. We discover de novo frameshift variants in HMGB1 that cause brachyphalangy, polydactyly and tibial aplasia syndrome, a rare complex malformation syndrome. The frameshifts replace the intrinsically disordered acidic tail of HMGB1 with an arginine-rich basic tail. The mutant tail alters HMGB1 phase separation, enhances its partitioning into the nucleolus and causes nucleolar dysfunction. We built a catalogue of more than 200,000 variants in disordered carboxy-terminal tails and identified more than 600 frameshifts that create arginine-rich basic tails in transcription factors and other proteins. For 12 out of the 13 disease-associated variants tested, the mutation enhanced partitioning into the nucleolus, and several variants altered rRNA biogenesis. These data identify the cause of a rare complex syndrome and suggest that a large number of genetic variants may dysregulate nucleoli and other biomolecular condensates in humans.
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Affiliation(s)
- Martin A. Mensah
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Henri Niskanen
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandre P. Magalhaes
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Shaon Basu
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Kircher
- grid.484013.a0000 0004 6879 971XExploratory Diagnostic Sciences, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.4562.50000 0001 0057 2672Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel Germany
| | - Henrike L. Sczakiel
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alisa M. V. Reiter
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonas Elsner
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Meinecke
- grid.13648.380000 0001 2180 3484Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Saskia Biskup
- grid.498061.20000 0004 6008 5552Center for Genomics and Transcriptomics (CeGaT), Tübingen, Germany
| | - Brian H. Y. Chung
- grid.194645.b0000000121742757Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Gregor Dombrowsky
- grid.412468.d0000 0004 0646 2097Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany ,grid.5560.60000 0001 1009 3608Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | - Christel Eckmann-Scholz
- grid.412468.d0000 0004 0646 2097Department of Obstetrics and Gynecology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Marc Phillip Hitz
- grid.412468.d0000 0004 0646 2097Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany ,grid.5560.60000 0001 1009 3608Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | - Alexander Hoischen
- grid.10417.330000 0004 0444 9382Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul-Martin Holterhus
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, Pediatric Endocrinology and Diabetes, University Hospital Schleswig-Holstein, Schleswig-Holstein, Germany
| | - Wiebke Hülsemann
- grid.440182.b0000 0004 0580 3398Handchirurgie, Katholisches Kinderkrankenhaus Wilhelmstift, Hamburg, Germany
| | - Kimia Kahrizi
- grid.472458.80000 0004 0612 774XGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Vera M. Kalscheuer
- grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anita Kan
- grid.415550.00000 0004 1764 4144Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Mandy Krumbiegel
- grid.5330.50000 0001 2107 3311Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ingo Kurth
- grid.412301.50000 0000 8653 1507Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, Aachen, Germany
| | - Jonas Leubner
- grid.6363.00000 0001 2218 4662Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ann Carolin Longardt
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Center Schleswig‐Holstein, Kiel, Germany
| | - Jörg D. Moritz
- grid.412468.d0000 0004 0646 2097Department of Radiology and Neuroradiology, Pediatric Radiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Hossein Najmabadi
- grid.472458.80000 0004 0612 774XGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Karolina Skipalova
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lot Snijders Blok
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andreas Tzschach
- grid.5963.9Institute of Human Genetics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eberhard Wiedersberg
- grid.491868.a0000 0000 9601 2399Zentrum für Kinder-und Jugendmedizin, Helios Kliniken Schwerin, Schwerin, Germany
| | - Martin Zenker
- grid.5807.a0000 0001 1018 4307Institute of Human Genetics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Carla Garcia-Cabau
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - René Buschow
- grid.419538.20000 0000 9071 0620Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Xavier Salvatella
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Passeig Lluís Companys 23, Barcelona, Spain
| | - Matthew L. Kraushar
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stefan Mundlos
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany ,grid.506128.8BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Almuth Caliebe
- grid.4562.50000 0001 0057 2672Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel Germany
| | - Malte Spielmann
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany.
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response. Genes (Basel) 2022; 14:genes14010112. [PMID: 36672853 PMCID: PMC9859207 DOI: 10.3390/genes14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
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7
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Vickridge E, Faraco CCF, Tehrani PS, Ramdzan ZM, Djerir B, Rahimian H, Leduy L, Maréchal A, Gingras AC, Nepveu A. The DNA repair function of BCL11A suppresses senescence and promotes continued proliferation of triple-negative breast cancer cells. NAR Cancer 2022; 4:zcac028. [PMID: 36186110 PMCID: PMC9516615 DOI: 10.1093/narcan/zcac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
We identified the BCL11A protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro, DNA repair assays demonstrate that both BCL11A and a small recombinant BCL11A160-520 protein that is devoid of DNA binding and transcription regulatory domains can stimulate the enzymatic activities of two base excision repair enzymes: NTHL1 and DNA Pol β. Increased DNA repair efficiency, in particular of the base excision repair pathway, is essential for many cancer cells to proliferate in the presence of elevated reactive oxygen species (ROS) produced by cancer-associated metabolic changes. BCL11A is highly expressed in triple-negative breast cancers (TNBC) where its knockdown was reported to reduce clonogenicity and cause tumour regression. We show that BCL11A knockdown in TNBC cells delays repair of oxidative DNA damage, increases the number of oxidized bases and abasic sites in genomic DNA, slows down proliferation and induces cellular senescence. These phenotypes are rescued by ectopic expression of the short BCL11A160-520 protein. We further show that the BCL11A160-520 protein accelerates the repair of oxidative DNA damage and cooperates with RAS in cell transformation assays, thereby enabling cells to avoid senescence and continue to proliferate in the presence of high ROS levels.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Camila C F Faraco
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Payman S Tehrani
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Zubaidah M Ramdzan
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Billel Djerir
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Hedyeh Rahimian
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Alexandre Maréchal
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alain Nepveu
- To whom correspondence should be addressed. Tel: +1 514 398 5839; Fax: +1 514 398 6769;
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8
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Turgimbayeva A, Zein U, Zharkov DO, Ramankulov Y, Saparbaev M, Abeldenov S. Cloning and characterization of the major AP endonuclease from Staphylococcus aureus. DNA Repair (Amst) 2022; 119:103390. [DOI: 10.1016/j.dnarep.2022.103390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/19/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
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9
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Vickridge E, Faraco CCF, Nepveu A. Base excision repair accessory factors in senescence avoidance and resistance to treatments. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:703-720. [PMID: 36176767 PMCID: PMC9511810 DOI: 10.20517/cdr.2022.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 06/16/2023]
Abstract
Cancer cells, in which the RAS and PI3K pathways are activated, produce high levels of reactive oxygen species (ROS), which cause oxidative DNA damage and ultimately cellular senescence. This process has been documented in tissue culture, mouse models, and human pre-cancerous lesions. In this context, cellular senescence functions as a tumour suppressor mechanism. Some rare cancer cells, however, manage to adapt to avoid senescence and continue to proliferate. One well-documented mode of adaptation involves increased production of antioxidants often associated with inactivation of the KEAP1 tumour suppressor gene and the resulting upregulation of the NRF2 transcription factor. In this review, we detail an alternative mode of adaptation to oxidative DNA damage induced by ROS: the increased activity of the base excision repair (BER) pathway, achieved through the enhanced expression of BER enzymes and DNA repair accessory factors. These proteins, exemplified here by the CUT domain proteins CUX1, CUX2, and SATB1, stimulate the activity of BER enzymes. The ensued accelerated repair of oxidative DNA damage enables cancer cells to avoid senescence despite high ROS levels. As a by-product of this adaptation, these cancer cells exhibit increased resistance to genotoxic treatments including ionizing radiation, temozolomide, and cisplatin. Moreover, considering the intrinsic error rate associated with DNA repair and translesion synthesis, the elevated number of oxidative DNA lesions caused by high ROS leads to the accumulation of mutations in the cancer cell population, thereby contributing to tumour heterogeneity and eventually to the acquisition of resistance, a major obstacle to clinical treatment.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- These authors contributed equally to this work
| | - Camila C. F. Faraco
- Goodman Cancer Institute, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Departments of Biochemistry, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- These authors contributed equally to this work
| | - Alain Nepveu
- Goodman Cancer Institute, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Departments of Biochemistry, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Medicine, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Oncology, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
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10
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Park SB, Jung WK, Yu HY, Kim YH, Kim J. Effect of Aucubin-Containing Eye Drops on Tear Hyposecretion and Lacrimal Gland Damage Induced by Urban Particulate Matter in Rats. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092926. [PMID: 35566278 PMCID: PMC9104073 DOI: 10.3390/molecules27092926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022]
Abstract
Exposure to particulate matter is a causative factor of dry eye disease. We aimed to investigate the beneficial effect of eye drops containing aucubin on dry eye disease induced by urban particulate matter (UPM). Dry eye was induced in male SD rats (6 weeks old) by topical exposure to UPM thrice a day for 5 d. Eye drops containing 0.1% aucubin or 0.5% aucubin were topically administered directly into the eye after UPM exposure for an additional 5 d. Tear secretion was evaluated using a phenol red thread tear test and corneal irregularity. The oxidative damage in the lacrimal gland was evaluated using TUNEL and immunohistochemical staining. The topical administration of aucubin significantly attenuated UPM-induced tear hyposecretion (control group: 9.25 ± 0.62 mm, UPM group: 4.55 ± 0.25 mm, 0.1% aucubin: 7.12 ± 0.58 mm, and 0.5% aucubin: 7.88 ± 0.75 mm) and corneal irregularity (control group: 0.00 ± 0.00, UPM group: 3.40 ± 0.29, 0.1% aucubin: 1.80 ± 0.27, and 0.5% aucubin: 1.15 ± 0.27). In addition, aucubin also reduced the UPM-induced apoptotic injury of lacrimal gland cells induced by oxidative stress through the increased expression of HMGB1 and RAGE. These findings indicate that the topical administration of aucubin eye drops showed a beneficial effect against UPM-induced abnormal ocular changes, such as tear hyposecretion and lacrimal gland damage. Therefore, our results reveal the pharmacological activities of aucubin in dry eye disease.
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Affiliation(s)
| | | | | | | | - Junghyun Kim
- Correspondence: ; Tel.: +82-63-270-4032; Fax: +82-63-270-4025
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11
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Lin X, Jiang W, Rudolph J, Lee BJ, Luger K, Zha S. PARP inhibitors trap PARP2 and alter the mode of recruitment of PARP2 at DNA damage sites. Nucleic Acids Res 2022; 50:3958-3973. [PMID: 35349716 PMCID: PMC9023293 DOI: 10.1093/nar/gkac188] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/24/2022] [Accepted: 03/23/2022] [Indexed: 12/11/2022] Open
Abstract
Dual-inhibitors of PARP1 and PARP2 are promising anti-cancer drugs. In addition to blocking PARP1&2 enzymatic activity, PARP inhibitors also extend the lifetime of DNA damage-induced PARP1&2 foci, termed trapping. Trapping is important for the therapeutic effects of PARP inhibitors. Using live-cell imaging, we found that PARP inhibitors cause persistent PARP2 foci by switching the mode of PARP2 recruitment from a predominantly PARP1- and PAR-dependent rapid exchange to a WGR domain-mediated stalling of PARP2 on DNA. Specifically, PARP1-deletion markedly reduces but does not abolish PARP2 foci. The residual PARP2 foci in PARP1-deficient cells are DNA-dependent and abrogated by the R140A mutation in the WGR domain. Yet, PARP2-R140A forms normal foci in PARP1-proficient cells. In PARP1-deficient cells, PARP inhibitors - niraparib, talazoparib, and, to a lesser extent, olaparib - enhance PARP2 foci by preventing PARP2 exchange. This trapping of PARP2 is independent of auto-PARylation and is abolished by the R140A mutation in the WGR domain and the H415A mutation in the catalytic domain. Taken together, we found that PARP inhibitors trap PARP2 by physically stalling PARP2 on DNA via the WGR-DNA interaction while suppressing the PARP1- and PAR-dependent rapid exchange of PARP2.
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Affiliation(s)
- Xiaohui Lin
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO80309, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Department of Pathology and Cell Biology, Herbert Irvine Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
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12
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Yasom S, Watcharanurak P, Bhummaphan N, Thongsroy J, Puttipanyalears C, Settayanon S, Chalertpet K, Khumsri W, Kongkaew A, Patchsung M, Siriwattanakankul C, Pongpanich M, Pin‐on P, Jindatip D, Wanotayan R, Odton M, Supasai S, Oo TT, Arunsak B, Pratchayasakul W, Chattipakorn N, Chattipakorn S, Mutirangura A. The roles of HMGB1-produced DNA gaps in DNA protection and aging biomarker reversal. FASEB Bioadv 2022; 4:408-434. [PMID: 35664831 PMCID: PMC9164245 DOI: 10.1096/fba.2021-00131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/23/2022] [Accepted: 02/28/2022] [Indexed: 11/24/2022] Open
Abstract
The endogenous DNA damage triggering an aging progression in the elderly is prevented in the youth, probably by naturally occurring DNA gaps. Decreased DNA gaps are found during chronological aging in yeast. So we named the gaps "Youth-DNA-GAPs." The gaps are hidden by histone deacetylation to prevent DNA break response and were also reduced in cells lacking either the high-mobility group box (HMGB) or the NAD-dependent histone deacetylase, SIR2. A reduction in DNA gaps results in shearing DNA strands and decreasing cell viability. Here, we show the roles of DNA gaps in genomic stability and aging prevention in mammals. The number of Youth-DNA-GAPs were low in senescent cells, two aging rat models, and the elderly. Box A domain of HMGB1 acts as molecular scissors in producing DNA gaps. Increased gaps consolidated DNA durability, leading to DNA protection and improved aging features in senescent cells and two aging rat models similar to those of young organisms. Like the naturally occurring Youth-DNA-GAPs, Box A-produced DNA gaps avoided DNA double-strand break response by histone deacetylation and SIRT1, a Sir2 homolog. In conclusion, Youth-DNA-GAPs are a biomarker determining the DNA aging stage (young/old). Box A-produced DNA gaps ultimately reverse aging features. Therefore, DNA gap formation is a potential strategy to monitor and treat aging-associated diseases.
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Affiliation(s)
- Sakawdaurn Yasom
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand,Interdisciplinary Program of Biomedical Sciences, Graduate SchoolChulalongkorn UniversityBangkokThailand
| | - Papitchaya Watcharanurak
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand,Interdisciplinary Program of Biomedical Sciences, Graduate SchoolChulalongkorn UniversityBangkokThailand
| | - Narumol Bhummaphan
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | | | - Charoenchai Puttipanyalears
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Sirapat Settayanon
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand,Interdisciplinary Program of Biomedical Sciences, Graduate SchoolChulalongkorn UniversityBangkokThailand
| | - Kanwalat Chalertpet
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand,Interdisciplinary Program of Biomedical Sciences, Graduate SchoolChulalongkorn UniversityBangkokThailand
| | - Wilunplus Khumsri
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand,Interdisciplinary Program of Biomedical Sciences, Graduate SchoolChulalongkorn UniversityBangkokThailand
| | - Aphisek Kongkaew
- Research Administration Section, Faculty of MedicineChiang Mai UniversityChiang MaiThailand
| | - Maturada Patchsung
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Chutha Siriwattanakankul
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of ScienceChulalongkorn UniversityBangkokThailand,Omics Sciences and Bioinformatics Center, Faculty of ScienceChulalongkorn UniversityBangkokThailand
| | - Piyapat Pin‐on
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Depicha Jindatip
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Rujira Wanotayan
- Department of Radiological Technology, Faculty of Medical TechnologyMahidol UniversityNakhon PathomThailand
| | - Mingkwan Odton
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical MedicineMahidol UniversityBangkokThailand
| | - Suangsuda Supasai
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical MedicineMahidol UniversityBangkokThailand
| | - Thura Tun Oo
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of MedicineChiang Mai UniversityChiang MaiThailand,Center of Excellence in Cardiac Electrophysiology ResearchChiang Mai UniversityChiang MaiThailand
| | - Busarin Arunsak
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of MedicineChiang Mai UniversityChiang MaiThailand,Center of Excellence in Cardiac Electrophysiology ResearchChiang Mai UniversityChiang MaiThailand
| | - Wasana Pratchayasakul
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of MedicineChiang Mai UniversityChiang MaiThailand,Center of Excellence in Cardiac Electrophysiology ResearchChiang Mai UniversityChiang MaiThailand
| | - Nipon Chattipakorn
- Center of Excellence in Cardiac Electrophysiology ResearchChiang Mai UniversityChiang MaiThailand,Cardiac Electrophysiology Unit, Department of Physiology, Faculty of MedicineChiang Mai UniversityChiang MaiThailand
| | - Siriporn Chattipakorn
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of MedicineChiang Mai UniversityChiang MaiThailand,Center of Excellence in Cardiac Electrophysiology ResearchChiang Mai UniversityChiang MaiThailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, Faculty of MedicineChulalongkorn UniversityBangkokThailand
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13
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Wei X, Wang Z, Hinson C, Yang K. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3638-3657. [PMID: 35349719 PMCID: PMC9023300 DOI: 10.1093/nar/gkac185] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Caroline Hinson
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kun Yang
- To whom correspondence should be addressed. Tel: +1 512 471 4843;
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14
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Polydatin Alleviates Diabetes-Induced Hyposalivation through Anti-Glycation Activity in db/db Mouse. Pharmaceutics 2021; 14:pharmaceutics14010051. [PMID: 35056946 PMCID: PMC8777620 DOI: 10.3390/pharmaceutics14010051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/03/2022] Open
Abstract
Polydatin (resveratrol-3-O-β-mono-D-glucoside) is a polyphenol that can be easily accessed from peanuts, grapes, and red wine, and is known to have antiglycation, antioxidant, and anti-inflammatory effects. Diabetes mellitus is a very common disease, and diabetic complications are very common complications. The dry mouth symptom is one of the most common oral complaints in patients with diabetes mellitus. Diabetes mellitus is thought to promote hyposalivation. In this study, we aimed to investigate the improvement effect of polydatin on diabetes-induced hyposalivation in db/db mouse model of type 2 diabetes. We examined salivary flow rate, TUNEL assay, PAS staining, and immunohistochemical staining for AGEs, RAGE, HMGB1, 8-OHdG, and AQP5 to evaluate the efficacy of polydatin in the submandibular salivary gland. Diabetic db/db mice had a decreased salivary flow rate and salivary gland weight. The salivary gland of the vehicle-treated db/db mice showed an increased apoptotic cell injury. The AGEs were highly accumulated, and its receptor, RAGE expression was also enhanced. Expressions of HMGB1, an oxidative cell damage marker, and 8-OHdG, an oxidative DNA damage marker, increased greatly. However, polydatin ameliorated this hypofunction of the salivary gland and inhibited diabetes-related salivary cell injury. Furthermore, polydatin improved mucin accumulation, which is used as a damage marker for salivary gland acinar cells, and decreased expression of water channel AQP5 was improved by polydatin. In conclusion, polydatin has a potent protective effect on diabetes-related salivary gland hypofunction through its antioxidant and anti-glycation activities, and its AQP5 upregulation. This result suggests the possibility of the use of polydatin as a therapeutic drug to improve hyposalivation caused by diabetes.
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15
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Jang S, Schaich MA, Khuu C, Schnable BL, Majumdar C, Watkins SC, David SS, Van Houten B. Single molecule analysis indicates stimulation of MUTYH by UV-DDB through enzyme turnover. Nucleic Acids Res 2021; 49:8177-8188. [PMID: 34232996 PMCID: PMC8373069 DOI: 10.1093/nar/gkab591] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 06/09/2021] [Accepted: 06/24/2021] [Indexed: 11/30/2022] Open
Abstract
The oxidative base damage, 8-oxo-7,8-dihydroguanine (8-oxoG) is a highly mutagenic lesion because replicative DNA polymerases insert adenine (A) opposite 8-oxoG. In mammalian cells, the removal of A incorporated across from 8-oxoG is mediated by the glycosylase MUTYH during base excision repair (BER). After A excision, MUTYH binds avidly to the abasic site and is thus product inhibited. We have previously reported that UV-DDB plays a non-canonical role in BER during the removal of 8-oxoG by 8-oxoG glycosylase, OGG1 and presented preliminary data that UV-DDB can also increase MUTYH activity. In this present study we examine the mechanism of how UV-DDB stimulates MUTYH. Bulk kinetic assays show that UV-DDB can stimulate the turnover rate of MUTYH excision of A across from 8-oxoG by 4-5-fold. Electrophoretic mobility shift assays and atomic force microscopy suggest transient complex formation between MUTYH and UV-DDB, which displaces MUTYH from abasic sites. Using single molecule fluorescence analysis of MUTYH bound to abasic sites, we show that UV-DDB interacts directly with MUTYH and increases the mobility and dissociation rate of MUTYH. UV-DDB decreases MUTYH half-life on abasic sites in DNA from 8800 to 590 seconds. Together these data suggest that UV-DDB facilitates productive turnover of MUTYH at abasic sites during 8-oxoG:A repair.
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Affiliation(s)
- Sunbok Jang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Matthew A Schaich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Cindy Khuu
- Department of Chemistry and Biochemistry, Molecular, Cell and Development Graduate Group, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Brittani L Schnable
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburg, PA 15260, USA
| | - Chandrima Majumdar
- Department of Chemistry and Biochemistry, Molecular, Cell and Development Graduate Group, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Simon C Watkins
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Sheila S David
- Department of Chemistry and Biochemistry, Molecular, Cell and Development Graduate Group, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Bennett Van Houten
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburg, PA 15260, USA
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16
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Liu TC, Guo KW, Chu JW, Hsiao YY. Understanding APE1 cellular functions by the structural preference of exonuclease activities. Comput Struct Biotechnol J 2021; 19:3682-3691. [PMID: 34285771 PMCID: PMC8258793 DOI: 10.1016/j.csbj.2021.06.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/17/2022] Open
Abstract
Mammalian apurinic/apyrimidinic (AP) endonuclease 1 (APE1) has versatile enzymatic functions, including redox, endonuclease, and exonuclease activities. APE1 is thus broadly associated with pathways in DNA repair, cancer cell growth, and drug resistance. Unlike its AP site-specific endonuclease activity in Base excision repair (BER), the 3′-5′ exonucleolytic cleavage of APE1 using the same active site exhibits complex substrate selection patterns, which are key to the biological functions. This work aims to integrate molecular structural information and biocatalytic properties to deduce the substrate recognition mechanism of APE1 as an exonuclease and make connection to its diverse functionalities in the cell. In particular, an induced space-filling model emerges in which a bridge-like structure is formed by Arg177 and Met270 (RM bridge) upon substrate binding, causing the active site to adopt a long and narrow product pocket for hosting the leaving group of an AP site or the 3′-end nucleotide. Rather than distinguishing bases as other exonucleases, the hydrophobicity and steric hindrance due to the APE1 product pocket provides selectivity for substrate structures, such as matched or mismatched blunt-ended dsDNA, recessed dsDNA, gapped dsDNA, and nicked dsDNA with 3′-end overhang shorter than 2 nucleotides. These dsDNAs are similar to the native substrates in BER proofreading, BER for trinucleotide repeats (TNR), Nucleotide incision repair (NIR), DNA single-strand breaks (SSB), SSB with damaged bases, and apoptosis. Integration of in vivo studies, in vitro biochemical assays, and structural analysis is thus essential for linking the APE1 exonuclease activity to the specific roles in cellular functions.
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Affiliation(s)
- Tung-Chang Liu
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan
| | - Kai-Wei Guo
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan
| | - Jhih-Wei Chu
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Yuan Hsiao
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Drug Development and Value Creation Research Center, Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
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Ramdzan ZM, Vickridge E, Faraco CCF, Nepveu A. CUT Domain Proteins in DNA Repair and Cancer. Cancers (Basel) 2021; 13:cancers13122953. [PMID: 34204734 PMCID: PMC8231510 DOI: 10.3390/cancers13122953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 01/19/2023] Open
Abstract
Simple Summary Genetic integrity is ensured by complex groups of proteins involved in DNA repair. In particular, base damage is repaired by enzymes of the base excision repair pathway. Recent studies have revealed that some transcription factors can function as accessory factors that stimulate the enzymatic activities of these DNA repair enzymes. It is well known that defects in DNA repair mechanisms cause the accumulation of changes in DNA, called mutations, that increase the possibility that cells become tumorigenic. Paradoxically, once they have emerged certain cancer cells are acutely dependent on the heightened activities of base excision repair enzymes because their metabolism generates highly reactive molecules that cause multiple types of damage to bases. In this context, the function of accessory factors becomes essential to cancer cell survival. As a by-product of this adaptation, cancer cells become more resistant to therapies that cause DNA damage, such as chemotherapy and radiation. Abstract Recent studies revealed that CUT domains function as accessory factors that accelerate DNA repair by stimulating the enzymatic activities of the base excision repair enzymes OGG1, APE1, and DNA pol β. Strikingly, the role of CUT domain proteins in DNA repair is exploited by cancer cells to facilitate their survival. Cancer cells in which the RAS pathway is activated produce an excess of reactive oxygen species (ROS) which, if not counterbalanced by increased production of antioxidants, causes sustained oxidative DNA damage and, ultimately, cell senescence. These cancer cells can adapt by increasing their capacity to repair oxidative DNA damage in part through elevated expression of CUT domain proteins such as CUX1, CUX2, or SATB1. In particular, CUX1 overexpression was shown to cooperate with RAS in the formation of mammary and lung tumors in mice. Conversely, knockdown of CUX1, CUX2, or SATB1 was found to be synthetic lethal in cancer cells exhibiting high ROS levels as a consequence of activating mutations in KRAS, HRAS, BRAF, or EGFR. Importantly, as a byproduct of their adaptation, cancer cells that overexpress CUT domain proteins exhibit increased resistance to genotoxic treatments such as ionizing radiation, temozolomide, and cisplatin.
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Affiliation(s)
- Zubaidah M. Ramdzan
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada; (Z.M.R.); (E.V.); (C.C.F.F.)
| | - Elise Vickridge
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada; (Z.M.R.); (E.V.); (C.C.F.F.)
| | - Camila C. F. Faraco
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada; (Z.M.R.); (E.V.); (C.C.F.F.)
- Departments of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada
| | - Alain Nepveu
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada; (Z.M.R.); (E.V.); (C.C.F.F.)
- Departments of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada
- Departments of Medicine, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada
- Departments of Oncology, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada
- Correspondence: ; Tel.: +514-398-5839; Fax: +514-398-6769
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18
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Chikhirzhina EV, Starkova TY, Polyanichko AM. The Structural Organization of the HMGB1 Nuclear Protein and Its Effect on the Formation of Ordered Supramolecular Complexes. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921030039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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19
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Abstract
Poly(ADP-ribosyl)ation is one of immediate cellular responses to DNA damage and is catalyzed by poly(ADP-ribose) polymerases (PARPs). PARP1 is a well-known regulator of DNA repair. Another member of this family, PARP2, was discovered later. The study of PARP1 and PARP2 functions started a long time ago, and special attention has been given to the role of these enzymes in base excision repair. This review summarizes my lab's data on the functions of PARP1 and PARP2 in base excision repair as well as the results obtained in the course of our collaboration with Dr. Samuel H. Wilson.
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Affiliation(s)
- Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Lavrentiev Ave. 8, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
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20
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Ilina ES, Lavrik OI, Khodyreva SN. 5'-Deoxyribose Phosphate Lyase Activity of Apurinic/Apyrimidinic Endonuclease 1. Mol Biol 2021. [DOI: 10.1134/s0026893321020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Kladova OA, Kuznetsov NA, Fedorova OS. Initial stages of DNA Base Excision Repair in Nucleosomes. Mol Biol 2021. [DOI: 10.1134/s0026893321020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Peng Y, Pei H. DNA alkylation lesion repair: outcomes and implications in cancer chemotherapy. J Zhejiang Univ Sci B 2021; 22:47-62. [PMID: 33448187 DOI: 10.1631/jzus.b2000344] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, represent a major form of DNA damage in cells. The repair of alkylation damage is critical in all cells because such damage is cytotoxic and potentially mutagenic. Alkylation chemotherapy is a major therapeutic modality for many tumors, underscoring the importance of the repair pathways in cancer cells. Several different pathways exist for alkylation repair, including base excision and nucleotide excision repair, direct reversal by methyl-guanine methyltransferase (MGMT), and dealkylation by the AlkB homolog (ALKBH) protein family. However, maintaining a proper balance between these pathways is crucial for the favorable response of an organism to alkylating agents. Here, we summarize the progress in the field of DNA alkylation lesion repair and describe the implications for cancer chemotherapy.
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Affiliation(s)
- Yihan Peng
- Department of Biochemistry and Molecular Medicine, the George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA.,GW Cancer Center, the George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Huadong Pei
- Department of Biochemistry and Molecular Medicine, the George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA. .,GW Cancer Center, the George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA.
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Ramdzan ZM, Vickridge E, Li L, Faraco CCF, Djerir B, Leduy L, Maréchal A, Nepveu A. CUT Domains Stimulate Pol β Enzymatic Activities to Accelerate Completion of Base Excision Repair. J Mol Biol 2021; 433:166806. [PMID: 33450246 DOI: 10.1016/j.jmb.2020.166806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/11/2020] [Accepted: 12/30/2020] [Indexed: 01/19/2023]
Abstract
The full-length CUX1 protein isoform was previously shown to function as an auxiliary factor in base excision repair (BER). Specifically, CUT domains within CUX1 stimulate the enzymatic activities of the OGG1 DNA glycosylase and APE1 endonuclease. Moreover, ectopic expression of CUX1 or CUT domains increased the resistance of cancer cells to treatments that cause oxidative DNA damage and mono-alkylation of bases. Stimulation of OGG1 AP/lyase and APE1 endonuclease activities, however, cannot explain how CUT domains confer resistance to these treatments since these enzymes produce DNA single-strand breaks that are highly toxic to cells. In the present study, we show that CUT domains stimulate the polymerase and deoxyribose phosphate (dRP)-lyase activities of DNA polymerase β to promote BER completion. In agreement with these results, CUX1 knockdown decreases BER completion in cell extracts and causes an increase in the number of abasic sites in genomic DNA following temozolomide treatment. We also show that CUT domains stimulate bypass of intrastrand G-crosslinks by Pol β in vitro, while the resistance of cancer cells to cisplatin treatment is reduced by CUX1 knockdown but restored by ectopic expression of CUT domains. Altogether our results establish CUX1 as an important auxiliary factor that stimulates multiple steps of base excision repair, from the recognition and removal of altered bases to the addition of new nucleotides and removal of 5'-deoxyribose phosphate required for ligation and BER completion. These findings provide a mechanistic explanation for the observed correlation between CUX1 expression and the resistance of cancer cells to genotoxic treatments.
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Affiliation(s)
- Zubaidah M Ramdzan
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Elise Vickridge
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Li Li
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Camila C F Faraco
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada; Departments of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Billel Djerir
- Department of Biology, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Lam Leduy
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Alexandre Maréchal
- Department of Biology, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada; Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Alain Nepveu
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada; Departments of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada; Medicine, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada; Oncology, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada.
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Zhao L, Deng J, Ma LB, Zhang WP, Khalil MM, Karrow NA, Qi DS, Sun LH. Dietary Se deficiency dysregulates metabolic and cell death signaling in aggravating the AFB1 hepatotoxicity of chicks. Food Chem Toxicol 2020; 149:111938. [PMID: 33348051 DOI: 10.1016/j.fct.2020.111938] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/31/2022]
Abstract
The objective of this study was to use isobaric tags for relative and absolute quantitation (iTRAQ) proteomic technology to systematically analyze the hepatotoxic mechanism of aflatoxin B1 (AFB1) and its prevention by Se in broilers. Four groups of day-old broilers were allocated into a 2 × 2 factorial design trial that fed a Se-deficient based diet (BD) or the BD + 1.0 mg AFB1/kg, 0.3 mg Se/kg, or 1.0 mg AFB1/kg plus 0.3 mg Se/kg for 3 wk. Dietary AFB1 increased serum ALT and decreased total protein and albumin concentrations, and induced hepatic histopathological lesions in Se adequate groups. Notably, Se deficiency exacerbated these AFB1-induced changes. Furthermore, Se deficiency reduced hepatic glutathione peroxidase but increased thioredoxin reductase and glutathione S-transferase activities and 8-hydroxydeoxyguanosine concentration in AFB1 administrated groups. Moreover, AFB1 dysregulated 261 co-differentially expressed proteins (DEPs) in both Se adequate and deficiency diets, and Se deficiency dysregulated 64 DEPs in AFB1 administrated diets. These DEPs are mainly related to phase I and II metabolizing enzymes, heat shock proteins, DNA repair, fatty acid metabolism and apoptosis. The in vitro study has verified that aldo-keto reductase family1, member10 plays an important role in AFB1-induced hepatotoxicity and Se-mediated detoxification of AFB1 in a chicken leghorn male hepatoma cells. Conclusively, this study has analyzed the hepatic proteome response to dietary AFB1 and Se, and thus shed new light on the mechanisms of hepatotoxicity of AFB1 and its detoxification by Se in broilers.
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Affiliation(s)
- Ling Zhao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiang Deng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Li-Bao Ma
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Wan-Po Zhang
- Department of Veterinary Pathology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | | | | | - De-Sheng Qi
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Lv-Hui Sun
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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25
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Mustafa AI, Khashaba RA, Fawzy E, Baghdady SMA, Rezk SM. Cross talk between oxidative stress and inflammation in alopecia areata. J Cosmet Dermatol 2020; 20:2305-2310. [PMID: 33099870 DOI: 10.1111/jocd.13814] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Although the etiopathogenesis of alopecia areata (AA) is still unclear, inflammation, oxidative stress, and subsequent DNA damage might be considered role players in disease development. AIM We aimed at exploring the potential link between oxidative DNA damage and inflammation in AA patients through measuring 8-hydroxy deoxyguanosine (8-OHdG), high mobility group box 1 protein (HMGB1), and one of the inflammatory mediators, C-reactive protein (CRP). METHODS A total of 79 subjects (49 AA patients in addition to 30 apparently healthy control subjects) were tested for serum levels of 8-OHdG, HMBG1, and CRP. RESULTS Compared with the control group, serum 8-OHdG, HMBG1, and CRP levels were significantly elevated in the studied patients group (0.031, <0.001, and <0.001, respectively). Moreover, logistic regression analysis revealed that disease course, serum levels of 8-OHdG, and HMBG1 were considered independent predictors for AA severity in both uni- and multivariable analyses. CONCLUSION Our results suggest a possible role of oxidative stress together with proinflammatory biomarkers in development of AA and their benefit in predicting a severe form of the disease.
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Affiliation(s)
- Amany Ibrahim Mustafa
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Benha University, Benha, Egypt
| | - Rana Atef Khashaba
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Benha University, Benha, Egypt
| | - Eman Fawzy
- Department of Laboratory Medicine, Mansoura Fever Hospital, Ministry of Health, Mansoura, Egypt
| | | | - Shymaa Mostafa Rezk
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Benha University, Benha, Egypt
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26
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Chikhirzhina E, Starkova T, Beljajev A, Polyanichko A, Tomilin A. Functional Diversity of Non-Histone Chromosomal Protein HmgB1. Int J Mol Sci 2020; 21:E7948. [PMID: 33114717 PMCID: PMC7662367 DOI: 10.3390/ijms21217948] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/27/2022] Open
Abstract
The functioning of DNA in the cell nucleus is ensured by a multitude of proteins, whose interactions with DNA as well as with other proteins lead to the formation of a complicated, organized, and quite dynamic system known as chromatin. This review is devoted to the description of properties and structure of the progenitors of the most abundant non-histone protein of the HMGB family-the HmgB1 protein. The proteins of the HMGB family are also known as "architectural factors" of chromatin, which play an important role in gene expression, transcription, DNA replication, and repair. However, as soon as HmgB1 goes outside the nucleus, it acquires completely different functions, post-translational modifications, and change of its redox state. Despite a lot of evidence of the functional activity of HmgB1, there are still many issues to be solved related to the mechanisms of the influence of HmgB1 on the development and treatment of different diseases-from oncological and cardiovascular diseases to pathologies during pregnancy and childbirth. Here, we describe molecular structure of the HmgB1 protein and discuss general mechanisms of its interactions with other proteins and DNA in cell.
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Affiliation(s)
| | | | | | - Alexander Polyanichko
- Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, 194064 St. Petersburg, Tikhoretsky Av. 4, Russia; (T.S.); (A.B.); (A.T.)
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27
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Zhao Z, Hu Z, Zeng R, Yao Y. HMGB1 in kidney diseases. Life Sci 2020; 259:118203. [PMID: 32781069 DOI: 10.1016/j.lfs.2020.118203] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 12/20/2022]
Abstract
High mobility group box 1 (HMGB1) is a highly conserved nucleoprotein involving in numerous biological processes, and well known to trigger immune responses as the damage-associated molecular pattern (DAMP) in the extracellular environment. The role of HMGB1 is distinct due to its multiple functions in different subcellular location. In the nucleus, HMGB1 acts as a chaperone to regulate DNA events including DNA replication, repair and nucleosome stability. While in the cytoplasm, it is engaged in regulating autophagy and apoptosis. A great deal of research has explored its function in the pathogenesis of renal diseases. This review mainly focuses on the role of HMGB1 and summarizes the pathway and treatment targeting HMGB1 in the various renal diseases which may open the windows of opportunities for the development of desirable therapeutic ends in these pathological conditions.
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Affiliation(s)
- Zhi Zhao
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, Hubei 430030, China
| | - Zhizhi Hu
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, Hubei 430030, China
| | - Rui Zeng
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, Hubei 430030, China.
| | - Ying Yao
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, Hubei 430030, China.
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Rapoport BL, Steel HC, Theron AJ, Heyman L, Smit T, Ramdas Y, Anderson R. High Mobility Group Box 1 in Human Cancer. Cells 2020; 9:E1664. [PMID: 32664328 PMCID: PMC7407638 DOI: 10.3390/cells9071664] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
High mobility group box 1 (HMGB1) is an extremely versatile protein that is located predominantly in the nucleus of quiescent eukaryotic cells, where it is critically involved in maintaining genomic structure and function. During cellular stress, however, this multifaceted, cytokine-like protein undergoes posttranslational modifications that promote its translocation to the cytosol, from where it is released extracellularly, either actively or passively, according to cell type and stressor. In the extracellular milieu, HMGB1 triggers innate inflammatory responses that may be beneficial or harmful, depending on the magnitude and duration of release of this pro-inflammatory protein at sites of tissue injury. Heightened awareness of the potentially harmful activities of HMGB1, together with a considerable body of innovative, recent research, have revealed that excessive production of HMGB1, resulting from misdirected, chronic inflammatory responses, appears to contribute to all the stages of tumorigenesis. In the setting of established cancers, the production of HMGB1 by tumor cells per se may also exacerbate inflammation-related immunosuppression. These pro-inflammatory mechanisms of HMGB1-orchestrated tumorigenesis, as well as the prognostic potential of detection of elevated expression of this protein in the tumor microenvironment, represent the major thrusts of this review.
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Affiliation(s)
- Bernardo L. Rapoport
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa; (H.C.S.); (A.J.T.); (R.A.)
- The Medical Oncology Centre of Rosebank, Johannesburg 2196, South Africa; (L.H.); (T.S.)
| | - Helen C. Steel
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa; (H.C.S.); (A.J.T.); (R.A.)
| | - Annette J. Theron
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa; (H.C.S.); (A.J.T.); (R.A.)
| | - Liezl Heyman
- The Medical Oncology Centre of Rosebank, Johannesburg 2196, South Africa; (L.H.); (T.S.)
| | - Teresa Smit
- The Medical Oncology Centre of Rosebank, Johannesburg 2196, South Africa; (L.H.); (T.S.)
| | - Yastira Ramdas
- The Breast Care Centre, Netcare Milpark, 9 Guild Road, Parktown, Johannesburg 2193, South Africa;
| | - Ronald Anderson
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa; (H.C.S.); (A.J.T.); (R.A.)
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Sahakian L, Filippone RT, Stavely R, Robinson AM, Yan XS, Abalo R, Eri R, Bornstein JC, Kelley MR, Nurgali K. Inhibition of APE1/Ref-1 Redox Signaling Alleviates Intestinal Dysfunction and Damage to Myenteric Neurons in a Mouse Model of Spontaneous Chronic Colitis. Inflamm Bowel Dis 2020; 27:388-406. [PMID: 32618996 PMCID: PMC8287929 DOI: 10.1093/ibd/izaa161] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) associates with damage to the enteric nervous system (ENS), leading to gastrointestinal (GI) dysfunction. Oxidative stress is important for the pathophysiology of inflammation-induced enteric neuropathy and GI dysfunction. Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/Ref-1) is a dual functioning protein that is an essential regulator of the cellular response to oxidative stress. In this study, we aimed to determine whether an APE1/Ref-1 redox domain inhibitor, APX3330, alleviates inflammation-induced oxidative stress that leads to enteric neuropathy in the Winnie murine model of spontaneous chronic colitis. METHODS Winnie mice received APX3330 or vehicle via intraperitoneal injections over 2 weeks and were compared with C57BL/6 controls. In vivo disease activity and GI transit were evaluated. Ex vivo experiments were performed to assess functional parameters of colonic motility, immune cell infiltration, and changes to the ENS. RESULTS Targeting APE1/Ref-1 redox activity with APX3330 improved disease severity, reduced immune cell infiltration, restored GI function ,and provided neuroprotective effects to the enteric nervous system. Inhibition of APE1/Ref-1 redox signaling leading to reduced mitochondrial superoxide production, oxidative DNA damage, and translocation of high mobility group box 1 protein (HMGB1) was involved in neuroprotective effects of APX3330 in enteric neurons. CONCLUSIONS This study is the first to investigate inhibition of APE1/Ref-1's redox activity via APX3330 in an animal model of chronic intestinal inflammation. Inhibition of the redox function of APE1/Ref-1 is a novel strategy that might lead to a possible application of APX3330 for the treatment of IBD.
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Affiliation(s)
- Lauren Sahakian
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia
| | - Rhiannon T Filippone
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia
| | - Rhian Stavely
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia,Department of Pediatric Surgery, Pediatric Surgery Research Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ainsley M Robinson
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia
| | - Xu Sean Yan
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia
| | - Raquel Abalo
- Área de Farmacología y Nutrición y Unidad Asociada al Instituto de Química Médica (IQM) del Consejo Superior de Investigaciones Científicas (CSIC), Universidad Rey Juan Carlos (URJC), Alcorcón, Madrid, Spain,High Performance Research Group in Physiopathology and Pharmacology of the Digestive System at URJC, Alcorcón, Madrid, Spain
| | - Rajaraman Eri
- University of Tasmania, School of Health Sciences, Launceston, Tasmania, Australia
| | - Joel C Bornstein
- Department of Physiology, Melbourne University, Melbourne, Australia
| | - Mark R Kelley
- Indiana University Simon Comprehensive Cancer Center, Departments of Pediatrics, Biochemistry & Molecular Biology and Pharmacology & Toxicology, Program in Pediatric Molecular Oncology & Experimental Therapeutics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine Indianapolis, USA
| | - Kulmira Nurgali
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia,Department of Medicine Western Health, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia,Regenerative Medicine and Stem Cells Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, Victoria, Australia,Address correspondence to: Kulmira Nurgali, Level 4, Research Labs, Western Centre for Health Research & Education, Sunshine Hospital, 176 Furlong Road, St Albans, 3021, VIC, Australia. E-mail:
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Kosova AA, Kutuzov MM, Evdokimov AN, Ilina ES, Belousova EA, Romanenko SA, Trifonov VA, Khodyreva SN, Lavrik OI. Poly(ADP-ribosyl)ation and DNA repair synthesis in the extracts of naked mole rat, mouse, and human cells. Aging (Albany NY) 2020; 11:2852-2873. [PMID: 31085801 PMCID: PMC6535076 DOI: 10.18632/aging.101959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022]
Abstract
DNA repair capacity in cells of naked mole rat (Hgl), a species known for its longevity and resistance to cancer, is still poorly characterized. Here, using the whole-cell extracts (WCEs) of Hgl, mouse and human cells, we studied the interrelation between DNA synthesis on the substrates of base excision repair and the activity of poly(ADP-ribose) polymerases (PARPs) responsible for the transfer of the ADP-ribose moieties onto different targets. The level of PAR synthesis was more than ten-fold higher in human WCE as compared to rodent WCEs, while the efficiency of DNA synthesis was comparable. Under conditions of PAR synthesis, the efficiency of DNA synthesis was only slightly enhanced in all extracts and in mouse WCEs unusual products of the primer elongation were detected. The results obtained with WCEs, recombinant proteins and recently found ability of PARPs to attach the ADP-ribose moieties to DNA allowed us to attribute these products to primer mono(ADP-ribosyl)ation (MARylation) at the 5ʹ-terminal phosphate by PARP3 during the DNA synthesis. PARP1/PARP2 can then transfer the ADP-ribose moieties onto initial ADP-ribose. Our results suggest that MARylation/PARylation of DNA in the extracts depends on the ratios between PARPs and can be controlled by DNA-binding proteins.
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Affiliation(s)
- Anastasiya A Kosova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Mikhail M Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexei N Evdokimov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ekaterina S Ilina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ekaterina A Belousova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Svetlana A Romanenko
- Novosibirsk State University, Novosibirsk 630090, Russia.,Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Vladimir A Trifonov
- Novosibirsk State University, Novosibirsk 630090, Russia.,Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Svetlana N Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
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Khodyreva S, Lavrik O. Non-canonical interaction of DNA repair proteins with intact and cleaved AP sites. DNA Repair (Amst) 2020; 90:102847. [DOI: 10.1016/j.dnarep.2020.102847] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/06/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023]
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32
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Prasad R, Horton JK, Wilson SH. WITHDRAWN: Requirements for PARP-1 covalent crosslinking to DNA (PARP-1 DPC). DNA Repair (Amst) 2020; 89:102824. [PMID: 32151818 DOI: 10.1016/j.dnarep.2020.102824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 02/06/2023]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published in DNA Repair, 90C (2020) 102850, https://doi.org/10.1016/j.dnarep.2020.102850. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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Prasad R, Horton JK, Wilson SH. Requirements for PARP-1 covalent crosslinking to DNA (PARP-1 DPC). DNA Repair (Amst) 2020; 90:102850. [PMID: 32438305 DOI: 10.1016/j.dnarep.2020.102850] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, North Carolina, 27709, USA
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, North Carolina, 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, North Carolina, 27709, USA.
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34
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Mukherjee A, Vasquez KM. Targeting Chromosomal Architectural HMGB Proteins Could Be the Next Frontier in Cancer Therapy. Cancer Res 2020; 80:2075-2082. [PMID: 32152151 DOI: 10.1158/0008-5472.can-19-3066] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/24/2020] [Accepted: 03/04/2020] [Indexed: 12/18/2022]
Abstract
Chromatin-associated architectural proteins are part of a fundamental support system for cellular DNA-dependent processes and can maintain/modulate the efficiency of DNA replication, transcription, and DNA repair. Interestingly, prognostic outcomes of many cancer types have been linked with the expression levels of several of these architectural proteins. The high mobility group box (HMGB) architectural protein family has been well studied in this regard. The differential expression levels of HMGB proteins and/or mRNAs and their implications in cancer etiology and prognosis present the potential of novel targets that can be explored to increase the efficacy of existing cancer therapies. HMGB1, the most studied member of the HMGB protein family, has pleiotropic roles in cells including an association with nucleotide excision repair, base excision repair, mismatch repair, and DNA double-strand break repair. Moreover, the HMGB proteins have been identified in regulating DNA damage responses and cell survival following treatment with DNA-damaging agents and, as such, may play roles in modulating the efficacy of chemotherapeutic drugs by modulating DNA repair pathways. Here, we discuss the functions of HMGB proteins in DNA damage processing and their potential roles in cancer etiology, prognosis, and therapeutics.
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Affiliation(s)
- Anirban Mukherjee
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, Texas
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, Texas.
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35
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Fang Q, Andrews J, Sharma N, Wilk A, Clark J, Slyskova J, Koczor CA, Lans H, Prakash A, Sobol RW. Stability and sub-cellular localization of DNA polymerase β is regulated by interactions with NQO1 and XRCC1 in response to oxidative stress. Nucleic Acids Res 2020; 47:6269-6286. [PMID: 31287140 PMCID: PMC6614843 DOI: 10.1093/nar/gkz293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 03/24/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
Protein–protein interactions regulate many essential enzymatic processes in the cell. Somatic mutations outside of an enzyme active site can therefore impact cellular function by disruption of critical protein–protein interactions. In our investigation of the cellular impact of the T304I cancer mutation of DNA Polymerase β (Polβ), we find that mutation of this surface threonine residue impacts critical Polβ protein–protein interactions. We show that proteasome-mediated degradation of Polβ is regulated by both ubiquitin-dependent and ubiquitin-independent processes via unique protein–protein interactions. The ubiquitin-independent proteasome pathway regulates the stability of Polβ in the cytosol via interaction between Polβ and NAD(P)H quinone dehydrogenase 1 (NQO1) in an NADH-dependent manner. Conversely, the interaction of Polβ with the scaffold protein X-ray repair cross complementing 1 (XRCC1) plays a role in the localization of Polβ to the nuclear compartment and regulates the stability of Polβ via a ubiquitin-dependent pathway. Further, we find that oxidative stress promotes the dissociation of the Polβ/NQO1 complex, enhancing the interaction of Polβ with XRCC1. Our results reveal that somatic mutations such as T304I in Polβ impact critical protein–protein interactions, altering the stability and sub-cellular localization of Polβ and providing mechanistic insight into how key protein–protein interactions regulate cellular responses to stress.
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Affiliation(s)
- Qingming Fang
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Joel Andrews
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Nidhi Sharma
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Anna Wilk
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Jennifer Clark
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Jana Slyskova
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Christopher A Koczor
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.,Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Aishwarya Prakash
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
| | - Robert W Sobol
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, USA
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36
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Jia L, Song H, Fan W, Song Y, Wang G, Li X, He Y, Yao A. The association between high mobility group box 1 chromatin protein and mitotic chromosomes in glioma cells. Oncol Lett 2020; 19:745-752. [PMID: 31897190 PMCID: PMC6924194 DOI: 10.3892/ol.2019.11170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/01/2019] [Indexed: 11/06/2022] Open
Abstract
High mobility group box 1 (HMGB1) is an abundant non-histone nuclear protein that functions as a structural protein of chromatin, regulating genome replication and recombination, mRNA transcription and DNA repair. HMGB1 has been implicated in the tumorigenesis of various cancer types, and the upregulation of HMGB1 has been demonstrated in glioma cells. However, the association between HMGB1 and the mitotic chromosomes in glioma remains uncharacterized. In the present study, the sub-cellular localization of HMGB1 in glioma tissues and cells was investigated. In addition, enhanced green fluorescent protein (EGFP)-tagging of the human HMGB1 protein and chromosome spreading were used to investigate the combination of HMGB1 with mitotic chromosomes. The results of the current study indicated that HMGB1 was localized to the nucleus and the cytoplasm, and it was determined to combine with the condensed chromosomes of proliferating cells in paraformaldehyde (PFA)-fixed glioma tissues. However, HMGB1 was also associated with interphase (but not mitotic chromosomes) when fixed with chilled methanol and 5% (v/v) acetic acid or PFA in vitro. Data from live cell imaging and chromosome spreading indicated the association of HMGB1 with mitotic chromosomes in glioma cells. The present results suggest that HMGB1 combines with mitotic chromosomes in glioma cells, and that the use of fixatives may result in the dissociation of the HMGB1-DNA interaction. Therefore, in live specimens and chromosome spreads, EGFP fusion proteins may represent an accurate indicator for the determination of the correct localization and interaction of HMGB1 in glioma cells.
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Affiliation(s)
- Liyun Jia
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Huiling Song
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Wange Fan
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Yanan Song
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Gang Wang
- Henan Eye Institute, Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan 450003, P.R. China
| | - Xueli Li
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Ying He
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Anhui Yao
- Department of Neurosurgery, The General Hospital of Chinese People's Liberation Army, Beijing 100084, P.R. China.,Department of Neurosurgery, No. 988 Hospital of Joint Logistic Support Force, Zhengzhou, Henan 450042, P.R. China
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37
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Recognition of DNA adducts by edited and unedited forms of DNA glycosylase NEIL1. DNA Repair (Amst) 2019; 85:102741. [PMID: 31733589 DOI: 10.1016/j.dnarep.2019.102741] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/18/2022]
Abstract
Pre-mRNA encoding human NEIL1 undergoes editing by adenosine deaminase ADAR1 that converts a single adenosine to inosine, and this conversion results in an amino acid change of lysine 242 to arginine. Previous investigations of the catalytic efficiencies of the two forms of the enzyme revealed differential release of thymine glycol (ThyGly) from synthetic oligodeoxynucleotides, with the unedited form, NEIL1 K242 being ≈30-fold more efficient than the edited NEIL1 K242R. In contrast, when these enzymes were reacted with oligodeoxynucleotides containing guanidinohydantoin or spiroiminohydantoin, the edited K242R form was ≈3-fold more efficient than the unedited NEIL1. However, no prior studies have investigated the efficiencies of these two forms of NEIL1 on either high-molecular weight DNA containing multiple oxidatively-induced base damages, or oligodeoxynucleotides containing a bulky alkylated formamidopyrimidine. To understand the extent of changes in substrate recognition, γ-irradiated calf thymus DNA was treated with either edited or unedited NEIL1 and the released DNA base lesions analyzed by gas chromatography-tandem mass spectrometry. Of all the measured DNA lesions, imidazole ring-opened 4,6-diamino-5-formamidopyrimidine (FapyAde) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua) were preferentially released by both NEIL1 enzymes with K242R being ≈1.3 and 1.2-fold more efficient than K242 on excision of FapyAde and FapyGua, respectively. Consistent with the prior literature, large differences (≈7.5 to 12-fold) were measured in the excision of ThyGly from genomic DNA by the unedited versus edited NEIL1. In contrast, the edited NEIL1 was more efficient (≈3 to 5-fold) on release of 5-hydroxycytosine. Excision kinetics on DNA containing a site-specific aflatoxin B1-FapyGua adduct revealed an ≈1.4-fold higher rate by the unedited NEIL1. Molecular modeling provides insight into these differential substrate specificities. The results of this study and in particular, the comparison of substrate specificities of unedited and edited NEIL1 using biologically and clinically important base lesions, are critical for defining its role in preservation of genomic integrity.
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38
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Neuroinflammation in Gulf War Illness is linked with HMGB1 and complement activation, which can be discerned from brain-derived extracellular vesicles in the blood. Brain Behav Immun 2019; 81:430-443. [PMID: 31255677 DOI: 10.1016/j.bbi.2019.06.040] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 12/31/2022] Open
Abstract
Cognitive dysfunction and neuroinflammation are conspicuously observed in Gulf War Illness (GWI). We investigated whether brain inflammation in GWI is associated with activation of high mobility group box-1 (HMGB1) and complement-related proteins in neurons and astrocytes, and brain inflammation can be tracked through neuron-derived extracellular vesicles (NDEVs) and astrocyte-derived EVs (ADEVs) found in the circulating blood. We exposed animals to GWI-related chemicals pyridostigmine bromide, DEET and permethrin, and moderate stress for 28 days. We performed behavioral tests 10 months post-exposure and quantified activated microglia and reactive astrocytes in the cerebral cortex. Then, we measured the concentration of HMGB1, proinflammatory cytokines, and complement activation-related proteins in the cerebral cortex, and NDEVs and ADEVs in the circulating blood. Cognitive impairments persisted in GWI rats at 10 months post-exposure, which were associated with increased density of activated microglia and reactive astrocytes in the cerebral cortex. Moreover, the level of HMGB1 was elevated in the cerebral cortex with altered expression in the cytoplasm of neuronal soma and dendrites as well as the extracellular space. Also, higher levels of proinflammatory cytokines (TNFa, IL-1b, and IL-6), and complement activation-related proteins (C3 and TccC5b-9) were seen in the cerebral cortex. Remarkably, increased levels of HMGB1 and proinflammatory cytokines observed in the cerebral cortex of GWI rats could also be found in NDEVs isolated from the blood. Similarly, elevated levels of complement proteins seen in the cerebral cortex could be found in ADEVs. The results provide new evidence that persistent cognitive dysfunction and chronic neuroinflammation in a model of GWI are linked with elevated HMGB1 concentration and complement activation. Furthermore, the results demonstrated that multiple biomarkers of neuroinflammation could be tracked reliably via analyses of NDEVs and ADEVs in the circulating blood. Execution of such a liquid biopsy approach is especially useful in clinical trials for monitoring the remission, persistence or progression of brain inflammation in GWI patients with drug treatment.
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Evdokimov A, Kutuzov M, Petruseva I, Lukjanchikova N, Kashina E, Kolova E, Zemerova T, Romanenko S, Perelman P, Prokopov D, Seluanov A, Gorbunova V, Graphodatsky A, Trifonov V, Khodyreva S, Lavrik O. Naked mole rat cells display more efficient excision repair than mouse cells. Aging (Albany NY) 2019; 10:1454-1473. [PMID: 29930219 PMCID: PMC6046242 DOI: 10.18632/aging.101482] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/13/2018] [Indexed: 12/29/2022]
Abstract
Naked mole rat (NMR) is the long-lived and tumor-resistant rodent. NMRs possess multiple adaptations that may contribute to longevity and cancer-resistance. However, whether NMRs have more efficient DNA repair have not been directly tested. Here we compared base excision repair (BER) and nucleotide excision repair (NER) systems in extracts from NMR and mouse fibroblasts after UVC irradiation. Transcript levels of the key repair enzymes demonstrated in most cases higher inducibility in the mouse vs the NMR cells. Ratios of repair enzymes activities in the extracts somewhat varied depending on post-irradiation time. NMR cell extracts were 2–3-fold more efficient at removing the bulky lesions, 1.5–3-fold more efficient at removing uracil, and about 1.4-fold more efficient at cleaving the AP-site than the mouse cells, while DNA polymerase activities being as a whole higher in the mouse demonstrate different patterns of product distribution. The level of poly(ADP-ribose) synthesis was 1.4–1.8-fold higher in the NMR cells. Furthermore, NMR cell extracts displayed higher binding of PARP1 to DNA probes containing apurinic/apyrimidinic site or photo-reactive DNA lesions. Cumulatively, our results suggest that the NMR has more efficient excision repair systems than the mouse, which may contribute to longevity and cancer resistance of this species.
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Affiliation(s)
- Alexei Evdokimov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Mikhail Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Irina Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | | | - Elena Kashina
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Ekaterina Kolova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Tatyana Zemerova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | | | - Polina Perelman
- Institute of Molecular and Cellular Biology, Novosibirsk 630090, Russia
| | - Dmitry Prokopov
- Institute of Molecular and Cellular Biology, Novosibirsk 630090, Russia
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | | | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Novosibirsk 630090, Russia
| | - Svetlana Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Olga Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
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40
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Mandke P, Vasquez KM. Interactions of high mobility group box protein 1 (HMGB1) with nucleic acids: Implications in DNA repair and immune responses. DNA Repair (Amst) 2019; 83:102701. [PMID: 31563843 DOI: 10.1016/j.dnarep.2019.102701] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/10/2023]
Abstract
High mobility group box protein 1 (HMGB1) is a highly versatile, abundant, and ubiquitously expressed, non-histone chromosomal protein, which belongs to the HMGB family of proteins. These proteins form an integral part of the architectural protein repertoire to support chromatin structure in the nucleus. In the nucleus, the role of HMGB1 is attributed to its ability to bind to undamaged DNA, damaged DNA, and alternative (i.e. non-B) DNA structures with high affinity and subsequently induce bending of the DNA substrates. Due to its binding to DNA, HMGB1 has been implicated in critical biological processes, such as DNA transcription, replication, repair, and recombination. In addition to its intracellular functions, HMGB1 can also be released in the extracellular space where it elicits immunological responses. HMGB1 associates with many different molecules, including DNA, RNA, proteins, and lipopolysaccharides to modulate a variety of processes in both DNA metabolism and in innate immunity. In this review, we will focus on the implications of the interactions of HMGB1 with nucleic acids in DNA repair and immune responses. We report on the roles of HMGB1 in nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR) and DNA double-strand break repair (DSBR). We also report on its roles in immune responses via its potential effects on antigen receptor diversity generation [V(D)J recombination] and interactions with foreign and self-nucleic acids. HMGB1 expression is altered in a variety of cancers and immunological disorders. However, due to the diversity and complexity of the biological processes influenced by HMGB1 (and its family members), a detailed understanding of the intracellular and extracellular roles of HMGB1 in DNA damage repair and immune responses is warranted to ensure the development of effective HMGB1-related therapies.
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Affiliation(s)
- Pooja Mandke
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard, Austin, TX, 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard, Austin, TX, 78723, USA.
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Mutirangura A. A Hypothesis to Explain How the DNA of Elderly People Is Prone to Damage: Genome-Wide Hypomethylation Drives Genomic Instability in the Elderly by Reducing Youth-Associated Gnome-Stabilizing DNA Gaps. Epigenetics 2019. [DOI: 10.5772/intechopen.83372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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42
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Luo H, Wang L, Bao D, Wang L, Zhao H, Lian Y, Yan M, Mohan C, Li QZ. Novel Autoantibodies Related to Cell Death and DNA Repair Pathways in Systemic Lupus Erythematosus. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:248-259. [PMID: 31494269 PMCID: PMC6818352 DOI: 10.1016/j.gpb.2018.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 10/16/2018] [Accepted: 12/25/2018] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune syndrome characterized by various co-existing autoantibodies (autoAbs) in patients’ blood. However, the full spectrum of autoAbs in SLE has not been comprehensively elucidated. In this study, a commercial platform bearing 9400 antigens (ProtoArray) was used to identify autoAbs that were significantly elevated in the sera of SLE patients. By comparing the autoAb profiles of SLE patients with those of healthy controls, we identified 437 IgG and 1213 IgM autoAbs that the expression levels were significantly increased in SLE (P < 0.05). Use of the ProtoArray platform uncovered over 300 novel autoAbs targeting a broad range of nuclear, cytoplasmic, and membrane antigens. Molecular interaction network analysis revealed that the antigens targeted by the autoAbs were most significantly enriched in cell death, cell cycle, and DNA repair pathways. A group of autoAbs associated with cell apoptosis and DNA repair function, including those targeting APEX1, AURKA, POLB, AGO1, HMGB1, IFIT5, MAPKAPK3, PADI4, RGS3, SRP19, UBE2S, and VRK1, were further validated by ELISA and Western blot in a larger cohort. In addition, the levels of autoAbs against APEX1, HMGB1, VRK1, AURKA, PADI4, and SRP19 were positively correlated with the level of anti-dsDNA in SLE patients. Comprehensive autoAb screening has identified novel autoAbs, which may shed light on potential pathogenic pathways leading to lupus.
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Affiliation(s)
- Hui Luo
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ling Wang
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Nephrology, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, China
| | - Ding Bao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Li Wang
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hongjun Zhao
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yun Lian
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mei Yan
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, Houston, TX 77004, USA
| | - Quan-Zhen Li
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Rodriguez Y, Horton JK, Wilson SH. Histone H3 Lysine 56 Acetylation Enhances AP Endonuclease 1-Mediated Repair of AP Sites in Nucleosome Core Particles. Biochemistry 2019; 58:3646-3655. [PMID: 31407575 DOI: 10.1021/acs.biochem.9b00433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Deciphering factors modulating DNA repair in chromatin is of great interest because nucleosomal positioning influences mutation rates. H3K56 acetylation (Ac) is implicated in chromatin landscape regulation, impacting genomic stability, yet the effect of H3K56Ac on DNA base excision repair (BER) remains unclear. We determined whether H3K56Ac plays a role in regulating AP site incision by AP endonuclease 1 (APE1), an early step in BER. Our in vitro studies of acetylated, well-positioned nucleosome core particles (H3K56Ac-601-NCPs) demonstrate APE1 strand incision is enhanced compared with that of unacetylated WT-601-NCPs. The high-mobility group box 1 protein enhances APE1 activity in WT-601-NCPs, but this effect is not observed in H3K56Ac-601-NCPs. Therefore, our results suggest APE1 activity on NCPs can be modulated by H3K56Ac.
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Affiliation(s)
- Yesenia Rodriguez
- Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States
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Endutkin AV, Yudkina AV, Sidorenko VS, Zharkov DO. Transient protein-protein complexes in base excision repair. J Biomol Struct Dyn 2018; 37:4407-4418. [PMID: 30488779 DOI: 10.1080/07391102.2018.1553741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transient protein-protein complexes are of great importance for organizing multiple enzymatic reactions into productive reaction pathways. Base excision repair (BER), a process of critical importance for maintaining genome stability against a plethora of DNA-damaging factors, involves several enzymes, including DNA glycosylases, AP endonucleases, DNA polymerases, DNA ligases and accessory proteins acting sequentially on the same damaged site in DNA. Rather than being assembled into one stable multisubunit complex, these enzymes pass the repair intermediates between them in a highly coordinated manner. In this review, we discuss the nature and the role of transient complexes arising during BER as deduced from structural and kinetic data. Almost all of the transient complexes are DNA-mediated, although some may also exist in solution and strengthen under specific conditions. The best-studied example, the interactions between DNA glycosylases and AP endonucleases, is discussed in more detail to provide a framework for distinguishing between stable and transient complexes based on the kinetic data. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia.,Podalirius Ltd. , Novosibirsk , Russia
| | - Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia
| | - Viktoriya S Sidorenko
- Department of Pharmacological Sciences, Stony Brook University , Stony Brook , NY , USA
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia
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Cheng P, Ma Y, Gao Z, Duan L. High Mobility Group Box 1 (HMGB1) Predicts Invasion and Poor Prognosis of Glioblastoma Multiforme via Activating AKT Signaling in an Autocrine Pathway. Med Sci Monit 2018; 24:8916-8924. [PMID: 30531692 PMCID: PMC6296343 DOI: 10.12659/msm.912104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background As a nuclear protein and a secreted protein, HMGB1 is involved in many cellular processes such as proliferation, transcription, and inflammation. The overexpression of HMGB1 in various types of cancers is reported, but its clinical significance and prognostic value in glioblastoma multiforme (GBM) has not been well defined. Material/Methods The expression of HMGB1 in 116 patients with GBM was investigated with immunohistochemistry, and was detected with qRT-PCR in 12 pairs of tumor tissues and adjacent tissues. The correlations between HMGB1 and clinicopathological factors were analyzed with the chi-square test. Prognostic value of HMGB1 was evaluated with univariate analysis and multivariate analysis. By knocking down HMGB1 by siRNA, the functions of HMGB1 in progression of GBM cell lines were investigated by experiments in vitro. Results In our study, patients with high HMGB1 expression accounted for 42.2% of all the patients. High HMGB1 was correlated with low survival rates and was identified as an independent prognostic factor of GBM. Knockdown of intracellular HMGB1 remarkably decreased GBM cells proliferation and invasion. In hypoxia, intracellular HMGB1 of GBM cells was released out and activated AKT and ERK signaling pathways, thus promoting GBM cell invasion in this autocrine pathway. Conclusions HMGB1 is an independent prognostic biomarker for unfavorable prognosis of patients with GBM. Released HMGB1 of GBM cells can activate AKT and ERK signaling pathways and promote GBM cells invasion in this autocrine pathway, indicating that anti-HMGB1 therapy may be a promising treatment for GBM.
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Affiliation(s)
- Peng Cheng
- Department of Critical Care Medicine, Yidu Central Hospital of Weifang, Weifang, Shandong, China (mainland)
| | - Yun Ma
- Department of Critical Care Medicine, Yidu Central Hospital of Weifang, Weifang, Shandong, China (mainland)
| | - Zhiqiang Gao
- Department of Nephrology, Yidu Central Hospital of Weifang, Weifang, Shandong, China (mainland)
| | - Lingling Duan
- Department of Geriatric Medicine, Jinan Central Hospital of Shandong University, Jinan, Shandong, China (mainland)
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Prasad R, Horton JK, Dai DP, Wilson SH. Repair pathway for PARP-1 DNA-protein crosslinks. DNA Repair (Amst) 2018; 73:71-77. [PMID: 30466837 DOI: 10.1016/j.dnarep.2018.11.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/03/2018] [Accepted: 11/09/2018] [Indexed: 02/06/2023]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a regulatory enzyme involved in many different processes of DNA and RNA metabolism, including DNA repair. Previously, PARP-1 was found capable of forming a covalent DNA-protein crosslink (DPC) at the apurinic/apyrimidinic (AP) site in double-stranded DNA. The C1´ atom of the AP site participates in Schiff base formation with a lysine side chain in PARP-1, and a covalent bond is formed upon reduction of the Schiff base. The PARP-1 DPC is formed in vivo where DPC formation correlates with AP site induction by a monofunctional alkylating agent. Here, we examined repair of PARP-1 DPCs in mouse fibroblasts and found that a proteasome inhibitor, MG-132, reduces repair resulting in accumulation of PARP-1 DPCs and increased alkylating agent cytotoxicity. Using a model DNA substrate mimicking the PARP-1 DPC after proteasomal degradation, we found that repair is completed by a sub-pathway of base excision repair (BER). Tyrosyl-DNA phosphodiesterase 1 was proficient in removing the ring-open AP site sugar at the phosphodiester linkage, leaving an intermediate for processing by other BER enzymes. The results reveal proteasomal degradation of the PARP-1 DPC is active in mouse fibroblasts and that a model repair intermediate is processed by the BER machinery.
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Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Da-Peng Dai
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
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Ahmed AA, Smoczer C, Pace B, Patterson D, Cress Cabelof D. Loss of DNA polymerase β induces cellular senescence. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:603-612. [PMID: 29968395 PMCID: PMC6203593 DOI: 10.1002/em.22206] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/28/2018] [Accepted: 04/30/2018] [Indexed: 06/01/2023]
Abstract
We aim to establish that accelerated aging and premature cellular senescence seen in individuals with Down syndrome is related to reduced DNA polymeraseβ. We report here that primary fibroblasts from Down syndrome individuals exhibit greater SA-β-gal staining (fourfold increase, P < 0.001), increased p16 transcript abundance (threefold increase, P < 0.01), and reduced HMGB1 nuclear localization (1.5-fold lower, P < 0.01). We also find that DNA polymerase β expression is significantly reduced in Down syndrome primary fibroblasts (53% decline, P < 0.01). To evaluate whether DNA polymerase β might be causative in senescence induction, we evaluated the impact of murine DNA polymerase β nullizygosity on senescence. We find that unexposed DNA polymerase β -null primary fibroblasts exhibit a robust increase in the number of senescent cells compared to wild-type (11-fold, P < 0.001), demonstrating that loss DNA polymerase β is sufficient to induce senescence. We also see an additional increase in response to hydroxyurea (threefold greater than WT-HU, P < 0.05). These data demonstrate that loss of DNA polymerase β is sufficient to induce senescence. Additionally, we report a significant induction in spontaneous DNA double strand breaks in DNA polymerase β null MEFs (fivefold increase from wild-type, P < 0.0001). Our findings strongly suggest that DNA polymerase β is causative in senescence induction, reasonably pointing to DNA polymerase β as a likely factor driving the premature senescence in Down syndrome. Environ. Mol. Mutagen. 59:603-612, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Aqila A. Ahmed
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
| | - Cristine Smoczer
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
| | - Brianna Pace
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
| | - David Patterson
- Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, United States
- Knoebel Institute for Healthy Aging and Department of Biological Sciences, University of Denver, Denver, Colorado, United States
| | - Diane Cress Cabelof
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
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Thongsroy J, Patchsung M, Pongpanich M, Settayanon S, Mutirangura A. Reduction in replication-independent endogenous DNA double-strand breaks promotes genomic instability during chronological aging in yeast. FASEB J 2018; 32:fj201800218RR. [PMID: 29812972 DOI: 10.1096/fj.201800218rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mechanism that causes genomic instability in nondividing aging cells is unknown. Our previous study of mutant yeast suggested that 2 types of replication-independent endogenous DNA double-strand breaks (RIND-EDSBs) exist and that they play opposing roles. The first type, known as physiologic RIND-EDSBs, were ubiquitous in the G0 phase of both yeast and human cells in certain genomic locations and may act as epigenetic markers. Low RIND-EDSB levels were found in mutants that lacked chromatin-condensing proteins, such as the high-mobility group box (HMGB) proteins and Sir2. The second type is referred to as pathologic RIND-EDSBs. High pathological RIND-EDSB levels were found in DSB repair mutants. Under normal physiologic conditions, these excess RIND-EDSBs are repaired in much the same way as DNA lesions. Here, chronological aging in yeast reduced physiological RIND-EDSBs and cell viability. A strong correlation was observed between the reduction in RIND-EDSBs and viability in aging yeast cells ( r = 0.94, P < 0.0001). We used galactose-inducible HO endonuclease (HO) and nhp6a∆, an HMGB protein mutant, to evaluate the consequences of reduced physiological RIND-EDSB levels. The HO-induced cells exhibited a sustained reduction in RIND-EDSBs at various levels for several days. Interestingly, we found that lower physiologic RIND-EDSB levels resulted in decreased cell viability ( r = 0.69, P < 0.0001). Treatment with caffeine, a DSB repair inhibitor, increased pathological RIND-EDSBs, which were distinguished from physiologic RIND-EDSBs by their lack of sequences prior to DSB in untreated cells [odds ratio (OR) ≤1]. Caffeine treatment in both the HO-induced and nhp6a∆ cells markedly increased OR ≤1 breaks. Therefore, physiological RIND-EDSBs play an epigenetic role in preventing pathological RIND-EDSBs, a type of DNA damage. In summary, the reduction of physiological RIND-EDSB level is a genomic instability mechanism in chronologically aging cells.-Thongsroy, J., Patchsung, M., Pongpanich, M., Settayanon, S., Mutirangura, A. Reduction in replication-independent endogenous DNA double-strand breaks promotes genomic instability during chronological aging in yeast.
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Affiliation(s)
- Jirapan Thongsroy
- School of Medicine, Walailak University, Nakhon Si Thammarat, Thailand
| | - Maturada Patchsung
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Sirapat Settayanon
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center for Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Moor NA, Lavrik OI. Protein–Protein Interactions in DNA Base Excision Repair. BIOCHEMISTRY (MOSCOW) 2018; 83:411-422. [DOI: 10.1134/s0006297918040120] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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50
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Hombach-Klonisch S, Mehrpour M, Shojaei S, Harlos C, Pitz M, Hamai A, Siemianowicz K, Likus W, Wiechec E, Toyota BD, Hoshyar R, Seyfoori A, Sepehri Z, Ande SR, Khadem F, Akbari M, Gorman AM, Samali A, Klonisch T, Ghavami S. Glioblastoma and chemoresistance to alkylating agents: Involvement of apoptosis, autophagy, and unfolded protein response. Pharmacol Ther 2018; 184:13-41. [DOI: 10.1016/j.pharmthera.2017.10.017] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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