1
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Dyrkheeva NS, Zakharenko AL, Malakhova AA, Okorokova LS, Shtokalo DN, Medvedev SP, Tupikin AA, Kabilov MR, Lavrik OI. Transcriptomic analysis of HEK293A cells with a CRISPR/Cas9-mediated TDP1 knockout. Biochim Biophys Acta Gen Subj 2024; 1868:130616. [PMID: 38621596 DOI: 10.1016/j.bbagen.2024.130616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a human DNA repair protein. It is a member of the phospholipase D family based on structural similarity. TDP1 is a key enzyme of the repair of stalled topoisomerase 1 (TOP1)-DNA complexes. Previously, with the CRISPR/Cas9 method, we obtained HEK293A cells with a homozygous knockout of the TDP1 gene and used the TDP1 knockout cells as a cellular model for studying mechanisms of action of an anticancer therapy. In the present work, we hypothesized that the TDP1 knockout would alter the expression of DNA repair-related genes. By transcriptomic analysis, we investigated for the first time the effect of the TDP1 gene knockout on genes' expression changes in the human HEK293A cell line. We obtained original data implying a role of TDP1 in other processes besides the repair of the DNA-TOP1 complex. Differentially expressed gene analysis revealed that TDP1 may participate in cell adhesion and communication, spermatogenesis, mitochondrial function, neurodegeneration, a cytokine response, and the MAPK signaling pathway.
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Affiliation(s)
- Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Alexandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Anastasia A Malakhova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | | | - Dmitry N Shtokalo
- AcademGene LLC, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; A.P. Ershov Institute of Informatics Systems, SB RAS, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Sergey P Medvedev
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Alexey A Tupikin
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
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2
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Marques C, Held A, Dorfman K, Sung J, Song C, Kavuturu AS, Aguilar C, Russo T, Oakley DH, Albers MW, Hyman BT, Petrucelli L, Lagier-Tourenne C, Wainger BJ. Neuronal STING activation in amyotrophic lateral sclerosis and frontotemporal dementia. Acta Neuropathol 2024; 147:56. [PMID: 38478117 PMCID: PMC10937762 DOI: 10.1007/s00401-024-02688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 03/17/2024]
Abstract
The stimulator of interferon genes (STING) pathway has been implicated in neurodegenerative diseases, including Parkinson's disease and amyotrophic lateral sclerosis (ALS). While prior studies have focused on STING within immune cells, little is known about STING within neurons. Here, we document neuronal activation of the STING pathway in human postmortem cortical and spinal motor neurons from individuals affected by familial or sporadic ALS. This process takes place selectively in the most vulnerable cortical and spinal motor neurons but not in neurons that are less affected by the disease. Concordant STING activation in layer V cortical motor neurons occurs in a mouse model of C9orf72 repeat-associated ALS and frontotemporal dementia (FTD). To establish that STING activation occurs in a neuron-autonomous manner, we demonstrate the integrity of the STING signaling pathway, including both upstream activators and downstream innate immune response effectors, in dissociated mouse cortical neurons and neurons derived from control human induced pluripotent stem cells (iPSCs). Human iPSC-derived neurons harboring different familial ALS-causing mutations exhibit increased STING signaling with DNA damage as a main driver. The elevated downstream inflammatory markers present in ALS iPSC-derived neurons can be suppressed with a STING inhibitor. Our results reveal an immunophenotype that consists of innate immune signaling driven by the STING pathway and occurs specifically within vulnerable neurons in ALS/FTD.
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Affiliation(s)
- Christine Marques
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aaron Held
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katherine Dorfman
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Joon Sung
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine Song
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Amey S Kavuturu
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Corey Aguilar
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Tommaso Russo
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Derek H Oakley
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Mark W Albers
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Alzheimer Disease Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Bradley T Hyman
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Alzheimer Disease Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | | | - Clotilde Lagier-Tourenne
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Brian J Wainger
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA.
- Department of Anesthesiology, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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3
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Rahmoon MA, Elghaish RA, Ibrahim AA, Alaswad Z, Gad MZ, El-Khamisy SF, Elserafy M. High Glucose Increases DNA Damage and Elevates the Expression of Multiple DDR Genes. Genes (Basel) 2023; 14:144. [PMID: 36672885 PMCID: PMC9858638 DOI: 10.3390/genes14010144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/19/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
The DNA Damage Response (DDR) pathways sense DNA damage and coordinate robust DNA repair and bypass mechanisms. A series of repair proteins are recruited depending on the type of breaks and lesions to ensure overall survival. An increase in glucose levels was shown to induce genome instability, yet the links between DDR and glucose are still not well investigated. In this study, we aimed to identify dysregulation in the transcriptome of normal and cancerous breast cell lines upon changing glucose levels. We first performed bioinformatics analysis using a microarray dataset containing the triple-negative breast cancer (TNBC) MDA-MB-231 and the normal human mammary epithelium MCF10A cell lines grown in high glucose (HG) or in the presence of the glycolysis inhibitor 2-deoxyglucose (2DG). Interestingly, multiple DDR genes were significantly upregulated in both cell lines grown in HG. In the wet lab, we remarkably found that HG results in severe DNA damage to TNBC cells as observed using the comet assay. In addition, several DDR genes were confirmed to be upregulated using qPCR analysis in the same cell line. Our results propose a strong need for DDR pathways in the presence of HG to oppose the severe DNA damage induced in cells.
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Affiliation(s)
- Mai A. Rahmoon
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- Department of Pharmaceutical Biology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Reem A. Elghaish
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Aya A. Ibrahim
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Zina Alaswad
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Mohamed Z. Gad
- Department of Biochemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Sherif F. El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- The Healthy Lifespan Institute and Institute of Neuroscience, School of Bioscience, University of Sheffield, Sheffield S10 2TN, UK
- The Institute of Cancer Therapeutics, University of Bradford, Bradford BD7 1 DP, UK
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
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4
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Bhattacharjee S, Rehman I, Basu S, Nandy S, Richardson JM, Das BB. Interplay between symmetric arginine dimethylation and ubiquitylation regulates TDP1 proteostasis for the repair of topoisomerase I-DNA adducts. Cell Rep 2022; 39:110940. [PMID: 35705029 DOI: 10.1016/j.celrep.2022.110940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 04/05/2022] [Accepted: 05/20/2022] [Indexed: 11/03/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase (TDP1) hydrolyzes the phosphodiester bond between a DNA 3' end and a tyrosyl moiety and is implicated in the repair of trapped topoisomerase I (Top1)-DNA covalent complexes (Top1cc). Protein arginine methyltransferase 5 (PRMT5) catalyzes arginine methylation of TDP1 at the residues R361 and R586. Here, we establish mechanistic crosstalk between TDP1 arginine methylation and ubiquitylation, which is critical for TDP1 homeostasis and cellular responses to Top1 poisons. We show that R586 methylation promotes TDP1 ubiquitylation, which facilitates ubiquitin/proteasome-dependent TDP1 turnover by impeding the binding of UCHL3 (deubiquitylase enzyme) with TDP1. TDP1-R586 also promotes TDP1-XRCC1 binding and XRCC1 foci formation at Top1cc-damage sites. Intriguingly, R361 methylation enhances the 3'-phosphodiesterase activity of TDP1 in real-time fluorescence-based cleavage assays, and this was rationalized using structural modeling. Together, our findings establish arginine methylation as a co-regulator of TDP1 proteostasis and activity, which modulates the repair of trapped Top1cc.
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Affiliation(s)
- Sangheeta Bhattacharjee
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ishita Rehman
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Saini Basu
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Souvik Nandy
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Benu Brata Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
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5
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Abstract
Covalent DNA-protein crosslinks (DPCs) are pervasive DNA lesions that interfere with essential chromatin processes such as transcription or replication. This review strives to provide an overview of the sources and principles of cellular DPC formation. DPCs are caused by endogenous reactive metabolites and various chemotherapeutic agents. However, in certain conditions DPCs also arise physiologically in cells. We discuss the cellular mechanisms resolving these threats to genomic integrity. Detection and repair of DPCs require not only the action of canonical DNA repair pathways but also the activity of specialized proteolytic enzymes-including proteases of the SPRTN/Wss1 family-to degrade the crosslinked protein. Loss of DPC repair capacity has dramatic consequences, ranging from genome instability in yeast and worms to cancer predisposition and premature aging in mice and humans. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pedro Weickert
- Department of Biochemistry, Ludwig Maximilians University, Munich, Germany; .,Gene Center, Ludwig Maximilians University, Munich, Germany
| | - Julian Stingele
- Department of Biochemistry, Ludwig Maximilians University, Munich, Germany; .,Gene Center, Ludwig Maximilians University, Munich, Germany
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6
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SenGupta T, Palikaras K, Esbensen YQ, Konstantinidis G, Galindo FJN, Achanta K, Kassahun H, Stavgiannoudaki I, Bohr VA, Akbari M, Gaare J, Tzoulis C, Tavernarakis N, Nilsen H. Base excision repair causes age-dependent accumulation of single-stranded DNA breaks that contribute to Parkinson disease pathology. Cell Rep 2021; 36:109668. [PMID: 34496255 PMCID: PMC8441048 DOI: 10.1016/j.celrep.2021.109668] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 05/26/2021] [Accepted: 08/13/2021] [Indexed: 01/24/2023] Open
Abstract
Aging, genomic stress, and mitochondrial dysfunction are risk factors for neurodegenerative pathologies, such as Parkinson disease (PD). Although genomic instability is associated with aging and mitochondrial impairment, the underlying mechanisms are poorly understood. Here, we show that base excision repair generates genomic stress, promoting age-related neurodegeneration in a Caenorhabditis elegans PD model. A physiological level of NTH-1 DNA glycosylase mediates mitochondrial and nuclear genomic instability, which promote degeneration of dopaminergic neurons in older nematodes. Conversely, NTH-1 deficiency protects against α-synuclein-induced neurotoxicity, maintaining neuronal function with age. This apparent paradox is caused by modulation of mitochondrial transcription in NTH-1-deficient cells, and this modulation activates LMD-3, JNK-1, and SKN-1 and induces mitohormesis. The dependance of neuroprotection on mitochondrial transcription highlights the integration of BER and transcription regulation during physiological aging. Finally, whole-exome sequencing of genomic DNA from patients with idiopathic PD suggests that base excision repair might modulate susceptibility to PD in humans. Incomplete base excision repair is a source of genomic stress during aging The NTH-1 DNA glycosylase is a key mediator of age-dependent genomic instability Compromised NTH-1 activity promotes neuroprotection in PD nematodes NTH-1 deficiency triggers LMD-3/JNK-1/SKN-1-dependent mitohormetic response
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Affiliation(s)
- Tanima SenGupta
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Konstantinos Palikaras
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Hellas, Greece; Department of Physiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ying Q Esbensen
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Georgios Konstantinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Hellas, Greece
| | - Francisco Jose Naranjo Galindo
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Kavya Achanta
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, SUND, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henok Kassahun
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
| | - Ioanna Stavgiannoudaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Hellas, Greece
| | - Vilhelm A Bohr
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, SUND, University of Copenhagen, 2200 Copenhagen, Denmark; DNA Repair Section, National Institute on Aging, 251 Bayview Boulevard, Baltimore, MD, USA
| | - Mansour Akbari
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, SUND, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Johannes Gaare
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway; Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway; Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Hellas, Greece; Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway.
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7
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Zhang L, Chen C, Fu J, Lilley B, Berlinicke C, Hansen B, Ding D, Wang G, Wang T, Shou D, Ye Y, Mulligan T, Emmerich K, Saxena MT, Hall KR, Sharrock AV, Brandon C, Park H, Kam TI, Dawson VL, Dawson TM, Shim JS, Hanes J, Ji H, Liu JO, Qian J, Ackerley DF, Rohrer B, Zack DJ, Mumm JS. Large-scale phenotypic drug screen identifies neuroprotectants in zebrafish and mouse models of retinitis pigmentosa. eLife 2021; 10:e57245. [PMID: 34184634 PMCID: PMC8425951 DOI: 10.7554/elife.57245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
Retinitis pigmentosa (RP) and associated inherited retinal diseases (IRDs) are caused by rod photoreceptor degeneration, necessitating therapeutics promoting rod photoreceptor survival. To address this, we tested compounds for neuroprotective effects in multiple zebrafish and mouse RP models, reasoning drugs effective across species and/or independent of disease mutation may translate better clinically. We first performed a large-scale phenotypic drug screen for compounds promoting rod cell survival in a larval zebrafish model of inducible RP. We tested 2934 compounds, mostly human-approved drugs, across six concentrations, resulting in 113 compounds being identified as hits. Secondary tests of 42 high-priority hits confirmed eleven lead candidates. Leads were then evaluated in a series of mouse RP models in an effort to identify compounds effective across species and RP models, that is, potential pan-disease therapeutics. Nine of 11 leads exhibited neuroprotective effects in mouse primary photoreceptor cultures, and three promoted photoreceptor survival in mouse rd1 retinal explants. Both shared and complementary mechanisms of action were implicated across leads. Shared target tests implicated parp1-dependent cell death in our zebrafish RP model. Complementation tests revealed enhanced and additive/synergistic neuroprotective effects of paired drug combinations in mouse photoreceptor cultures and zebrafish, respectively. These results highlight the value of cross-species/multi-model phenotypic drug discovery and suggest combinatorial drug therapies may provide enhanced therapeutic benefits for RP patients.
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Affiliation(s)
- Liyun Zhang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Conan Chen
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Jie Fu
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Brendan Lilley
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Cynthia Berlinicke
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Baranda Hansen
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Ding Ding
- Department of Biostatistics, Johns Hopkins UniversityBaltimoreUnited States
| | - Guohua Wang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Tao Wang
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- School of Chemistry, Xuzhou College of Industrial TechnologyXuzhouChina
- College of Light Industry and Food Engineering, Nanjing Forestry UniversityNanjingChina
| | - Daniel Shou
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Ying Ye
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Timothy Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Kevin Emmerich
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- Department of Genetic Medicine, Johns Hopkins UniversityBaltimoreUnited States
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Kelsi R Hall
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Abigail V Sharrock
- Department of Biostatistics, Johns Hopkins UniversityBaltimoreUnited States
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Carlene Brandon
- Department of Ophthalmology, Medical University of South CarolinaCharlestonUnited States
| | - Hyejin Park
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
| | - Tae-In Kam
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
- Institute for Cell Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Valina L Dawson
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
- Institute for Cell Engineering, Johns Hopkins UniversityBaltimoreUnited States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
| | - Ted M Dawson
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
- Institute for Cell Engineering, Johns Hopkins UniversityBaltimoreUnited States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
| | - Joong Sup Shim
- Faculty of Health Sciences, University of Macau, TaipaMacauChina
| | - Justin Hanes
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins UniversityBaltimoreUnited States
| | - Jun O Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins UniversityBaltimoreUnited States
- Department of Oncology, Johns Hopkins UniversityBaltimoreUnited States
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - David F Ackerley
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Baerbel Rohrer
- Department of Ophthalmology, Medical University of South CarolinaCharlestonUnited States
| | - Donald J Zack
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- Department of Genetic Medicine, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins UniversityBaltimoreUnited States
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- Department of Genetic Medicine, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
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8
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Kojima Y, Machida YJ. DNA-protein crosslinks from environmental exposure: Mechanisms of formation and repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:716-729. [PMID: 32329115 PMCID: PMC7575214 DOI: 10.1002/em.22381] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 05/19/2023]
Abstract
Many environmental carcinogens cause DNA damage, which can result in mutations and other alterations in genomic DNA if not repaired promptly. Because of the bulkiness of the lesions, DNA-protein crosslinks (DPCs) are one of the types of toxic DNA damage with potentially deleterious consequences. Despite the importance of DPCs, how cells remove these complex DNA adducts has been incompletely understood. However, major progress in the DPC repair field over the past 5 years now supports the view that cells are equipped with multiple mechanisms to cope with DPCs. Here, we first provide an overview of environmental substances that induce DPCs, describing the sources of exposure and mechanisms of DPC formation. We then review current models of DPC repair and discuss their significance for environmental carcinogens.
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Affiliation(s)
- Yusuke Kojima
- Department of Oncology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - Yuichi J. Machida
- Department of Oncology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA
- Correspondence to Yuichi J. Machida.
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9
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UCHL3 Regulates Topoisomerase-Induced Chromosomal Break Repair by Controlling TDP1 Proteostasis. Cell Rep 2019; 23:3352-3365. [PMID: 29898404 PMCID: PMC6019701 DOI: 10.1016/j.celrep.2018.05.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 04/17/2018] [Accepted: 05/11/2018] [Indexed: 11/21/2022] Open
Abstract
Genomic damage can feature DNA-protein crosslinks whereby their acute accumulation is utilized to treat cancer and progressive accumulation causes neurodegeneration. This is typified by tyrosyl DNA phosphodiesterase 1 (TDP1), which repairs topoisomerase-mediated chromosomal breaks. Although TDP1 levels vary in multiple clinical settings, the mechanism underpinning this variation is unknown. We reveal that TDP1 is controlled by ubiquitylation and identify UCHL3 as the deubiquitylase that controls TDP1 proteostasis. Depletion of UCHL3 increases TDP1 ubiquitylation and turnover rate and sensitizes cells to TOP1 poisons. Overexpression of UCHL3, but not a catalytically inactive mutant, suppresses TDP1 ubiquitylation and turnover rate. TDP1 overexpression in the topoisomerase therapy-resistant rhabdomyosarcoma is driven by UCHL3 overexpression. In contrast, UCHL3 is downregulated in spinocerebellar ataxia with axonal neuropathy (SCAN1), causing elevated levels of TDP1 ubiquitylation and faster turnover rate. These data establish UCHL3 as a regulator of TDP1 proteostasis and, consequently, a fine-tuner of protein-linked DNA break repair. TDP1 proteostasis is controlled by a UCHL3-dependent ubiquitylation mechanism UCHL3 depletion sensitizes mammalian cells to TOP1 inhibitors Increased TDP1 protein in rhabdomyosarcoma is driven by UCHL3 upregulation Decreased TDP1 protein in spinocerebellar ataxia is driven by UCHL3 downregulation
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10
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Ghosh A, Bhattacharjee S, Chowdhuri SP, Mallick A, Rehman I, Basu S, Das BB. SCAN1-TDP1 trapping on mitochondrial DNA promotes mitochondrial dysfunction and mitophagy. SCIENCE ADVANCES 2019; 5:eaax9778. [PMID: 31723605 PMCID: PMC6834389 DOI: 10.1126/sciadv.aax9778] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/17/2019] [Indexed: 05/03/2023]
Abstract
A homozygous mutation of human tyrosyl-DNA phosphodiesterase 1 (TDP1) causes the neurodegenerative syndrome, spinocerebellar ataxia with axonal neuropathy (SCAN1). TDP1 hydrolyzes the phosphodiester bond between DNA 3'-end and a tyrosyl moiety within trapped topoisomerase I (Top1)-DNA covalent complexes (Top1cc). TDP1 is critical for mitochondrial DNA (mtDNA) repair; however, the role of mitochondria remains largely unknown for the etiology of SCAN1. We demonstrate that mitochondria in cells expressing SCAN1-TDP1 (TDP1H493R) are selectively trapped on mtDNA in the regulatory non-coding region and promoter sequences. Trapped TDP1H493R-mtDNA complexes were markedly increased in the presence of the Top1 poison (mito-SN38) when targeted selectively into mitochondria in nanoparticles. TDP1H493R-trapping accumulates mtDNA damage and triggers Drp1-mediated mitochondrial fission, which blocks mitobiogenesis. TDP1H493R prompts PTEN-induced kinase 1-dependent mitophagy to eliminate dysfunctional mitochondria. SCAN1-TDP1 in mitochondria creates a pathological state that allows neurons to turn on mitophagy to rescue fit mitochondria as a mechanism of survival.
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Affiliation(s)
- Arijit Ghosh
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sangheeta Bhattacharjee
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Srijita Paul Chowdhuri
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Abhik Mallick
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - Ishita Rehman
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sudipta Basu
- Discipline of Chemistry, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Benu Brata Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
- Corresponding author.
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11
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Abstract
Nucleotide excision repair (NER) is a highly conserved mechanism to remove helix-distorting DNA lesions. A major substrate for NER is DNA damage caused by environmental genotoxins, most notably ultraviolet radiation. Xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy are three human disorders caused by inherited defects in NER. The symptoms and severity of these diseases vary dramatically, ranging from profound developmental delay to cancer predisposition and accelerated ageing. All three syndromes include developmental abnormalities, indicating an important role for optimal transcription and for NER in protecting against spontaneous DNA damage during embryonic development. Here, we review the current knowledge on genes that function in NER that also affect embryonic development, in particular the development of a fully functional nervous system.
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Affiliation(s)
- Sofia J Araújo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.,Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain
| | - Isao Kuraoka
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
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12
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DNA- and DNA-Protein-Crosslink Repair in Plants. Int J Mol Sci 2019; 20:ijms20174304. [PMID: 31484324 PMCID: PMC6747210 DOI: 10.3390/ijms20174304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/30/2019] [Accepted: 09/01/2019] [Indexed: 12/12/2022] Open
Abstract
DNA-crosslinks are one of the most severe types of DNA lesions. Crosslinks (CLs) can be subdivided into DNA-intrastrand CLs, DNA-interstrand CLs (ICLs) and DNA-protein crosslinks (DPCs), and arise by various exogenous and endogenous sources. If left unrepaired before the cell enters S-phase, ICLs and DPCs pose a major threat to genomic integrity by blocking replication. In order to prevent the collapse of replication forks and impairment of cell division, complex repair pathways have emerged. In mammals, ICLs are repaired by the so-called Fanconi anemia (FA) pathway, which includes 22 different FANC genes, while in plants only a few of these genes are conserved. In this context, two pathways of ICL repair have been defined, each requiring the interaction of a helicase (FANCJB/RTEL1) and a nuclease (FAN1/MUS81). Moreover, homologous recombination (HR) as well as postreplicative repair factors are also involved. Although DPCs possess a comparable toxic potential to cells, it has only recently been shown that at least three parallel pathways for DPC repair exist in plants, defined by the protease WSS1A, the endonuclease MUS81 and tyrosyl-DNA phosphodiesterase 1 (TDP1). The importance of crosslink repair processes are highlighted by the fact that deficiencies in the respective pathways are associated with diverse hereditary disorders.
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13
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DNA repair and neurological disease: From molecular understanding to the development of diagnostics and model organisms. DNA Repair (Amst) 2019; 81:102669. [PMID: 31331820 DOI: 10.1016/j.dnarep.2019.102669] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In both replicating and non-replicating cells, the maintenance of genomic stability is of utmost importance. Dividing cells can repair DNA damage during cell division, tolerate the damage by employing potentially mutagenic DNA polymerases or die via apoptosis. However, the options for accurate DNA repair are more limited in non-replicating neuronal cells. If DNA damage is left unresolved, neuronal cells die causing neurodegenerative disorders. A number of pathogenic variants of DNA repair proteins have been linked to multiple neurological diseases. The current challenge is to harness our knowledge of fundamental properties of DNA repair to improve diagnosis, prognosis and treatment of such debilitating disorders. In this perspective, we will focus on recent efforts in identifying novel DNA repair biomarkers for the diagnosis of neurological disorders and their use in monitoring the patient response to therapy. These efforts are greatly facilitated by the development of model organisms such as zebrafish, which will also be summarised.
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14
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Bermúdez-Guzmán L, Leal A. DNA repair deficiency in neuropathogenesis: when all roads lead to mitochondria. Transl Neurodegener 2019; 8:14. [PMID: 31110700 PMCID: PMC6511134 DOI: 10.1186/s40035-019-0156-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/24/2019] [Indexed: 12/18/2022] Open
Abstract
Mutations in DNA repair enzymes can cause two neurological clinical manifestations: a developmental impairment and a degenerative disease. Polynucleotide kinase 3'-phosphatase (PNKP) is an enzyme that is actively involved in DNA repair in both single and double strand break repair systems. Mutations in this protein or others in the same pathway are responsible for a complex group of diseases with a broad clinical spectrum. Besides, mitochondrial dysfunction also has been consolidated as a hallmark of brain degeneration. Here we provide evidence that supports a shared role between mitochondrial dysfunction and DNA repair defects in the pathogenesis of the nervous system. As models, we analyze PNKP-related disorders, focusing on Charcot-Marie-Tooth disease and ataxia. A better understanding of the molecular dynamics of this relationship could provide improved diagnosis and treatment for neurological diseases.
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Affiliation(s)
- Luis Bermúdez-Guzmán
- Section of Genetics and Biotechnology, School of Biology, Universidad de Costa Rica, San José, 11501 Costa Rica
| | - Alejandro Leal
- Section of Genetics and Biotechnology, School of Biology, Universidad de Costa Rica, San José, 11501 Costa Rica
- Neuroscience Research Center, Universidad de Costa Rica, San José, Costa Rica
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15
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Walker C, El-Khamisy SF. Perturbed autophagy and DNA repair converge to promote neurodegeneration in amyotrophic lateral sclerosis and dementia. Brain 2018; 141:1247-1262. [PMID: 29584802 PMCID: PMC5917746 DOI: 10.1093/brain/awy076] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/16/2018] [Accepted: 02/09/2018] [Indexed: 12/13/2022] Open
Abstract
Maintaining genomic stability constitutes a major challenge facing cells. DNA breaks can arise from direct oxidative damage to the DNA backbone, the inappropriate activities of endogenous enzymes such as DNA topoisomerases, or due to transcriptionally-derived RNA/DNA hybrids (R-loops). The progressive accumulation of DNA breaks has been linked to several neurological disorders. Recently, however, several independent studies have implicated nuclear and mitochondrial genomic instability, perturbed co-transcriptional processing, and impaired cellular clearance pathways as causal and intertwined mechanisms underpinning neurodegeneration. Here, we discuss this emerging paradigm in the context of amyotrophic lateral sclerosis and frontotemporal dementia, and outline how this knowledge paves the way to novel therapeutic interventions.
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Affiliation(s)
- Callum Walker
- Krebs Institute, Department of Molecular biology and biotechnology, University of Sheffield, UK
- The Institute of Cancer Research, London, UK
| | - Sherif F El-Khamisy
- Krebs Institute, Department of Molecular biology and biotechnology, University of Sheffield, UK
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
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16
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Meisenberg C, Ashour ME, El-Shafie L, Liao C, Hodgson A, Pilborough A, Khurram SA, Downs JA, Ward SE, El-Khamisy SF. Epigenetic changes in histone acetylation underpin resistance to the topoisomerase I inhibitor irinotecan. Nucleic Acids Res 2017; 45:1159-1176. [PMID: 28180300 PMCID: PMC5388393 DOI: 10.1093/nar/gkw1026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 10/08/2016] [Accepted: 10/18/2016] [Indexed: 02/06/2023] Open
Abstract
The topoisomerase I (TOP1) inhibitor irinotecan triggers cell death by trapping TOP1 on DNA, generating cytotoxic protein-linked DNA breaks (PDBs). Despite its wide application in a variety of solid tumors, the mechanisms of cancer cell resistance to irinotecan remains poorly understood. Here, we generated colorectal cancer (CRC) cell models for irinotecan resistance and report that resistance is neither due to downregulation of the main cellular target of irinotecan TOP1 nor upregulation of the key TOP1 PDB repair factor TDP1. Instead, the faster repair of PDBs underlies resistance, which is associated with perturbed histone H4K16 acetylation. Subsequent treatment of irinotecan-resistant, but not parental, CRC cells with histone deacetylase (HDAC) inhibitors can effectively overcome resistance. Immunohistochemical analyses of CRC tissues further corroborate the importance of histone H4K16 acetylation in CRC. Finally, the resistant clones exhibit cross-resistance with oxaliplatin but not with ionising radiation or 5-fluoruracil, suggesting that the latter two could be employed following loss of irinotecan response. These findings identify perturbed chromatin acetylation in irinotecan resistance and establish HDAC inhibitors as potential therapeutic means to overcome resistance.
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Affiliation(s)
- Cornelia Meisenberg
- Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK.,The Wellcome Trust DNA Repair Group, University of Sussex, Brighton, UK
| | - Mohamed E Ashour
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City for Science and Technology, Giza, Egypt.,Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK
| | - Lamia El-Shafie
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City for Science and Technology, Giza, Egypt
| | - Chunyan Liao
- Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK
| | - Adam Hodgson
- Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK
| | - Alice Pilborough
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, UK
| | - Syed A Khurram
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, UK
| | - Jessica A Downs
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Simon E Ward
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Sherif F El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City for Science and Technology, Giza, Egypt.,Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK.,The Wellcome Trust DNA Repair Group, University of Sussex, Brighton, UK
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17
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Abstract
Covalent DNA-protein crosslinks (DPCs, also known as protein adducts) of topoisomerases and other proteins with DNA are highly toxic DNA lesions. Of note, chemical agents that induce DPCs include widely used classes of chemotherapeutics. Their bulkiness blocks virtually every chromatin-based process and makes them intractable for repair by canonical repair pathways. Distinct DPC repair pathways employ unique points of attack and are crucial for the maintenance of genome stability. Tyrosyl-DNA phosphodiesterases (TDPs) directly hydrolyse the covalent linkage between protein and DNA. The MRE11-RAD50-NBS1 (MRN) nuclease complex targets the DNA component of DPCs, excising the fragment affected by the lesion, whereas proteases of the spartan (SPRTN)/weak suppressor of SMT3 protein 1 (Wss1) family target the protein component. Loss of these pathways renders cells sensitive to DPC-inducing chemotherapeutics, and DPC repair pathways are thus attractive targets for combination cancer therapy.
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Affiliation(s)
- Julian Stingele
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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18
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Walker C, Herranz-Martin S, Karyka E, Liao C, Lewis K, Elsayed W, Lukashchuk V, Chiang SC, Ray S, Mulcahy PJ, Jurga M, Tsagakis I, Iannitti T, Chandran J, Coldicott I, De Vos KJ, Hassan MK, Higginbottom A, Shaw PJ, Hautbergue GM, Azzouz M, El-Khamisy SF. C9orf72 expansion disrupts ATM-mediated chromosomal break repair. Nat Neurosci 2017; 20:1225-1235. [PMID: 28714954 PMCID: PMC5578434 DOI: 10.1038/nn.4604] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 06/12/2017] [Indexed: 12/14/2022]
Abstract
Hexanucleotide repeat expansions represent the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia, though the mechanisms by which such expansions cause neurodegeneration are poorly understood. We report elevated levels of DNA-RNA hybrids (R-loops) and double strand breaks in rat neurons, human cells and C9orf72 ALS patient spinal cord tissues. Accumulation of endogenous DNA damage is concomitant with defective ATM-mediated DNA repair signaling and accumulation of protein-linked DNA breaks. We reveal that defective ATM-mediated DNA repair is a consequence of P62 accumulation, which impairs H2A ubiquitylation and perturbs ATM signaling. Virus-mediated expression of C9orf72-related RNA and dipeptide repeats in the mouse central nervous system increases double strand breaks and ATM defects and triggers neurodegeneration. These findings identify R-loops, double strand breaks and defective ATM-mediated repair as pathological consequences of C9orf72 expansions and suggest that C9orf72-linked neurodegeneration is driven at least partly by genomic instability.
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Affiliation(s)
- Callum Walker
- SITraN and Krebs Institutes, Neurodegeneration and Genome Stability Group, University of Sheffield, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
- Krebs and Sheffield Institutes for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
| | - Saul Herranz-Martin
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Evangelia Karyka
- SITraN and Krebs Institutes, Neurodegeneration and Genome Stability Group, University of Sheffield, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
- Krebs and Sheffield Institutes for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
| | - Chunyan Liao
- Krebs and Sheffield Institutes for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
| | - Katherine Lewis
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Waheba Elsayed
- Krebs and Sheffield Institutes for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Vera Lukashchuk
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Shih-Chieh Chiang
- Krebs and Sheffield Institutes for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
| | - Swagat Ray
- Krebs and Sheffield Institutes for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
| | - Padraig J. Mulcahy
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Mateusz Jurga
- Krebs and Sheffield Institutes for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
| | - Ioannis Tsagakis
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Tommaso Iannitti
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Jayanth Chandran
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Ian Coldicott
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Kurt J. De Vos
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Mohamed K. Hassan
- Krebs and Sheffield Institutes for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Adrian Higginbottom
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Guillaume M. Hautbergue
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Mimoun Azzouz
- SITraN and Krebs Institutes, Neurodegeneration and Genome Stability Group, University of Sheffield, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, S10 2HQ, Sheffield, UK
| | - Sherif F. El-Khamisy
- SITraN and Krebs Institutes, Neurodegeneration and Genome Stability Group, University of Sheffield, UK
- Krebs and Sheffield Institutes for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
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19
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Chiang SC, Meagher M, Kassouf N, Hafezparast M, McKinnon PJ, Haywood R, El-Khamisy SF. Mitochondrial protein-linked DNA breaks perturb mitochondrial gene transcription and trigger free radical-induced DNA damage. SCIENCE ADVANCES 2017; 3:e1602506. [PMID: 28508041 PMCID: PMC5409496 DOI: 10.1126/sciadv.1602506] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/02/2017] [Indexed: 05/06/2023]
Abstract
Breakage of one strand of DNA is the most common form of DNA damage. Most damaged DNA termini require end-processing in preparation for ligation. The importance of this step is highlighted by the association of defects in the 3'-end processing enzyme tyrosyl DNA phosphodiesterase 1 (TDP1) and neurodegeneration and by the cytotoxic induction of protein-linked DNA breaks (PDBs) and oxidized nucleic acid intermediates during chemotherapy and radiotherapy. Although much is known about the repair of PDBs in the nucleus, little is known about this process in the mitochondria. We reveal that TDP1 resolves mitochondrial PDBs (mtPDBs), thereby promoting mitochondrial gene transcription. Overexpression of a toxic form of mitochondrial topoisomerase I (TOP1mt*), which generates excessive mtPDBs, results in a TDP1-dependent compensatory up-regulation of mitochondrial gene transcription. In the absence of TDP1, the imbalance in transcription of mitochondrial- and nuclear-encoded electron transport chain (ETC) subunits results in misassembly of ETC complex III. Bioenergetics profiling further reveals that TDP1 promotes oxidative phosphorylation under both basal and high energy demands. It is known that mitochondrial dysfunction results in free radical leakage and nuclear DNA damage; however, the detection of intermediates of radical damage to DNA is yet to be shown. Consequently, we report an increased accumulation of carbon-centered radicals in cells lacking TDP1, using electron spin resonance spectroscopy. Overexpression of the antioxidant enzyme superoxide dismutase 1 (SOD1) reduces carbon-centered adducts and protects TDP1-deficient cells from oxidative stress. Conversely, overexpression of the amyotrophic lateral sclerosis-associated mutant SOD1G93A leads to marked sensitivity. Whereas Tdp1 knockout mice develop normally, overexpression of SOD1G93A suggests early embryonic lethality. Together, our data show that TDP1 resolves mtPDBs, thereby regulating mitochondrial gene transcription and oxygen consumption by oxidative phosphorylation, thus conferring cellular protection against reactive oxygen species-induced damage.
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Affiliation(s)
- Shih-Chieh Chiang
- Krebs Institute and Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN Sheffield, U.K
| | - Martin Meagher
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Nick Kassouf
- RAFT Institute, Mount Vernon Hospital, Northwood, Middlesex HA6 2RN, U.K
| | - Majid Hafezparast
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, U.K
| | - Peter J. McKinnon
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105–3678, USA
| | - Rachel Haywood
- RAFT Institute, Mount Vernon Hospital, Northwood, Middlesex HA6 2RN, U.K
| | - Sherif F. El-Khamisy
- Krebs Institute and Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN Sheffield, U.K
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12588, Egypt
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20
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Atteya R, Ashour ME, Ibrahim EE, Farag MA, El-Khamisy SF. Chemical screening identifies the β-Carboline alkaloid harmine to be synergistically lethal with doxorubicin. Mech Ageing Dev 2017; 161:141-148. [PMID: 27282658 DOI: 10.1016/j.mad.2016.04.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 04/16/2016] [Accepted: 04/30/2016] [Indexed: 12/18/2022]
Abstract
Despite being an invaluable chemotherapeutic agent for several types of cancer, the clinical utility of doxorubicin is hampered by its age-related and dose-dependent cardiotoxicity. Co-administration of dexrazoxane as a cardioprotective agent has been proposed, however recent studies suggest that it attenuates doxorubicin-induced antitumor activity. Since compounds of natural origin present a rich territory for drug discovery, we set out to identify putative natural compounds with the view to mitigate or minimize doxorubicin cardiotoxicity. We identify the DYRK1A kinase inhibitor harmine, which phosphorylates Tau that is deregulated in Alzheimer's disease, as a potentiator of cell death induced by non-toxic doses of doxorubicin. These observations suggest that harmine or other compounds that target the DYRK1A kinase my offer a new therapeutic opportunity to suppress doxorubicin age-related and dose-dependent cardiotoxicity.
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Affiliation(s)
- Reham Atteya
- Center of Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed E Ashour
- Center of Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Elsayed E Ibrahim
- Center of Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed A Farag
- Deparrtment of Pharamcognosy, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Sherif F El-Khamisy
- Center of Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt; Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.
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21
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Reprint of "Oxidant and environmental toxicant-induced effects compromise DNA ligation during base excision DNA repair". DNA Repair (Amst) 2015; 36:86-90. [PMID: 26596511 DOI: 10.1016/j.dnarep.2015.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA lesions arise from many endogenous and environmental agents, and such lesions can promote deleterious events leading to genomic instability and cell death. Base excision repair (BER) is the main DNA repair pathway responsible for repairing single strand breaks, base lesions and abasic sites in mammalian cells. During BER, DNA substrates and repair intermediates are channeled from one step to the next in a sequential fashion so that release of toxic repair intermediates is minimized. This includes handoff of the product of gap-filling DNA synthesis to the DNA ligation step. The conformational differences in DNA polymerase β (pol β) associated with incorrect or oxidized nucleotide (8-oxodGMP) insertion could impact channeling of the repair intermediate to the final step of BER, i.e., DNA ligation by DNA ligase I or the DNA Ligase III/XRCC1 complex. Thus, modified DNA ligase substrates produced by faulty pol β gap-filling could impair coordination between pol β and DNA ligase. Ligation failure is associated with 5'-AMP addition to the repair intermediate and accumulation of strand breaks that could be more toxic than the initial DNA lesions. Here, we provide an overview of the consequences of ligation failure in the last step of BER. We also discuss DNA-end processing mechanisms that could play roles in reversal of impaired BER.
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Çağlayan M, Wilson SH. Oxidant and environmental toxicant-induced effects compromise DNA ligation during base excision DNA repair. DNA Repair (Amst) 2015; 35:85-9. [PMID: 26466358 DOI: 10.1016/j.dnarep.2015.09.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA lesions arise from many endogenous and environmental agents, and such lesions can promote deleterious events leading to genomic instability and cell death. Base excision repair (BER) is the main DNA repair pathway responsible for repairing single strand breaks, base lesions and abasic sites in mammalian cells. During BER, DNA substrates and repair intermediates are channeled from one step to the next in a sequential fashion so that release of toxic repair intermediates is minimized. This includes handoff of the product of gap-filling DNA synthesis to the DNA ligation step. The conformational differences in DNA polymerase β (pol β) associated with incorrect or oxidized nucleotide (8-oxodGMP) insertion could impact channeling of the repair intermediate to the final step of BER, i.e., DNA ligation by DNA ligase I or the DNA Ligase III/XRCC1 complex. Thus, modified DNA ligase substrates produced by faulty pol β gap-filling could impair coordination between pol β and DNA ligase. Ligation failure is associated with 5'-AMP addition to the repair intermediate and accumulation of strand breaks that could be more toxic than the initial DNA lesions. Here, we provide an overview of the consequences of ligation failure in the last step of BER. We also discuss DNA-end processing mechanisms that could play roles in reversal of impaired BER.
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Affiliation(s)
- Melike Çağlayan
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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Carroll J, Page TKW, Chiang SC, Kalmar B, Bode D, Greensmith L, Mckinnon PJ, Thorpe JR, Hafezparast M, El-Khamisy SF. Expression of a pathogenic mutation of SOD1 sensitizes aprataxin-deficient cells and mice to oxidative stress and triggers hallmarks of premature ageing. Hum Mol Genet 2015; 24:828-40. [PMID: 25274775 PMCID: PMC4291253 DOI: 10.1093/hmg/ddu500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/02/2014] [Accepted: 09/26/2014] [Indexed: 11/13/2022] Open
Abstract
Aprataxin (APTX) deficiency causes progressive cerebellar degeneration, ataxia and oculomotor apraxia in man. Cell free assays and crystal structure studies demonstrate a role for APTX in resolving 5'-adenylated nucleic acid breaks, however, APTX function in vertebrates remains unclear due to the lack of an appropriate model system. Here, we generated a murine model in which a pathogenic mutant of superoxide dismutase 1 (SOD1(G93A)) is expressed in an Aptx-/- mouse strain. We report a delayed population doubling and accelerated senescence in Aptx-/- primary mouse fibroblasts, which is not due to detectable telomere instability or cell cycle deregulation but is associated with a reduction in transcription recovery following oxidative stress. Expression of SOD1(G93A) uncovers a survival defect ex vivo in cultured cells and in vivo in tissues lacking Aptx. The surviving neurons feature numerous and deep nuclear envelope invaginations, a hallmark of cellular stress. Furthermore, they possess an elevated number of high-density nuclear regions and a concomitant increase in histone H3 K9 trimethylation, hallmarks of silenced chromatin. Finally, the accelerated cellular senescence was also observed at the organismal level as shown by down-regulation of insulin-like growth factor 1 (IGF-1), a hallmark of premature ageing. Together, this study demonstrates a protective role of Aptx in vivo and suggests that its loss results in progressive accumulation of DNA breaks in the nervous system, triggering hallmarks of premature ageing, systemically.
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Affiliation(s)
- Jean Carroll
- Genome Damage and Stability Center, University of Sussex, Brighton BN1 9RQ, UK
| | - Tristan K W Page
- School of Life Science, University of Sussex, Brighton BN1 9QG, UK
| | - Shih-Chieh Chiang
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield S10 2TN, UK
| | - Bernadett Kalmar
- Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - David Bode
- School of Life Science, University of Sussex, Brighton BN1 9QG, UK
| | - Linda Greensmith
- Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Peter J Mckinnon
- Department of Genetics, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA and
| | - Julian R Thorpe
- School of Life Science, University of Sussex, Brighton BN1 9QG, UK
| | | | - Sherif F El-Khamisy
- Genome Damage and Stability Center, University of Sussex, Brighton BN1 9RQ, UK Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield S10 2TN, UK Center of Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
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Meisenberg C, Gilbert DC, Chalmers A, Haley V, Gollins S, Ward SE, El-Khamisy SF. Clinical and cellular roles for TDP1 and TOP1 in modulating colorectal cancer response to irinotecan. Mol Cancer Ther 2015; 14:575-85. [PMID: 25522766 PMCID: PMC4340569 DOI: 10.1158/1535-7163.mct-14-0762] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Colorectal cancer is the third most common cancer in the world. Despite surgery, up to 50% of patients relapse with incurable disease. First-line chemotherapy uses the topoisomerase 1 (TOP1) poison irinotecan, which triggers cell death by trapping TOP1 on DNA. The removal of TOP1 peptide from TOP1-DNA breaks is conducted by tyrosyl-DNA phosphodiesterase 1 (TDP1). Despite putative roles for TDP1 and TOP1 in colorectal cancer, their role in cellular and clinical responses to TOP1-targeting therapies remains unclear. Here, we show varying expression levels of TOP1 and TDP1 polypeptides in multiple colorectal cancer cell lines and in clinical colorectal cancer samples. TDP1 overexpression or TOP1 depletion is protective. Conversely, TDP1 depletion increases DNA-strand breakage and hypersensitivity to irinotecan in a TOP1-dependent manner, presenting a potential therapeutic opportunity in colorectal cancer. TDP1 protein levels correlate well with mRNA and with TDP1 catalytic activity. However, no correlation is observed between inherent TDP1 or TOP1 levels alone and irinotecan sensitivity, pointing at their limited utility as predictive biomarkers in colorectal cancer. These findings establish TDP1 as a potential therapeutic target for the treatment of colorectal cancer and question the validity of TOP1 or TDP1 on their own as predictive biomarkers for irinotecan response.
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Affiliation(s)
- Cornelia Meisenberg
- The Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Duncan C Gilbert
- Sussex Cancer Centre, Royal Sussex County Hospital, Brighton, United Kingdom
| | - Anthony Chalmers
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Vikki Haley
- Faculty of Science, Department of Life, Health and Chemical Sciences, The Open University, Milton Keynes, United Kingdom
| | - Simon Gollins
- North Wales Cancer Treatment Centre, Betsi Cadwaladr University of Health Board, Ysbty Glan Clwyd, Bodelwyddan, Rhyl, United Kingdom
| | - Simon E Ward
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sherif F El-Khamisy
- The Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom. Mammalian Genome Stability Group, Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom. Center of Genomics, Helmy Institute, Zewail City of Science and Technology, Giza, Egypt.
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Meisenberg C, Ward SE, Schmid P, El-Khamisy SF. TDP1/TOP1 Ratio as a Promising Indicator for the Response of Small Cell Lung Cancer to Topotecan. JOURNAL OF CANCER SCIENCE & THERAPY 2014; 6:258-267. [PMID: 25232464 PMCID: PMC4163653 DOI: 10.4172/1948-5956.1000280] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND AND OBJECTIVE Small cell lung cancer (SCLC) is one of the most challenging tumors to treat due to high proliferation rate, early metastatic dissemination and rapid development of chemotherapy resistance. The current treatment protocols involve the use of topoisomerase 1 (TOP1) poisons such as irinotecan and topotecan in combination with platinum-based compounds. TOP1 poisons kill cancer cells by trapping TOP1 on DNA, generating lethal DNA double-strand breaks. A potential mechanism employed by cancer cells to resist killing by TOP1 poisons is to overexpress enzymes involved in the repair of TOP1-DNA breaks. Tyrosyl DNA phosphodiesterase 1 (TDP1) is a key player in this process and despite its importance, no data is currently available to correlate TDP1 protein and mRNA levels with catalytic activity in SCLC. In addition, it is not known if TDP1 and TOP1 protein levels correlate with the cellular response of SCLC to TOP1 based therapies. METHODS AND RESULTS We report a remarkable variation in TDP1 and TOP1 protein levels in a panel of SCLC cell lines. TDP1 protein level correlates well with TDP1 mRNA and TDP1 catalytic activity, as measured by two newly developed independent activity assays, suggesting the potential utility of immunohistochemistry in assessing TDP1 levels in SCLC tissues. We further demonstrate that whilst TDP1 protein level alone does not correlate with topotecan sensitivity, TDP1/TOP1 ratio correlates well with sensitivity in 8 out of 10 cell lines examined. CONCLUSION This study provides the first cellular analyses of TDP1 and TOP1 in SCLC and suggests the potential utility of TDP1/TOP1 ratio to assess the response of SCLC to topotecan. The establishment and validation of an easy-to-use TDP1 enzymatic assay in cell extracts could be exploited as a diagnostic tool in the clinic. These findings may help in stratifying patients that are likely to benefit from TOP1 poisons and TDP1 inhibitors currently under development.
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Affiliation(s)
- Cornelia Meisenberg
- The Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Simon E Ward
- The Sussex Translational Drug Discovery Group, University of Sussex, Brighton, UK
| | - Peter Schmid
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK (former affiliation)
- Centre of Experimental Cancer Medicine, Barts Cancer Institute, Queen Mary University London, UK
| | - Sherif F El-Khamisy
- The Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
- Center of Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
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DNA repair abnormalities leading to ataxia: shared neurological phenotypes and risk factors. Neurogenetics 2014; 15:217-28. [PMID: 25038946 DOI: 10.1007/s10048-014-0415-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/11/2014] [Indexed: 02/06/2023]
Abstract
Since identification of mutations in the ATM gene leading to ataxia-telangiectasia, enormous efforts have been devoted to discovering the roles this protein plays in DNA repair as well as other cellular functions. Even before the identification of ATM mutations, it was clear that other diseases with different genomic loci had very similar neurological symptoms. There has been significant progress in understanding why cancer and immunodeficiency occur in ataxia-telangiectasia even though many details remain to be determined, but the field is no closer to determining why the nervous system requires ATM and other DNA repair genes. Even though rodent disease models have similar DNA repair abnormalities as the human diseases, they have no consistent, robust neuropathological phenotype making it difficult to understand the neurological underpinnings of disease. Therefore, it may be useful to reassess the neurological and neuropathological characteristics of ataxia-telangiectasia in human patients to look for potential commonalities in DNA repair diseases that result in ataxia. In doing so, it is clear that ataxia-telangiectasia and similar diseases share neurological features other than merely ataxia, such as length-dependent motor and sensory neuropathies, and that the neuroanatomical localization for these symptoms is understood. Cells affected in ataxia-telangiectasia and similar diseases are some of the largest single nucleated cells in the body. In addition, a subset of these diseases also has extrapyramidal movements and oculomotor apraxia. These neurological and neuropathological similarities may indicate a common DNA repair related pathogenesis with very large cell size as a critical risk factor.
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Marchand C, Huang SYN, Dexheimer TS, Lea WA, Mott BT, Chergui A, Naumova A, Stephen AG, Rosenthal AS, Rai G, Murai J, Gao R, Maloney DJ, Jadhav A, Jorgensen WL, Simeonov A, Pommier Y. Biochemical assays for the discovery of TDP1 inhibitors. Mol Cancer Ther 2014; 13:2116-26. [PMID: 25024006 DOI: 10.1158/1535-7163.mct-13-0952] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Drug screening against novel targets is warranted to generate biochemical probes and new therapeutic drug leads. TDP1 and TDP2 are two DNA repair enzymes that have yet to be successfully targeted. TDP1 repairs topoisomerase I-, alkylation-, and chain terminator-induced DNA damage, whereas TDP2 repairs topoisomerase II-induced DNA damage. Here, we report the quantitative high-throughput screening (qHTS) of the NIH Molecular Libraries Small Molecule Repository using recombinant human TDP1. We also developed a secondary screening method using a multiple loading gel-based assay where recombinant TDP1 is replaced by whole cell extract (WCE) from genetically engineered DT40 cells. While developing this assay, we determined the importance of buffer conditions for testing TDP1, and most notably the possible interference of phosphate-based buffers. The high specificity of endogenous TDP1 in WCE allowed the evaluation of a large number of hits with up to 600 samples analyzed per gel via multiple loadings. The increased stringency of the WCE assay eliminated a large fraction of the initial hits collected from the qHTS. Finally, inclusion of a TDP2 counter-screening assay allowed the identification of two novel series of selective TDP1 inhibitors.
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Affiliation(s)
- Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute;
| | - Shar-yin N Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute
| | - Thomas S Dexheimer
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Wendy A Lea
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Bryan T Mott
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Adel Chergui
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute
| | - Alena Naumova
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute
| | - Andrew G Stephen
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland; and
| | - Andrew S Rosenthal
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Ganesha Rai
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute
| | - Rui Gao
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute
| | - David J Maloney
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | | | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute;
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Abstract
TDP1 and TDP2 were discovered and named based on the fact they process 3'- and 5'-DNA ends by excising irreversible protein tyrosyl-DNA complexes involving topoisomerases I and II, respectively. Yet, both enzymes have an extended spectrum of activities. TDP1 not only excises trapped topoisomerases I (Top1 in the nucleus and Top1mt in mitochondria), but also repairs oxidative damage-induced 3'-phosphoglycolates and alkylation damage-induced DNA breaks, and excises chain terminating anticancer and antiviral nucleosides in the nucleus and mitochondria. The repair function of TDP2 is devoted to the excision of topoisomerase II- and potentially topoisomerases III-DNA adducts. TDP2 is also essential for the life cycle of picornaviruses (important human and bovine pathogens) as it unlinks VPg proteins from the 5'-end of the viral RNA genome. Moreover, TDP2 has been involved in signal transduction (under the former names of TTRAP or EAPII). The DNA repair partners of TDP1 include PARP1, XRCC1, ligase III and PNKP from the base excision repair (BER) pathway. By contrast, TDP2 repair functions are coordinated with Ku and ligase IV in the non-homologous end joining pathway (NHEJ). This article summarizes and compares the biochemistry, functions, and post-translational regulation of TDP1 and TDP2, as well as the relevance of TDP1 and TDP2 as determinants of response to anticancer agents. We discuss the rationale for developing TDP inhibitors for combinations with topoisomerase inhibitors (topotecan, irinotecan, doxorubicin, etoposide, mitoxantrone) and DNA damaging agents (temozolomide, bleomycin, cytarabine, and ionizing radiation), and as novel antiviral agents.
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Affiliation(s)
- Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA.
| | - Shar-yin N Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA
| | - Rui Gao
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA
| | - Benu Brata Das
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA; Laboratory of Molecular Biology, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA; Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku 606-8501, Japan
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA
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Murai J, Marchand C, Shahane SA, Sun H, Huang R, Zhang Y, Chergui A, Ji J, Doroshow JH, Jadhav A, Takeda S, Xia M, Pommier Y. Identification of novel PARP inhibitors using a cell-based TDP1 inhibitory assay in a quantitative high-throughput screening platform. DNA Repair (Amst) 2014; 21:177-82. [PMID: 24794403 DOI: 10.1016/j.dnarep.2014.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 03/21/2014] [Indexed: 10/25/2022]
Abstract
Anti-cancer topoisomerase I (Top1) inhibitors (camptothecin and its derivatives irinotecan and topotecan, and indenoisoquinolines) induce lethal DNA lesions by stabilizing Top1-DNA cleavage complex (Top1cc). These lesions are repaired by parallel repair pathways including the tyrosyl-DNA phosphodiesterase 1 (TDP1)-related pathway and homologous recombination. As TDP1-deficient cells in vertebrates are hypersensitive to Top1 inhibitors, small molecules inhibiting TDP1 should augment the cytotoxicity of Top1 inhibitors. We developed a cell-based high-throughput screening assay for the discovery of inhibitors for human TDP1 using a TDP1-deficient chicken DT40 cell line (TDP1-/-) complemented with human TDP1 (hTDP1). Any compounds showing a synergistic effect with the Top1 inhibitor camptothecin (CPT) in hTDP1 cells should either be a TDP1-related pathway inhibitor or an inhibitor of alternate repair pathways for Top1cc. We screened the 400,000-compound Small Molecule Library Repository (SMLR, NIH Molecular Libraries) against hTDP1 cells in the absence or presence of CPT. After confirmation in a secondary screen using both hTDP1 and TDP1-/- cells in the absence or presence of CPT, five compounds were confirmed as potential TDP1 pathway inhibitors. All five compounds showed synergistic effect with CPT in hTDP1 cells, but not in TDP1-/- cells, indicating that the compounds inhibited a TDP1-related repair pathway. Yet, in vitro gel-based assay revealed that the five compounds did not inhibit TDP1 catalytic activity directly. We tested the compounds for their ability to inhibit poly(ADP-ribose)polymerase (PARP) because PARP inhibitors are known to potentiate the cytotoxicity of CPT by inhibiting the recruitment of TDP1 to Top1cc. Accordingly, we found that the five compounds inhibit catalytic activity of PARP by ELISA and Western blotting. We identified the most potent compound (Cpd1) that offers characteristic close to veliparib, a leading clinical PARP inhibitor. Cpd1 may represent a new scaffold for the development of PARP inhibitors.
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Affiliation(s)
- Junko Murai
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Christophe Marchand
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Sampada A Shahane
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, United States
| | - Hongmao Sun
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, United States
| | - Ruili Huang
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, United States
| | - Yiping Zhang
- National Clinical Target Validation Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Adel Chergui
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jiuping Ji
- National Clinical Target Validation Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - James H Doroshow
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States; National Clinical Target Validation Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, United States
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Menghang Xia
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, United States
| | - Yves Pommier
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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Das BB, Huang SYN, Murai J, Rehman I, Amé JC, Sengupta S, Das SK, Majumdar P, Zhang H, Biard D, Majumder HK, Schreiber V, Pommier Y. PARP1-TDP1 coupling for the repair of topoisomerase I-induced DNA damage. Nucleic Acids Res 2014; 42:4435-49. [PMID: 24493735 PMCID: PMC3985661 DOI: 10.1093/nar/gku088] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARP) attach poly(ADP-ribose) (PAR) chains to various proteins including themselves and chromatin. Topoisomerase I (Top1) regulates DNA supercoiling and is the target of camptothecin and indenoisoquinoline anticancer drugs, as it forms Top1 cleavage complexes (Top1cc) that are trapped by the drugs. Endogenous and carcinogenic DNA lesions can also trap Top1cc. Tyrosyl-DNA phosphodiesterase 1 (TDP1), a key repair enzyme for trapped Top1cc, hydrolyzes the phosphodiester bond between the DNA 3'-end and the Top1 tyrosyl moiety. Alternative repair pathways for Top1cc involve endonuclease cleavage. However, it is unknown what determines the choice between TDP1 and the endonuclease repair pathways. Here we show that PARP1 plays a critical role in this process. By generating TDP1 and PARP1 double-knockout lymphoma chicken DT40 cells, we demonstrate that TDP1 and PARP1 are epistatic for the repair of Top1cc. The N-terminal domain of TDP1 directly binds the C-terminal domain of PARP1, and TDP1 is PARylated by PARP1. PARylation stabilizes TDP1 together with SUMOylation of TDP1. TDP1 PARylation enhances its recruitment to DNA damage sites without interfering with TDP1 catalytic activity. TDP1-PARP1 complexes, in turn recruit X-ray repair cross-complementing protein 1 (XRCC1). This work identifies PARP1 as a key component driving the repair of trapped Top1cc by TDP1.
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Affiliation(s)
- Benu Brata Das
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA, Laboratory of Molecular Biology, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India, Biotechnology and Cell Signaling, UMR7242 CNRS, Université de Strasbourg, Laboratory of Excellence Medalis, ESBS, Blvd Sébastien Brant, CS 10413, 67412 Illkirch, France, CEA-DSV-iMETI-SEPIA, BP6, 92265 Fontenay-aux-Roses cedex, France and Laboratory of Molecular Parasitology, Indian Institute of Chemical Biology, Kolkata 700032, India
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Gao R, Das BB, Chatterjee R, Abaan OD, Agama K, Matuo R, Vinson C, Meltzer PS, Pommier Y. Epigenetic and genetic inactivation of tyrosyl-DNA-phosphodiesterase 1 (TDP1) in human lung cancer cells from the NCI-60 panel. DNA Repair (Amst) 2013; 13:1-9. [PMID: 24355542 DOI: 10.1016/j.dnarep.2013.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/29/2013] [Accepted: 09/02/2013] [Indexed: 02/08/2023]
Abstract
Tyrosyl-DNA-phosphodiesterase 1 (TDP1) repairs 3'-blocking DNA lesions by catalytically hydrolyzing the tyrosyl-DNA-phosphodiester bond of trapped topoisomerase I (Top1) cleavage complexes (Top1cc). It also removes 3'-blocking residues derived from oxidative damage or incorporation of chain terminating anticancer and antiviral nucleosides. Thus, TDP1 is regarded as a determinant of resistance to Top1 inhibitors and chain terminating nucleosides, and possibly of genomic stability. In the 60 cell lines of the NCI Developmental Therapeutic Anticancer Screen (the NCI-60), whose whole genome transcriptome and mutations have recently been characterized, we discovered two human lung cancer cell lines deficient for TDP1 (NCI_H522 and HOP_62). HOP_62 shows undetectable TDP1 mRNA and NCI_H522 bears a homozygous deleterious mutation of TDP1 at a highly conserved amino acid residue (K292E). Absence of TDP1 protein and lack of TDP1 catalytic activity were demonstrated in cell lysates from both cell lines. Lack of TDP1 expression in HOP_62 was shown to be due to TDP1 promoter hypermethylation. Our study provides insights into the possible inactivation of TDP1 in cancers and its relationship to cellular response to Top1-targeted drugs. It also reveals two TDP1 knockout lung cancer cell lines for further TDP1 functional analyses.
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Affiliation(s)
- Rui Gao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benu Brata Das
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raghunath Chatterjee
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ogan D Abaan
- Molecular Genetics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Renata Matuo
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul S Meltzer
- Molecular Genetics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Studying the cerebellar DNA damage response in the tissue culture dish. Mech Ageing Dev 2013; 134:496-505. [DOI: 10.1016/j.mad.2013.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/29/2013] [Accepted: 04/01/2013] [Indexed: 11/30/2022]
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ATM deficiency results in accumulation of DNA-topoisomerase I covalent intermediates in neural cells. PLoS One 2013; 8:e58239. [PMID: 23626666 PMCID: PMC3634035 DOI: 10.1371/journal.pone.0058239] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 02/01/2013] [Indexed: 12/20/2022] Open
Abstract
Accumulation of peptide-linked DNA breaks contributes to neurodegeration in humans. This is typified by defects in tyrosyl DNA phosphodiesterase 1 (TDP1) and human hereditary ataxia. TDP1 primarily operates at single-strand breaks (SSBs) created by oxidative stress or by collision of transcription machinery with topoisomerase I intermediates (Top1-CCs). Cellular and cell-free studies have shown that Top1 at stalled Top1-CCs is first degraded to a small peptide resulting in Top1-SSBs, which are the primary substrates for TDP1. Here we established an assay to directly compare Top1-SSBs and Top1-CCs. We subsequently employed this assay to reveal an increased steady state level of Top1-CCs in neural cells lacking Atm; the protein mutated in ataxia telangiectasia. Our data suggest that the accumulation of endogenous Top1-CCs in Atm-/- neural cells is primarily due to elevated levels of reactive oxygen species. Biochemical purification of Top1-CCs from neural cell extract and the use of Top1 poisons further confirmed a role for Atm during the formation/resolution of Top1-CCs. Finally, we report that global transcription is reduced in Atm-/- neural cells and fails to recover to normal levels following Top1-mediated DNA damage. Together, these data identify a distinct role for ATM during the formation/resolution of neural Top1-CCs and suggest that their accumulation contributes to the neuropathology of ataxia telangiectasia.
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Zeng Z, Sharma A, Ju L, Murai J, Umans L, Vermeire L, Pommier Y, Takeda S, Huylebroeck D, Caldecott KW, El-Khamisy SF. TDP2 promotes repair of topoisomerase I-mediated DNA damage in the absence of TDP1. Nucleic Acids Res 2012; 40:8371-80. [PMID: 22740648 PMCID: PMC3458563 DOI: 10.1093/nar/gks622] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The abortive activity of topoisomerases can result in clastogenic and/or lethal DNA damage in which the topoisomerase is covalently linked to the 3′- or 5′-terminus of a DNA strand break. This type of DNA damage is implicated in chromosome translocations and neurological disease and underlies the clinical efficacy of an important class of anticancer topoisomerase ‘poisons’. Tyrosyl DNA phosphodiesterase-1 protects cells from abortive topoisomerase I (Top1) activity by hydrolyzing the 3′-phosphotyrosyl bond that links Top1 to a DNA strand break and is currently the only known human enzyme that displays this activity in cells. Recently, we identified a second tyrosyl DNA phosphodiesterase (TDP2; aka TTRAP/EAPII) that possesses weak 3′-tyrosyl DNA phosphodiesterase (3′-TDP) activity, in vitro. Herein, we have examined whether TDP2 contributes to the repair of Top1-mediated DNA breaks by deleting Tdp1 and Tdp2 separately and together in murine and avian cells. We show that while deletion of Tdp1 in wild-type DT40 cells and mouse embryonic fibroblasts decreases DNA strand break repair rates and cellular survival in response to Top1-induced DNA damage, deletion of Tdp2 does not. However, deletion of both Tdp1 and Tdp2 reduces rates of DNA strand break repair and cell survival below that observed in Tdp1−/− cells, suggesting that Tdp2 contributes to cellular 3′-TDP activity in the absence of Tdp1. Consistent with this idea, over-expression of human TDP2 in Tdp1−/−/Tdp2−/−/− DT40 cells increases DNA strand break repair rates and cell survival above that observed in Tdp1−/− DT40 cells, suggesting that Tdp2 over-expression can partially complement the defect imposed by loss of Tdp1. Finally, mice lacking both Tdp1 and Tdp2 exhibit greater sensitivity to Top1 poisons than do mice lacking Tdp1 alone, further suggesting that Tdp2 contributes to the repair of Top1-mediated DNA damage in the absence of Tdp1. In contrast, we failed to detect a contribution for Tdp1 to repair Top2-mediated damage. Together, our data suggest that Tdp1 and Tdp2 fulfil overlapping roles following Top1-induced DNA damage, but not following Top2-induced DNA damage, in vivo.
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Affiliation(s)
- Zhihong Zeng
- School of Life Sciences, Genome Damage and Stability Centre, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
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Seifried A, Schultz J, Gohla A. Human HAD phosphatases: structure, mechanism, and roles in health and disease. FEBS J 2012; 280:549-71. [PMID: 22607316 DOI: 10.1111/j.1742-4658.2012.08633.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Phosphatases of the haloacid dehalogenase (HAD) superfamily of hydrolases are an ancient and very large class of enzymes that have evolved to dephosphorylate a wide range of low- and high molecular weight substrates with often exquisite specificities. HAD phosphatases constitute approximately one-fifth of all human phosphatase catalytic subunits. While the overall sequence similarity between HAD phosphatases is generally very low, family members can be identified based on the presence of a characteristic Rossmann-like fold and the active site sequence DxDx(V/T). HAD phosphatases employ an aspartate residue as a nucleophile in a magnesium-dependent phosphoaspartyl transferase reaction. Although there is genetic evidence demonstrating a causal involvement of some HAD phosphatases in diseases such as cancer, cardiovascular, metabolic and neurological disorders, the physiological roles of many of these enzymes are still poorly understood. In this review, we discuss the structure and evolution of human HAD phosphatases, and summarize their known functions in health and disease.
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Affiliation(s)
- Annegrit Seifried
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
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Tyrosyl-DNA phosphodiesterase 1 initiates repair of apurinic/apyrimidinic sites. Biochimie 2012; 94:1749-53. [PMID: 22522093 PMCID: PMC3778944 DOI: 10.1016/j.biochi.2012.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 04/04/2012] [Indexed: 12/04/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) catalyzes the hydrolysis of the phosphodiester linkage between the DNA 3′ phosphate and a tyrosine residue as well as a variety of other DNA 3′ damaged termini. Recently we have shown that Tdp1 can liberate the 3′ DNA phosphate termini from apurinic/apyrimidinic (AP) sites. Here, we found that Tdp1 is more active in the cleavage of the AP sites inside bubble-DNA structure in comparison to ssDNA containing AP site. Furthermore, Tdp1 hydrolyzes AP sites opposite to bulky fluorescein adduct faster than AP sites located in dsDNA. Whilst the Tdp1 H493R (SCAN1) and H263A mutants retain the ability to bind an AP site-containing DNA, both mutants do not reveal endonuclease activity, further suggesting the specificity of the AP cleavage activity. We suggest that this Tdp1 activity can contribute to the repair of AP sites particularly in DNA structures containing ssDNA region or AP sites in the context of clustered DNA lesions.
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SUMO modification of the neuroprotective protein TDP1 facilitates chromosomal single-strand break repair. Nat Commun 2012; 3:733. [PMID: 22415824 PMCID: PMC3316882 DOI: 10.1038/ncomms1739] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 02/09/2012] [Indexed: 11/08/2022] Open
Abstract
Breaking and sealing one strand of DNA is an inherent feature of chromosome metabolism to overcome torsional barriers. Failure to reseal broken DNA strands results in protein-linked DNA breaks, causing neurodegeneration in humans. This is typified by defects in tyrosyl DNA phosphodiesterase 1 (TDP1), which removes stalled topoisomerase 1 peptides from DNA termini. Here we show that TDP1 is a substrate for modification by the small ubiquitin-like modifier SUMO. We purify SUMOylated TDP1 from mammalian cells and identify the SUMOylation site as lysine 111. While SUMOylation exhibits no impact on TDP1 catalytic activity, it promotes its accumulation at sites of DNA damage. A TDP1 SUMOylation-deficient mutant displays a reduced rate of repair of chromosomal single-strand breaks arising from transcription-associated topoisomerase 1 activity or oxidative stress. These data identify a role for SUMO during single-strand break repair, and suggest a mechanism for protecting the nervous system from genotoxic stress. Tyrosyl DNA phosphodiesterase 1 (TDP1) repairs DNA breaks and is mutated in the disease Spinocerebellar Ataxia with Axonal Neuropathy. Here TDP1 is shown to be post-translationally modified by sumoylation of lysine 111, and cells carrying a mutation at this residue are inefficient at single-strand DNA break repair.
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Abstract
The topoisomerase I (Top 1) poison irinotecan is an important component of the modern treatment of colorectal cancer. By stabilising Top 1-DNA complexes, irinotecan generates Top 1-linked DNA single-strand breaks that can evolve into double-strand breaks and ultimately cause cell death. However, cancer cells may overcome cell killing by releasing the stalled topoisomerase from DNA termini, thereby reducing the efficacy of Top 1 poisons in clinics. Thus, understanding the DNA repair mechanisms involved in the repair of Top 1-mediated DNA damage provides a useful tool to identify potential biomarkers that predict response to this class of chemotherapy. Furthermore, targeting these pathways could enhance the therapeutic benefits of Top 1 poisons. In this review, we describe the cellular mechanisms and consequences of targeting Top 1 activity in cells. We summarise preclinical data and discuss the potential clinical utility of small-molecule inhibitors of the key proteins.
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