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Atkinson J, Bezak E, Le H, Kempson I. DNA Double Strand Break and Response Fluorescent Assays: Choices and Interpretation. Int J Mol Sci 2024; 25:2227. [PMID: 38396904 PMCID: PMC10889524 DOI: 10.3390/ijms25042227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Accurately characterizing DNA double-stranded breaks (DSBs) and understanding the DNA damage response (DDR) is crucial for assessing cellular genotoxicity, maintaining genomic integrity, and advancing gene editing technologies. Immunofluorescence-based techniques have proven to be invaluable for quantifying and visualizing DSB repair, providing valuable insights into cellular repair processes. However, the selection of appropriate markers for analysis can be challenging due to the intricate nature of DSB repair mechanisms, often leading to ambiguous interpretations. This comprehensively summarizes the significance of immunofluorescence-based techniques, with their capacity for spatiotemporal visualization, in elucidating complex DDR processes. By evaluating the strengths and limitations of different markers, we identify where they are most relevant chronologically from DSB detection to repair, better contextualizing what each assay represents at a molecular level. This is valuable for identifying biases associated with each assay and facilitates accurate data interpretation. This review aims to improve the precision of DSB quantification, deepen the understanding of DDR processes, assay biases, and pathway choices, and provide practical guidance on marker selection. Each assay offers a unique perspective of the underlying processes, underscoring the need to select markers that are best suited to specific research objectives.
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Affiliation(s)
- Jake Atkinson
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia;
| | - Eva Bezak
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA 5095, Australia; (E.B.)
- Department of Physics, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Hien Le
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA 5095, Australia; (E.B.)
- Department of Radiation Oncology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Ivan Kempson
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia;
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2
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Qian H, Margaretha Plat A, Jonker A, Hoebe RA, Krawczyk P. Super-resolution GSDIM microscopy unveils distinct nanoscale characteristics of DNA repair foci under diverse genotoxic stress. DNA Repair (Amst) 2024; 134:103626. [PMID: 38232606 DOI: 10.1016/j.dnarep.2024.103626] [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: 09/07/2023] [Revised: 12/06/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
DNA double-strand breaks initiate the DNA damage response (DDR), leading to the accumulation of repair proteins at break sites and the formation of the-so-called foci. Various microscopy methods, such as wide-field, confocal, electron, and super-resolution microscopy, have been used to study these structures. However, the impact of different DNA-damaging agents on their (nano)structure remains unclear. Utilising GSDIM super-resolution microscopy, here we investigated the distribution of fluorescently tagged DDR proteins (53BP1, RNF168, MDC1) and γH2AX in U2OS cells treated with γ-irradiation, etoposide, cisplatin, or hydroxyurea. Our results revealed that both foci structure and their nanoscale ultrastructure, including foci size, nanocluster characteristics, fluorophore density and localisation, can be significantly altered by different inducing agents, even ones with similar mechanisms. Furthermore, distinct behaviours of DDR proteins were observed under the same treatment. These findings have implications for cancer treatment strategies involving these agents and provide insights into the nanoscale organisation of the DDR.
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Affiliation(s)
- Haibin Qian
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Audrey Margaretha Plat
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Ard Jonker
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Ron A Hoebe
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Przemek Krawczyk
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands.
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3
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Usluer S, Galhuber M, Khanna Y, Bourgeois B, Spreitzer E, Michenthaler H, Prokesch A, Madl T. Disordered regions mediate the interaction of p53 and MRE11. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119654. [PMID: 38123020 DOI: 10.1016/j.bbamcr.2023.119654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
The genome is frequently targeted by genotoxic agents, resulting in the formation of DNA scars. However, cells employ diverse repair mechanisms to restore DNA integrity. Among these processes, the Mre11-Rad50-Nbs1 complex detects double-strand breaks (DSBs) and recruits DNA damage response proteins such as ataxia-telangiectasia-mutated (ATM) kinase to DNA damage sites. ATM phosphorylates the transactivation domain (TAD) of the p53 tumor suppressor, which in turn regulates DNA repair, growth arrest, apoptosis, and senescence following DNA damage. The disordered glycine-arginine-rich (GAR) domain of double-strand break protein MRE11 (MRE11GAR) and its methylation are important for DSB repair, and localization to Promyelocytic leukemia nuclear bodies (PML-NBs). There is preliminary evidence that p53, PML protein, and MRE11 might co-localize and interact at DSB sites. To uncover the molecular details of these interactions, we aimed to identify the domains mediating the p53-MRE11 interaction and to elucidate the regulation of the p53-MRE11 interaction by post-translational modifications (PTMs) through a combination of biophysical techniques. We discovered that, in vitro, p53 binds directly to MRE11GAR mainly through p53TAD2 and that phosphorylation further enhances this interaction. Furthermore, we found that MRE11GAR methylation still allows for binding to p53. Overall, we demonstrated that p53 and MRE11 interaction is facilitated by disordered regions. We provide for the first time insight into the molecular details of the p53-MRE11 complex formation and elucidate potential regulatory mechanisms that will promote our understanding of the DNA damage response. Our findings suggest that PTMs regulate the p53-MRE11 interaction and subsequently their colocalization to PML-NBs upon DNA damage.
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Affiliation(s)
- Sinem Usluer
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Austria; Research Unit Integrative Structural Biology, Medical University of Graz, Austria
| | - Markus Galhuber
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Austria
| | - Yukti Khanna
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Austria; Research Unit Integrative Structural Biology, Medical University of Graz, Austria
| | - Benjamin Bourgeois
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Austria; Research Unit Integrative Structural Biology, Medical University of Graz, Austria
| | - Emil Spreitzer
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Austria; Research Unit Integrative Structural Biology, Medical University of Graz, Austria
| | - Helene Michenthaler
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Austria
| | - Andreas Prokesch
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Austria; BioTechMed-Graz, Austria
| | - Tobias Madl
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Austria; BioTechMed-Graz, Austria.
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Ryabchenko B, Šroller V, Horníková L, Lovtsov A, Forstová J, Huérfano S. The interactions between PML nuclear bodies and small and medium size DNA viruses. Virol J 2023; 20:82. [PMID: 37127643 PMCID: PMC10152602 DOI: 10.1186/s12985-023-02049-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/23/2023] [Indexed: 05/03/2023] Open
Abstract
Promyelocytic leukemia nuclear bodies (PM NBs), often referred to as membraneless organelles, are dynamic macromolecular protein complexes composed of a PML protein core and other transient or permanent components. PML NBs have been shown to play a role in a wide variety of cellular processes. This review describes in detail the diverse and complex interactions between small and medium size DNA viruses and PML NBs that have been described to date. The PML NB components that interact with small and medium size DNA viruses include PML protein isoforms, ATRX/Daxx, Sp100, Sp110, HP1, and p53, among others. Interaction between viruses and components of these NBs can result in different outcomes, such as influencing viral genome expression and/or replication or impacting IFN-mediated or apoptotic cell responses to viral infection. We discuss how PML NB components abrogate the ability of adenoviruses or Hepatitis B virus to transcribe and/or replicate their genomes and how papillomaviruses use PML NBs and their components to promote their propagation. Interactions between polyomaviruses and PML NBs that are poorly understood but nevertheless suggest that the NBs can serve as scaffolds for viral replication or assembly are also presented. Furthermore, complex interactions between the HBx protein of hepadnaviruses and several PML NBs-associated proteins are also described. Finally, current but scarce information regarding the interactions of VP3/apoptin of the avian anellovirus with PML NBs is provided. Despite the considerable number of studies that have investigated the functions of the PML NBs in the context of viral infection, gaps in our understanding of the fine interactions between viruses and the very dynamic PML NBs remain. The complexity of the bodies is undoubtedly a great challenge that needs to be further addressed.
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Affiliation(s)
- Boris Ryabchenko
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Vojtěch Šroller
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Lenka Horníková
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Alexey Lovtsov
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Jitka Forstová
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Sandra Huérfano
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic.
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Restier-Verlet J, Joubert A, Ferlazzo ML, Granzotto A, Sonzogni L, Al-Choboq J, El Nachef L, Le Reun E, Bourguignon M, Foray N. X-rays-Induced Bystander Effect Consists in the Formation of DNA Breaks in a Calcium-Dependent Manner: Influence of the Experimental Procedure and the Individual Factor. Biomolecules 2023; 13:biom13030542. [PMID: 36979480 PMCID: PMC10046354 DOI: 10.3390/biom13030542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/22/2023] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
Radiation-induced bystander effects (RIBE) describe the biological events occurring in non-targeted cells in the vicinity of irradiated ones. Various experimental procedures have been used to investigate RIBE. Interestingly, most micro-irradiation experiments have been performed with alpha particles, whereas most medium transfers have been done with X-rays. With their high fluence, synchrotron X-rays represent a real opportunity to study RIBE by applying these two approaches with the same radiation type. The RIBE induced in human fibroblasts by the medium transfer approach resulted in a generation of DNA double-strand breaks (DSB) occurring from 10 min to 4 h post-irradiation. Such RIBE was found to be dependent on dose and on the number of donor cells. The RIBE induced with the micro-irradiation approach produced DSB with the same temporal occurrence. Culture media containing high concentrations of phosphates were found to inhibit RIBE, while media rich in calcium increased it. The contribution of the RIBE to the biological dose was evaluated after synchrotron X-rays, media transfer, micro-irradiation, and 6 MeV photon irradiation mimicking a standard radiotherapy session: the RIBE may represent less than 1%, about 5%, and about 20% of the initial dose, respectively. However, RIBE may result in beneficial or otherwise deleterious effects in surrounding tissues according to their radiosensitivity status and their capacity to release Ca2+ ions in response to radiation.
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Affiliation(s)
- Juliette Restier-Verlet
- INSERM U1296 unit “Radiation: Defense/Health/Environment” Centre Léon-Bérard, 69008 Lyon, France
| | - Aurélie Joubert
- INSERM U1296 unit “Radiation: Defense/Health/Environment” Centre Léon-Bérard, 69008 Lyon, France
| | - Mélanie L. Ferlazzo
- INSERM U1296 unit “Radiation: Defense/Health/Environment” Centre Léon-Bérard, 69008 Lyon, France
| | - Adeline Granzotto
- INSERM U1296 unit “Radiation: Defense/Health/Environment” Centre Léon-Bérard, 69008 Lyon, France
| | - Laurène Sonzogni
- INSERM U1296 unit “Radiation: Defense/Health/Environment” Centre Léon-Bérard, 69008 Lyon, France
| | - Joëlle Al-Choboq
- INSERM U1296 unit “Radiation: Defense/Health/Environment” Centre Léon-Bérard, 69008 Lyon, France
| | - Laura El Nachef
- INSERM U1296 unit “Radiation: Defense/Health/Environment” Centre Léon-Bérard, 69008 Lyon, France
| | - Eymeric Le Reun
- INSERM U1296 unit “Radiation: Defense/Health/Environment” Centre Léon-Bérard, 69008 Lyon, France
| | - Michel Bourguignon
- INSERM U1296 unit “Radiation: Defense/Health/Environment” Centre Léon-Bérard, 69008 Lyon, France
- Department of Biophysics and Nuclear Medicine, Université Paris Saclay Versailles St Quentin en Yvelines, 78035 Versailles, France
| | - Nicolas Foray
- INSERM U1296 unit “Radiation: Defense/Health/Environment” Centre Léon-Bérard, 69008 Lyon, France
- Correspondence: ; Tel.: +33-4-78-78-28-28
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Cobb AM, De Silva SA, Hayward R, Sek K, Ulferts S, Grosse R, Shanahan CM. Filamentous nuclear actin regulation of PML NBs during the DNA damage response is deregulated by prelamin A. Cell Death Dis 2022; 13:1042. [PMID: 36522328 PMCID: PMC9755150 DOI: 10.1038/s41419-022-05491-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/16/2022]
Abstract
Nuclear actin participates in a continuously expanding list of core processes within eukaryotic nuclei, including the maintenance of genomic integrity. In response to DNA damage, nuclear actin polymerises into filaments that are involved in the repair of damaged DNA through incompletely defined mechanisms. We present data to show that the formation of nuclear F-actin in response to genotoxic stress acts as a scaffold for PML NBs and that these filamentous networks are essential for PML NB fission and recruitment of microbodies to DNA lesions. Further to this, we demonstrate that the accumulation of the toxic lamin A precursor prelamin A induces mislocalisation of nuclear actin to the nuclear envelope and prevents the establishment of nucleoplasmic F-actin networks in response to stress. Consequently, PML NB dynamics and recruitment to DNA lesions is ablated, resulting in impaired DNA damage repair. Inhibition of nuclear export of formin mDia2 restores nuclear F-actin formation by augmenting polymerisation of nuclear actin in response to stress and rescues PML NB localisation to sites of DNA repair, leading to reduced levels of DNA damage.
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Affiliation(s)
- Andrew M. Cobb
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Shanelle A. De Silva
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Robert Hayward
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Karolina Sek
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Svenja Ulferts
- grid.5963.9Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Robert Grosse
- grid.5963.9Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Catherine M. Shanahan
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
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Magliocco AM, Moughan J, Miyamoto DT, Simko J, Shipley WU, Gray PJ, Hagan MP, Parliament M, Tester WJ, Zietman AL, McCarthy S, Saeed-Vafa D, Xiong Y, Ayral T, Hartford AC, Patel A, Rosenthal SA, Chafe S, Greenberg R, Schwartz MA, Augspurger ME, Keech JA, Winter KA, Feng FY, Efstathiou JA. Analysis of MRE11 and Mortality Among Adults With Muscle-Invasive Bladder Cancer Managed With Trimodality Therapy. JAMA Netw Open 2022; 5:e2242378. [PMID: 36383379 PMCID: PMC9669810 DOI: 10.1001/jamanetworkopen.2022.42378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
IMPORTANCE Bladder-preserving trimodality therapy can be an effective alternative to radical cystectomy for treatment of muscle-invasive bladder cancer (MIBC), but biomarkers are needed to guide optimal patient selection. The DNA repair protein MRE11 is a candidate response biomarker that has not been validated in prospective cohorts using standardized measurement approaches. OBJECTIVE To evaluate MRE11 expression as a prognostic biomarker in MIBC patients receiving trimodality therapy using automated quantitative image analysis. DESIGN, SETTING, AND PARTICIPANTS This prognostic study analyzed patients with MIBC pooled from 6 prospective phase I/II, II, or III trials of trimodality therapy (Radiation Therapy Oncology Group [RTOG] 8802, 8903, 9506, 9706, 9906, and 0233) across 37 participating institutions in North America from 1988 to 2007. Eligible patients had nonmetastatic MIBC and were enrolled in 1 of the 6 trimodality therapy clinical trials. Analyses were completed August 2020. EXPOSURES Trimodality therapy with transurethral bladder tumor resection and cisplatin-based chemoradiation therapy. MAIN OUTCOMES AND MEASURES MRE11 expression and association with disease-specific (bladder cancer) mortality (DSM), defined as death from bladder cancer. Pretreatment tumor tissues were processed for immunofluorescence with anti-MRE11 antibody and analyzed using automated quantitative image analysis to calculate a normalized score for MRE11 based on nuclear-to-cytoplasmic (NC) signal ratio. RESULTS Of 465 patients from 6 trials, 168 patients had available tissue, of which 135 were analyzable for MRE11 expression (median age of 65 years [minimum-maximum, 34-90 years]; 111 [82.2%] men). Median (minimum-maximum) follow-up for alive patients was 5.0 (0.6-11.7) years. Median (Q1-Q3) MRE11 NC signal ratio was 2.41 (1.49-3.34). Patients with an MRE11 NC ratio above 1.49 (ie, above first quartile) had a significantly lower DSM (HR, 0.50; 95% CI, 0.26-0.93; P = .03). The 4-year DSM was 41.0% (95% CI, 23.2%-58.0%) for patients with an MRE11 NC signal ratio of 1.49 or lower vs 21.0% (95% CI, 13.4%-29.8%) for a ratio above 1.49. MRE11 NC signal ratio was not significantly associated with overall survival (HR, 0.84; 95% CI, 0.49-1.44). CONCLUSIONS AND RELEVANCE Higher MRE11 NC signal ratios were associated with better DSM after trimodality therapy. Lower MRE11 NC signal ratios identified a poor prognosis subgroup that may benefit from intensification of therapy.
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Affiliation(s)
| | - Jennifer Moughan
- NRG Oncology Statistics and Data Management Center/ACR, Philadelphia, Pennsylvania
| | - David T. Miyamoto
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jeff Simko
- Department of Radiation Oncology, University of California, San Francisco
| | - William U. Shipley
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Phillip J. Gray
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael P. Hagan
- Hunter Holmes McGuire Veterans Administration Medical Center, Richmond, Virginia
| | | | | | - Anthony L. Zietman
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Yin Xiong
- H. Lee Moffitt Cancer Center, Tampa, Florida
| | | | | | - Ashish Patel
- MD Anderson Cancer Center at Cooper, Camden, New Jersey
| | | | - Susan Chafe
- Cross Cancer Institute, Edmonton, Alberta, Canada
| | | | | | | | - John A. Keech
- MultiCare Gig Harbor Medical Park, Gig Harbor, Washington
| | - Kathryn A. Winter
- NRG Oncology Statistics and Data Management Center/ACR, Philadelphia, Pennsylvania
| | - Felix Y. Feng
- Department of Radiation Oncology, University of California, San Francisco
| | - Jason A. Efstathiou
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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Ali A, Xiao W, Babar ME, Bi Y. Double-Stranded Break Repair in Mammalian Cells and Precise Genome Editing. Genes (Basel) 2022; 13:genes13050737. [PMID: 35627122 PMCID: PMC9142082 DOI: 10.3390/genes13050737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, double-strand breaks (DSBs) are repaired predominantly by error-prone non-homologous end joining (NHEJ), but less prevalently by error-free template-dependent homologous recombination (HR). DSB repair pathway selection is the bedrock for genome editing. NHEJ results in random mutations when repairing DSB, while HR induces high-fidelity sequence-specific variations, but with an undesirable low efficiency. In this review, we first discuss the latest insights into the action mode of NHEJ and HR in a panoramic view. We then propose the future direction of genome editing by virtue of these advancements. We suggest that by switching NHEJ to HR, full fidelity genome editing and robust gene knock-in could be enabled. We also envision that RNA molecules could be repurposed by RNA-templated DSB repair to mediate precise genetic editing.
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Affiliation(s)
- Akhtar Ali
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan
| | - Wei Xiao
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
| | - Masroor Ellahi Babar
- The University of Agriculture Dera Ismail Khan, Dera Ismail Khan 29220, Pakistan;
| | - Yanzhen Bi
- Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (A.A.); (W.X.)
- Correspondence: ; Tel.: +86-151-0714-8708
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9
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HiIDDD: a high-throughput imaging pipeline for the quantitative detection of DNA damage in primary human immune cells. Sci Rep 2022; 12:6335. [PMID: 35428779 PMCID: PMC9022135 DOI: 10.1038/s41598-022-10018-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/25/2022] [Indexed: 11/21/2022] Open
Abstract
DNA damage is a prominent biomarker for numerous diseases, including cancer, as well as for the aging process. Detection of DNA damage routinely relies on traditional microscopy or cytometric methods. However, these techniques are typically of limited throughput and are not ideally suited for large-scale longitudinal and population studies that require analysis of large sample sets. We have developed HiIDDD (High-throughput Immune cell DNA Damage Detection), a robust, quantitative and single-cell assay that measures DNA damage by high-throughput imaging using the two major DNA damage markers 53BP1 and \documentclass[12pt]{minimal}
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\begin{document}$$\upgamma$$\end{document}γ-H2AX. We demonstrate sensitive detection with low inter-assay variability of DNA damage in various types of freshly isolated and cryopreserved primary human immune cells, including CD4 + and CD8 + T cells, B cells and monocytes. As proof of principle, we demonstrate parallel batch processing of several immune cell types from multiple donors. We find common patterns of DNA damage in multiple immune cell types of donors of varying ages, suggesting that immune cell properties are specific to individuals. These results establish a novel high-throughput assay for the evaluation of DNA damage in large-scale studies.
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Mirman Z, Sasi NK, King A, Chapman JR, de Lange T. 53BP1-shieldin-dependent DSB processing in BRCA1-deficient cells requires CST-Polα-primase fill-in synthesis. Nat Cell Biol 2022; 24:51-61. [PMID: 35027730 PMCID: PMC8849574 DOI: 10.1038/s41556-021-00812-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/09/2021] [Indexed: 12/19/2022]
Abstract
The efficacy of poly(ADP)-ribose polymerase 1 inhibition (PARPi) in BRCA1-deficient cells depends on 53BP1 and shieldin, which have been proposed to limit single-stranded DNA at double-strand breaks (DSBs) by blocking resection and/or through CST-Polα-primase-mediated fill-in. We show that primase (like 53BP1-shieldin and CST-Polα) promotes radial chromosome formation in PARPi-treated BRCA1-deficient cells and demonstrate shieldin-CST-Polα-primase-dependent incorporation of BrdU at DSBs. In the absence of 53BP1 or shieldin, radial formation in BRCA1-deficient cells was restored by the tethering of CST near DSBs, arguing that in this context, shieldin acts primarily by recruiting CST. Furthermore, a SHLD1 mutant defective in CST binding (SHLD1Δ) was non-functional in BRCA1-deficient cells and its function was restored after reconnecting SHLD1Δ to CST. Interestingly, at dysfunctional telomeres and at DNA breaks in class switch recombination where CST has been implicated, SHLD1Δ was fully functional, perhaps because these DNA ends carry CST recognition sites that afford SHLD1-independent binding of CST. These data establish that in BRCA1-deficient cells, CST-Polα-primase is the major effector of shieldin-dependent DSB processing.
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Affiliation(s)
- Zachary Mirman
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Nanda Kumar Sasi
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Ashleigh King
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - J Ross Chapman
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA.
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11
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Williams RM, Zhang X. Roles of ATM and ATR in DNA double strand breaks and replication stress. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 161:27-38. [DOI: 10.1016/j.pbiomolbio.2020.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022]
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12
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Nomura D, Abe R, Tsukimoto M. Involvement of TRPM8 Channel in Radiation-Induced DNA Damage Repair Mechanism Contributing to Radioresistance of B16 Melanoma. Biol Pharm Bull 2021; 44:642-652. [PMID: 33658452 DOI: 10.1248/bpb.b20-00934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Radiation is an effective cancer treatment, but cancer cells can acquire radioresistance, which is associated with increased DNA damage response and enhanced proliferative capacity, and therefore, it is important to understand the intracellular biochemical responses to γ-irradiation. The transient receptor potential melastatin 8 (TRPM8) channel plays roles in the development and progression of tumors, but it is unclear whether it is involved in the DNA damage response induced by γ-irradiation. Here, we show that a TRPM8 channel inhibitor suppresses the DNA damage response (phosphorylated histone variant H2AX-p53-binding protein 1 (γH2AX-53BP1) focus formation) and colony formation of B16 melanoma cells. Furthermore, the TRPM8 channel-specific agonist WS-12 enhanced the DNA damage response and increased the survival fraction after γ-irradiation. We found that the TRPM8 channel inhibitor enhanced G2/M phase arrest after γ-irradiation. Phosphorylation of ataxia telangiectasia mutated and p53, which both contribute to the DNA damage response was also suppressed after γ-irradiation. In addition, the TRPM8 channel inhibitor enhanced the γ-irradiation-induced suppression of tumor growth in vivo. We conclude that the TRPM8 channel is involved in radiation-induced DNA damage repair and contributes to the radioresistance of B16 melanoma cells. TRPM8 channel inhibitors might be clinically useful as radiosensitizers to enhance radiation therapy of melanoma.
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Affiliation(s)
- Daichi Nomura
- Department of Radiation Biosciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science
| | - Ryo Abe
- Research Institute for Biomedical Sciences, Tokyo University of Science.,Strategic Innovation and Research Center, Teikyo University
| | - Mitsutoshi Tsukimoto
- Department of Radiation Biosciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science
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13
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Roles of ATM and ATR in DNA double strand breaks and replication stress. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:109-119. [PMID: 33887296 DOI: 10.1016/j.pbiomolbio.2021.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023]
Abstract
The maintenance of genome integrity is critical for the faithful replication of the genome during cell division and for protecting cells from accumulation of DNA damage, which if left unrepaired leads to a loss of genetic information, a breakdown in cell function and ultimately cell death and cancer. ATM and ATR are master kinases that are integral to homologous recombination-mediated repair of double strand breaks and preventing accumulation of dangerous DNA structures and genome instability during replication stress. While the roles of ATM and ATR are heavily intertwined in response to double strand breaks, their roles diverge in the response to replication stress. This review summarises our understanding of the players and their mode of actions in recruitment, activation and activity of ATM and ATR in response to DNA damage and replication stress and discusses how controlling localisation of these kinases and their activators allows them to orchestrate a stress-specific response.
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14
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Na J, Newman JA, Then CK, Syed J, Vendrell I, Torrecilla I, Ellermann S, Ramadan K, Fischer R, Kiltie AE. SPRTN protease-cleaved MRE11 decreases DNA repair and radiosensitises cancer cells. Cell Death Dis 2021; 12:165. [PMID: 33558481 PMCID: PMC7870818 DOI: 10.1038/s41419-021-03437-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 12/21/2022]
Abstract
The human MRE11/RAD50/NBS1 (MRN) complex plays a crucial role in sensing and repairing DNA DSB. MRE11 possesses dual 3'-5' exonuclease and endonuclease activity and forms the core of the multifunctional MRN complex. We previously identified a C-terminally truncated form of MRE11 (TR-MRE11) associated with post-translational MRE11 degradation. Here we identified SPRTN as the essential protease for the formation of TR-MRE11 and characterised the role of this MRE11 form in its DNA damage response (DDR). Using tandem mass spectrometry and site-directed mutagenesis, the SPRTN-dependent cleavage site for MRE11 was identified between 559 and 580 amino acids. Despite the intact interaction of TR-MRE11 with its constitutive core complex proteins RAD50 and NBS1, both nuclease activities of truncated MRE11 were dramatically reduced due to its deficient binding to DNA. Furthermore, lack of the MRE11 C-terminal decreased HR repair efficiency, very likely due to abolished recruitment of TR-MRE11 to the sites of DNA damage, which consequently led to increased cellular radiosensitivity. The presence of this DNA repair-defective TR-MRE11 could explain our previous finding that the high MRE11 protein expression by immunohistochemistry correlates with improved survival following radical radiotherapy in bladder cancer patients.
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Affiliation(s)
- Juri Na
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Chee Kin Then
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Junetha Syed
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Iolanda Vendrell
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ignacio Torrecilla
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sophie Ellermann
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Kristijan Ramadan
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anne E Kiltie
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
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15
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Targeting DNA Repair and Chromatin Crosstalk in Cancer Therapy. Cancers (Basel) 2021; 13:cancers13030381. [PMID: 33498525 PMCID: PMC7864178 DOI: 10.3390/cancers13030381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/09/2021] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Targeting aberrant DNA repair in cancers in addition to transcription and replication is an area of interest for cancer researchers. Inhibition of DNA repair selectively in cancer cells leads to cytotoxic or cytostatic effects and overcomes survival advantages imparted by chromosomal translocations or mutations. In this review, we highlight the relevance of DNA repair-linked events in developmental diseases and cancers and also discuss mechanisms to overcome these events that participate in different cellular processes. Abstract Aberrant DNA repair pathways that underlie developmental diseases and cancers are potential targets for therapeutic intervention. Targeting DNA repair signal effectors, modulators and checkpoint proteins, and utilizing the synthetic lethality phenomena has led to seminal discoveries. Efforts to efficiently translate the basic findings to the clinic are currently underway. Chromatin modulation is an integral part of DNA repair cascades and an emerging field of investigation. Here, we discuss some of the key advancements made in DNA repair-based therapeutics and what is known regarding crosstalk between chromatin and repair pathways during various cellular processes, with an emphasis on cancer.
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16
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Miao T, Peng C, Tang Z, Zeng M, Wang S, Wang X, Guo L, Wang X, Zhao J, Zhao M, Chen J, Liu C. Implication of Ataxia-Telangiectasia-mutated kinase in epithelium-mesenchyme transition. Carcinogenesis 2021; 42:640-649. [PMID: 33417668 DOI: 10.1093/carcin/bgab002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/22/2020] [Accepted: 01/08/2021] [Indexed: 02/05/2023] Open
Abstract
Impairment of genome instability drives the development of cancer by disrupting anti-cancer barriers. Upon genotoxic insults, DNA damage responsive factors, notably ATM kinase, is crucial to protect genomic integrity while promoting cell death. Meanwhile, cytotoxic therapy-inducing DNA lesions is double-edged sword by causing cancer metastasis based on animal models and clinical observations. The underlying mechanisms for the procancer effect of cytotoxic therapies are poorly understood. Here, we report that cancer cells subjected to cytotoxic treatments elicit dramatic alteration of gene expression controlling the potential of epithelium-mesenchyme transition (EMT). Resultantly, EMT-dependent cell mobility is potently induced upon DNA damage. This stimulation of EMT is mainly Ataxia-Telangiectasia-mutated (ATM)-dependent, as the chemical inhibitor specifically inhibiting ATM kinase activity can suppress the EMT gene expression and thus cell mobility. At last, we show that cancer cells with ATM activation display increased metastatic potential in ovarian cancer tissues. Taken together, we reveal a novel role of ATM in promoting metastatic potential of cancer cells by favoring EMT gene expression.
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Affiliation(s)
- Tianyu Miao
- Vascular Surgery of West China Hospital, Sichuan University, Chengdu, PR China
| | - Changsheng Peng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Gynecology, West China Second University Hospital, Sichuan University, Chengdu, PR China
| | - Zizhi Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Gynecology, West China Second University Hospital, Sichuan University, Chengdu, PR China
| | - Ming Zeng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Gynecology, West China Second University Hospital, Sichuan University, Chengdu, PR China
| | - Shi Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Gynecology, West China Second University Hospital, Sichuan University, Chengdu, PR China
| | - Xiaojun Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Gynecology, West China Second University Hospital, Sichuan University, Chengdu, PR China
| | - Liandi Guo
- College of Pharmacy, Southwest Minzu University, Chengdu, PR China
| | - Xiaobo Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Gynecology, West China Second University Hospital, Sichuan University, Chengdu, PR China
| | - Jichun Zhao
- Vascular Surgery of West China Hospital, Sichuan University, Chengdu, PR China
| | - Mingcai Zhao
- Department of Clinical Laboratory, Suining Central Hospital, Suining, PR China
| | - Jie Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Gynecology, West China Second University Hospital, Sichuan University, Chengdu, PR China
| | - Cong Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Gynecology, West China Second University Hospital, Sichuan University, Chengdu, PR China
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17
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Chansel-Da Cruz M, Hohl M, Ceppi I, Kermasson L, Maggiorella L, Modesti M, de Villartay JP, Ileri T, Cejka P, Petrini JHJ, Revy P. A Disease-Causing Single Amino Acid Deletion in the Coiled-Coil Domain of RAD50 Impairs MRE11 Complex Functions in Yeast and Humans. Cell Rep 2020; 33:108559. [PMID: 33378670 PMCID: PMC7788285 DOI: 10.1016/j.celrep.2020.108559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/30/2020] [Accepted: 12/04/2020] [Indexed: 12/20/2022] Open
Abstract
The MRE11-RAD50-NBS1 complex plays a central role in response to DNA double-strand breaks. Here, we identify a patient with bone marrow failure and developmental defects caused by biallelic RAD50 mutations. One of the mutations creates a null allele, whereas the other (RAD50E1035Δ) leads to the loss of a single residue in the heptad repeats within the RAD50 coiled-coil domain. This mutation represents a human RAD50 separation-of-function mutation that impairs DNA repair, DNA replication, and DNA end resection without affecting ATM-dependent DNA damage response. Purified recombinant proteins indicate that RAD50E1035Δ impairs MRE11 nuclease activity. The corresponding mutation in Saccharomyces cerevisiae causes severe thermosensitive defects in both DNA repair and Tel1ATM-dependent signaling. These findings demonstrate that a minor heptad break in the RAD50 coiled coil suffices to impede MRE11 complex functions in human and yeast. Furthermore, these results emphasize the importance of the RAD50 coiled coil to regulate MRE11-dependent DNA end resection in humans.
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Affiliation(s)
- Marie Chansel-Da Cruz
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France; Genomic Vision, R&D Innovation Department, Bagneux, France
| | - Marcel Hohl
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Laëtitia Kermasson
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | | | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Jean-Pierre de Villartay
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Talia Ileri
- Ankara University School of Medicine, Pediatric Hematology and Oncology, Ankara, Turkey
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - John H J Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France.
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18
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Robu M, Shah RG, Shah GM. Methods to Study Intracellular Movement and Localization of the Nucleotide Excision Repair Proteins at the DNA Lesions in Mammalian Cells. Front Cell Dev Biol 2020; 8:590242. [PMID: 33282869 PMCID: PMC7705073 DOI: 10.3389/fcell.2020.590242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/27/2020] [Indexed: 11/13/2022] Open
Abstract
Nucleotide excision repair (NER) is the most versatile DNA repair pathway that removes a wide variety of DNA lesions caused by different types of physical and chemical agents, such as ultraviolet radiation (UV), environmental carcinogen benzo[a]pyrene and anti-cancer drug carboplatin. The mammalian NER utilizes more than 30 proteins, in a multi-step process that begins with the lesion recognition within seconds of DNA damage to completion of repair after few hours to several days. The core proteins and their biochemical reactions are known from in vitro DNA repair assays using purified proteins, but challenge was to understand the dynamics of their rapid recruitment and departure from the lesion site and their coordination with other proteins and post-translational modifications to execute the sequential steps of repair. Here, we provide a brief overview of various techniques developed by different groups over last 20 years to overcome these challenges. However, more work is needed for a comprehensive knowledge of all aspects of mammalian NER. With this aim, here we provide detailed protocols of three simple yet innovative methods developed by many teams that range from local UVC irradiation to in situ extraction and sub-cellular fractionation that will permit study of endogenous as well as exogenous NER proteins in any cellular model. These methods do not require unique reagents or specialized instruments, and will allow many more laboratories to explore this repair pathway in different models. These techniques would reveal intracellular movement of these proteins to the DNA lesion site, their interactions with other proteins during repair and the effect of post-translational modifications on their functions. We also describe how these methods led us to identify hitherto unexpected role of poly(ADP-ribose) polymerase-1 (PARP1) in NER. Collectively these three simple techniques can provide an initial assessment of the functions of known and unknown proteins in the core or auxiliary events associated with mammalian NER. The results from these techniques could serve as a solid foundation and a justification for more detailed studies in NER using specialized reagents and more sophisticated tools. They can also be suitably modified to study other cellular processes beyond DNA repair.
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Affiliation(s)
- Mihaela Robu
- CHU de Québec Université Laval Research Centre (site CHUL), Laboratory for Skin Cancer Research and Axe Neuroscience, Québec, QC, Canada
| | - Rashmi G Shah
- CHU de Québec Université Laval Research Centre (site CHUL), Laboratory for Skin Cancer Research and Axe Neuroscience, Québec, QC, Canada
| | - Girish M Shah
- CHU de Québec Université Laval Research Centre (site CHUL), Laboratory for Skin Cancer Research and Axe Neuroscience, Québec, QC, Canada
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19
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Medhi D, Jasin M. CRISPR at lightning speeds. Science 2020; 368:1180-1181. [PMID: 32527814 DOI: 10.1126/science.abc3997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Darpan Medhi
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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20
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Vítor AC, Huertas P, Legube G, de Almeida SF. Studying DNA Double-Strand Break Repair: An Ever-Growing Toolbox. Front Mol Biosci 2020; 7:24. [PMID: 32154266 PMCID: PMC7047327 DOI: 10.3389/fmolb.2020.00024] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/04/2020] [Indexed: 12/29/2022] Open
Abstract
To ward off against the catastrophic consequences of persistent DNA double-strand breaks (DSBs), eukaryotic cells have developed a set of complex signaling networks that detect these DNA lesions, orchestrate cell cycle checkpoints and ultimately lead to their repair. Collectively, these signaling networks comprise the DNA damage response (DDR). The current knowledge of the molecular determinants and mechanistic details of the DDR owes greatly to the continuous development of ground-breaking experimental tools that couple the controlled induction of DSBs at distinct genomic positions with assays and reporters to investigate DNA repair pathways, their impact on other DNA-templated processes and the specific contribution of the chromatin environment. In this review, we present these tools, discuss their pros and cons and illustrate their contribution to our current understanding of the DDR.
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Affiliation(s)
- Alexandra C Vítor
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Pablo Huertas
- Department of Genetics, University of Seville, Seville, Spain.,Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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21
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Inhibition of FGFR2-Signaling Attenuates a Homology-Mediated DNA Repair in GIST and Sensitizes Them to DNA-Topoisomerase II Inhibitors. Int J Mol Sci 2020; 21:ijms21010352. [PMID: 31948066 PMCID: PMC6982350 DOI: 10.3390/ijms21010352] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/28/2019] [Accepted: 01/03/2020] [Indexed: 01/30/2023] Open
Abstract
Deregulation of receptor tyrosine kinase (RTK)-signaling is frequently observed in many human malignancies, making activated RTKs the promising therapeutic targets. In particular, activated RTK-signaling has a strong impact on tumor resistance to various DNA damaging agents, e.g., ionizing radiation and chemotherapeutic drugs. We showed recently that fibroblast growth factor receptor (FGFR)-signaling might be hyperactivated in imatinib (IM)-resistant gastrointestinal stromal tumors (GIST) and inhibition of this pathway sensitized tumor cells to the low doses of chemotherapeutic agents, such as topoisomerase II inhibitors. Here, we report that inhibition of FGFR-signaling in GISTs attenuates the repair of DNA double-strand breaks (DSBs), which was evidenced by the delay in γ-H2AX decline after doxorubicin (Dox)-induced DNA damage. A single-cell gel electrophoresis (Comet assay) data showed an increase of tail moment in Dox-treated GIST cells cultured in presence of BGJ398, a selective FGFR1-4 inhibitor, thereby revealing the attenuated DNA repair. By utilizing GFP-based reporter constructs to assess the efficiency of DSBs repair via homologous recombination (HR) and non-homologous end-joining (NHEJ), we found for the first time that FGFR inhibition in GISTs attenuated the homology-mediated DNA repair. Of note, FGFR inhibition/depletion did not reduce the number of BrdU and phospho-RPA foci in Dox-treated cells, suggesting that inhibition of FGFR-signaling has no impact on the processing of DSBs. In contrast, the number of Dox-induced Rad51 foci were decreased when FGFR2-mediated signaling was interrupted/inhibited by siRNA FGFR2 or BGJ398. Moreover, Rad51 and -H2AX foci were mislocalized in FGFR-inhibited GIST and the amount of Rad51 was substantially decreased in -H2AX-immunoprecipitated complexes, thereby illustrating the defect of Rad51 recombinase loading to the Dox-induced DSBs. Finally, as a result of the impaired homology-mediated DNA repair, the increased numbers of hypodiploid (i.e., apoptotic) cells were observed in FGFR2-inhibited GISTs after Dox treatment. Collectively, our data illustrates for the first time that inhibition of FGF-signaling in IM-resistant GIST interferes with the efficiency of DDR signaling and attenuates the homology-mediated DNA repair, thus providing the molecular mechanism of GIST’s sensitization to DNA damaging agents, e.g., DNA-topoisomerase II inhibitors.
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22
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Ticli G, Prosperi E. In Situ Analysis of DNA-Protein Complex Formation upon Radiation-Induced DNA Damage. Int J Mol Sci 2019; 20:ijms20225736. [PMID: 31731696 PMCID: PMC6888283 DOI: 10.3390/ijms20225736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 01/05/2023] Open
Abstract
The importance of determining at the cellular level the formation of DNA–protein complexes after radiation-induced lesions to DNA is outlined by the evidence that such interactions represent one of the first steps of the cellular response to DNA damage. These complexes are formed through recruitment at the sites of the lesion, of proteins deputed to signal the presence of DNA damage, and of DNA repair factors necessary to remove it. Investigating the formation of such complexes has provided, and will probably continue to, relevant information about molecular mechanisms and spatiotemporal dynamics of the processes that constitute the first barrier of cell defense against genome instability and related diseases. In this review, we will summarize and discuss the use of in situ procedures to detect the formation of DNA-protein complexes after radiation-induced DNA damage. This type of analysis provides important information on the spatial localization and temporal resolution of the formation of such complexes, at the single-cell level, allowing the study of heterogeneous cell populations.
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Affiliation(s)
- Giulio Ticli
- Istituto di Genetica Molecolare “Luca Cavalli Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy;
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27100 Pavia, Italy
| | - Ennio Prosperi
- Istituto di Genetica Molecolare “Luca Cavalli Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy;
- Correspondence:
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23
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Pike AM, Strong MA, Ouyang JPT, Greider CW. TIN2 Functions with TPP1/POT1 To Stimulate Telomerase Processivity. Mol Cell Biol 2019; 39:e00593-18. [PMID: 31383750 PMCID: PMC6791651 DOI: 10.1128/mcb.00593-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/10/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
TIN2 is an important regulator of telomere length, and mutations in TINF2, the gene encoding TIN2, cause short-telomere syndromes. While the genetics underscore the importance of TIN2, the mechanism through which TIN2 regulates telomere length remains unclear. Here, we tested the effects of human TIN2 on telomerase activity. We identified a new isoform in human cells, TIN2M, that is expressed at levels similar to those of previously studied TIN2 isoforms. All three TIN2 isoforms localized to and maintained telomere integrity in vivo, and localization was not disrupted by telomere syndrome mutations. Using direct telomerase activity assays, we discovered that TIN2 stimulated telomerase processivity in vitro All of the TIN2 isoforms stimulated telomerase to similar extents. Mutations in the TPP1 TEL patch abrogated this stimulation, suggesting that TIN2 functions with TPP1/POT1 to stimulate telomerase processivity. We conclude from our data and previously published work that TIN2/TPP1/POT1 is a functional shelterin subcomplex.
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Affiliation(s)
- Alexandra M Pike
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Margaret A Strong
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John Paul T Ouyang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Graduate Program in Biochemistry Cell and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Carol W Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Graduate Program in Biochemistry Cell and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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24
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Zhong Y, Pan B, Zhu J, Fu H, Zheng X. RNase L facilitates the repair of DNA double-strand breaks through the nonhomologous end-joining pathway. FEBS Lett 2019; 593:1190-1200. [PMID: 31062340 DOI: 10.1002/1873-3468.13426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/18/2019] [Accepted: 03/24/2019] [Indexed: 11/08/2022]
Abstract
RNA molecules have been found to play important roles in DNA double-strand break (DSB) repair, but the exact underlying mechanism remains unclear. Here, we aimed to clarify the function of RNase L, an important ribonuclease in the immune system of vertebrates, in DSB repair. Knockdown of RNase L reduces cell survival after induction of DSBs by ionizing radiation or camptothecin and causes a significant decrease in DSB repair, as evidenced by an increase in the extent of phosphorylation of histone H2AX on Ser139 (γH2AX) and γH2AX nuclear foci formation. Thus, our findings indicate that RNase L interacts with the core factors involved in DNA end joining, such as XRCC4 and Lig4, and facilitates DSB repair through the nonhomologous end-joining pathway.
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Affiliation(s)
- Yiran Zhong
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, China
| | - Bingxin Pan
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, China.,Anhui Medical University, Hefei, China
| | - Jie Zhu
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, China
| | - Hanjiang Fu
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, China
| | - Xiaofei Zheng
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, China
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25
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Vinutha K, Pavan G, Pattar S, Kumari NS, Vidya S. Aqueous extract from Madhuca indica bark protects cells from oxidative stress caused by electron beam radiation: in vitro, in vivo and in silico approach. Heliyon 2019; 5:e01749. [PMID: 31193873 PMCID: PMC6543085 DOI: 10.1016/j.heliyon.2019.e01749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/18/2019] [Accepted: 05/13/2019] [Indexed: 12/14/2022] Open
Abstract
In an endeavor to find the novel natural radioprotector to secure normal cells surrounding cancerous cell during radiation exposure, Madhuca indica (M. indica) aqueous stem bark extract was evaluated for radioprotective activity using in vitro, in vivo, and in silico models. M. indica extract exhibited concentration dependent protective effect on electron beam radiation (EBR) induced damage to pBR322 DNA; the highest protection was achieved at 150 μg concentrations. Similarly, M. indica extract (400 mg/kg) administrated to mice prior to irradiation protected DNA from the radiation damage, which was confirmed by inhibiting comet parameters. The study showed a significant increase in the levels of glutathione and superoxide dismutase levels. The study also revealed that administration of M. Indica at the different dose to mice significantly reduced EBR induced MDA, sialic acid and nitric acid levels. Further extract prevented histophatological changes of skin and liver. In contrast, protein-protein interaction studies were performed to find the hub protein, involved in radiation-induced DNA damage. Among 437 proteins that are found expressed during radiation, p53 was found to be a master protein regulating the whole pathway. Molecular interaction between p53 and M. indica extract was predicted by quantitative structure-activity relationship and ADMET properties. Biomolecules such as quercetin, myricetin, and 7-hydroxyflavone were found to be promising inhibitors of p53 protein and may help in the protection of EBR induced DNA damage during cancer treatment.
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Affiliation(s)
- K. Vinutha
- Department of Biotechnology, NMAM Institute of Technology, 574110, Udupi (Dist), Nitte, Karnataka, India
| | - Gollapalli Pavan
- Department of Biotechnology Vignan's Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Guntur (Dt), Andhra Pradesh, 522203, India
| | - Sharath Pattar
- National Bureau of Agriculturally Important Insects, P.Bag No: 2491, H.A. Farm Post, Bellary Rd, Hebbal, Bengaluru, Karnataka, 560024, India
| | - N Suchetha Kumari
- University Enclave, Medical Sciences Complex, Deralakatte, Mangalore, 575018, India
| | - S.M. Vidya
- Department of Biotechnology, NMAM Institute of Technology, 574110, Udupi (Dist), Nitte, Karnataka, India
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26
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Adenovirus 5 E1A Interacts with E4orf3 To Regulate Viral Chromatin Organization. J Virol 2019; 93:JVI.00157-19. [PMID: 30842325 DOI: 10.1128/jvi.00157-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/27/2019] [Indexed: 01/05/2023] Open
Abstract
Human adenovirus expresses several early proteins that control various aspects of the viral replication program, including an orchestrated expression of viral genes. Two of the earliest viral transcriptional units activated after viral genome entry into the host cell nucleus are the E1 and E4 units, which each express a variety of proteins. Chief among these are the E1A proteins that function to reprogram the host cell and activate transcription of all other viral genes. The E4 gene encodes multiple proteins, including E4orf3, which functions to disrupt cellular antiviral defenses, including the DNA damage response pathway and activation of antiviral genes. Here we report that E1A directly interacts with E4orf3 via the conserved N terminus of E1A to regulate the expression of viral genes. We show that E4orf3 indiscriminately drives high nucleosomal density of viral genomes, which is restrictive to viral gene expression and which E1A overcomes via a direct interaction with E4orf3. We also show that during infection E1A colocalizes with E4orf3 to nuclear tracks that are associated with heterochromatin formation. The inability of E1A to interact with E4orf3 has a significant negative impact on overall viral replication, the ability of the virus to reprogram the host cell, and the levels of viral gene expression. Together these results show that E1A and E4orf3 work together to fine-tune the viral replication program during the course of infection and highlight a novel mechanism that regulates viral gene expression.IMPORTANCE To successfully replicate, human adenovirus needs to carry out a rapid yet ordered transcriptional program that executes and drives viral replication. Early in infection, the viral E1A proteins are the key activators and regulators of viral transcription. Here we report, for the first time, that E1A works together with E4orf3 to perfect the viral transcriptional program and identify a novel mechanism by which the virus can adjust viral gene expression by modifying its genome's nucleosomal organization via cooperation between E1A and E4orf3.
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27
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Djuzenova CS, Fiedler V, Memmel S, Katzer A, Sisario D, Brosch PK, Göhrung A, Frister S, Zimmermann H, Flentje M, Sukhorukov VL. Differential effects of the Akt inhibitor MK-2206 on migration and radiation sensitivity of glioblastoma cells. BMC Cancer 2019; 19:299. [PMID: 30943918 PMCID: PMC6446411 DOI: 10.1186/s12885-019-5517-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/25/2019] [Indexed: 01/29/2023] Open
Abstract
Background Most tumor cells show aberrantly activated Akt which leads to increased cell survival and resistance to cancer radiotherapy. Therefore, targeting Akt can be a promising strategy for radiosensitization. Here, we explore the impact of the Akt inhibitor MK-2206 alone and in combination with the dual PI3K and mTOR inhibitor PI-103 on the radiation sensitivity of glioblastoma cells. In addition, we examine migration of drug-treated cells. Methods Using single-cell tracking and wound healing migration tests, colony-forming assay, Western blotting, flow cytometry and electrorotation we examined the effects of MK-2206 and PI-103 and/or irradiation on the migration, radiation sensitivity, expression of several marker proteins, DNA damage, cell cycle progression and the plasma membrane properties in two glioblastoma (DK-MG and SNB19) cell lines, previously shown to differ markedly in their migratory behavior and response to PI3K/mTOR inhibition. Results We found that MK-2206 strongly reduces the migration of DK-MG but only moderately reduces the migration of SNB19 cells. Surprisingly, MK-2206 did not cause radiosensitization, but even increased colony-forming ability after irradiation. Moreover, MK-2206 did not enhance the radiosensitizing effect of PI-103. The results appear to contradict the strong depletion of p-Akt in MK-2206-treated cells. Possible reasons for the radioresistance of MK-2206-treated cells could be unaltered or in case of SNB19 cells even increased levels of p-mTOR and p-S6, as compared to the reduced expression of these proteins in PI-103-treated samples. We also found that MK-2206 did not enhance IR-induced DNA damage, neither did it cause cell cycle distortion, nor apoptosis nor excessive autophagy. Conclusions Our study provides proof that MK-2206 can effectively inhibit the expression of Akt in two glioblastoma cell lines. However, due to an aberrant activation of mTOR in response to Akt inhibition in PTEN mutated cells, the therapeutic window needs to be carefully defined, or a combination of Akt and mTOR inhibitors should be considered. Electronic supplementary material The online version of this article (10.1186/s12885-019-5517-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cholpon S Djuzenova
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany.
| | - Vanessa Fiedler
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany
| | - Simon Memmel
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany
| | - Astrid Katzer
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany
| | - Dmitri Sisario
- Department of Biotechnology and Biophysics, University of Würzburg, 97074, Würzburg, Germany
| | - Philippa K Brosch
- Department of Biotechnology and Biophysics, University of Würzburg, 97074, Würzburg, Germany
| | - Alexander Göhrung
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany
| | - Svenja Frister
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany
| | - Heiko Zimmermann
- Fraunhofer-Institut für Biomedizinische Technik, Joseph-von-Fraunhofer-Weg 1, 66280, Sulzbach, Germany.,Professur für Molekulare und Zelluläre Biotechnologie/Nanotechnologie, Universität des Saarlandes, Campus Saarbrücken, 66123, Saarbrücken, Germany.,Marine Sciences, Universidad Católica del Norte, Casa Central, Angamos 0610, Antafogasta/Coquimbo, Chile
| | - Michael Flentje
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany
| | - Vladimir L Sukhorukov
- Department of Biotechnology and Biophysics, University of Würzburg, 97074, Würzburg, Germany
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28
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Li CG, Mahon C, Sweeney NM, Verschueren E, Kantamani V, Li D, Hennigs JK, Marciano DP, Diebold I, Abu-Halawa O, Elliott M, Sa S, Guo F, Wang L, Cao A, Guignabert C, Sollier J, Nickel NP, Kaschwich M, Cimprich KA, Rabinovitch M. PPARγ Interaction with UBR5/ATMIN Promotes DNA Repair to Maintain Endothelial Homeostasis. Cell Rep 2019; 26:1333-1343.e7. [PMID: 30699358 PMCID: PMC6436616 DOI: 10.1016/j.celrep.2019.01.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/30/2018] [Accepted: 01/03/2019] [Indexed: 01/13/2023] Open
Abstract
Using proteomic approaches, we uncovered a DNA damage response (DDR) function for peroxisome proliferator activated receptor γ (PPARγ) through its interaction with the DNA damage sensor MRE11-RAD50-NBS1 (MRN) and the E3 ubiquitin ligase UBR5. We show that PPARγ promotes ATM signaling and is essential for UBR5 activity targeting ATM interactor (ATMIN). PPARγ depletion increases ATMIN protein independent of transcription and suppresses DDR-induced ATM signaling. Blocking ATMIN in this context restores ATM activation and DNA repair. We illustrate the physiological relevance of PPARγ DDR functions by using pulmonary arterial hypertension (PAH) as a model that has impaired PPARγ signaling related to endothelial cell (EC) dysfunction and unresolved DNA damage. In pulmonary arterial ECs (PAECs) from PAH patients, we observed disrupted PPARγ-UBR5 interaction, heightened ATMIN expression, and DNA lesions. Blocking ATMIN in PAH PAEC restores ATM activation. Thus, impaired PPARγ DDR functions may explain the genomic instability and loss of endothelial homeostasis in PAH.
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Affiliation(s)
- Caiyun G Li
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Cathal Mahon
- California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA 94158, USA
| | - Nathaly M Sweeney
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Erik Verschueren
- California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA 94158, USA
| | - Vivek Kantamani
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Dan Li
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Jan K Hennigs
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - David P Marciano
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Isabel Diebold
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Ossama Abu-Halawa
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Matthew Elliott
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Silin Sa
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Feng Guo
- Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Lingli Wang
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Aiqin Cao
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Christophe Guignabert
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Julie Sollier
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Nils P Nickel
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Mark Kaschwich
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Marlene Rabinovitch
- The Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics and Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA.
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29
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Awate S, Dhar S, Sommers JA, Brosh RM. Cellular Assays to Study the Functional Importance of Human DNA Repair Helicases. Methods Mol Biol 2019; 1999:185-207. [PMID: 31127577 PMCID: PMC9123881 DOI: 10.1007/978-1-4939-9500-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA helicases represent a specialized class of enzymes that play crucial roles in the DNA damage response. Using the energy of nucleoside triphosphate binding and hydrolysis, helicases behave as molecular motors capable of efficiently disrupting the many noncovalent hydrogen bonds that stabilize DNA molecules with secondary structure. In addition to their importance in DNA damage sensing and signaling, DNA helicases facilitate specific steps in DNA repair mechanisms that require polynucleotide tract unwinding or resolution. Because they play fundamental roles in the DNA damage response and DNA repair, defects in helicases disrupt cellular homeostasis. Thus, helicase deficiency or inhibition may result in reduced cell proliferation and survival, apoptosis, DNA damage induction, defective localization of repair proteins to sites of genomic DNA damage, chromosomal instability, and defective DNA repair pathways such as homologous recombination of double-strand breaks. In this chapter, we will describe step-by-step protocols to assay the functional importance of human DNA repair helicases in genome stability and cellular homeostasis.
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Affiliation(s)
- Sanket Awate
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD, USA
| | - Srijita Dhar
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD, USA
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD, USA.
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30
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Gustafsson NMS, Färnegårdh K, Bonagas N, Ninou AH, Groth P, Wiita E, Jönsson M, Hallberg K, Lehto J, Pennisi R, Martinsson J, Norström C, Hollers J, Schultz J, Andersson M, Markova N, Marttila P, Kim B, Norin M, Olin T, Helleday T. Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination. Nat Commun 2018; 9:3872. [PMID: 30250201 PMCID: PMC6155239 DOI: 10.1038/s41467-018-06287-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022] Open
Abstract
The glycolytic PFKFB3 enzyme is widely overexpressed in cancer cells and an emerging anti-cancer target. Here, we identify PFKFB3 as a critical factor in homologous recombination (HR) repair of DNA double-strand breaks. PFKFB3 rapidly relocates into ionizing radiation (IR)-induced nuclear foci in an MRN-ATM-γH2AX-MDC1-dependent manner and co-localizes with DNA damage and HR repair proteins. PFKFB3 relocalization is critical for recruitment of HR proteins, HR activity, and cell survival upon IR. We develop KAN0438757, a small molecule inhibitor that potently targets PFKFB3. Pharmacological PFKFB3 inhibition impairs recruitment of ribonucleotide reductase M2 and deoxynucleotide incorporation upon DNA repair, and reduces dNTP levels. Importantly, KAN0438757 induces radiosensitization in transformed cells while leaving non-transformed cells unaffected. In summary, we identify a key role for PFKFB3 enzymatic activity in HR repair and present KAN0438757, a selective PFKFB3 inhibitor that could potentially be used as a strategy for the treatment of cancer.
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Affiliation(s)
- Nina M S Gustafsson
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden.
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden.
| | - Katarina Färnegårdh
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Organic Chemistry, Stockholm University, Box 1030, S-171 21, Solna, Sweden
| | - Nadilly Bonagas
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | - Anna Huguet Ninou
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Petra Groth
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | - Elisee Wiita
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | | | - Kenth Hallberg
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
- Sprint Bioscience, 141 57, Huddinge, Sweden
| | - Jemina Lehto
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Rosa Pennisi
- Department of Sciences, Roma Tre University, 446 00146 Rome, Italy
| | | | | | - Jessica Hollers
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Johan Schultz
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | | | | | - Petra Marttila
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Pharmacy, Kyung-Hee University, 02447, Seoul, South Korea
| | - Martin Norin
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Thomas Olin
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden.
- Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, S10 2RX, Sheffield, UK.
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31
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Kannappan R, Mattapally S, Wagle PA, Zhang J. Transactivation domain of p53 regulates DNA repair and integrity in human iPS cells. Am J Physiol Heart Circ Physiol 2018; 315:H512-H521. [PMID: 29775409 PMCID: PMC6172637 DOI: 10.1152/ajpheart.00160.2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/23/2018] [Accepted: 05/03/2018] [Indexed: 12/12/2022]
Abstract
The role of p53 transactivation domain (p53-TAD), a multifunctional and dynamic domain, on DNA repair and retaining DNA integrity in human induced pluripotent stem cells (hiPSCs) has never been studied. p53-TAD was knocked out in iPSCs using CRISPR/Cas9 and was confirmed by DNA sequencing. p53-TAD knockout (KO) cells were characterized by accelerated proliferation, decreased population doubling time, and unaltered Bcl-2, Bcl-2-binding component 3, insulin-like growth factor 1 receptor, and Bax and altered Mdm2, p21, and p53-induced death domain transcript expression. In p53-TAD KO cells, the p53-regulated DNA repair proteins xeroderma pigmentosum group A, DNA polymerase H, and DNA-binding protein 2 expression were found to be reduced compared with p53 wild-type cells. Exposure to a low dose of doxorubicin (Doxo) induced similar DNA damage and DNA damage response (DDR) as measured by RAD50 and MRE11 expression, checkpoint kinase 2 activation, and γH2A.X recruitment at DNA strand breaks in both cell groups, indicating that silence of p53-TAD does not affect the DDR mechanism upstream of p53. After removal of Doxo, p53 wild-type hiPSCs underwent DNA repair, corrected their damaged DNA, and restored DNA integrity. Conversely, p53-TAD KO hiPSCs did not undergo complete DNA repair and failed to restore DNA integrity. More importantly, continuous culture of p53-TAD KO hiPSCs underwent G2/M cell cycle arrest and expressed the cellular senescent marker p16INK4a. Our data clearly show that silence of the TAD of p53 did not affect DDR but affected the DNA repair process, implying the crucial role of p53-TAD in maintaining DNA integrity. Therefore, activating p53-TAD domain using small molecules may promote DNA repair and integrity of cells and prevent cellular senescence.
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Affiliation(s)
- Ramaswamy Kannappan
- Department of Biomedical Engineering, School of Medicine, School of Engineering, The University of Alabama at Birmingham , Birmingham, Alabama
| | - Saidulu Mattapally
- Department of Biomedical Engineering, School of Medicine, School of Engineering, The University of Alabama at Birmingham , Birmingham, Alabama
| | - Pooja A Wagle
- Department of Biomedical Engineering, School of Medicine, School of Engineering, The University of Alabama at Birmingham , Birmingham, Alabama
| | - Jianyi Zhang
- Department of Biomedical Engineering, School of Medicine, School of Engineering, The University of Alabama at Birmingham , Birmingham, Alabama
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32
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Carruthers RD, Ahmed SU, Ramachandran S, Strathdee K, Kurian KM, Hedley A, Gomez-Roman N, Kalna G, Neilson M, Gilmour L, Stevenson KH, Hammond EM, Chalmers AJ. Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells. Cancer Res 2018; 78:5060-5071. [PMID: 29976574 PMCID: PMC6128404 DOI: 10.1158/0008-5472.can-18-0569] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/25/2018] [Accepted: 06/28/2018] [Indexed: 11/16/2022]
Abstract
Glioblastoma (GBM) is a lethal primary brain tumor characterized by treatment resistance and inevitable tumor recurrence, both of which are driven by a subpopulation of GBM cancer stem-like cells (GSC) with tumorigenic and self-renewal properties. Despite having broad implications for understanding GSC phenotype, the determinants of upregulated DNA-damage response (DDR) and subsequent radiation resistance in GSC are unknown and represent a significant barrier to developing effective GBM treatments. In this study, we show that constitutive DDR activation and radiation resistance are driven by high levels of DNA replication stress (RS). CD133+ GSC exhibited reduced DNA replication velocity and a higher frequency of stalled replication forks than CD133- non-GSC in vitro; immunofluorescence studies confirmed these observations in a panel of orthotopic xenografts and human GBM specimens. Exposure of non-GSC to low-level exogenous RS generated radiation resistance in vitro, confirming RS as a novel determinant of radiation resistance in tumor cells. GSC exhibited DNA double-strand breaks, which colocalized with "replication factories" and RNA: DNA hybrids. GSC also demonstrated increased expression of long neural genes (>1 Mbp) containing common fragile sites, supporting the hypothesis that replication/transcription collisions are the likely cause of RS in GSC. Targeting RS by combined inhibition of ATR and PARP (CAiPi) provided GSC-specific cytotoxicity and complete abrogation of GSC radiation resistance in vitro These data identify RS as a cancer stem cell-specific target with significant clinical potential.Significance: These findings shed new light on cancer stem cell biology and reveal novel therapeutics with the potential to improve clinical outcomes by overcoming inherent radioresistance in GBM. Cancer Res; 78(17); 5060-71. ©2018 AACR.
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Affiliation(s)
- Ross D Carruthers
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom.
| | - Shafiq U Ahmed
- School of Pharmacy and Pharmaceutical Sciences, Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, United Kingdom
| | - Shaliny Ramachandran
- Cancer Research UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Karen Strathdee
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Kathreena M Kurian
- Department of Neuropathology, Brain Tumour Research Group, Frenchay Hospital, North Bristol NHS Trust Bristol, Bristol, United Kingdom
| | - Ann Hedley
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Natividad Gomez-Roman
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Gabriela Kalna
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Mathew Neilson
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Lesley Gilmour
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Katrina H Stevenson
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Ester M Hammond
- Cancer Research UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Anthony J Chalmers
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
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Ortega-Pierres M, Jex AR, Ansell BR, Svärd SG. Recent advances in the genomic and molecular biology of Giardia. Acta Trop 2018; 184:67-72. [PMID: 28888474 DOI: 10.1016/j.actatropica.2017.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/05/2017] [Indexed: 01/01/2023]
Abstract
Giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders. Robust tools for analyzing gene function in this parasite have been developed and a range of genetic tools are now available. These together with public databases have provided insights on the function of different genes in Giardia. In this review we provide a current perspective on different molecular aspects of Giardia related to genomics, regulation of encystation, trophozoite transcriptional responses to physiological and xenobiotic (drug-induced) stress, and mechanisms of drug resistance. We also examine recent insights that have contributed to gain knowledge in the study of VSPs, antigenic variation, epigenetics, DNA repair and in the direct manipulation of gene function in Giardia, with a particular focus on the inducible Cre/loxP system.
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Mirman Z, Lottersberger F, Takai H, Kibe T, Gong Y, Takai K, Bianchi A, Zimmermann M, Durocher D, de Lange T. 53BP1-RIF1-shieldin counteracts DSB resection through CST- and Polα-dependent fill-in. Nature 2018; 560:112-116. [PMID: 30022158 PMCID: PMC6072559 DOI: 10.1038/s41586-018-0324-7] [Citation(s) in RCA: 272] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/10/2018] [Indexed: 12/29/2022]
Abstract
Resection of double-strand breaks (DSBs) dictates the choice between Homology-Directed Repair (HDR), which requires a 3′ overhang, and classical Non-Homologous End Joining (c-NHEJ), which can join unresected ends1,2. BRCA1 mutant cancers show minimal DSB resection, rendering them HDR deficient and sensitive to PARP1 inhibitors (PARPi)3–8. When BRCA1 is absent, DSB resection is thought to be prevented by 53BP1, Rif1, and the Rev7/Shld1/Shld2/Shld3 (Shieldin) complex and loss of these factors diminishes PARPi sensitivity4,6–9. Here we address the mechanism by which 53BP1/Rif1/Shieldin regulate the generation of recombinogenic 3′ overhangs. We report that CST (Ctc1, Stn1, Ten110), an RPA-like complex that functions as a Polymeraseα/primase accessory factor11 is a downstream effector in the 53BP1 pathway. CST interacts with Shieldin and localizes with Polα to sites of DNA damage in a 53BP1- and Shieldin-dependent manner. Like loss of 53BP1/Rif1/Shieldin, CST depletion leads to increased resection. Furthermore, in BRCA1-deficient cells, CST blocks Rad51 loading and promotes PARPi efficacy. Finally, Polα inhibition diminishes the effect of PARPi in BRCA1-deficient cells. These data suggest that CST/Polα-mediated fill-in contributes to the control of DSB repair by 53BP1, Rif1, and Shieldin.
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Affiliation(s)
- Zachary Mirman
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Francisca Lottersberger
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA.,Department of Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Hiroyuki Takai
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Tatsuya Kibe
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Yi Gong
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Kaori Takai
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Alessandro Bianchi
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Michal Zimmermann
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA.
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35
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Li Z, Li Y, Tang M, Peng B, Lu X, Yang Q, Zhu Q, Hou T, Li M, Liu C, Wang L, Xu X, Zhao Y, Wang H, Yang Y, Zhu WG. Destabilization of linker histone H1.2 is essential for ATM activation and DNA damage repair. Cell Res 2018; 28:756-770. [PMID: 29844578 PMCID: PMC6028381 DOI: 10.1038/s41422-018-0048-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/06/2018] [Accepted: 05/07/2018] [Indexed: 12/22/2022] Open
Abstract
Linker histone H1 is a master regulator of higher order chromatin structure, but its involvement in the DNA damage response and repair is unclear. Here, we report that linker histone H1.2 is an essential regulator of ataxia telangiectasia mutated (ATM) activation. We show that H1.2 protects chromatin from aberrant ATM activation through direct interaction with the ATM HEAT repeat domain and inhibition of MRE11-RAD50-NBS1 (MRN) complex-dependent ATM recruitment. Upon DNA damage, H1.2 undergoes rapid PARP1-dependent chromatin dissociation through poly-ADP-ribosylation (PARylation) of its C terminus and further proteasomal degradation. Inhibition of H1.2 displacement by PARP1 depletion or an H1.2 PARylation-dead mutation compromises ATM activation and DNA damage repair, thus leading to impaired cell survival. Taken together, our findings suggest that linker histone H1.2 functions as a physiological barrier for ATM to target the chromatin, and PARylation-mediated active H1.2 turnover is required for robust ATM activation and DNA damage repair.
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Affiliation(s)
- Zhiming Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yinglu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ming Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Bin Peng
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Xiaopeng Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Qiaoyan Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Qian Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Tianyun Hou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Meiting Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Chaohua Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Lina Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xingzhi Xu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Ying Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Haiying Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yang Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China.
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Paquin KL, Howlett NG. Understanding the Histone DNA Repair Code: H4K20me2 Makes Its Mark. Mol Cancer Res 2018; 16:1335-1345. [PMID: 29858375 DOI: 10.1158/1541-7786.mcr-17-0688] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/28/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022]
Abstract
Chromatin is a highly compact structure that must be rapidly rearranged in order for DNA repair proteins to access sites of damage and facilitate timely and efficient repair. Chromatin plasticity is achieved through multiple processes, including the posttranslational modification of histone tails. In recent years, the impact of histone posttranslational modification on the DNA damage response has become increasingly well recognized, and chromatin plasticity has been firmly linked to efficient DNA repair. One particularly important histone posttranslational modification process is methylation. Here, we focus on the regulation and function of H4K20 methylation (H4K20me) in the DNA damage response and describe the writers, erasers, and readers of this important chromatin mark as well as the combinatorial histone posttranslational modifications that modulate H4K20me recognition. Finally, we discuss the central role of H4K20me in determining if DNA double-strand breaks (DSB) are repaired by the error-prone, nonhomologous DNA end joining pathway or the error-free, homologous recombination pathway. This review article discusses the regulation and function of H4K20me2 in DNA DSB repair and outlines the components and modifications that modulate this important chromatin mark and its fundamental impact on DSB repair pathway choice. Mol Cancer Res; 16(9); 1335-45. ©2018 AACR.
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Affiliation(s)
- Karissa L Paquin
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island
| | - Niall G Howlett
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island.
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Hollingworth R, Horniblow RD, Forrest C, Stewart GS, Grand RJ. Localization of Double-Strand Break Repair Proteins to Viral Replication Compartments following Lytic Reactivation of Kaposi's Sarcoma-Associated Herpesvirus. J Virol 2017; 91:e00930-17. [PMID: 28855246 PMCID: PMC5660498 DOI: 10.1128/jvi.00930-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/10/2017] [Indexed: 12/11/2022] Open
Abstract
Double-strand breaks (DSBs) in DNA are recognized by the Ku70/80 heterodimer and the MRE11-RAD50-NBS1 (MRN) complex and result in activation of the DNA-PK and ATM kinases, which play key roles in regulating the cellular DNA damage response (DDR). DNA tumor viruses such as Kaposi's sarcoma-associated herpesvirus (KSHV) are known to interact extensively with the DDR during the course of their replicative cycles. Here we show that during lytic amplification of KSHV DNA, the Ku70/80 heterodimer and the MRN complex consistently colocalize with viral genomes in replication compartments (RCs), whereas other DSB repair proteins form foci outside RCs. Depletion of MRE11 and abrogation of its exonuclease activity negatively impact viral replication, while in contrast, knockdown of Ku80 and inhibition of the DNA-PK enzyme, which are involved in nonhomologous end joining (NHEJ) repair, enhance amplification of viral DNA. Although the recruitment of DSB-sensing proteins to KSHV RCs is a consistent occurrence across multiple cell types, activation of the ATM-CHK2 pathway during viral replication is a cell line-specific event, indicating that recognition of viral DNA by the DDR does not necessarily result in activation of downstream signaling pathways. We have also observed that newly replicated viral DNA is not associated with cellular histones. Since the presence and modification of these DNA-packaging proteins provide a scaffold for docking of multiple DNA repair factors, the absence of histone deposition may allow the virus to evade localization of DSB repair proteins that would otherwise have a detrimental effect on viral replication.IMPORTANCE Tumor viruses are known to interact with machinery responsible for detection and repair of double-strand breaks (DSBs) in DNA, although detail concerning how Kaposi's sarcoma-associated herpesvirus (KSHV) modulates these cellular pathways during its lytic replication phase was previously lacking. By undertaking a comprehensive assessment of the localization of DSB repair proteins during KSHV replication, we have determined that a DNA damage response (DDR) is directed to viral genomes but is distinct from the response to cellular DNA damage. We also demonstrate that although recruitment of the MRE11-RAD50-NBS1 (MRN) DSB-sensing complex to viral genomes and activation of the ATM kinase can promote KSHV replication, proteins involved in nonhomologous end joining (NHEJ) repair restrict amplification of viral DNA. Overall, this study extends our understanding of the virus-host interactions that occur during lytic replication of KSHV and provides a deeper insight into how the DDR is manipulated during viral infection.
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Affiliation(s)
- Robert Hollingworth
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Richard D Horniblow
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Calum Forrest
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Roger J Grand
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
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38
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Saki M, Makino H, Javvadi P, Tomimatsu N, Ding LH, Clark JE, Gavin E, Takeda K, Andrews J, Saha D, Story MD, Burma S, Nirodi CS. EGFR Mutations Compromise Hypoxia-Associated Radiation Resistance through Impaired Replication Fork-Associated DNA Damage Repair. Mol Cancer Res 2017; 15:1503-1516. [PMID: 28801308 PMCID: PMC5668182 DOI: 10.1158/1541-7786.mcr-17-0136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/29/2017] [Accepted: 08/03/2017] [Indexed: 12/20/2022]
Abstract
EGFR signaling has been implicated in hypoxia-associated resistance to radiation or chemotherapy. Non-small cell lung carcinomas (NSCLC) with activating L858R or ΔE746-E750 EGFR mutations exhibit elevated EGFR activity and downstream signaling. Here, relative to wild-type (WT) EGFR, mutant (MT) EGFR expression significantly increases radiosensitivity in hypoxic cells. Gene expression profiling in human bronchial epithelial cells (HBEC) revealed that MT-EGFR expression elevated transcripts related to cell cycle and replication in aerobic and hypoxic conditions and downregulated RAD50, a critical component of nonhomologous end joining and homologous recombination DNA repair pathways. NSCLCs and HBEC with MT-EGFR revealed elevated basal and hypoxia-induced γ-H2AX-associated DNA lesions that were coincident with replication protein A in the S-phase nuclei. DNA fiber analysis showed that, relative to WT-EGFR, MT-EGFR NSCLCs harbored significantly higher levels of stalled replication forks and decreased fork velocities in aerobic and hypoxic conditions. EGFR blockade by cetuximab significantly increased radiosensitivity in hypoxic cells, recapitulating MT-EGFR expression and closely resembling synthetic lethality of PARP inhibition.Implications: This study demonstrates that within an altered DNA damage response of hypoxic NSCLC cells, mutant EGFR expression, or EGFR blockade by cetuximab exerts a synthetic lethality effect and significantly compromises radiation resistance in hypoxic tumor cells. Mol Cancer Res; 15(11); 1503-16. ©2017 AACR.
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Affiliation(s)
- Mohammad Saki
- Department of Oncologic Sciences, University of South Alabama Mitchell Cancer Institute, Mobile, Alabama
| | - Haruhiko Makino
- Division of Medical Oncology and Molecular Respirology, Faculty of Medicine Tottori University, Yonago, Tottori, Japan
| | - Prashanthi Javvadi
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Nozomi Tomimatsu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Liang-Hao Ding
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jennifer E Clark
- Department of Oncologic Sciences, University of South Alabama Mitchell Cancer Institute, Mobile, Alabama
| | - Elaine Gavin
- Department of Oncologic Sciences, University of South Alabama Mitchell Cancer Institute, Mobile, Alabama
| | - Kenichi Takeda
- Division of Medical Oncology and Molecular Respirology, Faculty of Medicine Tottori University, Yonago, Tottori, Japan
| | - Joel Andrews
- Department of Oncologic Sciences, University of South Alabama Mitchell Cancer Institute, Mobile, Alabama
| | - Debabrata Saha
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Michael D Story
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sandeep Burma
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Chaitanya S Nirodi
- Department of Oncologic Sciences, University of South Alabama Mitchell Cancer Institute, Mobile, Alabama.
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39
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Horton SJ, Giotopoulos G, Yun H, Vohra S, Sheppard O, Bashford-Rogers R, Rashid M, Clipson A, Chan WI, Sasca D, Yiangou L, Osaki H, Basheer F, Gallipoli P, Burrows N, Erdem A, Sybirna A, Foerster S, Zhao W, Sustic T, Petrunkina Harrison A, Laurenti E, Okosun J, Hodson D, Wright P, Smith KG, Maxwell P, Fitzgibbon J, Du MQ, Adams DJ, Huntly BJP. Early loss of Crebbp confers malignant stem cell properties on lymphoid progenitors. Nat Cell Biol 2017; 19:1093-1104. [PMID: 28825697 PMCID: PMC5633079 DOI: 10.1038/ncb3597] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/20/2017] [Indexed: 12/13/2022]
Abstract
Loss-of-function mutations of cyclic-AMP response element binding protein, binding protein (CREBBP) are prevalent in lymphoid malignancies. However, the tumour suppressor functions of CREBBP remain unclear. We demonstrate that loss of Crebbp in murine haematopoietic stem and progenitor cells (HSPCs) leads to increased development of B-cell lymphomas. This is preceded by accumulation of hyperproliferative lymphoid progenitors with a defective DNA damage response (DDR) due to a failure to acetylate p53. We identify a premalignant lymphoma stem cell population with decreased H3K27ac, which undergoes transcriptional and genetic evolution due to the altered DDR, resulting in lymphomagenesis. Importantly, when Crebbp is lost later in lymphopoiesis, cellular abnormalities are lost and tumour generation is attenuated. We also document that CREBBP mutations may occur in HSPCs from patients with CREBBP-mutated lymphoma. These data suggest that earlier loss of Crebbp is advantageous for lymphoid transformation and inform the cellular origins and subsequent evolution of lymphoid malignancies.
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Affiliation(s)
- Sarah J Horton
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - George Giotopoulos
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Haiyang Yun
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Shabana Vohra
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Olivia Sheppard
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Rachael Bashford-Rogers
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Mamunur Rashid
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Alexandra Clipson
- Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Wai-In Chan
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Daniel Sasca
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Loukia Yiangou
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Hikari Osaki
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Faisal Basheer
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Paolo Gallipoli
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Natalie Burrows
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Ayşegül Erdem
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - Sarah Foerster
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Wanfeng Zhao
- Department of Pathology, Cambridge University Hospitals, Hills Road, Cambridge CB2 0QQ, UK
| | - Tonci Sustic
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - Elisa Laurenti
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jessica Okosun
- Barts Cancer Institute, Charterhouse Square, London EC1M 6BQ, UK
| | - Daniel Hodson
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Penny Wright
- Department of Pathology, Cambridge University Hospitals, Hills Road, Cambridge CB2 0QQ, UK
| | - Ken G Smith
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Patrick Maxwell
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Jude Fitzgibbon
- Barts Cancer Institute, Charterhouse Square, London EC1M 6BQ, UK
| | - Ming Q Du
- Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Brian J P Huntly
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
- Department of Haematology, Cambridge University Hospitals, Hills Road, Cambridge CB2 0QQ, UK
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40
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Liu C, Vyas A, Kassab MA, Singh AK, Yu X. The role of poly ADP-ribosylation in the first wave of DNA damage response. Nucleic Acids Res 2017; 45:8129-8141. [PMID: 28854736 PMCID: PMC5737498 DOI: 10.1093/nar/gkx565] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 06/15/2017] [Accepted: 06/20/2017] [Indexed: 01/11/2023] Open
Abstract
Poly ADP-ribose polymerases (PARPs) catalyze massive protein poly ADP-ribosylation (PARylation) within seconds after the induction of DNA single- or double-strand breaks. PARylation occurs at or near the sites of DNA damage and promotes the recruitment of DNA repair factors via their poly ADP-ribose (PAR) binding domains. Several novel PAR-binding domains have been recently identified. Here, we summarize these and other recent findings suggesting that PARylation may be the critical event that mediates the first wave of the DNA damage response. We also discuss the potential for functional crosstalk with other DNA damage-induced post-translational modifications.
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Affiliation(s)
- Chao Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Aditi Vyas
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Muzaffer A. Kassab
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Anup K. Singh
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
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Rohban S, Cerutti A, Morelli MJ, d'Adda di Fagagna F, Campaner S. The cohesin complex prevents Myc-induced replication stress. Cell Death Dis 2017; 8:e2956. [PMID: 28749464 PMCID: PMC5550886 DOI: 10.1038/cddis.2017.345] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 11/25/2022]
Abstract
The cohesin complex is mutated in cancer and in a number of rare syndromes collectively known as Cohesinopathies. In the latter case, cohesin deficiencies have been linked to transcriptional alterations affecting Myc and its target genes. Here, we set out to understand to what extent the role of cohesins in controlling cell cycle is dependent on Myc expression and activity. Inactivation of the cohesin complex by silencing the RAD21 subunit led to cell cycle arrest due to both transcriptional impairment of Myc target genes and alterations of replication forks, which were fewer and preferentially unidirectional. Ectopic activation of Myc in RAD21 depleted cells rescued Myc-dependent transcription and promoted S-phase entry but failed to sustain S-phase progression due to a strong replicative stress response, which was associated to a robust DNA damage response, DNA damage checkpoint activation and synthetic lethality. Thus, the cohesin complex is dispensable for Myc-dependent transcription but essential to prevent Myc-induced replicative stress. This suggests the presence of a feed-forward regulatory loop where cohesins by regulating Myc level control S-phase entry and prevent replicative stress.
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Affiliation(s)
- Sara Rohban
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Aurora Cerutti
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, CNR – Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, CNR – Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Stefano Campaner
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
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42
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de Campos Nebel M, Palmitelli M, González-Cid M. Measurement of Drug-Stabilized Topoisomerase II Cleavage Complexes by Flow Cytometry. ACTA ACUST UNITED AC 2017; 81:7.48.1-7.48.8. [PMID: 28678420 DOI: 10.1002/cpcy.21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The poisoning of Topoisomerase II (Top2) has been found to be useful as a therapeutic strategy for the treatment of several tumors. The mechanism of Top2 poisons involves a drug-mediated stabilization of a Top2-DNA complex, termed Top2 cleavage complex (Top2cc), which maintains a 5' end of DNA covalently bound to a tyrosine from Top2 through a phosphodiester group. Drug-stabilized Top2cc leads to Top2-linked-DNA breaks, which are believed to mediate their cytotoxicity. Several time-consuming or cell type-limiting assays have been used in the past to study drug-stabilized Top2cc. Here, we describe a flow cytometry-based method that allows a rapid assessment of drug-induced Top2cc, which is suitable for high throughput analysis in almost any kind of human cell. The analyses of the drug-induced Top2cc in the cell cycle context and the possibility to track its removal are additional benefits from this methodology. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marcelo de Campos Nebel
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET. Ciudad Autónoma de Buenos Aires, Argentina
| | - Micaela Palmitelli
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET. Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcela González-Cid
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET. Ciudad Autónoma de Buenos Aires, Argentina
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43
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Vélez-Cruz R, Manickavinayaham S, Biswas AK, Clary RW, Premkumar T, Cole F, Johnson DG. RB localizes to DNA double-strand breaks and promotes DNA end resection and homologous recombination through the recruitment of BRG1. Genes Dev 2017; 30:2500-2512. [PMID: 27940962 PMCID: PMC5159665 DOI: 10.1101/gad.288282.116] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/03/2016] [Indexed: 11/24/2022]
Abstract
The retinoblastoma (RB) tumor suppressor is recognized as a master regulator that controls entry into the S phase of the cell cycle. Its loss leads to uncontrolled cell proliferation and is a hallmark of cancer. RB works by binding to members of the E2F family of transcription factors and recruiting chromatin modifiers to the promoters of E2F target genes. Here we show that RB also localizes to DNA double-strand breaks (DSBs) dependent on E2F1 and ATM kinase activity and promotes DSB repair through homologous recombination (HR), and its loss results in genome instability. RB is necessary for the recruitment of the BRG1 ATPase to DSBs, which stimulates DNA end resection and HR. A knock-in mutation of the ATM phosphorylation site on E2F1 (S29A) prevents the interaction between E2F1 and TopBP1 and recruitment of RB, E2F1, and BRG1 to DSBs. This knock-in mutation also impairs DNA repair, increases genomic instability, and renders mice hypersensitive to IR. Importantly, depletion of RB in osteosarcoma and breast cancer cell lines results in sensitivity to DNA-damaging drugs, which is further exacerbated by poly-ADP ribose polymerase (PARP) inhibitors. We uncovered a novel, nontranscriptional function for RB in HR, which could contribute to genome instability associated with RB loss.
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Affiliation(s)
- Renier Vélez-Cruz
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville Texas 78957, USA
| | - Swarnalatha Manickavinayaham
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville Texas 78957, USA
| | - Anup K Biswas
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville Texas 78957, USA
| | - Regina Weaks Clary
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville Texas 78957, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77225, USA
| | - Tolkappiyan Premkumar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville Texas 78957, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77225, USA
| | - Francesca Cole
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville Texas 78957, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77225, USA
| | - David G Johnson
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville Texas 78957, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77225, USA
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44
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Ghelli Luserna di Rora’ A, Iacobucci I, Martinelli G. The cell cycle checkpoint inhibitors in the treatment of leukemias. J Hematol Oncol 2017; 10:77. [PMID: 28356161 PMCID: PMC5371185 DOI: 10.1186/s13045-017-0443-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/15/2017] [Indexed: 01/25/2023] Open
Abstract
The inhibition of the DNA damage response (DDR) pathway in the treatment of cancers has recently reached an exciting stage with several cell cycle checkpoint inhibitors that are now being tested in several clinical trials in cancer patients. Although the great amount of pre-clinical and clinical data are from the solid tumor experience, only few studies have been done on leukemias using specific cell cycle checkpoint inhibitors. This review aims to summarize the most recent data found on the biological mechanisms of the response to DNA damages highlighting the role of the different elements of the DDR pathway in normal and cancer cells and focusing on the main genetic alteration or aberrant gene expression that has been found on acute and chronic leukemias. This review, for the first time, outlines the most important pre-clinical and clinical data available on the efficacy of cell cycle checkpoint inhibitors in single agent and in combination with different agents normally used for the treatment of acute and chronic leukemias.
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Affiliation(s)
| | - I. Iacobucci
- Department of Hematology and Medical Sciences “L. and A. Seràgnoli”, Bologna University, Bologna, Italy
- Present: Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - G. Martinelli
- Department of Hematology and Medical Sciences “L. and A. Seràgnoli”, Bologna University, Bologna, Italy
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45
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Gong Y, Handa N, Kowalczykowski SC, de Lange T. PHF11 promotes DSB resection, ATR signaling, and HR. Genes Dev 2017; 31:46-58. [PMID: 28115467 PMCID: PMC5287112 DOI: 10.1101/gad.291807.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 12/22/2016] [Indexed: 02/05/2023]
Abstract
Resection of double-strand breaks (DSBs) plays a critical role in their detection and appropriate repair. The 3' ssDNA protrusion formed through resection activates the ATR-dependent DNA damage response (DDR) and is required for DSB repair by homologous recombination (HR). Here we report that PHF11 (plant homeodomain finger 11) encodes a previously unknown DDR factor involved in 5' end resection, ATR signaling, and HR. PHF11 was identified based on its association with deprotected telomeres and localized to sites of DNA damage in S phase. Depletion of PHF11 diminished the ATR signaling response to telomere dysfunction and genome-wide DNA damage, reduced end resection at sites of DNA damage, resulted in compromised HR and misrejoining of S-phase DSBs, and increased the sensitivity to DNA-damaging agents. PHF11 interacted with the ssDNA-binding protein RPA and was found in a complex with several nucleases, including the 5' dsDNA exonuclease EXO1. Biochemical experiments demonstrated that PHF11 stimulates EXO1 by overcoming its inhibition by RPA, suggesting that PHF11 acts (in part) by promoting 5' end resection at RPA-bound sites of DNA damage. These findings reveal a role for PHF11 in DSB resection, DNA damage signaling, and DSB repair.
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Affiliation(s)
- Yi Gong
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10065, USA
| | - Naofumi Handa
- Department of Microbiology and Molecular Genetics, University of California at Davis, Davis, California 95616, USA
,Department of Molecular and Cellular Biology, University of California at Davis, Davis, California 95616, USA
| | - Stephen C. Kowalczykowski
- Department of Microbiology and Molecular Genetics, University of California at Davis, Davis, California 95616, USA
,Department of Molecular and Cellular Biology, University of California at Davis, Davis, California 95616, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10065, USA
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46
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Roos WP, Krumm A. The multifaceted influence of histone deacetylases on DNA damage signalling and DNA repair. Nucleic Acids Res 2016; 44:10017-10030. [PMID: 27738139 PMCID: PMC5137451 DOI: 10.1093/nar/gkw922] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/02/2016] [Accepted: 10/05/2016] [Indexed: 12/16/2022] Open
Abstract
Histone/protein deacetylases play multiple roles in regulating gene expression and protein activation and stability. Their deregulation during cancer initiation and progression cause resistance to therapy. Here, we review the role of histone deacetylases (HDACs) and the NAD+ dependent sirtuins (SIRTs) in the DNA damage response (DDR). These lysine deacetylases contribute to DNA repair by base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), non-homologous end joining (NHEJ), homologous recombination (HR) and interstrand crosslink (ICL) repair. Furthermore, we discuss possible mechanisms whereby these histone/protein deacetylases facilitate the switch between DNA double-strand break (DSB) repair pathways, how SIRTs play a central role in the crosstalk between DNA repair and cell death pathways due to their dependence on NAD+, and the influence of small molecule HDAC inhibitors (HDACi) on cancer cell resistance to genotoxin based therapies. Throughout the review, we endeavor to identify the specific HDAC targeted by HDACi leading to therapy sensitization.
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Affiliation(s)
- Wynand Paul Roos
- Institute of Toxicology, Medical Center of the University Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | - Andrea Krumm
- Institute of Toxicology, Medical Center of the University Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
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47
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Legartová S, Sehnalová P, Malyšková B, Küntziger T, Collas P, Cmarko D, Raška I, Sorokin DV, Kozubek S, Bártová E. Localized Movement and Levels of 53BP1 Protein Are Changed by γ-irradiation in PML Deficient Cells. J Cell Biochem 2016; 117:2583-96. [PMID: 27526954 DOI: 10.1002/jcb.25551] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 03/23/2016] [Indexed: 01/07/2023]
Abstract
We studied epigenetics, distribution pattern, kinetics, and diffusion of proteins recruited to spontaneous and γ-radiation-induced DNA lesions. We showed that PML deficiency leads to an increased number of DNA lesions, which was accompanied by changes in histone signature. In PML wt cells, we observed two mobile fractions of 53BP1 protein with distinct diffusion in spontaneous lesions. These protein fractions were not detected in PML-deficient cells, characterized by slow-diffusion of 53BP1. Single particle tracking analysis revealed limited local motion of 53BP1 foci in PML double null cells and local motion 53BP1 foci was even more reduced after γ-irradiation. However, radiation did not change co-localization between 53BP1 nuclear bodies and interchromatin granule-associated zones (IGAZs), nuclear speckles, or chromocenters. This newly observed interaction pattern imply that 53BP1 protein could be a part of not only DNA repair, but also process mediated via components accumulated in IGAZs, nuclear speckles, or paraspeckles. Together, PML deficiency affected local motion of 53BP1 nuclear bodies and changed composition and a number of irradiation-induced foci. J. Cell. Biochem. 117: 2583-2596, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Petra Sehnalová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Barbora Malyšková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | | | - Philippe Collas
- Department of Biochemistry, Institute of Basic Medical Sciences, University of Oslo, Norwegian Center for Stem Cell Research, Oslo, Norway
| | - Dušan Cmarko
- Institute of Cellular Biology and Pathology, the First Faculty of Medicine, Charles University in Prague, Albertov 4, Prague, 128 01, Czech Republic
| | - Ivan Raška
- Institute of Cellular Biology and Pathology, the First Faculty of Medicine, Charles University in Prague, Albertov 4, Prague, 128 01, Czech Republic
| | - Dmitry V Sorokin
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic.,Faculty of Informatics, Masaryk University, Botanická 68a, Brno, 602 00, Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic. .,Institute of Cellular Biology and Pathology, the First Faculty of Medicine, Charles University in Prague, Albertov 4, Prague, 128 01, Czech Republic.
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48
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de Campos-Nebel M, Palmitelli M, González-Cid M. A flow cytometry-based method for a high-throughput analysis of drug-stabilized topoisomerase II cleavage complexes in human cells. Cytometry A 2016; 89:852-60. [PMID: 27517472 DOI: 10.1002/cyto.a.22919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/27/2016] [Accepted: 07/15/2016] [Indexed: 11/08/2022]
Abstract
Topoisomerase II (Top2) is an important target for anticancer therapy. A variety of drugs that poison Top2, including several epipodophyllotoxins, anthracyclines, and anthracenediones, are widely used in the clinic for both hematologic and solid tumors. The poisoning of Top2 involves the formation of a reaction intermediate Top2-DNA, termed Top2 cleavage complex (Top2cc), which is persistent in the presence of the drug and involves a 5' end of DNA covalently bound to a tyrosine from the enzyme through a phosphodiester group. Drug-induced Top2cc leads to Top2 linked-DNA breaks which are the major responsible for their cytotoxicity. While biochemical detection is very laborious, quantification of drug-induced Top2cc by immunofluorescence-based microscopy techniques is time consuming and requires extensive image segmentation for the analysis of a small population of cells. Here, we developed a flow cytometry-based method for the analysis of drug-induced Top2cc. This method allows a rapid analysis of a high number of cells in their cell cycle phase context. Moreover, it can be applied to almost any human cell type, including clinical samples. The methodology is useful for a high-throughput analysis of drugs that poison Top2, allowing not just the discrimination of the Top2 isoform that is targeted but also to track its removal. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
- Marcelo de Campos-Nebel
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET, Buenos Aires, Argentina.
| | - Micaela Palmitelli
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET, Buenos Aires, Argentina
| | - Marcela González-Cid
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET, Buenos Aires, Argentina
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49
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Konishi A, Izumi T, Shimizu S. TRF2 Protein Interacts with Core Histones to Stabilize Chromosome Ends. J Biol Chem 2016; 291:20798-810. [PMID: 27514743 PMCID: PMC5034068 DOI: 10.1074/jbc.m116.719021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Indexed: 12/03/2022] Open
Abstract
Mammalian chromosome ends are protected by a specialized nucleoprotein complex called telomeres. Both shelterin, a telomere-specific multi-protein complex, and higher order telomeric chromatin structures combine to stabilize the chromosome ends. Here, we showed that TRF2, a component of shelterin, binds to core histones to protect chromosome ends from inappropriate DNA damage response and loss of telomeric DNA. The N-terminal Gly/Arg-rich domain (GAR domain) of TRF2 directly binds to the globular domain of core histones. The conserved arginine residues in the GAR domain of TRF2 are required for this interaction. A TRF2 mutant with these arginine residues substituted by alanine lost the ability to protect telomeres and induced rapid telomere shortening caused by the cleavage of a loop structure of the telomeric chromatin. These findings showed a previously unnoticed interaction between the shelterin complex and nucleosomal histones to stabilize the chromosome ends.
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Affiliation(s)
- Akimitsu Konishi
- From the Department of Pathological Cell Biology and Medical Top Track Program, Medical Research Institute, Tokyo Medical and Dental University, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan, the Department of Biochemistry, Gunma University Graduate School of Medicine, 3-39-22 Showa, Maebashi, Gunma 371-8511, Japan, and the Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, New York 10065
| | - Takashi Izumi
- the Department of Biochemistry, Gunma University Graduate School of Medicine, 3-39-22 Showa, Maebashi, Gunma 371-8511, Japan, and
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50
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Kaushik Tiwari M, Adaku N, Peart N, Rogers FA. Triplex structures induce DNA double strand breaks via replication fork collapse in NER deficient cells. Nucleic Acids Res 2016; 44:7742-54. [PMID: 27298253 PMCID: PMC5027492 DOI: 10.1093/nar/gkw515] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 05/31/2016] [Indexed: 12/20/2022] Open
Abstract
Structural alterations in DNA can serve as natural impediments to replication fork stability and progression, resulting in DNA damage and genomic instability. Naturally occurring polypurine mirror repeat sequences in the human genome can create endogenous triplex structures evoking a robust DNA damage response. Failures to recognize or adequately process these genomic lesions can result in loss of genomic integrity. Nucleotide excision repair (NER) proteins have been found to play a prominent role in the recognition and repair of triplex structures. We demonstrate using triplex-forming oligonucleotides that chromosomal triplexes perturb DNA replication fork progression, eventually resulting in fork collapse and the induction of double strand breaks (DSBs). We find that cells deficient in the NER damage recognition proteins, XPA and XPC, accumulate more DSBs in response to chromosomal triplex formation than NER-proficient cells. Furthermore, we demonstrate that XPC-deficient cells are particularly prone to replication-associated DSBs in the presence of triplexes. In the absence of XPA or XPC, deleterious consequences of triplex-induced genomic instability may be averted by activating apoptosis via dual phosphorylation of the H2AX protein. Our results reveal that damage recognition by XPC and XPA is critical to maintaining replication fork integrity and preventing replication fork collapse in the presence of triplex structures.
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Affiliation(s)
- Meetu Kaushik Tiwari
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Nneoma Adaku
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Natoya Peart
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Faye A Rogers
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
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