1
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Mikhova M, Goff NJ, Janovič T, Heyza JR, Meek K, Schmidt JC. Single-molecule imaging reveals the kinetics of non-homologous end-joining in living cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.22.546088. [PMID: 38826211 PMCID: PMC11142080 DOI: 10.1101/2023.06.22.546088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Non-homologous end joining (NHEJ) is the predominant pathway that repairs DNA double-stranded breaks (DSBs) in vertebrates. However, due to challenges in detecting DSBs in living cells, the repair capacity of the NHEJ pathway is unknown. The DNA termini of many DSBs must be processed to allow ligation while minimizing genetic changes that result from break repair. Emerging models propose that DNA termini are first synapsed ~115Å apart in one of several long-range synaptic complexes before transitioning into a short-range synaptic complex that juxtaposes DNA ends to facilitate ligation. The transition from long-range to short-range synaptic complexes involves both conformational and compositional changes of the NHEJ factors bound to the DNA break. Importantly, it is unclear how NHEJ proceeds in vivo because of the challenges involved in analyzing recruitment of NHEJ factors to DSBs over time in living cells. Here, we develop a new approach to study the temporal and compositional dynamics of NHEJ complexes using live cell single-molecule imaging. Our results provide direct evidence for stepwise maturation of the NHEJ complex, pinpoint key regulatory steps in NHEJ progression, and define the overall repair capacity NHEJ in living cells.
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Affiliation(s)
- Mariia Mikhova
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
| | - Noah J. Goff
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing
- Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing
| | - Tomáš Janovič
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
| | - Joshua R. Heyza
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
| | - Katheryn Meek
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing
- Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing
| | - Jens C. Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing
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2
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Stilgoe A, Favre-Bulle IA, Watson ML, Gomez-Godinez V, Berns MW, Preece D, Rubinsztein-Dunlop H. Shining Light in Mechanobiology: Optical Tweezers, Scissors, and Beyond. ACS PHOTONICS 2024; 11:917-940. [PMID: 38523746 PMCID: PMC10958612 DOI: 10.1021/acsphotonics.4c00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/26/2024]
Abstract
Mechanobiology helps us to decipher cell and tissue functions by looking at changes in their mechanical properties that contribute to development, cell differentiation, physiology, and disease. Mechanobiology sits at the interface of biology, physics and engineering. One of the key technologies that enables characterization of properties of cells and tissue is microscopy. Combining microscopy with other quantitative measurement techniques such as optical tweezers and scissors, gives a very powerful tool for unraveling the intricacies of mechanobiology enabling measurement of forces, torques and displacements at play. We review the field of some light based studies of mechanobiology and optical detection of signal transduction ranging from optical micromanipulation-optical tweezers and scissors, advanced fluorescence techniques and optogenentics. In the current perspective paper, we concentrate our efforts on elucidating interesting measurements of forces, torques, positions, viscoelastic properties, and optogenetics inside and outside a cell attained when using structured light in combination with optical tweezers and scissors. We give perspective on the field concentrating on the use of structured light in imaging in combination with tweezers and scissors pointing out how novel developments in quantum imaging in combination with tweezers and scissors can bring to this fast growing field.
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Affiliation(s)
- Alexander
B. Stilgoe
- School of
Mathematics and Physics, The University
of Queensland, Brisbane, 4074, Australia
- ARC
CoE for Engineered Quantum Systems, The
University of Queensland, Brisbane, 4074, Australia
- ARC
CoE in Quantum Biotechnology, The University
of Queensland, 4074, Brisbane, Australia
| | - Itia A. Favre-Bulle
- School of
Mathematics and Physics, The University
of Queensland, Brisbane, 4074, Australia
- Queensland
Brain Institute, The University of Queensland, Brisbane, 4074, Australia
| | - Mark L. Watson
- School of
Mathematics and Physics, The University
of Queensland, Brisbane, 4074, Australia
- ARC
CoE for Engineered Quantum Systems, The
University of Queensland, Brisbane, 4074, Australia
| | - Veronica Gomez-Godinez
- Institute
of Engineering and Medicine, University
of California San Diego, San Diego, California 92093, United States
| | - Michael W. Berns
- Institute
of Engineering and Medicine, University
of California San Diego, San Diego, California 92093, United States
- Beckman
Laser Institute, University of California
Irvine, Irvine, California 92612, United States
| | - Daryl Preece
- Beckman
Laser Institute, University of California
Irvine, Irvine, California 92612, United States
| | - Halina Rubinsztein-Dunlop
- School of
Mathematics and Physics, The University
of Queensland, Brisbane, 4074, Australia
- ARC
CoE for Engineered Quantum Systems, The
University of Queensland, Brisbane, 4074, Australia
- ARC
CoE in Quantum Biotechnology, The University
of Queensland, 4074, Brisbane, Australia
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3
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Pinto Jurado E, Smith R, Bigot N, Chapuis C, Timinszky G, Huet S. The recruitment of ACF1 and SMARCA5 to DNA lesions relies on ADP-ribosylation dependent chromatin unfolding. Mol Biol Cell 2024; 35:br7. [PMID: 38170578 PMCID: PMC10916859 DOI: 10.1091/mbc.e23-07-0281] [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: 07/24/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
ADP-ribosylation signaling orchestrates the recruitment of various repair actors and chromatin remodeling processes promoting access to lesions during the early stages of the DNA damage response. The chromatin remodeler complex ACF, composed of the ATPase subunit SMARCA5/SNF2H and the cofactor ACF1/BAZ1A, is among the factors that accumulate at DNA lesions in an ADP-ribosylation dependent manner. In this work, we show that each subunit of the ACF complex accumulates to DNA breaks independently from its partner. Furthermore, we demonstrate that the recruitment of SMARCA5 and ACF1 to sites of damage is not due to direct binding to the ADP-ribose moieties but due to facilitated DNA binding at relaxed ADP-ribosylated chromatin. Therefore, our work provides new insights regarding the mechanisms underlying the timely accumulation of ACF1 and SMARCA5 to DNA lesions, where they contribute to efficient DNA damage resolution.
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Affiliation(s)
- Eva Pinto Jurado
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes), F-35000 Rennes, France
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, 6720 Szeged, Hungary
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes), F-35000 Rennes, France
| | - Nicolas Bigot
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes), F-35000 Rennes, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes), F-35000 Rennes, France
| | - Gyula Timinszky
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes), F-35000 Rennes, France
- Institut Universitaire de France, F-75000 Paris, France
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4
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Vickridge E, Faraco CCF, Lo F, Rahimian H, Liu Z, Tehrani P, Djerir B, Ramdzan ZM, Leduy L, Maréchal A, Gingras AC, Nepveu A. The function of BCL11B in base excision repair contributes to its dual role as an oncogene and a haplo-insufficient tumor suppressor gene. Nucleic Acids Res 2024; 52:223-242. [PMID: 37956270 PMCID: PMC10783527 DOI: 10.1093/nar/gkad1037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Genetic studies in mice and human cancers established BCL11B as a haploinsufficient tumor suppressor gene. Paradoxically, BCL11B is overexpressed in some human cancers where its knockdown is synthetic lethal. We identified the BCL11B protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro DNA repair assays demonstrated that both BCL11B and a small recombinant BCL11B213-560 protein lacking transcription regulation potential can stimulate the enzymatic activities of two base excision repair (BER) enzymes: NTHL1 and Pol β. In cells, BCL11B is rapidly recruited to sites of DNA damage caused by laser microirradiation. BCL11B knockdown delays, whereas ectopic expression of BCL11B213-560 accelerates, the repair of oxidative DNA damage. Inactivation of one BCL11B allele in TK6 lymphoblastoid cells causes an increase in spontaneous and radiation-induced mutation rates. In turn, ectopic expression of BCL11B213-560 cooperates with the RAS oncogene in cell transformation by reducing DNA damage and cellular senescence. These findings indicate that BCL11B functions as a BER accessory factor, safeguarding normal cells from acquiring mutations. Paradoxically, it also enables the survival of cancer cells that would otherwise undergo senescence or apoptosis due to oxidative DNA damage resulting from the elevated production of reactive oxygen species.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Camila C F Faraco
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Fanny Lo
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Hedyeh Rahimian
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Zi Yang Liu
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Payman S Tehrani
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario Canada
| | - Billel Djerir
- Department of Biology and Cancer Research Institute, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Zubaidah M Ramdzan
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Alexandre Maréchal
- Department of Biology and Cancer Research Institute, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alain Nepveu
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Medicine, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Oncology, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
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5
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Danovski G, Dyankova-Danovska T, Stamatov R, Aleksandrov R, Kanev PB, Stoynov S. CellTool: An Open-Source Software Combining Bio-Image Analysis and Mathematical Modeling for the Study of DNA Repair Dynamics. Int J Mol Sci 2023; 24:16784. [PMID: 38069107 PMCID: PMC10706408 DOI: 10.3390/ijms242316784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Elucidating the dynamics of DNA repair proteins is essential to understanding the mechanisms that preserve genomic stability and prevent carcinogenesis. However, the measurement and modeling of protein dynamics at DNA lesions via currently available image analysis tools is cumbersome. Therefore, we developed CellTool-a stand-alone open-source software with a graphical user interface for the analysis of time-lapse microscopy images. It combines data management, image processing, mathematical modeling, and graphical presentation of data in a single package. Multiple image filters, segmentation, and particle tracking algorithms, combined with direct visualization of the obtained results, make CellTool an ideal application for the comprehensive analysis of DNA repair protein dynamics. This software enables the fitting of obtained kinetic data to predefined or custom mathematical models. Importantly, CellTool provides a platform for easy implementation of custom image analysis packages written in a variety of programing languages. Using CellTool, we demonstrate that the ALKB homolog 2 (ALKBH2) demethylase is excluded from DNA damage sites despite recruitment of its putative interaction partner proliferating cell nuclear antigen (PCNA). Further, CellTool facilitates the straightforward fluorescence recovery after photobleaching (FRAP) analysis of BRCA1 associated RING domain 1 (BARD1) exchange at complex DNA lesions. In summary, the software presented herein enables the time-efficient analysis of a wide range of time-lapse microscopy experiments through a user-friendly interface.
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Affiliation(s)
| | | | | | | | | | - Stoyno Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl. 21, 1113 Sofia, Bulgaria; (T.D.-D.); (R.S.); (R.A.); (P.-B.K.)
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6
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Heemskerk T, van de Kamp G, Essers J, Kanaar R, Paul MW. Multi-scale cellular imaging of DNA double strand break repair. DNA Repair (Amst) 2023; 131:103570. [PMID: 37734176 DOI: 10.1016/j.dnarep.2023.103570] [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: 04/30/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Live-cell and high-resolution fluorescence microscopy are powerful tools to study the organization and dynamics of DNA double-strand break repair foci and specific repair proteins in single cells. This requires specific induction of DNA double-strand breaks and fluorescent markers to follow the DNA lesions in living cells. In this review, where we focused on mammalian cell studies, we discuss different methods to induce DNA double-strand breaks, how to visualize and quantify repair foci in living cells., We describe different (live-cell) imaging modalities that can reveal details of the DNA double-strand break repair process across multiple time and spatial scales. In addition, recent developments are discussed in super-resolution imaging and single-molecule tracking, and how these technologies can be applied to elucidate details on structural compositions or dynamics of DNA double-strand break repair.
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Affiliation(s)
- Tim Heemskerk
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Gerarda van de Kamp
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Radiotherapy, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Maarten W Paul
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.
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7
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Cintori L, Di Guilmi AM, Canitrot Y, Huet S, Campalans A. Spatio-temporal dynamics of the DNA glycosylase OGG1 in finding and processing 8-oxoguanine. DNA Repair (Amst) 2023; 129:103550. [PMID: 37542751 DOI: 10.1016/j.dnarep.2023.103550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023]
Abstract
OGG1 is the DNA glycosylase responsible for the removal of the oxidative lesion 8-oxoguanine (8-oxoG) from DNA. The recognition of this lesion by OGG1 is a complex process that involves scanning the DNA for the presence of 8-oxoG, followed by recognition and lesion removal. Structural data have shown that OGG1 evolves through different stages of conformation onto the DNA, corresponding to elementary steps of the 8-oxoG recognition and extrusion from the double helix. Single-molecule studies of OGG1 on naked DNA have shown that OGG1 slides in persistent contact with the DNA, displaying different binding states probably corresponding to the different conformation stages. However, in cells, the DNA is not naked and OGG1 has to navigate into a complex and highly crowded environment within the nucleus. To ensure rapid detection of 8-oxoG, OGG1 alternates between 3D diffusion and sliding along the DNA. This process is regulated by the local chromatin state but also by protein co-factors that could facilitate the detection of oxidized lesions. We will review here the different methods that have been used over the last years to better understand how OGG1 detects and process 8-oxoG lesions.
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Affiliation(s)
- Luana Cintori
- Molecular, Cellular and Developmental Biology unit, Centre de Biologie Integrative, University of Toulouse, CNRS, F-31062 Toulouse, France
| | - Anne-Marie Di Guilmi
- Université de Paris-Cite, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France; Université Paris-Saclay, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | - Yvan Canitrot
- Molecular, Cellular and Developmental Biology unit, Centre de Biologie Integrative, University of Toulouse, CNRS, F-31062 Toulouse, France
| | - Sebastien Huet
- Université Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, ´ Sante, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France; Institut Universitaire de France, Paris, France
| | - Anna Campalans
- Université de Paris-Cite, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France; Université Paris-Saclay, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France.
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8
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Heyza JR, Mikhova M, Schmidt JC. Live cell single-molecule imaging to study DNA repair in human cells. DNA Repair (Amst) 2023; 129:103540. [PMID: 37467632 PMCID: PMC10530516 DOI: 10.1016/j.dnarep.2023.103540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023]
Abstract
The genetic material in human cells is continuously exposed to a wide variety of insults that can induce different DNA lesions. To maintain genomic stability and prevent potentially deleterious genetic changes caused by DNA damage, mammalian cells have evolved a number of pathways that repair specific types of DNA damage. These DNA repair pathways vary in their accuracy, some providing high-fidelity repair while others are error-prone and are only activated as a last resort. Adding additional complexity to cellular mechanisms of DNA repair is the DNA damage response which is a sophisticated a signaling network that coordinates repair outcomes, cell-cycle checkpoint activation, and cell fate decisions. As a result of the sheer complexity of the various DNA repair pathways and the DNA damage response there are large gaps in our understanding of the molecular mechanisms underlying DNA damage repair in human cells. A key unaddressed question is how the dynamic recruitment of DNA repair factors contributes to repair kinetics and repair pathway choice in human cells. Methodological advances in live cell single-molecule imaging over the last decade now allow researchers to directly observe and analyze the dynamics of DNA repair proteins in living cells with high spatiotemporal resolution. Live cell single-molecule imaging combined with single-particle tracking can provide direct insight into the biochemical reactions that control DNA repair and has the power to identify previously unobservable processes in living cells. This review summarizes the main considerations for experimental design and execution for live cell single-molecule imaging experiments and describes how they can be used to define the molecular mechanisms of DNA damage repair in mammalian cells.
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Affiliation(s)
- Joshua R Heyza
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Mariia Mikhova
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Jens C Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI, USA.
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D’Augustin O, Gaudon V, Siberchicot C, Smith R, Chapuis C, Depagne J, Veaute X, Busso D, Di Guilmi AM, Castaing B, Radicella JP, Campalans A, Huet S. Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells. Nucleic Acids Res 2023; 51:4942-4958. [PMID: 37021552 PMCID: PMC10250219 DOI: 10.1093/nar/gkad243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 02/28/2023] [Accepted: 03/24/2023] [Indexed: 04/07/2023] Open
Abstract
The DNA-glycosylase OGG1 oversees the detection and clearance of the 7,8-dihydro-8-oxoguanine (8-oxoG), which is the most frequent form of oxidized base in the genome. This lesion is deeply buried within the double-helix and its detection requires careful inspection of the bases by OGG1 via a mechanism that remains only partially understood. By analyzing OGG1 dynamics in the nucleus of living human cells, we demonstrate that the glycosylase constantly samples the DNA by rapidly alternating between diffusion within the nucleoplasm and short transits on the DNA. This sampling process, that we find to be tightly regulated by the conserved residue G245, is crucial for the rapid recruitment of OGG1 at oxidative lesions induced by laser micro-irradiation. Furthermore, we show that residues Y203, N149 and N150, while being all involved in early stages of 8-oxoG probing by OGG1 based on previous structural data, differentially regulate the sampling of the DNA and recruitment to oxidative lesions.
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Affiliation(s)
- Ostiane D’Augustin
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France
- Université de Paris-Cité, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | | | - Capucine Siberchicot
- Université de Paris-Cité, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France
| | - Jordane Depagne
- Université de Paris-Cité, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
| | - Xavier Veaute
- Université de Paris-Cité, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
| | - Didier Busso
- Université de Paris-Cité, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA/IBFJ/IRCM/CIGEx, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
| | - Anne-Marie Di Guilmi
- Université de Paris-Cité, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | | | - J Pablo Radicella
- Université de Paris-Cité, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | - Anna Campalans
- Université de Paris-Cité, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, CEA/IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France
- Institut Universitaire de France, Paris, France
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10
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Fluorescence and phosphorescence lifetime imaging reveals a significant cell nuclear viscosity and refractive index changes upon DNA damage. Sci Rep 2023; 13:422. [PMID: 36624137 PMCID: PMC9829731 DOI: 10.1038/s41598-022-26880-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Cytoplasmic viscosity is a crucial parameter in determining rates of diffusion-limited reactions. Changes in viscosity are associated with several diseases, whilst nuclear viscosity determines gene integrity, regulation and expression. Yet how drugs including DNA-damaging agents affect viscosity is unknown. We demonstrate the use of a platinum complex, Pt[L]Cl, that localizes efficiently mostly in the nucleus as a probe for nuclear viscosity. The phosphorescence lifetime of Pt[L]Cl is sensitive to viscosity and provides an excellent tool to investigate the impact of DNA damage. We show using Fluorescence Lifetime Imaging (FLIM) that the lifetime of both green and red fluorescent proteins (FP) are also sensitive to changes in cellular viscosity and refractive index. However, Pt[L]Cl proved to be a more sensitive viscosity probe, by virtue of microsecond phosphorescence lifetime versus nanosecond fluorescence lifetime of FP, hence greater sensitivity to bimolecular reactions. DNA damage was inflicted by either a two-photon excitation, one-photon excitation microbeam and X-rays. DNA damage of live cells causes significant increase in the lifetime of either Pt[L]Cl (HeLa cells, 12.5-14.1 µs) or intracellularly expressed mCherry (HEK293 cells, 1.54-1.67 ns), but a decrease in fluorescence lifetime of GFP from 2.65 to 2.29 ns (in V15B cells). These values represent a viscosity change from 8.59 to 20.56 cP as well as significant changes in the refractive index (RI), according to independent calibration. Interestingly DNA damage localized to a submicron region following a laser microbeam induction showed a whole cell viscosity change, with those in the nucleus being greater than the cytoplasm. We also found evidence of a by-stander effect, whereby adjacent un-irradiated cells also showed nuclear viscosity change. Finally, an increase in viscosity following DNA damage was also observed in bacterial cells with an over-expressed mNeonGreen FP, evidenced by the change in its lifetime from 2.8 to 2.4 ns.
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11
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Efficacy of Low-Level Laser Therapy in a Rabbit Model of Rhinosinusitis. Int J Mol Sci 2023; 24:ijms24010760. [PMID: 36614203 PMCID: PMC9820841 DOI: 10.3390/ijms24010760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023] Open
Abstract
Little is known about alternative treatment options for rhinosinusitis (RS). We aimed to evaluate the efficacy of low-level laser therapy (LLLT) for RS in experimentally induced rabbit models of RS. A total of 18 rabbits were divided into four groups: a negative control group (n = 3), an RS group without treatment (n = 5, positive control group), an RS group with natural recovery (n = 5, natural recovery group), and an RS group with laser irradiation (n = 5, laser-treated group). Computed tomography and histopathological staining were performed for each group. mRNA and protein expression levels of local cytokines (IFN-γ, IL-17, and IL-5) were also measured. Tissue inflammation revealed a significant improvement in the laser-treated group compared with the RS and natural recovery groups (p < 0.01). In addition, sinus opacification in the CT scans and cytokine expression was reduced in the laser-treated group, though without statistical significance. LLLT could be an effective option for the management of RS concerning radiological, histological, and molecular parameters.
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12
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NEIL3 contributes to the Fanconi anemia/BRCA pathway by promoting the downstream double-strand break repair step. Cell Rep 2022; 41:111600. [PMID: 36351389 DOI: 10.1016/j.celrep.2022.111600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/30/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022] Open
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13
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Dikec J, Bechoua N, Winckler P, Perrier-Cornet JM. Effects of pulsed near infrared light (NIR) on Bacillus subtilis spores. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 234:112530. [PMID: 35930949 DOI: 10.1016/j.jphotobiol.2022.112530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
In this study, we develop a characterization of bacterial spore resistance to NIR pulsed light under modalities traditionally used in multiphoton microscopy. Energy dose and laser power are both key parameters in spore and bacterial cell inactivation. Surprisingly, spores and vegetative cells seem to show a similar sensitivity to pulsed NIR, spores being only 2-fold more resistant than their vegetative counterparts. This work enables us to eliminate certain hypotheses concerning the main driver of spore inactivation processes. Our findings suggest that damage leading to inactivation is mainly caused by photochemical reactions characterized by multiple possible pathways, including DNA damage or oxidation processes.
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Affiliation(s)
- J Dikec
- UMR Procédés Alimentaires et Microbiologiques, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1, Esplanade Erasme, 21000 Dijon, France
| | - N Bechoua
- UMR Procédés Alimentaires et Microbiologiques, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1, Esplanade Erasme, 21000 Dijon, France
| | - P Winckler
- UMR Procédés Alimentaires et Microbiologiques, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1, Esplanade Erasme, 21000 Dijon, France; Dimacell Imaging Facility, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1 Esplanade Erasme, 21000 Dijon, France
| | - J M Perrier-Cornet
- UMR Procédés Alimentaires et Microbiologiques, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1, Esplanade Erasme, 21000 Dijon, France; Dimacell Imaging Facility, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1 Esplanade Erasme, 21000 Dijon, France.
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14
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Angelov D, Boopathi R, Lone IN, Menoni H, Dimitrov S, Cadet J. Capturing Protein-Nucleic Acid Interactions by High-Intensity Laser-Induced Covalent Crosslinking. Photochem Photobiol 2022; 99:296-312. [PMID: 35997098 DOI: 10.1111/php.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Interactions of DNA with structural proteins such as histones, regulatory proteins, and enzymes play a crucial role in major cellular processes such as transcription, replication and repair. The in vivo mapping and characterization of the binding sites of the involved biomolecules are of primary importance for a better understanding of genomic deployment that is implicated in tissue and developmental stage-specific gene expression regulation. The most powerful and commonly used approach to date is immunoprecipitation of chemically cross-linked chromatin (XChIP) coupled with sequencing analysis (ChIP-seq). While the resolution and the sensitivity of the high-throughput sequencing techniques have been constantly improved little progress has been achieved in the crosslinking step. Because of its low efficiency the use of the conventional UVC lamps remains very limited while the formaldehyde method was established as the "gold standard" crosslinking agent. Efficient biphotonic crosslinking of directly interacting nucleic acid-protein complexes by a single short UV laser pulse has been introduced as an innovative technique for overcoming limitations of conventionally used chemical and photochemical approaches. In this survey, the main available methods including the laser approach are critically reviewed for their ability to generate DNA-protein crosslinks in vitro model systems and cells.
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Affiliation(s)
- Dimitar Angelov
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, CNRS UMR 5239, 46 Allée d'Italie, 69007, Lyon, France.,Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balçova, Izmir 35330, Turkey
| | - Ramachandran Boopathi
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, CNRS UMR 5239, 46 Allée d'Italie, 69007, Lyon, France.,Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balçova, Izmir 35330, Turkey
| | - Hervé Menoni
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France
| | - Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
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15
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Prasetyanto EA, Wasisto HS, Septiadi D. Cellular lasers for cell imaging and biosensing. Acta Biomater 2022; 143:39-51. [PMID: 35314365 DOI: 10.1016/j.actbio.2022.03.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/08/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
The possibility to produce laser action involving biomaterials, in particular (single) biological cells, has fostered the development of cellular lasers as a novel approach in biophotonics. In this respect, cells that are engineered to carry gain medium (e.g., fluorescent dyes or proteins) are placed inside an optical cavity (i.e., typically a sandwich of highly reflective mirrors), allowing the generation of stimulated emission upon sufficient optical pumping. In another scenario, micron-sized optical resonators supporting whispering-gallery mode (WGM) or semiconductor-based laser probes can be internalized by the cells and support light amplification. This review summarizes the recent advances in the fields of biolasers and cellular lasers, and most importantly, highlights their potential applications in the fields of in vitro and in vivo cell imaging and analysis. They include biosensing (e.g., in vitro detection of sodium chloride (NaCl) concentration), cancer cell imaging, laser-emission-based microscope, cell tracking, cell distinction study, and tissue contraction monitoring in zebrafish. Lastly, several fundamental issues in developing cellular lasers including laser probe fabrication, biocompatibility of the system, and alteration of local refractive index of optical cavities due to protein absorption or probe aggregation are described. Cellular lasers are foreseen as a promising tool to study numerous biological and biophysical phenomena. STATEMENT OF SIGNIFICANCE: Biolasers are generation of laser involving biological materials. Biomaterials, including single cells, can be engineered to incorporate laser probes or fluorescent proteins or fluorophores, and the resulting light emission can be coupled to optical resonator, allowing generation of cellular laser emission upon optical pumping. Unlike fluorescence, this stimulated emission is very sensitive and is capable of detecting small alterations in the optical property of the cells and their environment. In this review, recent development and applications of cellular lasers in the fields of in vitro and in vivo cell imaging, cell tracking, biosensing, and cell/tissue analysis are highlighted. Several challenges in developing cellular lasers including probe fabrication and biocompatibility as well as alteration of cellular environment are explained.
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Affiliation(s)
- Eko Adi Prasetyanto
- Department of Pharmacy, School of Medicine and Health Sciences, Atma Jaya Catholic University, Jl. Pluit Raya 2, Jakarta 14440, Indonesia
| | | | - Dedy Septiadi
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, Fribourg 1700, Switzerland.
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16
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Rawal CC, Butova NL, Mitra A, Chiolo I. An Expanding Toolkit for Heterochromatin Repair Studies. Genes (Basel) 2022; 13:genes13030529. [PMID: 35328082 PMCID: PMC8955653 DOI: 10.3390/genes13030529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/04/2022] Open
Abstract
Pericentromeric heterochromatin is mostly composed of repetitive DNA sequences prone to aberrant recombination. Cells have developed highly specialized mechanisms to enable ‘safe’ homologous recombination (HR) repair while preventing aberrant recombination in this domain. Understanding heterochromatin repair responses is essential to understanding the critical mechanisms responsible for genome integrity and tumor suppression. Here, we review the tools, approaches, and methods currently available to investigate double-strand break (DSB) repair in pericentromeric regions, and also suggest how technologies recently developed for euchromatin repair studies can be adapted to characterize responses in heterochromatin. With this ever-growing toolkit, we are witnessing exciting progress in our understanding of how the ‘dark matter’ of the genome is repaired, greatly improving our understanding of genome stability mechanisms.
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17
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Levone BR, Lombardi S, Barabino SM. Laser microirradiation as a tool to investigate the role of liquid-liquid phase separation in DNA damage repair. STAR Protoc 2022; 3:101146. [PMID: 35146448 PMCID: PMC8819395 DOI: 10.1016/j.xpro.2022.101146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Here we describe a protocol for the generation of site-specific DNA damage, including double and single strand breaks, using the 405 nm laser of a confocal microscope in cells pre-sensitized with Hoechst. This is a simple approach, particularly useful to assess the involvement of proteins and the roles of liquid-liquid phase separation in DNA damage repair. Examples of transfection protocol, drug concentrations, and microscopy are provided, although optimization may be needed for specific experimental setups and cell lines used. For complete details on the use and execution of this protocol, please refer to Levone et al. (2021). Protocol for the generation of site-specific DNA damage in living cells Using a 405 nm laser of a confocal microscope in pre-sensitized cells Analysis of the kinetics of proteins in DNA damage repair Analysis of the roles of liquid–liquid phase separation in DNA damage repair
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Affiliation(s)
- Brunno Rocha Levone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20125 Milan, Italy
- Corresponding author
| | - Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20125 Milan, Italy
| | - Silvia M.L. Barabino
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20125 Milan, Italy
- Corresponding author
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18
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Rosin FCP, de Paula Novaes C, dos Santos AF, Deboni MCZ, Corrêa L. Photobiomodulation Therapy Minimises the DNA Damage in 5FU‐treated Gingival Fibroblasts. Photochem Photobiol 2022; 98:1201-1206. [DOI: 10.1111/php.13609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | - Luciana Corrêa
- Pathology Department School of Dentistry University of São Paulo
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19
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Prajapati S, Locatelli M, Sawyer C, Holmes J, Bonin K, Black P, Vidi PA. Characterization and implementation of a miniature X-ray system for live cell microscopy. Mutat Res 2021; 824:111772. [PMID: 34923215 DOI: 10.1016/j.mrfmmm.2021.111772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/03/2021] [Accepted: 12/07/2021] [Indexed: 11/19/2022]
Abstract
The study of radiation effects on biological tissues is a diverse field of research with direct applications to improve human health, in particular in the contexts of radiation therapy and space exploration. Understanding the DNA damage response following radiation exposure, which is a key determinant for mutagenesis, requires reproducible methods for delivering known doses of ionizing radiation (IR) in a controlled environment. Multiple IR sources, including research X-ray and gamma-ray irradiators are routinely used in basic and translational research with cell and animal models. These systems are however not ideal when a high temporal resolution is needed, for example to study early DNA damage responses with live cell microscopy. Here, we characterize the dose rate and beam properties of a commercial, miniature, affordable, and versatile X-ray source (Mini-X). We describe how to use Mini-X on the stage of a fluorescence microscope to deliver high IR dose rates (up to 29 Gy/min) or lower dose rates (≤ 0.1 Gy/min) in live cell imaging experiments. This article provides a blueprint for radiation biology applications with high temporal resolution, with a step-by-step guide to implement a miniature X-ray system on an imaging platform, and the information needed to characterize the system.
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Affiliation(s)
- Surendra Prajapati
- Department of Radiation Physics, UT MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Maëlle Locatelli
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Caleb Sawyer
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Julia Holmes
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Keith Bonin
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27109, USA; Comprehensive Cancer Center of Wake Forest University, USA
| | - Paul Black
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA; Comprehensive Cancer Center of Wake Forest University, USA.
| | - Pierre-Alexandre Vidi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA; Institut de Cancérologie de l'Ouest, 49055, Angers, France; Comprehensive Cancer Center of Wake Forest University, USA.
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20
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Talone B, Bazzarelli M, Schirato A, Dello Vicario F, Viola D, Jacchetti E, Bregonzio M, Raimondi MT, Cerullo G, Polli D. Phototoxicity induced in living HeLa cells by focused femtosecond laser pulses: a data-driven approach. BIOMEDICAL OPTICS EXPRESS 2021; 12:7886-7905. [PMID: 35003873 PMCID: PMC8713694 DOI: 10.1364/boe.441225] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Nonlinear optical microscopy is a powerful label-free imaging technology, providing biochemical and structural information in living cells and tissues. A possible drawback is photodamage induced by high-power ultrashort laser pulses. Here we present an experimental study on thousands of HeLa cells, to characterize the damage induced by focused femtosecond near-infrared laser pulses as a function of laser power, scanning speed and exposure time, in both wide-field and point-scanning illumination configurations. Our data-driven approach offers an interpretation of the underlying damage mechanisms and provides a predictive model that estimates its probability and extension and a safety limit for the working conditions in nonlinear optical microscopy. In particular, we demonstrate that cells can withstand high temperatures for a short amount of time, while they die if exposed for longer times to mild temperatures. It is thus better to illuminate the samples with high irradiances: thanks to the nonlinear imaging mechanism, much stronger signals will be generated, enabling fast imaging and thus avoiding sample photodamage.
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Affiliation(s)
- B. Talone
- Department of Physics, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | | | - A. Schirato
- Department of Physics, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
- Istituto Italiano di Tecnologia, via Morego 30, I- 16163, Genoa, Italy
| | | | - D. Viola
- Department of Physics, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | - E. Jacchetti
- Department of Chemistry, Materials and Chemical Engineering ’G. Natta’, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | - M. Bregonzio
- 3rdPlace SRL, Foro Bonaparte 71, 20121 Milan, Italy
| | - M. T. Raimondi
- Department of Chemistry, Materials and Chemical Engineering ’G. Natta’, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
| | - G. Cerullo
- Department of Physics, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
- Istituto di Fotonica e Nanotecnologie (IFN), Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - D. Polli
- Department of Physics, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milan, Italy
- Istituto di Fotonica e Nanotecnologie (IFN), Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
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21
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Park SH, Kim Y, Ra JS, Wie MW, Kang MS, Kang S, Myung K, Lee KY. Timely termination of repair DNA synthesis by ATAD5 is important in oxidative DNA damage-induced single-strand break repair. Nucleic Acids Res 2021; 49:11746-11764. [PMID: 34718749 PMCID: PMC8599757 DOI: 10.1093/nar/gkab999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Reactive oxygen species (ROS) generate oxidized bases and single-strand breaks (SSBs), which are fixed by base excision repair (BER) and SSB repair (SSBR), respectively. Although excision and repair of damaged bases have been extensively studied, the function of the sliding clamp, proliferating cell nuclear antigen (PCNA), including loading/unloading, remains unclear. We report that, in addition to PCNA loading by replication factor complex C (RFC), timely PCNA unloading by the ATPase family AAA domain-containing protein 5 (ATAD5)-RFC-like complex is important for the repair of ROS-induced SSBs. We found that PCNA was loaded at hydrogen peroxide (H2O2)-generated direct SSBs after the 3'-terminus was converted to the hydroxyl moiety by end-processing enzymes. However, PCNA loading rarely occurred during BER of oxidized or alkylated bases. ATAD5-depleted cells were sensitive to acute H2O2 treatment but not methyl methanesulfonate treatment. Unexpectedly, when PCNA remained on DNA as a result of ATAD5 depletion, H2O2-induced repair DNA synthesis increased in cancerous and normal cells. Based on higher H2O2-induced DNA breakage and SSBR protein enrichment by ATAD5 depletion, we propose that extended repair DNA synthesis increases the likelihood of DNA polymerase stalling, shown by increased PCNA monoubiquitination, and consequently, harmful nick structures are more frequent.
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Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Youyoung Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Min Woo Wie
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
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22
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Madhavan BK, Han Z, Sickmann A, Pepperkok R, Nawroth PP, Kumar V. A laser-mediated photo-manipulative toolbox for generation and real-time monitoring of DNA lesions. STAR Protoc 2021; 2:100700. [PMID: 34401774 PMCID: PMC8350334 DOI: 10.1016/j.xpro.2021.100700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
With the advancement of laser-based microscopy tools, it is now possible to explore mechano-kinetic processes occurring inside the cell. Here, we describe the advanced protocol for studying the DNA repair kinetics in real time using the laser to induce the DNA damage. This protocol can be used for inducing, testing, and studying the repair mechanisms associated with DNA double-strand breaks, interstrand cross-link repair, and single-strand break repair. For complete details on the use and execution of this protocol, please refer to Kumar et al. (2017, 2020).
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Affiliation(s)
- Bindhu K Madhavan
- Department of Internal Medicine-I and Clinical Chemistry, University Hospital of Heidelberg, Im Neuenheimer Feld 410, Heidelberg 69120, Germany
| | - Zhe Han
- Department of Internal Medicine-I and Clinical Chemistry, University Hospital of Heidelberg, Im Neuenheimer Feld 410, Heidelberg 69120, Germany
| | - Albert Sickmann
- Leibniz Institute for Analytical Sciences, Dortmund 44227, Germany
| | - Rainer Pepperkok
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg 69117, Germany
| | - Peter P Nawroth
- Department of Internal Medicine-I and Clinical Chemistry, University Hospital of Heidelberg, Im Neuenheimer Feld 410, Heidelberg 69120, Germany.,German Center for Diabetes Research (DZD), Neuherberg 85764, Germany.,Joint Heidelberg-IDC Translational Diabetes Program, Helmholtz-Zentrum, Heidelberg 69120, Germany
| | - Varun Kumar
- Department of Internal Medicine-I and Clinical Chemistry, University Hospital of Heidelberg, Im Neuenheimer Feld 410, Heidelberg 69120, Germany.,European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg 69117, Germany.,German Center for Diabetes Research (DZD), Neuherberg 85764, Germany
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23
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Babukov Y, Aleksandrov R, Ivanova A, Atemin A, Stoynov S. DNArepairK: An Interactive Database for Exploring the Impact of Anticancer Drugs onto the Dynamics of DNA Repair Proteins. Biomedicines 2021; 9:1238. [PMID: 34572428 PMCID: PMC8470695 DOI: 10.3390/biomedicines9091238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/06/2021] [Accepted: 09/11/2021] [Indexed: 11/23/2022] Open
Abstract
Cells are constantly exposed to numerous mutagens that produce diverse types of DNA lesions. Eukaryotic cells have evolved an impressive array of DNA repair mechanisms that are able to detect and repair these lesions, thus preventing genomic instability. The DNA repair process is subjected to precise spatiotemporal coordination, and repair proteins are recruited to lesions in an orderly fashion, depending on their function. Here, we present DNArepairK, a unique open-access database that contains the kinetics of recruitment and removal of 70 fluorescently tagged DNA repair proteins to complex DNA damage sites in living HeLa Kyoto cells. An interactive graphical representation of the data complemented with live cell imaging movies facilitates straightforward comparisons between the dynamics of proteins contributing to different DNA repair pathways. Notably, most of the proteins included in DNArepairK are represented by their kinetics in both nontreated and PARP1/2 inhibitor-treated (talazoparib) cells, thereby providing an unprecedented overview of the effects of anticancer drugs on the regular dynamics of the DNA damage response. We believe that the exclusive dataset available in DNArepairK will be of value to scientists exploring the DNA damage response but, also, to inform and guide the development and evaluation of novel DNA repair-targeting anticancer drugs.
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Affiliation(s)
- Yordan Babukov
- Faculty of Mathematics and Informatics, Sofia University, St. Kliment Ohridski, 5 James Bourchier Blvd., 1164 Sofia, Bulgaria;
| | - Radoslav Aleksandrov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria; (R.A.); (A.I.); (A.A.)
| | - Aneliya Ivanova
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria; (R.A.); (A.I.); (A.A.)
| | - Aleksandar Atemin
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria; (R.A.); (A.I.); (A.A.)
| | - Stoyno Stoynov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria; (R.A.); (A.I.); (A.A.)
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24
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Zentout S, Smith R, Jacquier M, Huet S. New Methodologies to Study DNA Repair Processes in Space and Time Within Living Cells. Front Cell Dev Biol 2021; 9:730998. [PMID: 34589495 PMCID: PMC8473836 DOI: 10.3389/fcell.2021.730998] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/25/2021] [Indexed: 01/02/2023] Open
Abstract
DNA repair requires a coordinated effort from an array of factors that play different roles in the DNA damage response from recognizing and signaling the presence of a break, creating a repair competent environment, and physically repairing the lesion. Due to the rapid nature of many of these events, live-cell microscopy has become an invaluable method to study this process. In this review we outline commonly used tools to induce DNA damage under the microscope and discuss spatio-temporal analysis tools that can bring added information regarding protein dynamics at sites of damage. In particular, we show how to go beyond the classical analysis of protein recruitment curves to be able to assess the dynamic association of the repair factors with the DNA lesions as well as the target-search strategies used to efficiently find these lesions. Finally, we discuss how the use of mathematical models, combined with experimental evidence, can be used to better interpret the complex dynamics of repair proteins at DNA lesions.
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Affiliation(s)
- Siham Zentout
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
| | - Marine Jacquier
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
- Institut Universitaire de France, Paris, France
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25
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Berzsenyi I, Pantazi V, Borsos BN, Pankotai T. Systematic overview on the most widespread techniques for inducing and visualizing the DNA double-strand breaks. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108397. [PMID: 34893162 DOI: 10.1016/j.mrrev.2021.108397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
DNA double-strand breaks (DSBs) are one of the most frequent causes of initiating cancerous malformations, therefore, to reduce the risk, cells have developed sophisticated DNA repair mechanisms. These pathways ensure proper cellular function and genome integrity. However, any alteration or malfunction during DNA repair can influence cellular homeostasis, as improper recognition of the DNA damage or dysregulation of the repair process can lead to genome instability. Several powerful methods have been established to extend our current knowledge in the field of DNA repair. For this reason, in this review, we focus on the methods used to study DSB repair, and we summarize the advantages and disadvantages of the most commonly used techniques currently available for the site-specific induction of DSBs and the subsequent tracking of the repair processes in human cells. We highlight methods that are suitable for site-specific DSB induction (by restriction endonucleases, CRISPR-mediated DSB induction and laser microirradiation) as well as approaches [e.g., fluorescence-, confocal- and super-resolution microscopy, chromatin immunoprecipitation (ChIP), DSB-labeling and sequencing techniques] to visualize and follow the kinetics of DSB repair.
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Affiliation(s)
- Ivett Berzsenyi
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
| | - Vasiliki Pantazi
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
| | - Barbara N Borsos
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
| | - Tibor Pankotai
- Institute of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, 1 Állomás Street H-6725, Szeged, Hungary.
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26
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Madhavan BK, Han Z, Singh B, Bordt N, Kaymak S, Bandapalli OR, Kihm L, Shahzad K, Isermann B, Herzig S, Nawroth P, Kumar V. Elevated Expression of the RAGE Variant- V in SCLC Mitigates the Effect of Chemotherapeutic Drugs. Cancers (Basel) 2021; 13:cancers13112843. [PMID: 34200336 PMCID: PMC8201239 DOI: 10.3390/cancers13112843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Radiomimetic drugs induce extensive genotoxic insults to their target cells. Irreparable DNA damage leaves cells with the choice between a program leading to cell death or senescence, but not DNA repair. Among the challenges of an advanced stage of small cell lung carcinoma (SCLC), the resistance to radiomimetic drugs is the most prominent one. In SCLC, the initial chemotherapeutic treatment primes cell to modify their DNA repair and cell cycle regulatory systems, using alternative but highly efficient forms of DNA repair and auxiliary factors. This modulated system now bypasses several regulatory controls. Thus, at this stage, cells become resistant to any beneficial effects of chemotherapeutic drugs. In the present study, we observed that variant-V of the receptor for advanced glycation end-products (RAGE) is abundantly expressed in advancing and metastasizing SCLC. Therefore, it may serve as a potential target for specific therapeutic interventions directed to SCLC. Abstract Small cell lung carcinoma (SCLC) is a highly aggressive malignancy with a very high mortality rate. A prominent part of this is because these carcinomas are refractory to chemotherapies, such as etoposide or cisplatin, making effective treatment almost impossible. Here, we report that elevated expression of the RAGE variant-V in SCLC promotes homology-directed DNA DSBs repair when challenged with anti-cancer drugs. This variant exclusively localizes to the nucleus, interacts with members of the double-strand break (DSB) repair machinery and thus promotes the recruitment of DSBs repair factors at the site of damage. Increased expression of this variant thus, promotes timely DNA repair. Congruently, the tumor cells expressing high levels of variant-V can tolerate chemotherapeutic drug treatment better than the RAGE depleted cells. Our findings reveal a yet undisclosed role of the RAGE variant-V in the homology-directed DNA repair. This variant thus can be a potential target to be considered for future therapeutic approaches in advanced SSLC.
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Affiliation(s)
- Bindhu K. Madhavan
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Zhe Han
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Bishal Singh
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Nico Bordt
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Serap Kaymak
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Obul Reddy Bandapalli
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany;
- Medical Faculty, Heidelberg University, 69117 Heidelberg, Germany
| | - Lars Kihm
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Khurrum Shahzad
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany; (K.S.); (B.I.)
| | - Berend Isermann
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany; (K.S.); (B.I.)
| | - Stephan Herzig
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
- Molecular Metabolic Control, Technical University Munich, 80333 Munich, Germany
- Helmholtz Center Munich, Institute for Diabetes and Cancer, D-85764 Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Programm, Helmholtz-Zentrum, 69120 Heidelberg, Germany
| | - Peter Nawroth
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
- Joint Heidelberg-IDC Translational Diabetes Programm, Helmholtz-Zentrum, 69120 Heidelberg, Germany
| | - Varun Kumar
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, 69117 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-56-6960
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27
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Image entropy-based label-free functional characterization of human induced pluripotent stem cell-derived 3D cardiac spheroids. Biosens Bioelectron 2021; 179:113055. [PMID: 33582565 DOI: 10.1016/j.bios.2021.113055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 11/22/2022]
Abstract
Human induced pluripotent stem cell-derived cardiac spheroids (iPSC-CSs) in 3D possess tremendous potential for treating heart diseases and screening drugs for their cardiac effect. The beating pattern (including beating frequency and amplitude) of iPSC-CSs is a direct indicator of their health and function. However, detecting the beating pattern of 3D cardiac spheroid is not well studied and the probes commonly used for labeling cardiomyocytes for their beating pattern detection is toxic during long-term culture. Here, we reveal that the beating pattern of 3D iPSC-CSs can be conveniently detected/quantified by calculating the relative change of entropy in all the frames/images of non-fluorescent optical signal without labeling any cells. The entropy rate superpixel segmentation method is used for image segmentation in frames containing multiple or aggregated iPSC-CSs to identify individual iPSC-CSs, enabling rapid detection/quantification of the beating pattern of each iPSC-CS. Moreover, the responses of iPSC-CSs to both anticancer and cardiac drugs can be reliably detected with the image entropy-based label-free method in terms of their beating patterns. This novel label-free approach may be valuable for convenient and efficient functional evaluation of 3D and 2D cardiac constructs, which is important not only for drug screening but also the advancement of manufacturing functional cardiac constructs to treat heart diseases.
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28
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Harrell K, Day M, Smolikove S. Recruitment of MRE-11 to complex DNA damage is modulated by meiosis-specific chromosome organization. Mutat Res 2021; 822:111743. [PMID: 33975127 DOI: 10.1016/j.mrfmmm.2021.111743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/11/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022]
Abstract
DNA double-strand breaks (DSBs) are one of the most dangerous assaults on the genome, and yet their natural and programmed production are inherent to life. When DSBs arise close together they are particularly deleterious, and their repair may require an altered form of the DNA damage response. Our understanding of how clustered DSBs are repaired in the germline is unknown. Using laser microirradiation, we examine early events in the repair of clustered DSBs in germ cells within Caenorhabditis elegans. We use precise temporal resolution to show how the recruitment of MRE-11 to complex damage is regulated, and that clustered DNA damage can recruit proteins from various repair pathways. Abrogation of non-homologous end joining or COM-1 attenuates the recruitment of MRE-11 through distinct mechanisms. The synaptonemal complex plays both positive and negative regulatory roles in these mutant contexts. These findings indicate that MRE-11 is regulated by modifying its accessibility to chromosomes.
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Affiliation(s)
- Kailey Harrell
- Department of Biology, University of Iowa, Iowa City, IA, 52241, USA
| | - Madison Day
- Department of Biology, University of Iowa, Iowa City, IA, 52241, USA
| | - Sarit Smolikove
- Department of Biology, University of Iowa, Iowa City, IA, 52241, USA.
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29
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Super-resolution mapping of cellular double-strand break resection complexes during homologous recombination. Proc Natl Acad Sci U S A 2021; 118:2021963118. [PMID: 33707212 PMCID: PMC7980414 DOI: 10.1073/pnas.2021963118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Homologous recombination (HR) is a major pathway for repair of DNA double-strand breaks (DSBs). The initial step that drives the HR process is resection of DNA at the DSB, during which a multitude of nucleases, mediators, and signaling proteins accumulates at the damage foci in a manner that remains elusive. Using single-molecule localization super-resolution (SR) imaging assays, we specifically visualize the spatiotemporal behavior of key mediator and nuclease proteins as they resect DNA at single-ended double-strand breaks (seDSBs) formed at collapsed replication forks. By characterizing these associations, we reveal the in vivo dynamics of resection complexes involved in generating the long single-stranded DNA (ssDNA) overhang prior to homology search. We show that 53BP1, a protein known to antagonize HR, is recruited to seDSB foci during early resection but is spatially separated from repair activities. Contemporaneously, CtBP-interacting protein (CtIP) and MRN (MRE11-RAD51-NBS1) associate with seDSBs, interacting with each other and BRCA1. The HR nucleases EXO1 and DNA2 are also recruited and colocalize with each other and with the repair helicase Bloom syndrome protein (BLM), demonstrating multiple simultaneous resection events. Quantification of replication protein A (RPA) accumulation and ssDNA generation shows that resection is completed 2 to 4 h after break induction. However, both BRCA1 and BLM persist later into HR, demonstrating potential roles in homology search and repair resolution. Furthermore, we show that initial recruitment of BRCA1 and removal of Ku are largely independent of MRE11 exonuclease activity but dependent on MRE11 endonuclease activity. Combined, our observations provide a detailed description of resection during HR repair.
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30
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RNF8 ubiquitinates RecQL4 and promotes its dissociation from DNA double strand breaks. Oncogenesis 2021; 10:24. [PMID: 33674555 PMCID: PMC7935965 DOI: 10.1038/s41389-021-00315-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 11/08/2022] Open
Abstract
Ubiquitination-dependent DNA damage response (DDR) signals play a critical role in the cellular choice of DNA damage repair pathways. Human DNA helicase RecQL4 participates in DNA replication and repair, and loss of RecQL4 is associated with autosomal recessive genetic disorders characterized by genomic instability features. In an earlier study, RecQL4 was isolated as a stable complex that contained two ubiquitin ligases of the N-end rule (UBR1 and UBR2). However, it is unknown whether or not RecQL4 ubiquitination status is critical for its DNA repair function. Here, we report that RecQL4 directly interacts with RNF8 (a RING finger ubiquitin E3 ligase), and both co-localize at DNA double-strand break (DSB) sites. Our findings indicate that RNF8 ubiquitinates RecQL4 protein mainly at the lysine sites of 876, 1048, and 1101, thereby facilitating the dissociation of RecQL4 from DSB sites. RecQL4 mutant at ubiquitination sites had a significantly prolonged retention at DSBs, which hinders the recruitment of its direct downstream DSB repair proteins (CtIP & Ku80). Interestingly, reduced DSB repair capacity observed in RecQL4 depleted cells was restored only by the reconstitution of wild-type RecQL4, but not the ubiquitination mutant. Additionally, RecQL4 directly interacts with WRAP53β that is known to recruit RNF8 to DSBs and WRAP53β enhances the association of RecQL4 with RNF8. WRAP53β silencing resulted in a nearly diminished recruitment of RNF8 to DSBs and in a greatly attenuated dissociation of RecQL4 from the DSB sites. Collectively, our study demonstrates that the ubiquitination event mediated by RNF8 constitutes an essential component for RecQL4's function in DSB repair.
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31
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Fu B, He G, Mu W, Li Y, Feng B, Zhang K, Wang H, Zhang J, Zhang S, Jia Z, Shi Y, Li Y, Ding S, Tao X. Laser damage mechanism and in situ observation of stacking fault relaxation in a β-Ga 2O 3 single crystal by the EFG method. CrystEngComm 2021. [DOI: 10.1039/d1ce00131k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We for the first time built up a laser damage mechanism and in situ observed stacking fault relaxation in a β-Ga2O3 single crystal.
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32
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Kaufmann T, Herbert S, Hackl B, Besold JM, Schramek C, Gotzmann J, Elsayad K, Slade D. Direct measurement of protein-protein interactions by FLIM-FRET at UV laser-induced DNA damage sites in living cells. Nucleic Acids Res 2020; 48:e122. [PMID: 33053171 PMCID: PMC7708043 DOI: 10.1093/nar/gkaa859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/04/2020] [Accepted: 09/22/2020] [Indexed: 01/27/2023] Open
Abstract
Protein-protein interactions are essential to ensure timely and precise recruitment of chromatin remodellers and repair factors to DNA damage sites. Conventional analyses of protein-protein interactions at a population level may mask the complexity of interaction dynamics, highlighting the need for a method that enables quantification of DNA damage-dependent interactions at a single-cell level. To this end, we integrated a pulsed UV laser on a confocal fluorescence lifetime imaging (FLIM) microscope to induce localized DNA damage. To quantify protein-protein interactions in live cells, we measured Förster resonance energy transfer (FRET) between mEGFP- and mCherry-tagged proteins, based on the fluorescence lifetime reduction of the mEGFP donor protein. The UV-FLIM-FRET system offers a unique combination of real-time and single-cell quantification of DNA damage-dependent interactions, and can distinguish between direct protein-protein interactions, as opposed to those mediated by chromatin proximity. Using the UV-FLIM-FRET system, we show the dynamic changes in the interaction between poly(ADP-ribose) polymerase 1, amplified in liver cancer 1, X-ray repair cross-complementing protein 1 and tripartite motif containing 33 after DNA damage. This new set-up complements the toolset for studying DNA damage response by providing single-cell quantitative and dynamic information about protein-protein interactions at DNA damage sites.
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Affiliation(s)
- Tanja Kaufmann
- Department of Biochemistry, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria
| | - Sébastien Herbert
- Department of Biochemistry, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria
| | - Benjamin Hackl
- Department of Biochemistry, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria
| | - Johanna Maria Besold
- Department of Biochemistry, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria
| | - Christopher Schramek
- Department of Biochemistry, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria
| | - Josef Gotzmann
- Department of Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Kareem Elsayad
- VBCF Advanced Microscopy Facility, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Dea Slade
- Department of Biochemistry, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria
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Blázquez-Castro A, Fernández-Piqueras J, Santos J. Genetic Material Manipulation and Modification by Optical Trapping and Nanosurgery-A Perspective. Front Bioeng Biotechnol 2020; 8:580937. [PMID: 33072730 PMCID: PMC7530750 DOI: 10.3389/fbioe.2020.580937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/01/2020] [Indexed: 11/13/2022] Open
Abstract
Light can be employed as a tool to alter and manipulate matter in many ways. An example has been the implementation of optical trapping, the so called optical tweezers, in which light can hold and move small objects with 3D control. Of interest for the Life Sciences and Biotechnology is the fact that biological objects in the size range from tens of nanometers to hundreds of microns can be precisely manipulated through this technology. In particular, it has been shown possible to optically trap and move genetic material (DNA and chromatin) using optical tweezers. Also, these biological entities can be severed, rearranged and reconstructed by the combined use of laser scissors and optical tweezers. In this review, the background, current state and future possibilities of optical tweezers and laser scissors to manipulate, rearrange and alter genetic material (DNA, chromatin and chromosomes) will be presented. Sources of undesirable effects by the optical procedure and measures to avoid them will be discussed. In addition, first tentative approaches at cellular-level genetic and organelle surgery, in which genetic material or DNA-carrying organelles are extracted out or introduced into cells, will be presented.
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Affiliation(s)
- Alfonso Blázquez-Castro
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Madrid, Spain.,Genome Dynamics and Function Program, Genome Decoding Unit, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Autonomous University of Madrid, Madrid, Spain
| | - José Fernández-Piqueras
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Madrid, Spain.,Genome Dynamics and Function Program, Genome Decoding Unit, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Autonomous University of Madrid, Madrid, Spain.,Institute of Health Research Jiménez Diaz Foundation, Madrid, Spain.,Consortium for Biomedical Research in Rare Diseases (CIBERER), Carlos III Institute of Health, Madrid, Spain
| | - Javier Santos
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Madrid, Spain.,Genome Dynamics and Function Program, Genome Decoding Unit, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Autonomous University of Madrid, Madrid, Spain.,Institute of Health Research Jiménez Diaz Foundation, Madrid, Spain.,Consortium for Biomedical Research in Rare Diseases (CIBERER), Carlos III Institute of Health, Madrid, Spain
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34
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Aleksandrov R, Hristova R, Stoynov S, Gospodinov A. The Chromatin Response to Double-Strand DNA Breaks and Their Repair. Cells 2020; 9:cells9081853. [PMID: 32784607 PMCID: PMC7464352 DOI: 10.3390/cells9081853] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular DNA is constantly being damaged by numerous internal and external mutagenic factors. Probably the most severe type of insults DNA could suffer are the double-strand DNA breaks (DSBs). They sever both DNA strands and compromise genomic stability, causing deleterious chromosomal aberrations that are implicated in numerous maladies, including cancer. Not surprisingly, cells have evolved several DSB repair pathways encompassing hundreds of different DNA repair proteins to cope with this challenge. In eukaryotic cells, DSB repair is fulfilled in the immensely complex environment of the chromatin. The chromatin is not just a passive background that accommodates the multitude of DNA repair proteins, but it is a highly dynamic and active participant in the repair process. Chromatin alterations, such as changing patterns of histone modifications shaped by numerous histone-modifying enzymes and chromatin remodeling, are pivotal for proficient DSB repair. Dynamic chromatin changes ensure accessibility to the damaged region, recruit DNA repair proteins, and regulate their association and activity, contributing to DSB repair pathway choice and coordination. Given the paramount importance of DSB repair in tumorigenesis and cancer progression, DSB repair has turned into an attractive target for the development of novel anticancer therapies, some of which have already entered the clinic.
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35
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Berns MW. Laser Scissors and Tweezers to Study Chromosomes: A Review. Front Bioeng Biotechnol 2020; 8:721. [PMID: 32850689 PMCID: PMC7401452 DOI: 10.3389/fbioe.2020.00721] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/08/2020] [Indexed: 01/22/2023] Open
Abstract
Starting in 1969 laser scissors have been used to study and manipulate chromosomes in mitotic animal cells. Key studies demonstrated that using the “hot spot” in the center of a focused Gaussian laser beam it was possible to delete the ribosomal genes (secondary constriction), and this deficiency was maintained in clonal daughter cells. It wasn’t until 2020 that it was demonstrated that cells with focal-point damaged chromosomes could replicate due to the cell’s DNA damage repair molecular machinery. A series of studies leading up to this conclusion involved using cells expressing different GFP DNA damage recognition and repair molecules. With the advent of optical tweezers in 1987, laser tweezers have been used to study the behavior and forces on chromosomes in mitotic and meiotic cells. The combination of laser scissors and tweezers were employed since 1991 to study various aspects of chromosome behavior during cell division. These studies involved holding chromosomes in an optical while gradually reducing the laser power until the chromosome recovered their movement toward the cell pole. It was determined in collaborative studies with Prof. Arthur Forer from York University, Toronto, Canada, cells from diverse group vertebrate and invertebrates, that forces necessary to move chromosomes to cell poles during cell division were between 2 and 17pN, orders of magnitude below the 700 pN generally found in the literature.
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Affiliation(s)
- Michael W Berns
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, Irvine, CA, United States.,Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States.,Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States.,Department of Surgery, School of Medicine, University of California, Irvine, Irvine, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, San Diego, CA, United States.,Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
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36
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Jiang S, Williams K, Kong X, Zeng W, Nguyen NV, Ma X, Tawil R, Yokomori K, Mortazavi A. Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei. PLoS Genet 2020; 16:e1008754. [PMID: 32365093 PMCID: PMC7224571 DOI: 10.1371/journal.pgen.1008754] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/14/2020] [Accepted: 04/03/2020] [Indexed: 12/22/2022] Open
Abstract
FSHD is characterized by the misexpression of DUX4 in skeletal muscle. Although DUX4 upregulation is thought to be the pathogenic cause of FSHD, DUX4 is lowly expressed in patient samples, and analysis of the consequences of DUX4 expression has largely relied on artificial overexpression. To better understand the native expression profile of DUX4 and its targets, we performed bulk RNA-seq on a 6-day differentiation time-course in primary FSHD2 patient myoblasts. We identify a set of 54 genes upregulated in FSHD2 cells, termed FSHD-induced genes. Using single-cell and single-nucleus RNA-seq on myoblasts and differentiated myotubes, respectively, we captured, for the first time, DUX4 expressed at the single-nucleus level in a native state. We identified two populations of FSHD myotube nuclei based on low or high enrichment of DUX4 and FSHD-induced genes ("FSHD-Lo" and "FSHD Hi", respectively). FSHD-Hi myotube nuclei coexpress multiple DUX4 target genes including DUXA, LEUTX and ZSCAN4, and also upregulate cell cycle-related genes with significant enrichment of E2F target genes and p53 signaling activation. We found more FSHD-Hi nuclei than DUX4-positive nuclei, and confirmed with in situ RNA/protein detection that DUX4 transcribed in only one or two nuclei is sufficient for DUX4 protein to activate target genes across multiple nuclei within the same myotube. DUXA (the DUX4 paralog) is more widely expressed than DUX4, and depletion of DUXA suppressed the expression of LEUTX and ZSCAN4 in late, but not early, differentiation. The results suggest that the DUXA can take over the role of DUX4 to maintain target gene expression. These results provide a possible explanation as to why it is easier to detect DUX4 target genes than DUX4 itself in patient cells and raise the possibility of a self-sustaining network of gene dysregulation triggered by the limited DUX4 expression.
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Affiliation(s)
- Shan Jiang
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Katherine Williams
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Weihua Zeng
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Nam Viet Nguyen
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Xinyi Ma
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
- * E-mail: (KY); (AM)
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
- * E-mail: (KY); (AM)
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37
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Gomez Godinez V, Kabbara S, Sherman A, Wu T, Cohen S, Kong X, Maravillas-Montero JL, Shi Z, Preece D, Yokomori K, Berns MW. DNA damage induced during mitosis undergoes DNA repair synthesis. PLoS One 2020; 15:e0227849. [PMID: 32343690 PMCID: PMC7188217 DOI: 10.1371/journal.pone.0227849] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/01/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the mitotic DNA damage response (DDR) is critical to our comprehension of cancer, premature aging and developmental disorders which are marked by DNA repair deficiencies. In this study we use a micro-focused laser to induce DNA damage in selected mitotic chromosomes to study the subsequent repair response. Our findings demonstrate that (1) mitotic cells are capable of DNA repair as evidenced by DNA synthesis at damage sites, (2) Repair is attenuated when DNA-PKcs and ATM are simultaneously compromised, (3) Laser damage may permit the observation of previously undetected DDR proteins when damage is elicited by other methods in mitosis, and (4) Twenty five percent of mitotic DNA-damaged cells undergo a subsequent mitosis. Together these findings suggest that mitotic DDR is more complex than previously thought and may involve factors from multiple repair pathways that are better understood in interphase.
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Affiliation(s)
- Veronica Gomez Godinez
- Institute of Engineering in Medicine, University of California-San Diego, San Diego, California, United States of America
| | - Sami Kabbara
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, California, United States of America
- Beckman Laser Institute, University of California-Irvine, Irvine, California, United States of America
| | - Adria Sherman
- Institute of Engineering in Medicine, University of California-San Diego, San Diego, California, United States of America
- Beckman Laser Institute, University of California-Irvine, Irvine, California, United States of America
| | - Tao Wu
- Beckman Laser Institute, University of California-Irvine, Irvine, California, United States of America
- Department of Biomedical Engineering, University of California-Irvine, Irvine, California, United States of America
| | - Shirli Cohen
- Institute of Engineering in Medicine, University of California-San Diego, San Diego, California, United States of America
| | - Xiangduo Kong
- Department of Biological Chemistry, University of California-Irvine, Irvine, California, United States of America
| | | | - Zhixia Shi
- Institute of Engineering in Medicine, University of California-San Diego, San Diego, California, United States of America
| | - Daryl Preece
- Beckman Laser Institute, University of California-Irvine, Irvine, California, United States of America
- Department of Biomedical Engineering, University of California-Irvine, Irvine, California, United States of America
| | - Kyoko Yokomori
- Department of Biological Chemistry, University of California-Irvine, Irvine, California, United States of America
| | - Michael W. Berns
- Institute of Engineering in Medicine, University of California-San Diego, San Diego, California, United States of America
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, California, United States of America
- Beckman Laser Institute, University of California-Irvine, Irvine, California, United States of America
- Department of Biomedical Engineering, University of California-Irvine, Irvine, California, United States of America
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38
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Wang J, Potocny AM, Rosenthal J, Day ES. Gold Nanoshell-Linear Tetrapyrrole Conjugates for Near Infrared-Activated Dual Photodynamic and Photothermal Therapies. ACS OMEGA 2020; 5:926-940. [PMID: 31956847 PMCID: PMC6964518 DOI: 10.1021/acsomega.9b04150] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/12/2019] [Indexed: 05/09/2023]
Abstract
Photodynamic therapy (PDT) is a treatment in which photoactive compounds delivered to cancerous tissues are excited with light and then transfer the absorbed energy to adjacent tissue oxygen molecules to generate toxic singlet oxygen (1O2). As 1O2 is produced only where light and photosensitizers (PSs) are combined, PDT holds promise as a minimally invasive, highly selective treatment for certain cancers. The practical application of PDT requires easily synthesized, water-soluble PSs that have low dark toxicities, high 1O2 quantum yields, and efficient absorption of 650-850 nm near-infrared (NIR) light, which deeply penetrates tissue. We recently developed a linear tetrapyrrole metal complex, Pd[DMBil1]-PEG750, that meets most of these criteria. This complex is remarkably effective as a PS for PDT against triple-negative breast cancer (TNBC) cells but, critically, it does not absorb NIR light, which is necessary to treat deeper tumors. To enable NIR activation, we synthesized a new derivative, Pd[DMBil1]-PEG5000-SH, which bears a thiol functionality that facilitates conjugation to NIR-absorbing gold nanoshells (NSs). Upon excitation with pulsed 800 nm light, NSs emit two-photon-induced photoluminescence spanning 500-700 nm, which can sensitize the attached PSs to initiate PDT. Additionally, NSs produce heat upon 800 nm irradiation, endowing the NS-PS conjugates with an auxiliary photothermal therapeutic (PTT) capability. Here, we demonstrate that NS-PS conjugates are potent mediators of NIR-activated tandem PDT/PTT against TNBC cells in vitro. We show that Pd[DMBil1]-PEG5000-SH retains the photophysical properties of the parent Pd[DMBil1] complex, and that NS-PS generate 1O2 under pulsed 800 nm irradiation, confirming activation of the PSs by photoluminescence emitted from NSs. TNBC cells readily internalize NS PS conjugates, which generate reactive oxygen species in the cells upon pulsed NIR irradiation to damage DNA and induce apoptosis. Together, these findings demonstrate that exploiting photoluminescent NSs as carriers of efficient Pd[DMBil1] PSs is an effective strategy to enable NIR light-activated tandem PDT/PTT.
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Affiliation(s)
- Jianxin Wang
- Department
of Biomedical Engineering, Department of Chemistry and Biochemistry, and Department of
Material Science & Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Andrea M. Potocny
- Department
of Biomedical Engineering, Department of Chemistry and Biochemistry, and Department of
Material Science & Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Joel Rosenthal
- Department
of Biomedical Engineering, Department of Chemistry and Biochemistry, and Department of
Material Science & Engineering, University
of Delaware, Newark, Delaware 19716, United States
- E-mail: (J.R.)
| | - Emily S. Day
- Department
of Biomedical Engineering, Department of Chemistry and Biochemistry, and Department of
Material Science & Engineering, University
of Delaware, Newark, Delaware 19716, United States
- Helen
F. Graham Cancer Center and Research Institute, Newark, Delaware 19713, United States
- E-mail: (E.S.D.)
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39
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Kochan JA, van den Belt M, von der Lippe J, Desclos ECB, Steurer B, Hoebe RA, Scutigliani EM, Verhoeven J, Stap J, Bosch R, Rijpkema M, van Oven C, van Veen HA, Stellingwerf I, Vriend LEM, Marteijn JA, Aten JA, Krawczyk PM. Ultra-soft X-ray system for imaging the early cellular responses to X-ray induced DNA damage. Nucleic Acids Res 2019; 47:e100. [PMID: 31318974 PMCID: PMC6753493 DOI: 10.1093/nar/gkz609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/18/2019] [Accepted: 07/10/2019] [Indexed: 11/14/2022] Open
Abstract
The majority of the proteins involved in processing of DNA double-strand breaks (DSBs) accumulate at the damage sites. Real-time imaging and analysis of these processes, triggered by the so-called microirradiation using UV lasers or heavy particle beams, yielded valuable insights into the underlying DSB repair mechanisms. To study the temporal organization of DSB repair responses triggered by a more clinically-relevant DNA damaging agent, we developed a system coined X-ray multi-microbeam microscope (XM3), capable of simultaneous high dose-rate (micro)irradiation of large numbers of cells with ultra-soft X-rays and imaging of the ensuing cellular responses. Using this setup, we analyzed the changes in real-time kinetics of MRE11, MDC1, RNF8, RNF168 and 53BP1—proteins involved in the signaling axis of mammalian DSB repair—in response to X-ray and UV laser-induced DNA damage, in non-cancerous and cancer cells and in the presence or absence of a photosensitizer. Our results reveal, for the first time, the kinetics of DSB signaling triggered by X-ray microirradiation and establish XM3 as a powerful platform for real-time analysis of cellular DSB repair responses.
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Affiliation(s)
- Jakub A Kochan
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.,Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Matthias van den Belt
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Julia von der Lippe
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Emilie C B Desclos
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Barbara Steurer
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Ron A Hoebe
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Enzo M Scutigliani
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Jan Verhoeven
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Jan Stap
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Ruben Bosch
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Meindert Rijpkema
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Carel van Oven
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Henk A van Veen
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Irene Stellingwerf
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Lianne E M Vriend
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Jurgen A Marteijn
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Jacob A Aten
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Przemek M Krawczyk
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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40
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The Impact of Dose Rate on DNA Double-Strand Break Formation and Repair in Human Lymphocytes Exposed to Fast Neutron Irradiation. Int J Mol Sci 2019; 20:ijms20215350. [PMID: 31661782 PMCID: PMC6862539 DOI: 10.3390/ijms20215350] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/16/2019] [Accepted: 10/19/2019] [Indexed: 12/12/2022] Open
Abstract
The lack of information on how biological systems respond to low-dose and low dose-rate exposures makes it difficult to accurately assess the carcinogenic risks. This is of critical importance to space radiation, which remains a serious concern for long-term manned space exploration. In this study, the γ-H2AX foci assay was used to follow DNA double-strand break (DSB) induction and repair following exposure to neutron irradiation, which is produced as secondary radiation in the space environment. Human lymphocytes were exposed to high dose-rate (HDR: 0.400 Gy/min) and low dose-rate (LDR: 0.015 Gy/min) p(66)/Be(40) neutrons. DNA DSB induction was investigated 30 min post exposure to neutron doses ranging from 0.125 to 2 Gy. Repair kinetics was studied at different time points after a 1 Gy neutron dose. Our results indicated that γ-H2AX foci formation was 40% higher at HDR exposure compared to LDR exposure. The maximum γ-H2AX foci levels decreased gradually to 1.65 ± 0.64 foci/cell (LDR) and 1.29 ± 0.45 (HDR) at 24 h postirradiation, remaining significantly higher than background levels. This illustrates a significant effect of dose rate on neutron-induced DNA damage. While no significant difference was observed in residual DNA damage after 24 h, the DSB repair half-life of LDR exposure was slower than that of HDR exposure. The results give a first indication that the dose rate should be taken into account for cancer risk estimations related to neutrons.
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41
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Siebenwirth C, Greubel C, Drexler GA, Reindl J, Walsh DWM, Schwarz B, Sammer M, Baur I, Pospiech H, Schmid TE, Dollinger G, Friedl AA. Local inhibition of rRNA transcription without nucleolar segregation after targeted ion irradiation of the nucleolus. J Cell Sci 2019; 132:jcs.232181. [PMID: 31492757 PMCID: PMC6803363 DOI: 10.1242/jcs.232181] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/29/2019] [Indexed: 12/18/2022] Open
Abstract
Nucleoli have attracted interest for their role as cellular stress sensors and as potential targets for cancer treatment. The effect of DNA double-strand breaks (DSBs) in nucleoli on rRNA transcription and nucleolar organisation appears to depend on the agent used to introduce DSBs, DSB frequency and the presence (or not) of DSBs outside the nucleoli. To address the controversy, we targeted nucleoli with carbon ions at the ion microbeam SNAKE. Localized ion irradiation with 1-100 carbon ions per point (about 0.3-30 Gy per nucleus) did not lead to overall reduced ribonucleotide incorporation in the targeted nucleolus or other nucleoli of the same cell. However, both 5-ethynyluridine incorporation and Parp1 protein levels were locally decreased at the damaged nucleolar chromatin regions marked by γH2AX, suggesting localized inhibition of rRNA transcription. This locally restricted transcriptional inhibition was not accompanied by nucleolar segregation, a structural reorganisation observed after inhibition of rRNA transcription by treatment with actinomycin D or UV irradiation. The presented data indicate that even multiple complex DSBs do not lead to a pan-nucleolar response if they affect only a subnucleolar region.
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Affiliation(s)
- Christian Siebenwirth
- Bundeswehr Institute of Radiobiology, 80937 Munich, Germany .,Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany.,Department of Radiation Therapy and Radiooncology, Technical University of Munich, 81675 Munich, Germany
| | - Christoph Greubel
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Guido A Drexler
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Judith Reindl
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Dietrich W M Walsh
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Benjamin Schwarz
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Matthias Sammer
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Iris Baur
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Helmut Pospiech
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Thomas E Schmid
- Department of Radiation Therapy and Radiooncology, Technical University of Munich, 81675 Munich, Germany
| | - Günther Dollinger
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Anna A Friedl
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
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42
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Garbrecht J, Hornegger H, Herbert S, Kaufmann T, Gotzmann J, Elsayad K, Slade D. Simultaneous dual-channel imaging to quantify interdependent protein recruitment to laser-induced DNA damage sites. Nucleus 2019; 9:474-491. [PMID: 30205747 PMCID: PMC6284507 DOI: 10.1080/19491034.2018.1516485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Fluorescence microscopy in combination with the induction of localized DNA damage using focused light beams has played a major role in the study of protein recruitment kinetics to DNA damage sites in recent years. Currently published methods are dedicated to the study of single fluorophore/single protein kinetics. However, these methods may be limited when studying the relative recruitment dynamics between two or more proteins due to cell-to-cell variability in gene expression and recruitment kinetics, and are not suitable for comparative analysis of fast-recruiting proteins. To tackle these limitations, we have established a time-lapse fluorescence microscopy method based on simultaneous dual-channel acquisition following UV-A-induced local DNA damage coupled with a standardized image and recruitment analysis workflow. Simultaneous acquisition is achieved by spectrally splitting the emitted light into two light paths, which are simultaneously imaged on two halves of the same camera chip. To validate this method, we studied the recruitment of poly(ADP-ribose) polymerase 1 (PARP1), poly (ADP-ribose) glycohydrolase (PARG), proliferating cell nuclear antigen (PCNA) and the chromatin remodeler ALC1. In accordance with the published data based on single fluorophore imaging, simultaneous dual-channel imaging revealed that PARP1 regulates fast recruitment and dissociation of PARG and that in PARP1-depleted cells PARG and PCNA are recruited with comparable kinetics. This approach is particularly advantageous for analyzing the recruitment sequence of fast-recruiting proteins such as PARP1 and ALC1, and revealed that PARP1 is recruited faster than ALC1. Split-view imaging can be incorporated into any laser microirradiation-adapted microscopy setup together with a recruitment-dedicated image analysis package.
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Affiliation(s)
- Joachim Garbrecht
- a Department of Biochemistry, Max F. Perutz Laboratories , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Harald Hornegger
- a Department of Biochemistry, Max F. Perutz Laboratories , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Sebastien Herbert
- a Department of Biochemistry, Max F. Perutz Laboratories , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Tanja Kaufmann
- a Department of Biochemistry, Max F. Perutz Laboratories , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Josef Gotzmann
- b Department of Medical Biochemistry, Max F. Perutz Laboratories (MFPL) , Medical University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Kareem Elsayad
- c VBCF-Advanced Microscopy , Vienna Biocenter (VBC) , Vienna , Austria
| | - Dea Slade
- a Department of Biochemistry, Max F. Perutz Laboratories , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
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43
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Menoni H, Wienholz F, Theil AF, Janssens RC, Lans H, Campalans A, Radicella JP, Marteijn JA, Vermeulen W. The transcription-coupled DNA repair-initiating protein CSB promotes XRCC1 recruitment to oxidative DNA damage. Nucleic Acids Res 2019; 46:7747-7756. [PMID: 29955842 PMCID: PMC6125634 DOI: 10.1093/nar/gky579] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 06/22/2018] [Indexed: 02/05/2023] Open
Abstract
Transcription-coupled nucleotide excision repair factor Cockayne syndrome protein B (CSB) was suggested to function in the repair of oxidative DNA damage. However thus far, no clear role for CSB in base excision repair (BER), the dedicated pathway to remove abundant oxidative DNA damage, could be established. Using live cell imaging with a laser-assisted procedure to locally induce 8-oxo-7,8-dihydroguanine (8-oxoG) lesions, we previously showed that CSB is recruited to these lesions in a transcription-dependent but NER-independent fashion. Here we showed that recruitment of the preferred 8-oxoG-glycosylase 1 (OGG1) is independent of CSB or active transcription. In contrast, recruitment of the BER-scaffolding protein, X-ray repair cross-complementing protein 1 (XRCC1), to 8-oxoG lesions is stimulated by CSB and transcription. Remarkably, recruitment of XRCC1 to BER-unrelated single strand breaks (SSBs) does not require CSB or transcription. Together, our results suggest a specific transcription-dependent role for CSB in recruiting XRCC1 to BER-generated SSBs, whereas XRCC1 recruitment to SSBs generated independently of BER relies predominantly on PARP activation. Based on our results, we propose a model in which CSB plays a role in facilitating BER progression at transcribed genes, probably to allow XRCC1 recruitment to BER-intermediates masked by RNA polymerase II complexes stalled at these intermediates.
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Affiliation(s)
- Hervé Menoni
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands.,Laboratoire de Biologie et Modélisation de la Cellule (LBMC) CNRS, ENSL, UCBL UMR 5239, Université de Lyon, Ecole Normale Supérieure de Lyon, 69007 Lyon
| | - Franziska Wienholz
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Anna Campalans
- CEA, Institute of Cellular and Molecular Radiobiology, F-96265 Fontenay aux Roses, France.,UMR967 CEA, INSERM, Universités Paris-Diderot et Paris-Sud, F-92265 Fontenay aux Roses, France
| | - J Pablo Radicella
- CEA, Institute of Cellular and Molecular Radiobiology, F-96265 Fontenay aux Roses, France.,UMR967 CEA, INSERM, Universités Paris-Diderot et Paris-Sud, F-92265 Fontenay aux Roses, France
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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Murata MM, Kong X, Moncada E, Chen Y, Imamura H, Wang P, Berns MW, Yokomori K, Digman MA. NAD+ consumption by PARP1 in response to DNA damage triggers metabolic shift critical for damaged cell survival. Mol Biol Cell 2019; 30:2584-2597. [PMID: 31390283 PMCID: PMC6740200 DOI: 10.1091/mbc.e18-10-0650] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA damage signaling is critical for the maintenance of genome integrity and cell fate decision. Poly(ADP-ribose) polymerase 1 (PARP1) is a DNA damage sensor rapidly activated in a damage dose- and complexity-dependent manner playing a critical role in the initial chromatin organization and DNA repair pathway choice at damage sites. However, our understanding of a cell-wide consequence of its activation in damaged cells is still limited. Using the phasor approach to fluorescence lifetime imaging microscopy and fluorescence-based biosensors in combination with laser microirradiation, we found a rapid cell-wide increase of the bound NADH fraction in response to nuclear DNA damage, which is triggered by PARP-dependent NAD+ depletion. This change is linked to the metabolic balance shift to oxidative phosphorylation (oxphos) over glycolysis. Inhibition of oxphos, but not glycolysis, resulted in parthanatos due to rapid PARP-dependent ATP deprivation, indicating that oxphos becomes critical for damaged cell survival. The results reveal the novel prosurvival response to PARP activation through a change in cellular metabolism and demonstrate how unique applications of advanced fluorescence imaging and laser microirradiation-induced DNA damage can be a powerful tool to interrogate damage-induced metabolic changes at high spatiotemporal resolution in a live cell.
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Affiliation(s)
- Michael M Murata
- Department of Biomedical Engineering, School of Engineering, University of California, Irvine, Irvine, CA 92697
| | - Xiangduo Kong
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697
| | - Emmanuel Moncada
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, Irvine, CA 92697
| | - Yumay Chen
- Department of Medicine, School of Medicine, University of California, Irvine, Irvine, CA 92697.,UC Irvine Diabetes Center, University of California, Irvine, Irvine, CA 92697
| | - Hiromi Imamura
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Ping Wang
- Department of Medicine, School of Medicine, University of California, Irvine, Irvine, CA 92697.,UC Irvine Diabetes Center, University of California, Irvine, Irvine, CA 92697
| | - Michael W Berns
- Department of Biomedical Engineering, School of Engineering, University of California, Irvine, Irvine, CA 92697.,Beckman Laser Institute and Medical Clinic, University of California, Irvine, Irvine, CA 92697
| | - Kyoko Yokomori
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697
| | - Michelle A Digman
- Department of Biomedical Engineering, School of Engineering, University of California, Irvine, Irvine, CA 92697
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45
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Optical Tweezers: Phototoxicity and Thermal Stress in Cells and Biomolecules. MICROMACHINES 2019; 10:mi10080507. [PMID: 31370251 PMCID: PMC6722566 DOI: 10.3390/mi10080507] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022]
Abstract
For several decades optical tweezers have proven to be an invaluable tool in the study and analysis of myriad biological responses and applications. However, as with every tool, they can have undesirable or damaging effects upon the very sample they are helping to study. In this review the main negative effects of optical tweezers upon biostructures and living systems will be presented. There are three main areas on which the review will focus: linear optical excitation within the tweezers, non-linear photonic effects, and thermal load upon the sampled volume. Additional information is provided on negative mechanical effects of optical traps on biological structures. Strategies to avoid or, at least, minimize these negative effects will be introduced. Finally, all these effects, undesirable for the most, can have positive applications under the right conditions. Some hints in this direction will also be discussed.
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46
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Schaser AJ, Osterberg VR, Dent SE, Stackhouse TL, Wakeham CM, Boutros SW, Weston LJ, Owen N, Weissman TA, Luna E, Raber J, Luk KC, McCullough AK, Woltjer RL, Unni VK. Alpha-synuclein is a DNA binding protein that modulates DNA repair with implications for Lewy body disorders. Sci Rep 2019; 9:10919. [PMID: 31358782 PMCID: PMC6662836 DOI: 10.1038/s41598-019-47227-z] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 07/12/2019] [Indexed: 02/04/2023] Open
Abstract
Alpha-synuclein is a presynaptic protein that forms abnormal cytoplasmic aggregates in Lewy body disorders. Although nuclear alpha-synuclein localization has been described, its function in the nucleus is not well understood. We demonstrate that alpha-synuclein modulates DNA repair. First, alpha-synuclein colocalizes with DNA damage response components within discrete foci in human cells and mouse brain. Removal of alpha-synuclein in human cells leads to increased DNA double-strand break (DSB) levels after bleomycin treatment and a reduced ability to repair these DSBs. Similarly, alpha-synuclein knock-out mice show increased neuronal DSBs that can be rescued by transgenic reintroduction of human alpha-synuclein. Alpha-synuclein binds double-stranded DNA and helps to facilitate the non-homologous end-joining reaction. Using a new, in vivo imaging approach that we developed, we find that serine-129-phosphorylated alpha-synuclein is rapidly recruited to DNA damage sites in living mouse cortex. We find that Lewy inclusion-containing neurons in both mouse model and human-derived patient tissue demonstrate increased DSB levels. Based on these data, we propose a model whereby cytoplasmic aggregation of alpha-synuclein reduces its nuclear levels, increases DSBs, and may contribute to programmed cell death via nuclear loss-of-function. This model could inform development of new treatments for Lewy body disorders by targeting alpha-synuclein-mediated DNA repair mechanisms.
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Affiliation(s)
- Allison J Schaser
- Department of Neurology & Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Valerie R Osterberg
- Department of Neurology & Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Sydney E Dent
- Department of Neurology & Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Teresa L Stackhouse
- Department of Neurology & Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Colin M Wakeham
- Neuroscience Graduate Program, Vollum Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Sydney W Boutros
- Departments of Behavioral Neuroscience, Neurology, and Radiation Medicine and Division of Neuroscience, ONPRC, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Leah J Weston
- Department of Neurology & Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Nichole Owen
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Tamily A Weissman
- Department of Biology, Lewis & Clark College, Portland, OR, 97219, USA
| | - Esteban Luna
- Department of Pathology and Laboratory Medicine and Center for Neurodegenerative Disease Research, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Jacob Raber
- Departments of Behavioral Neuroscience, Neurology, and Radiation Medicine and Division of Neuroscience, ONPRC, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Kelvin C Luk
- Department of Pathology and Laboratory Medicine and Center for Neurodegenerative Disease Research, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Amanda K McCullough
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Randall L Woltjer
- Department of Pathology, Division of Neuropathology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Vivek K Unni
- Department of Neurology & Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR, 97239, USA.
- OHSU Parkinson Center, Oregon Health & Science University, Portland, OR, 97239, USA.
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Abstract
All organisms must protect their genome from constantly occurring DNA damage. To this end, cells have evolved complex pathways for repairing sites of DNA lesions, and multiple in vitro and in vivo techniques have been developed to study these processes. In this review, we discuss the commonly used laser microirradiation method for monitoring the accumulation of repair proteins at DNA damage sites in cells, and we outline several strategies for deriving kinetic models from such experimental data. We discuss an example of how in vitro measurements and in vivo microirradation experiments complement each other to provide insight into the mechanism of PARP1 recruitment to DNA lesions. We also discuss a strategy to combine data obtained for the recruitment of many different proteins in a move toward fully quantitating the spatiotemporal relationships between various damage responses, and we outline potential venues for future development in the field.
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48
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Belmouaddine H, Madugundu GS, Wagner JR, Couairon A, Houde D, Sanche L. DNA Base Modifications Mediated by Femtosecond Laser-Induced Cold Low-Density Plasma in Aqueous Solutions. J Phys Chem Lett 2019; 10:2753-2760. [PMID: 31039309 DOI: 10.1021/acs.jpclett.9b00652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Applications based on near-infrared femtosecond laser-induced plasma in biological materials involve numerous ionization events that inevitably mediate physicochemical effects. Here, the physical chemistry underlying the action of such plasma is characterized in a system of biological interest. We have implemented wavefront shaping techniques to control the generation of laser-induced low electron density plasma channels in DNA aqueous solutions, which minimize the unwanted thermo-mechanical effects associated with plasma of higher density. The number of DNA base modifications per unit of absolute energy deposited by such cold plasma is compared to those induced by either ultraviolet or standard ionizing radiation (γ-rays). Analyses of various photoinduced, oxidative, and reductive DNA base products show that the effects of laser-induced cold plasma are mainly mediated by reactive radical species produced upon the ionization of water, rather than by the direct interaction of the strong laser field with DNA. In the plasma environment, reactions among densely produced primary radicals result in a dramatic decrease in the yields of DNA damages relative to sparse ionizing radiation. This intense radical production also drives the local depletion of oxygen.
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Affiliation(s)
- Hakim Belmouaddine
- Department of Nuclear Medicine and Radiobiology , Faculty of Medicine and Health Sciences, University of Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - Guru S Madugundu
- Department of Nuclear Medicine and Radiobiology , Faculty of Medicine and Health Sciences, University of Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - J Richard Wagner
- Department of Nuclear Medicine and Radiobiology , Faculty of Medicine and Health Sciences, University of Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - Arnaud Couairon
- CPHT, CNRS, Ecole polytechnique, IP Paris , F-91128 Palaiseau , France
| | - Daniel Houde
- Department of Nuclear Medicine and Radiobiology , Faculty of Medicine and Health Sciences, University of Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology , Faculty of Medicine and Health Sciences, University of Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
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49
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Advanced drug delivery systems and artificial skin grafts for skin wound healing. Adv Drug Deliv Rev 2019; 146:209-239. [PMID: 30605737 DOI: 10.1016/j.addr.2018.12.014] [Citation(s) in RCA: 295] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/27/2018] [Accepted: 12/27/2018] [Indexed: 12/14/2022]
Abstract
Cutaneous injuries, especially chronic wounds, burns, and skin wound infection, require painstakingly long-term treatment with an immense financial burden to healthcare systems worldwide. However, clinical management of chronic wounds remains unsatisfactory in many cases. Various strategies including growth factor and gene delivery as well as cell therapy have been used to enhance the healing of non-healing wounds. Drug delivery systems across the nano, micro, and macroscales can extend half-life, improve bioavailability, optimize pharmacokinetics, and decrease dosing frequency of drugs and genes. Replacement of the damaged skin tissue with substitutes comprising cell-laden scaffold can also restore the barrier and regulatory functions of skin at the wound site. This review covers comprehensively the advanced treatment strategies to improve the quality of wound healing.
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50
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Hurst V, Gasser SM. The study of protein recruitment to laser-induced DNA lesions can be distorted by photoconversion of the DNA binding dye Hoechst. F1000Res 2019; 8:104. [PMID: 30828443 PMCID: PMC6392149 DOI: 10.12688/f1000research.17865.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/04/2019] [Indexed: 01/07/2023] Open
Abstract
A commonly used approach for assessing DNA repair factor recruitment in mammalian cells is to induce DNA damage with a laser in the UV or near UV range and follow the local increase of GFP-tagged proteins at the site of damage. Often these measurements are performed in the presence of the blue DNA dye Hoechst, which is used as a photosensitizer. However, a light-induced switch of Hoechst from a blue-light to a green-light emitter will give a false positive signal at the site of damage. Thus, photoconversion signals must be subtracted from the overall green-light emission to determine true recruitment. Here we demonstrate the photoconversion effect and suggest control experiments to exclude false-positive results.
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Affiliation(s)
- Verena Hurst
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, CH-4058, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, CH-4056, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, CH-4058, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, CH-4056, Switzerland
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