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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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2
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De Falco M, De Felice M. Take a Break to Repair: A Dip in the World of Double-Strand Break Repair Mechanisms Pointing the Gaze on Archaea. Int J Mol Sci 2021; 22:ijms222413296. [PMID: 34948099 PMCID: PMC8708640 DOI: 10.3390/ijms222413296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
All organisms have evolved many DNA repair pathways to counteract the different types of DNA damages. The detection of DNA damage leads to distinct cellular responses that bring about cell cycle arrest and the induction of DNA repair mechanisms. In particular, DNA double-strand breaks (DSBs) are extremely toxic for cell survival, that is why cells use specific mechanisms of DNA repair in order to maintain genome stability. The choice among the repair pathways is mainly linked to the cell cycle phases. Indeed, if it occurs in an inappropriate cellular context, it may cause genome rearrangements, giving rise to many types of human diseases, from developmental disorders to cancer. Here, we analyze the most recent remarks about the main pathways of DSB repair with the focus on homologous recombination. A thorough knowledge in DNA repair mechanisms is pivotal for identifying the most accurate treatments in human diseases.
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3
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Topological Analysis of γH2AX and MRE11 Clusters Detected by Localization Microscopy during X-ray-Induced DNA Double-Strand Break Repair. Cancers (Basel) 2021; 13:cancers13215561. [PMID: 34771723 PMCID: PMC8582740 DOI: 10.3390/cancers13215561] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/30/2022] Open
Abstract
DNA double-strand breaks (DSBs), known as the most severe damage in chromatin, were induced in breast cancer cells and normal skin fibroblasts by 2 Gy ionizing photon radiation. In response to DSB induction, phosphorylation of the histone variant H2AX to γH2AX was observed in the form of foci visualized by specific antibodies. By means of super-resolution single-molecule localization microscopy (SMLM), it has been recently shown in a first article about these data that these foci can be separated into clusters of about the same size (diameter ~400 nm). The number of clusters increased with the dose applied and decreased with the repair time. It has also been shown that during the repair period, antibody-labeled MRE11 clusters of about half of the γH2AX cluster diameter were formed inside several γH2AX clusters. MRE11 is part of the MRE11-RAD50-NBS1 (MRN) complex, which is known as a DNA strand resection and broken-end bridging component in homologous recombination repair (HRR) and alternative non-homologous end joining (a-NHEJ). This article is a follow-up of the former ones applying novel procedures of mathematics (topology) and similarity measurements on the data set: to obtain a measure for cluster shape and shape similarities, topological quantifications employing persistent homology were calculated and compared. In addition, based on our findings that γH2AX clusters associated with heterochromatin show a high degree of similarity independently of dose and repair time, these earlier published topological analyses and similarity calculations comparing repair foci within individual cells were extended by topological data averaging (2nd-generation heatmaps) over all cells analyzed at a given repair time point; thereby, the two dimensions (0 and 1) expressed by components and holes were studied separately. Finally, these mean value heatmaps were averaged, in addition. For γH2AX clusters, in both normal fibroblast and MCF-7 cancer cell lines, an increased similarity was found at early time points (up to 60 min) after irradiation for both components and holes of clusters. In contrast, for MRE11, the peak in similarity was found at later time points (2 h up to 48 h) after irradiation. In general, the normal fibroblasts showed quicker phosphorylation of H2AX and recruitment of MRE11 to γH2AX clusters compared to breast cancer cells and a shorter time interval of increased similarity for γH2AX clusters. γH2AX foci and randomly distributed MRE11 molecules naturally occurring in non-irradiated control cells did not show any significant topological similarity.
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4
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Haas KT, Peaucelle A. Protocol for multicolor three-dimensional dSTORM data analysis using MATLAB-based script package Grafeo. STAR Protoc 2021; 2:100808. [PMID: 34541556 PMCID: PMC8437824 DOI: 10.1016/j.xpro.2021.100808] [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: 11/30/2022] Open
Abstract
This protocol describes the step-by-step analysis of the multicolor (one-, two-, or three-color) two- and three-dimensional dSTORM (direct STochastic Optical Reconstruction Microscopy) data using MATLAB-based script package Grafeo. Grafeo primarily uses pointillist data visualization and analysis frameworks, including the nearest neighbors, approach, Voronoi tessellation, Delaunay triangulation, Ripley’s (K, L) and two-point correlation functions, and graph-based clustering. For complete details on the use and execution of this protocol, please refer to Peaucelle et al. (2020), Haas et al., 2018, Haas et al. (2020b). Multicolor 3D dSTORM data visualization using scatter plots and Voronoi Diagrams Procedure for data filtering Spatial statistics, cluster, and colocalization analysis Graph-based cluster analysis with Delaunay triangulation
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Affiliation(s)
- Kalina Tamara Haas
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Alexis Peaucelle
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
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5
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Mhaskar AN, Koornneef L, Zelensky AN, Houtsmuller AB, Baarends WM. High Resolution View on the Regulation of Recombinase Accumulation in Mammalian Meiosis. Front Cell Dev Biol 2021; 9:672191. [PMID: 34109178 PMCID: PMC8181746 DOI: 10.3389/fcell.2021.672191] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 11/19/2022] Open
Abstract
A distinguishing feature of meiotic DNA double-strand breaks (DSBs), compared to DSBs in somatic cells, is the fact that they are induced in a programmed and specifically orchestrated manner, which includes chromatin remodeling prior to DSB induction. In addition, the meiotic homologous recombination (HR) repair process that follows, is different from HR repair of accidental DSBs in somatic cells. For instance, meiotic HR involves preferred use of the homolog instead of the sister chromatid as a repair template and subsequent formation of crossovers and non-crossovers in a tightly regulated manner. An important outcome of this distinct repair pathway is the pairing of homologous chromosomes. Central to the initial steps in homology recognition during meiotic HR is the cooperation between the strand exchange proteins (recombinases) RAD51 and its meiosis-specific paralog DMC1. Despite our understanding of their enzymatic activity, details on the regulation of their assembly and subsequent molecular organization at meiotic DSBs in mammals have remained largely enigmatic. In this review, we summarize recent mouse data on recombinase regulation via meiosis-specific factors. Also, we reflect on bulk “omics” studies of initial meiotic DSB processing, compare these with studies using super-resolution microscopy in single cells, at single DSB sites, and explore the implications of these findings for our understanding of the molecular mechanisms underlying meiotic HR regulation.
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Affiliation(s)
- Aditya N Mhaskar
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands
| | - Lieke Koornneef
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Alex N Zelensky
- Department of Molecular Genetics, Erasmus MC, Rotterdam, Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC, Rotterdam, Netherlands.,Department of Pathology, Erasmus MC, Rotterdam, Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands
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6
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Herbert KJ, Puliyadi R, Prevo R, Rodriguez-Berriguete G, Ryan A, Ramadan K, Higgins GS. Targeting TOPK sensitises tumour cells to radiation-induced damage by enhancing replication stress. Cell Death Differ 2021; 28:1333-1346. [PMID: 33168956 PMCID: PMC8027845 DOI: 10.1038/s41418-020-00655-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 10/22/2020] [Accepted: 10/22/2020] [Indexed: 01/04/2023] Open
Abstract
T-LAK-originated protein kinase (TOPK) overexpression is a feature of multiple cancers, yet is absent from most phenotypically normal tissues. As such, TOPK expression profiling and the development of TOPK-targeting pharmaceutical agents have raised hopes for its future potential in the development of targeted therapeutics. Results presented in this paper confirm the value of TOPK as a potential target for the treatment of solid tumours, and demonstrate the efficacy of a TOPK inhibitor (OTS964) when used in combination with radiation treatment. Using H460 and Calu-6 lung cancer xenograft models, we show that pharmaceutical inhibition of TOPK potentiates the efficacy of fractionated irradiation. Furthermore, we provide in vitro evidence that TOPK plays a hitherto unknown role during S phase, showing that TOPK depletion increases fork stalling and collapse under conditions of replication stress and exogenous DNA damage. Transient knockdown of TOPK was shown to impair recovery from fork stalling and to increase the formation of replication-associated single-stranded DNA foci in H460 lung cancer cells. We also show that TOPK interacts directly with CHK1 and Cdc25c, two key players in the checkpoint signalling pathway activated after replication fork collapse. This study thus provides novel insights into the mechanism by which TOPK activity supports the survival of cancer cells, facilitating checkpoint signalling in response to replication stress and DNA damage.
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Affiliation(s)
- Katharine J Herbert
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Rathi Puliyadi
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Remko Prevo
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Gonzalo Rodriguez-Berriguete
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Anderson Ryan
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Kristijan Ramadan
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Geoff S Higgins
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.
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7
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Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins. Mol Cell 2021; 81:1058-1073.e7. [PMID: 33421363 PMCID: PMC7941204 DOI: 10.1016/j.molcel.2020.12.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/02/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022]
Abstract
Homologous recombination (HR) is an essential DNA double-strand break (DSB) repair mechanism, which is frequently inactivated in cancer. During HR, RAD51 forms nucleoprotein filaments on RPA-coated, resected DNA and catalyzes strand invasion into homologous duplex DNA. How RAD51 displaces RPA and assembles into long HR-proficient filaments remains uncertain. Here, we employed single-molecule imaging to investigate the mechanism of nematode RAD-51 filament growth in the presence of BRC-2 (BRCA2) and RAD-51 paralogs, RFS-1/RIP-1. BRC-2 nucleates RAD-51 on RPA-coated DNA, whereas RFS-1/RIP-1 acts as a "chaperone" to promote 3' to 5' filament growth via highly dynamic engagement with 5' filament ends. Inhibiting ATPase or mutation in the RFS-1 Walker box leads to RFS-1/RIP-1 retention on RAD-51 filaments and hinders growth. The rfs-1 Walker box mutants display sensitivity to DNA damage and accumulate RAD-51 complexes non-functional for HR in vivo. Our work reveals the mechanism of RAD-51 nucleation and filament growth in the presence of recombination mediators.
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8
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Scott DE, Francis-Newton NJ, Marsh ME, Coyne AG, Fischer G, Moschetti T, Bayly AR, Sharpe TD, Haas KT, Barber L, Valenzano CR, Srinivasan R, Huggins DJ, Lee M, Emery A, Hardwick B, Ehebauer M, Dagostin C, Esposito A, Pellegrini L, Perrior T, McKenzie G, Blundell TL, Hyvönen M, Skidmore J, Venkitaraman AR, Abell C. A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death. Cell Chem Biol 2021; 28:835-847.e5. [PMID: 33662256 PMCID: PMC8219027 DOI: 10.1016/j.chembiol.2021.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/18/2020] [Accepted: 02/03/2021] [Indexed: 12/11/2022]
Abstract
BRCA2 controls RAD51 recombinase during homologous DNA recombination (HDR) through eight evolutionarily conserved BRC repeats, which individually engage RAD51 via the motif Phe-x-x-Ala. Using structure-guided molecular design, templated on a monomeric thermostable chimera between human RAD51 and archaeal RadA, we identify CAM833, a 529 Da orthosteric inhibitor of RAD51:BRC with a Kd of 366 nM. The quinoline of CAM833 occupies a hotspot, the Phe-binding pocket on RAD51 and the methyl of the substituted α-methylbenzyl group occupies the Ala-binding pocket. In cells, CAM833 diminishes formation of damage-induced RAD51 nuclear foci; inhibits RAD51 molecular clustering, suppressing extended RAD51 filament assembly; potentiates cytotoxicity by ionizing radiation, augmenting 4N cell-cycle arrest and apoptotic cell death and works with poly-ADP ribose polymerase (PARP)1 inhibitors to suppress growth in BRCA2-wildtype cells. Thus, chemical inhibition of the protein-protein interaction between BRCA2 and RAD51 disrupts HDR and potentiates DNA damage-induced cell death, with implications for cancer therapy.
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Affiliation(s)
- Duncan E Scott
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Nicola J Francis-Newton
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - May E Marsh
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Tommaso Moschetti
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Andrew R Bayly
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Timothy D Sharpe
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kalina T Haas
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Lorraine Barber
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Chiara R Valenzano
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rajavel Srinivasan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - David J Huggins
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Miyoung Lee
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Amy Emery
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Bryn Hardwick
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Matthias Ehebauer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Claudio Dagostin
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Alessandro Esposito
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Trevor Perrior
- Excellium Consulting, Brook Farm Barn, Lackford, Bury St Edmunds IP28 6HL, UK
| | - Grahame McKenzie
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - John Skidmore
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK.
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Activation of DNA damage response signaling in mammalian cells by ionizing radiation. Free Radic Res 2021; 55:581-594. [PMID: 33455476 DOI: 10.1080/10715762.2021.1876853] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cellular responses to DNA damage are fundamental to preserve genomic integrity during various endogenous and exogenous stresses. Following radiation therapy and chemotherapy, this DNA damage response (DDR) also determines development of carcinogenesis and therapeutic outcome. In humans, DNA damage activates a robust network of signal transduction cascades, driven primarily through phosphorylation events. These responses primarily involve two key non-redundant signal transducing proteins of phosphatidylinositol 3-kinase-like (PIKK) family - ATR and ATM, and their downstream kinases (hChk1 and hChk2). They further phosphorylate effectors proteins such as p53, Cdc25A and Cdc25C which function either to activate the DNA damage checkpoints and cell death mechanisms, or DNA repair pathways. Identification of molecular pathways that determine signaling after DNA damage and trigger DNA repair in response to differing types of DNA lesions allows for a far better understanding of the consequences of radiation and chemotherapy on normal and tumor cells. Here we highlight the network of DNA damage response pathways that are activated after treatment with different types of radiation. Further, we discuss regulation of cell cycle checkpoint and DNA repair processes in the context of DDR in response to radiation.
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Peaucelle A, Wightman R, Haas KT. Multicolor 3D-dSTORM Reveals Native-State Ultrastructure of Polysaccharides' Network during Plant Cell Wall Assembly. iScience 2020; 23:101862. [PMID: 33336161 PMCID: PMC7733027 DOI: 10.1016/j.isci.2020.101862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/07/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
The plant cell wall, a form of the extracellular matrix, is a complex and dynamic network of polymers mediating a plethora of physiological functions. How polysaccharides assemble into a coherent and heterogeneous matrix remains mostly undefined. Further progress requires improved molecular-level visualization methods that would gain a deeper understanding of the cell wall nanoarchitecture. dSTORM, a type of super-resolution microscopy, permits quantitative nanoimaging of the cell wall. However, due to the lack of single-cell model systems and the requirement of tissue-level imaging, its use in plant science is almost absent. Here we overcome these limitations; we compare two methods to achieve three-dimensional dSTORM and identify optimal photoswitching dyes for tissue-level multicolor nanoscopy. Combining dSTORM with spatial statistics, we reveal and characterize the ultrastructure of three major polysaccharides, callose, mannan, and cellulose, in the plant cell wall precursor and provide evidence for cellulose structural re-organization related to callose content.
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Affiliation(s)
- Alexis Peaucelle
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Raymond Wightman
- Microscopy Core Facility, Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Kalina Tamara Haas
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
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11
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Haas KT, Rivière M, Wightman R, Peaucelle A. Multitarget Immunohistochemistry for Confocal and Super-resolution Imaging of Plant Cell Wall Polysaccharides. Bio Protoc 2020; 10:e3783. [PMID: 33659438 PMCID: PMC7842508 DOI: 10.21769/bioprotoc.3783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/21/2020] [Accepted: 08/17/2020] [Indexed: 11/02/2022] Open
Abstract
The plant cell wall (PCW) is a pecto-cellulosic extracellular matrix that envelopes the plant cell. By integrating extra-and intra-cellular cues, PCW mediates a plethora of essential physiological functions. Notably, it permits controlled and oriented tissue growth by tuning its local mechano-chemical properties. To refine our knowledge of these essential properties of PCW, we need an appropriate tool for the accurate observation of the native (in muro) structure of the cell wall components. The label-free techniques, such as AFM, EM, FTIR, and Raman microscopy, are used; however, they either do not have the chemical or spatial resolution. Immunolabeling with electron microscopy allows observation of the cell wall nanostructure, however, it is mostly limited to single and, less frequently, multiple labeling. Immunohistochemistry (IHC) is a versatile tool to analyze the distribution and localization of multiple biomolecules in the tissue. The subcellular resolution of chemical changes in the cell wall component can be observed with standard diffraction-limited optical microscopy. Furthermore, novel chemical imaging tools such as multicolor 3D dSTORM (Three-dimensional, direct Stochastic Optical Reconstruction Microscopy) nanoscopy makes it possible to resolve the native structure of the cell wall polymers with nanometer precision and in three dimensions. Here we present a protocol for preparing multi-target immunostaining of the PCW components taking as example Arabidopsis thaliana, Star fruit (Averrhoa carambola), and Maize thin tissue sections. This protocol is compatible with the standard confocal microscope, dSTORM nanoscope, and can also be implemented for other optical nanoscopy such as STED (Stimulated Emission Depletion Microscopy). The protocol can be adapted for any other subcellular compartments, plasma membrane, cytoplasmic, and intracellular organelles.
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Affiliation(s)
- Kalina T. Haas
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Methieu Rivière
- Faculty of Life Sciences, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Raymond Wightman
- Microscopy Core Facility, Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Alexis Peaucelle
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
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12
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Wassing IE, Esashi F. RAD51: Beyond the break. Semin Cell Dev Biol 2020; 113:38-46. [PMID: 32938550 PMCID: PMC8082279 DOI: 10.1016/j.semcdb.2020.08.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/14/2020] [Accepted: 08/28/2020] [Indexed: 01/30/2023]
Abstract
As the primary catalyst of homologous recombination (HR) in vertebrates, RAD51 has been extensively studied in the context of repair of double-stranded DNA breaks (DSBs). With recent advances in the understanding of RAD51 function extending beyond DSBs, the importance of RAD51 throughout DNA metabolism has become increasingly clear. Here we review the suggested roles of RAD51 beyond HR, specifically focusing on their interplay with DNA replication and the maintenance of genomic stability, in which RAD51 function emerges as a double-edged sword.
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Affiliation(s)
- Isabel E Wassing
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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13
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Tang HL, Xu L, Chen XQ. [Bortezomib interferes with DNA repair and exerts synergistic anti-multiple myeloma activity with doxorubicin]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2020; 41:417-421. [PMID: 32447936 PMCID: PMC7364921 DOI: 10.3760/cma.j.issn.0253-2727.2020.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
目的 探讨系统性免疫球蛋白轻链淀粉样变性(AL)初治患者的外周血免疫细胞表型特征及其与临床指标的相关性。 方法 采用流式细胞仪多参数免疫荧光分析技术,对36例AL初诊患者和28名健康供者的外周血单个核细胞的表面抗原CD3、CD56、CD4、CD8、CD25、CD45RA、CD28、CD57及核内抗原FOXP3进行检测和比较。根据梅奥2012分期对AL患者进行分期,比较Ⅰ~Ⅱ、Ⅲ~Ⅳ期患者的免疫细胞表型差异。分析λ轻链型AL患者T细胞亚群比例与多项临床指标的相关性。 结果 AL患者的外周血T(CD3+CD56−)和NKT(CD3+CD56+)细胞比例,T细胞中的CD4+CD8−、CD4−CD8+、Treg(CD4+CD25+FOXP3+)细胞比例与健康供者相比差异无统计学意义(P>0.05)。AL患者的CD4−CD8+细胞中,CD57+细胞的比例较健康供者显著降低(P<0.05),但CD45RA+和CD28+细胞的比例在AL和健康供者间差异无统计学意义。Ⅰ~Ⅱ期和Ⅲ~Ⅳ期AL患者T细胞及其亚群的比例差异无统计学意义(P>0.05)。在λ轻链型AL患者中,外周血CD4−CD8+细胞的比例与24 h尿蛋白和血肌酐呈正相关(P<0.05),与eGFR呈负相关(P<0.05),与其他临床指标无显著相关性。与此相反,CD4+CD8−细胞的比例与eGFR呈正相关,而与24 h尿蛋白和血肌酐呈负相关(P<0.05)。 结论 AL患者外周血的T细胞亚群与健康供者相比差异无统计学意义,但CD8+ T细胞的比例与肾脏损伤程度呈正相关,提示CD8+ T细胞的比例在评估AL患者肾脏预后中具有一定的价值。
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Affiliation(s)
- H L Tang
- Department of Hematology, Xijing Hospital, Air Force Medical University, Hematologic Diseases Center of Chinese People's Liberation Army, Xi'an 710032, China
| | - L Xu
- Department of Hematology, Xijing Hospital, Air Force Medical University, Hematologic Diseases Center of Chinese People's Liberation Army, Xi'an 710032, China
| | - X Q Chen
- Department of Hematology, Xijing Hospital, Air Force Medical University, Hematologic Diseases Center of Chinese People's Liberation Army, Xi'an 710032, China
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14
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Khater IM, Nabi IR, Hamarneh G. A Review of Super-Resolution Single-Molecule Localization Microscopy Cluster Analysis and Quantification Methods. PATTERNS (NEW YORK, N.Y.) 2020; 1:100038. [PMID: 33205106 PMCID: PMC7660399 DOI: 10.1016/j.patter.2020.100038] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-molecule localization microscopy (SMLM) is a relatively new imaging modality, winning the 2014 Nobel Prize in Chemistry, and considered as one of the key super-resolution techniques. SMLM resolution goes beyond the diffraction limit of light microscopy and achieves resolution on the order of 10-20 nm. SMLM thus enables imaging single molecules and study of the low-level molecular interactions at the subcellular level. In contrast to standard microscopy imaging that produces 2D pixel or 3D voxel grid data, SMLM generates big data of 2D or 3D point clouds with millions of localizations and associated uncertainties. This unprecedented breakthrough in imaging helps researchers employ SMLM in many fields within biology and medicine, such as studying cancerous cells and cell-mediated immunity and accelerating drug discovery. However, SMLM data quantification and interpretation methods have yet to keep pace with the rapid advancement of SMLM imaging. Researchers have been actively exploring new computational methods for SMLM data analysis to extract biosignatures of various biological structures and functions. In this survey, we describe the state-of-the-art clustering methods adopted to analyze and quantify SMLM data and examine the capabilities and shortcomings of the surveyed methods. We classify the methods according to (1) the biological application (i.e., the imaged molecules/structures), (2) the data acquisition (such as imaging modality, dimension, resolution, and number of localizations), and (3) the analysis details (2D versus 3D, field of view versus region of interest, use of machine-learning and multi-scale analysis, biosignature extraction, etc.). We observe that the majority of methods that are based on second-order statistics are sensitive to noise and imaging artifacts, have not been applied to 3D data, do not leverage machine-learning formulations, and are not scalable for big-data analysis. Finally, we summarize state-of-the-art methodology, discuss some key open challenges, and identify future opportunities for better modeling and design of an integrated computational pipeline to address the key challenges.
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Affiliation(s)
- Ismail M. Khater
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ghassan Hamarneh
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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15
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Slotman JA, Paul MW, Carofiglio F, de Gruiter HM, Vergroesen T, Koornneef L, van Cappellen WA, Houtsmuller AB, Baarends WM. Super-resolution imaging of RAD51 and DMC1 in DNA repair foci reveals dynamic distribution patterns in meiotic prophase. PLoS Genet 2020; 16:e1008595. [PMID: 32502153 PMCID: PMC7310863 DOI: 10.1371/journal.pgen.1008595] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 06/23/2020] [Accepted: 05/05/2020] [Indexed: 11/19/2022] Open
Abstract
The recombinase RAD51, and its meiosis-specific paralog DMC1 localize at DNA double-strand break (DSB) sites in meiotic prophase. While both proteins are required during meiotic prophase, their spatial organization during meiotic DSB repair is not fully understood. Using super-resolution microscopy on mouse spermatocyte nuclei, we aimed to define their relative position at DSB foci, and how these vary in time. We show that a large fraction of meiotic DSB repair foci (38%) consisted of a single RAD51 nanofocus and a single DMC1 nanofocus (D1R1 configuration) that were partially overlapping with each other (average center-center distance around 70 nm). The vast majority of the rest of the foci had a similar large RAD51 and DMC1 nanofocus, but in combination with additional smaller nanofoci (D2R1, D1R2, D2R2, or DxRy configuration) at an average distance of around 250 nm. As prophase progressed, less D1R1 and more D2R1 foci were observed, where the large RAD51 nanofocus in the D2R1 foci elongated and gradually oriented towards the distant small DMC1 nanofocus. D1R2 foci frequency was relatively constant, and the single DMC1 nanofocus did not elongate, but was frequently observed between the two RAD51 nanofoci in early stages. D2R2 foci were rare (<10%) and nearest neighbour analyses also did not reveal cofoci formation between D1R1 foci. However, overall, foci localized nonrandomly along the SC, and the frequency of the distance distributions peaked at 800 nm, indicating interference and/or a preferred distance between two ends of a DSB. DMC1 nanofoci where somewhat further away from the axial or lateral elements of the synaptonemal complex (SC, connecting the chromosomal axes of homologs) compared to RAD51 nanofoci. In the absence of the transverse filament of the SC, early configurations were more prominent, and RAD51 nanofocus elongation occurred only transiently. This in-depth analysis of single cell landscapes of RAD51 and DMC1 accumulation patterns at DSB repair sites at super-resolution revealed the variability of foci composition, and defined functional consensus configurations that change over time.
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Affiliation(s)
- Johan A. Slotman
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Maarten W. Paul
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Fabrizia Carofiglio
- Department of Developmental Biology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - H. Martijn de Gruiter
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Tessa Vergroesen
- Department of Developmental Biology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Lieke Koornneef
- Department of Developmental Biology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Wiggert A. van Cappellen
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Adriaan B. Houtsmuller
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
| | - Willy M. Baarends
- Department of Developmental Biology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands
- * E-mail:
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16
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Haas KT, Wightman R, Meyerowitz EM, Peaucelle A. Pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells. Science 2020; 367:1003-1007. [PMID: 32108107 PMCID: PMC7932746 DOI: 10.1126/science.aaz5103] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 01/24/2020] [Indexed: 12/18/2022]
Abstract
The process by which plant cells expand and gain shape has presented a challenge for researchers. Current models propose that these processes are driven by turgor pressure acting on the cell wall. Using nanoimaging, we show that the cell wall contains pectin nanofilaments that possess an intrinsic expansion capacity. Additionally, we use growth models containing such structures to show that a complex plant cell shape can derive from chemically induced local and polarized expansion of the pectin nanofilaments without turgor-driven growth. Thus, the plant cell wall, outside of the cell itself, is an active participant in shaping plant cells. Extracellular matrix function may similarly guide cell shape in other kingdoms, including Animalia.
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Affiliation(s)
- Kalina T Haas
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK. .,Laboratoire Matière et Systèmes Complexes, Université Paris Diderot and CNRS UMR7057, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France
| | - Raymond Wightman
- Microscopy Core Facility, Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Elliot M Meyerowitz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering 156-29, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Alexis Peaucelle
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France.
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17
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[Bortezomib interferes with DNA repair and exerts synergistic anti-multiple myeloma activity with doxorubicin]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2020; 41. [PMID: 32536140 PMCID: PMC7342068 DOI: 10.3760/cma.j.issn.0253-2727.2020.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Peters DK, Garcea RL. Murine polyomavirus DNA transitions through spatially distinct nuclear replication subdomains during infection. PLoS Pathog 2020; 16:e1008403. [PMID: 32203554 PMCID: PMC7117779 DOI: 10.1371/journal.ppat.1008403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/02/2020] [Accepted: 02/13/2020] [Indexed: 12/16/2022] Open
Abstract
The replication of small DNA viruses requires both host DNA replication and repair factors that are often recruited to subnuclear domains termed viral replication centers (VRCs). Aside from serving as a spatial focus for viral replication, little is known about these dynamic areas in the nucleus. We investigated the organization and function of VRCs during murine polyomavirus (MuPyV) infection using 3D structured illumination microscopy (3D-SIM). We localized MuPyV replication center components, such as the viral large T-antigen (LT) and the cellular replication protein A (RPA), to spatially distinct subdomains within VRCs. We found that viral DNA (vDNA) trafficked sequentially through these subdomains post-synthesis, suggesting their distinct functional roles in vDNA processing. Additionally, we observed disruption of VRC organization and vDNA trafficking during mutant MuPyV infections or inhibition of DNA synthesis. These results reveal a dynamic organization of VRC components that coordinates virus replication.
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Affiliation(s)
- Douglas K. Peters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Robert L. Garcea
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
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19
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Pond KW, de Renty C, Yagle MK, Ellis NA. Rescue of collapsed replication forks is dependent on NSMCE2 to prevent mitotic DNA damage. PLoS Genet 2019; 15:e1007942. [PMID: 30735491 PMCID: PMC6383951 DOI: 10.1371/journal.pgen.1007942] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 02/21/2019] [Accepted: 01/07/2019] [Indexed: 12/12/2022] Open
Abstract
NSMCE2 is an E3 SUMO ligase and a subunit of the SMC5/6 complex that associates with the replication fork and protects against genomic instability. Here, we study the fate of collapsed replication forks generated by prolonged hydroxyurea treatment in human NSMCE2-deficient cells. Double strand breaks accumulate during rescue by converging forks in normal cells but not in NSMCE2-deficient cells. Un-rescued forks persist into mitosis, leading to increased mitotic DNA damage. Excess RAD51 accumulates and persists at collapsed forks in NSMCE2-deficient cells, possibly due to lack of BLM recruitment to stalled forks. Despite failure of BLM to accumulate at stalled forks, NSMCE2-deficient cells exhibit lower levels of hydroxyurea-induced sister chromatid exchange. In cells deficient in both NSMCE2 and BLM, hydroxyurea-induced double strand breaks and sister chromatid exchange resembled levels found in NSCME2-deficient cells. We conclude that the rescue of collapsed forks by converging forks is dependent on NSMCE2. DNA damage encountered by the replication fork causes fork stalling and is a major source of mutations when not adequately repaired. Fork stalling can lead to fork collapse, that is, a state of the fork in which normal DNA synthesis cannot be resumed at the site of stalling. Collapsed forks must be rescued by replication forks initiated nearby, but little is known about the rescue mechanism by which an active fork merges with a collapsed fork. We used an inhibitor of DNA replication to generate collapsed replication forks and then studied genetic control of collapsed-fork rescue. We found that NSMCE2, which is a gene product that is known to regulate repair responses to replication stress, is required for cells to effectively rescue collapsed replication forks in order to complete DNA synthesis. DNA double strand breaks that are associated with normal collapsed-fork rescue do not accumulate in cells that are deficient for NSMCE2, suggesting that DNA breakage is part of the rescue and repair mechanism. Failure to rescue collapsed forks leads to DNA damage in mitosis and DNA damage in the following cell cycle. Our work highlights a unique role for NSMCE2 in rescue of collapsed replication forks.
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Affiliation(s)
- Kelvin W. Pond
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Christelle de Renty
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
| | - Mary K. Yagle
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
| | - Nathan A. Ellis
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, United States of America
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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20
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Paul MW, de Gruiter HM, Lin Z, Baarends WM, van Cappellen WA, Houtsmuller AB, Slotman JA. SMoLR: visualization and analysis of single-molecule localization microscopy data in R. BMC Bioinformatics 2019; 20:30. [PMID: 30646838 PMCID: PMC6334411 DOI: 10.1186/s12859-018-2578-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/11/2018] [Indexed: 02/05/2023] Open
Abstract
Background Single-molecule localization microscopy is a super-resolution microscopy technique that allows for nanoscale determination of the localization and organization of proteins in biological samples. For biological interpretation of the data it is essential to extract quantitative information from the super-resolution data sets. Due to the complexity and size of these data sets flexible and user-friendly software is required. Results We developed SMoLR (Single Molecule Localization in R): a flexible framework that enables exploration and analysis of single-molecule localization data within the R programming environment. SMoLR is a package aimed at extracting, visualizing and analyzing quantitative information from localization data obtained by single-molecule microscopy. SMoLR is a platform not only to visualize nanoscale subcellular structures but additionally provides means to obtain statistical information about the distribution and localization of molecules within them. This can be done for individual images or SMoLR can be used to analyze a large set of super-resolution images at once. Additionally, we describe a method using SMoLR for image feature-based particle averaging, resulting in identification of common features among nanoscale structures. Conclusions Embedded in the extensive R programming environment, SMoLR allows scientists to study the nanoscale organization of biomolecules in cells by extracting and visualizing quantitative information and hence provides insight in a wide-variety of different biological processes at the single-molecule level. Electronic supplementary material The online version of this article (10.1186/s12859-018-2578-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maarten W Paul
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - H Martijn de Gruiter
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Zhanmin Lin
- Department of Neuroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands. .,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Johan A Slotman
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
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21
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Abstract
DNA damage possesses the capacity to threaten the genomic integrity of an organism. A multitude of proteins are involved in the detection and repair of DNA double-strand breaks (DSBs), a severe kind of DNA damage. The function of DNA repair proteins can be examined by biochemical assays in vitro as well as in cell-based studies. The Ca2+-binding protein S100A11 shows functional interactions with factors involved in the repair of DSBs by homologous recombination (HR), a high-fidelity DNA repair pathway, such as RAD51 and RAD54B. The key enzyme of the homologous recombination repair is RAD51 that catalyzes the invasion of single-stranded DNA (ssDNA) into double-stranded DNA (dsDNA) containing homologous regions and the exchange of these DNA molecules generating heteroduplex DNA (hDNA). In this chapter, we describe a protocol for the purification of S100A11 to near homogeneity. Using purified proteins, we show the ability of S100A11 to stimulate RAD51 in a DNA strand exchange assay. Additionally, we describe a protocol how S100A11 can be localized in sites of DNA repair by immunofluorescence staining. Furthermore, we present a protocol for assessment of chromosomal aberrations after depletion of S100A11 that illustrate the apparent involvement of S100A11 in genome integrity.
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22
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Whelan DR, Lee WTC, Yin Y, Ofri DM, Bermudez-Hernandez K, Keegan S, Fenyo D, Rothenberg E. Spatiotemporal dynamics of homologous recombination repair at single collapsed replication forks. Nat Commun 2018; 9:3882. [PMID: 30250272 PMCID: PMC6155164 DOI: 10.1038/s41467-018-06435-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 09/06/2018] [Indexed: 01/07/2023] Open
Abstract
Homologous recombination (HR) is a crucial pathway for the repair of DNA double-strand breaks. BRCA1/2 breast cancer proteins are key players in HR via their mediation of RAD51 nucleofilament formation and function; however, their individual roles and crosstalk in vivo are unknown. Here we use super-resolution (SR) imaging to map the spatiotemporal kinetics of HR proteins, revealing the interdependent relationships that govern the dynamic interplay and progression of repair events. We show that initial single-stranded DNA/RAD51 nucleofilament formation is mediated by RAD52 or, in the absence of RAD52, by BRCA2. In contrast, only BRCA2 can orchestrate later RAD51 recombinase activity during homology search and resolution. Furthermore, we establish that upstream BRCA1 activity is critical for BRCA2 function. Our analyses reveal the underlying epistatic landscape of RAD51 functional dependence on RAD52, BRCA1, and BRCA2 during HR and explain the phenotypic similarity of diseases associated with mutations in these proteins.
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Affiliation(s)
- Donna R Whelan
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA.,Department of Pharmacy and Applied Science, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| | - Wei Ting C Lee
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Yandong Yin
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Dylan M Ofri
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Keria Bermudez-Hernandez
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Sarah Keegan
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - David Fenyo
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA.
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