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Phasor histone FLIM-FRET microscopy quantifies spatiotemporal rearrangement of chromatin architecture during the DNA damage response. Proc Natl Acad Sci U S A 2019; 116:7323-7332. [PMID: 30918123 PMCID: PMC6462080 DOI: 10.1073/pnas.1814965116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
To investigate how chromatin architecture is spatiotemporally organized at a double-strand break (DSB) repair locus, we established a biophysical method to quantify chromatin compaction at the nucleosome level during the DNA damage response (DDR). The method is based on phasor image-correlation spectroscopy of histone fluorescence lifetime imaging microscopy (FLIM)-Förster resonance energy transfer (FRET) microscopy data acquired in live cells coexpressing H2B-eGFP and H2B-mCherry. This multiplexed approach generates spatiotemporal maps of nuclear-wide chromatin compaction that, when coupled with laser microirradiation-induced DSBs, quantify the size, stability, and spacing between compact chromatin foci throughout the DDR. Using this technology, we identify that ataxia-telangiectasia mutated (ATM) and RNF8 regulate rapid chromatin decompaction at DSBs and formation of compact chromatin foci surrounding the repair locus. This chromatin architecture serves to demarcate the repair locus from the surrounding nuclear environment and modulate 53BP1 mobility.
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52
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Mouche A, Archambeau J, Ricordel C, Chaillot L, Bigot N, Guillaudeux T, Grenon M, Pedeux R. ING3 is required for ATM signaling and DNA repair in response to DNA double strand breaks. Cell Death Differ 2019; 26:2344-2357. [PMID: 30804473 DOI: 10.1038/s41418-019-0305-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 01/16/2023] Open
Abstract
Inhibitor of Growth 3 (ING3) is a candidate tumor suppressor gene whose expression is lost in tumors such as hepatocellular carcinoma, head and neck squamous cell carcinoma and melanoma. In the present study, we show that ING3-depleted human cells and yeast cells deleted for its ortholog YNG2 are sensitive to DNA damage suggesting a conserved role in response to such stress. In human cells, ING3 is recruited to DNA double strand breaks and is required for ATM activation. Remarkably, in response to doxorubicin, ATM activation is dependent on ING3 but not on TIP60, whose recruitment to DNA breaks also depends on ING3. These events lead to ATM-mediated phosphorylation of NBS1 and the subsequent recruitment of RNF8, RNF168, 53BP1, and BRCA1, which are major mediators of the DNA damage response. Accordingly, upon genotoxic stress, DNA repair by non-homologous end joining (NHEJ) or homologous recombination (HR) were impaired in absence of ING3. Finally, immunoglobulin class switch recombination (CSR), a physiological mechanism requiring NHEJ repair, was impaired in the absence of ING3. Since deregulation of DNA double strand break repair is associated with genomic instability, we propose a novel function of ING3 as a caretaker tumor suppressor involved in the DNA damage signaling and repair.
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Affiliation(s)
- Audrey Mouche
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France.,INSERM U1236, MICMAC, Rennes, France
| | - Jérôme Archambeau
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France
| | - Charles Ricordel
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France
| | - Laura Chaillot
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France.,UMS Biosit, SFR Biologie-Santé, Rennes, France
| | - Nicolas Bigot
- Université de Rennes 1, Rennes, France.,INSERM U1236, MICMAC, Rennes, France.,Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Thierry Guillaudeux
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France.,UMS Biosit, SFR Biologie-Santé, Rennes, France
| | - Muriel Grenon
- Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Rémy Pedeux
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France. .,Université de Rennes 1, Rennes, France.
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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] [MESH Headings] [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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54
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Hurst V, Gasser SM. The study of protein recruitment to UV-induced DNA lesions can be distorted by photoconversion of DNA dyes like Hoechst or DAPI. F1000Res 2019; 8:104. [PMID: 30828443 PMCID: PMC6392149 DOI: 10.12688/f1000research.17865.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/22/2019] [Indexed: 07/18/2024] Open
Abstract
A common approach used to assess DNA repair factor binding in mammalian cells is to induce DNA damage with a UV laser and follow the movement of GFP-tagged proteins to the site of damage. Often these measurements are performed in the presence of the blue DNA intercalating dye Hoechst or DAPI, which is used to label nuclear DNA. A UV-induced switch of Hoechst and DAPI 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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55
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Aleksandrov R, Dotchev A, Poser I, Krastev D, Georgiev G, Panova G, Babukov Y, Danovski G, Dyankova T, Hubatsch L, Ivanova A, Atemin A, Nedelcheva-Veleva MN, Hasse S, Sarov M, Buchholz F, Hyman AA, Grill SW, Stoynov SS. Protein Dynamics in Complex DNA Lesions. Mol Cell 2019; 69:1046-1061.e5. [PMID: 29547717 DOI: 10.1016/j.molcel.2018.02.016] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/26/2017] [Accepted: 02/09/2018] [Indexed: 12/13/2022]
Abstract
A single mutagen can generate multiple different types of DNA lesions. How different repair pathways cooperate in complex DNA lesions, however, remains largely unclear. Here we measured, clustered, and modeled the kinetics of recruitment and dissociation of 70 DNA repair proteins to laser-induced DNA damage sites in HeLa cells. The precise timescale of protein recruitment reveals that error-prone translesion polymerases are considerably delayed compared to error-free polymerases. We show that this is ensured by the delayed recruitment of RAD18 to double-strand break sites. The time benefit of error-free polymerases disappears when PARP inhibition significantly delays PCNA recruitment. Moreover, removal of PCNA from complex DNA damage sites correlates with RPA loading during 5'-DNA end resection. Our systematic study of the dynamics of DNA repair proteins in complex DNA lesions reveals the multifaceted coordination between the repair pathways and provides a kinetics-based resource to study genomic instability and anticancer drug impact.
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Affiliation(s)
- Radoslav Aleksandrov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Anton Dotchev
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Ina Poser
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Dragomir Krastev
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Georgi Georgiev
- Faculty of Mathematics and Informatics, Sofia University, St. Kliment Ohridski, 5 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Greta Panova
- Department of Mathematics, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104, USA
| | - Yordan Babukov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria; Faculty of Mathematics and Informatics, Sofia University, St. Kliment Ohridski, 5 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Georgi Danovski
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Teodora Dyankova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Lars Hubatsch
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Aneliya Ivanova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Aleksandar Atemin
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Marina N Nedelcheva-Veleva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Susanne Hasse
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany; Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstr. 74, 01307 Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Stephan W Grill
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Stoyno S Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria.
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56
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Mussttaf RA, Jenkins DFL, Jha AN. Assessing the impact of low level laser therapy (LLLT) on biological systems: a review. Int J Radiat Biol 2019; 95:120-143. [DOI: 10.1080/09553002.2019.1524944] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ruwaidah A. Mussttaf
- School of Computing, Electronics and Mathematics, University of Plymouth, Plymouth, UK
| | - David F. L. Jenkins
- School of Computing, Electronics and Mathematics, University of Plymouth, Plymouth, UK
| | - Awadhesh N. Jha
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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57
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Duquette ML, Kim J, Shi LZ, Berns MW. LSD1 mediated changes in the local redox environment during the DNA damage response. PLoS One 2018; 13:e0201907. [PMID: 30096172 PMCID: PMC6086436 DOI: 10.1371/journal.pone.0201907] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022] Open
Abstract
The redox state of the cell can be affected by many cellular conditions. In this study we show that detectable reactive oxygen species (ROS) are also generated in response to DNA damage by the chromatin remodeling factor and monoamine oxidase LSD1/KDM1A. This raised the possibility that the localized generation of hydrogen peroxide produced by LSD1 may affect the function of proximally located DNA repair proteins. The two major pathways for repair of DNA double-strand breaks (DSBs) are homologous recombination (HR) and non-homologous end joining (NHEJ). Cells were exposed to low levels of ectopic H2O2, DNA breaks generated by laser light, and recruitment kinetics of NHEJ protein Ku80 to DNA damage sites determined. Ku80 recruitment to damage sites was significantly decreased in cells pretreated with H2O2 while HR end binding protein Nbs1 was increased. This suggests that the DNA repair pathway choice has the potential to be modulated by the local redox state. This has implications for chemotherapeutic approaches involving generating DNA damage to target actively dividing cancer cells, which may be more or less effective dependent on the redox state of the targeted cells and the predominant repair pathway required to repair the type of DNA damage generated.
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Affiliation(s)
- Michelle L. Duquette
- Institute of Engineering in Medicine, University of California, San Diego, CA, United States of America
- Department of Bioengineering, University of California, San Diego, CA, United States of America
- * E-mail:
| | - Justine Kim
- Institute of Engineering in Medicine, University of California, San Diego, CA, United States of America
| | - Linda Z. Shi
- Institute of Engineering in Medicine, University of California, San Diego, CA, United States of America
- Department of Bioengineering, University of California, San Diego, CA, United States of America
| | - Michael W. Berns
- Institute of Engineering in Medicine, University of California, San Diego, CA, United States of America
- Department of Bioengineering, University of California, San Diego, CA, United States of America
- Beckman Laser Institute, University of California, Irvine, Irvine, CA, United States of America
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58
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Abstract
![]()
The optical pickup
unit (OPU) within a CD/DVD/Blu-ray drive integrates
780, 650, and 405 nm wavelength lasers, diffraction-limited optics,
a high-bandwidth optoelectronic transducer up to 400 MHz, and a nanoresolution x-, z-axis, and tilt actuator in a compact
size. In addition, the OPU is a remarkable piece of engineering and
could enable different scientific applications such as sub-angstrom
displacement sensing, micro- and nanoimaging, and nanolithography.
Although off-the-shelf OPUs can be easily obtained, manufacturers
protect their datasheets under nondisclosure agreements to impede
their availability to the public. Thus, OPUs are black boxes that
few people can use for research, and only experienced researchers
can access all their functions. This review details the OPU mechanism
and components. In addition, we explain how to utilize three commercially
available triple-wavelength OPUs from scratch and optimize sensing
quality. Then, we discuss scientific research using OPUs, from standard
optical drive-based turnkey-biomarker array reading and OPU direct
bioapplications (cytometry, optical tweezing, bioimaging) to modified
OPU-based biosensing (DNA chip fluorescence scanning, biomolecular
diagnostics). We conclude by presenting future trends on optical storage
devices and potential applications. Hacking low-cost and high-performance
OPUs may spread micro- and nanoscale biosensing research from research
laboratories to citizen scientists around the globe.
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Affiliation(s)
- Edwin En-Te Hwu
- Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics (IDUN), Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Anja Boisen
- Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics (IDUN), Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby 2800, Denmark
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59
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Morotomi-Yano K, Saito S, Adachi N, Yano KI. Dynamic behavior of DNA topoisomerase IIβ in response to DNA double-strand breaks. Sci Rep 2018; 8:10344. [PMID: 29985428 PMCID: PMC6037730 DOI: 10.1038/s41598-018-28690-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/27/2018] [Indexed: 12/11/2022] Open
Abstract
DNA topoisomerase II (Topo II) is crucial for resolving topological problems of DNA and plays important roles in various cellular processes, such as replication, transcription, and chromosome segregation. Although DNA topology problems may also occur during DNA repair, the possible involvement of Topo II in this process remains to be fully investigated. Here, we show the dynamic behavior of human Topo IIβ in response to DNA double-strand breaks (DSBs), which is the most harmful form of DNA damage. Live cell imaging coupled with site-directed DSB induction by laser microirradiation demonstrated rapid recruitment of EGFP-tagged Topo IIβ to the DSB site. Detergent extraction followed by immunofluorescence showed the tight association of endogenous Topo IIβ with DSB sites. Photobleaching analysis revealed that Topo IIβ is highly mobile in the nucleus. The Topo II catalytic inhibitors ICRF-187 and ICRF-193 reduced the Topo IIβ mobility and thereby prevented Topo IIβ recruitment to DSBs. Furthermore, Topo IIβ knockout cells exhibited increased sensitivity to bleomycin and decreased DSB repair mediated by homologous recombination (HR), implicating the role of Topo IIβ in HR-mediated DSB repair. Taken together, these results highlight a novel aspect of Topo IIβ functions in the cellular response to DSBs.
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Affiliation(s)
- Keiko Morotomi-Yano
- Department of Bioelectrics, Institute of Pulsed Power Science, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Shinta Saito
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan
| | - Noritaka Adachi
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan.,Advanced Medical Research Center, Yokohama City University, Yokohama, 236-0004, Japan
| | - Ken-Ichi Yano
- Department of Bioelectrics, Institute of Pulsed Power Science, Kumamoto University, Kumamoto, 860-8555, Japan.
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60
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Kwok SJJ, Jo Y, Lin HH, Choi M, Yun SH. Millisecond cellular labelling in situ with two-photon photoconversion. BIOMEDICAL OPTICS EXPRESS 2018; 9:3067-3077. [PMID: 29984083 PMCID: PMC6033565 DOI: 10.1364/boe.9.003067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/23/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
In situ labeling of cells within living biological tissues using photoconversion has provided valuable information on cellular physiology in their natural environments. However, current photoconvertible probes typically require seconds to minutes of light exposure, limiting their uses in rapid biological processes such as intracellular diffusion and circulating cells. Here, we report that two-photon photoconversion of cyanine-based dyes offers unprecedentedly rapid photoconversion down to millisecond timescales per cell. We demonstrate potential biological applications including measuring intracellular diffusion kinetics in a spinal nerve, labeling of rapidly flowing cells in a microfluidic channel, and photoconversion of a circulating cell in vivo.
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Affiliation(s)
- Sheldon J J Kwok
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yongjae Jo
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, South Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon 16419, South Korea
| | - Harvey H Lin
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA
| | - Myunghwan Choi
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, South Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon 16419, South Korea
| | - Seok-Hyun Yun
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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61
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Schmalz MF, Wieser I, Schindler F, Czada C, Leitenstorfer A, Ferrando-May E. Highly standardized multicolor femtosecond fiber system for selective microphotomanipulation of deoxyribonucleic acid and chromatin. OPTICS LETTERS 2018; 43:2877-2880. [PMID: 29905713 DOI: 10.1364/ol.43.002877] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
We present a three-color femtosecond Er/Yb:fiber laser enabling highly specific and standardized nonlinear optical manipulation of live cells. The system simultaneously provides bandwidth-limited 80-fs pulses with identical intensity envelope centered at wavelengths of 515, 775, and 1035 nm in the focus of a confocal microscope. We achieve this goal by combining high-order dispersion control via, for example, chirped fiber Bragg gratings with proper bandwidth management in each nonlinear conversion step. Wavelength-selective and noninterfering induction of deoxyribonucleic acid (DNA) photoproducts and DNA strand breaks, as well as fluorescence photoactivation of a photoactivatable green fluorescent protein (PA-GFP)-histone fusion protein, are demonstrated. The capability to introduce different types of DNA lesions and perform photoswitching experiments in a selective manner is essential for quantitative studies on DNA repair and chromatin dynamics.
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62
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Hoischen C, Monajembashi S, Weisshart K, Hemmerich P. Multimodal Light Microscopy Approaches to Reveal Structural and Functional Properties of Promyelocytic Leukemia Nuclear Bodies. Front Oncol 2018; 8:125. [PMID: 29888200 PMCID: PMC5980967 DOI: 10.3389/fonc.2018.00125] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/05/2018] [Indexed: 12/11/2022] Open
Abstract
The promyelocytic leukemia (pml) gene product PML is a tumor suppressor localized mainly in the nucleus of mammalian cells. In the cell nucleus, PML seeds the formation of macromolecular multiprotein complexes, known as PML nuclear bodies (PML NBs). While PML NBs have been implicated in many cellular functions including cell cycle regulation, survival and apoptosis their role as signaling hubs along major genome maintenance pathways emerged more clearly. However, despite extensive research over the past decades, the precise biochemical function of PML in these pathways is still elusive. It remains a big challenge to unify all the different previously suggested cellular functions of PML NBs into one mechanistic model. With the advent of genetically encoded fluorescent proteins it became possible to trace protein function in living specimens. In parallel, a variety of fluorescence fluctuation microscopy (FFM) approaches have been developed which allow precise determination of the biophysical and interaction properties of cellular factors at the single molecule level in living cells. In this report, we summarize the current knowledge on PML nuclear bodies and describe several fluorescence imaging, manipulation, FFM, and super-resolution techniques suitable to analyze PML body assembly and function. These include fluorescence redistribution after photobleaching, fluorescence resonance energy transfer, fluorescence correlation spectroscopy, raster image correlation spectroscopy, ultraviolet laser microbeam-induced DNA damage, erythrocyte-mediated force application, and super-resolution microscopy approaches. Since most if not all of the microscopic equipment to perform these techniques may be available in an institutional or nearby facility, we hope to encourage more researches to exploit sophisticated imaging tools for their research in cancer biology.
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63
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Wakida NM, Cruz GMS, Ro CC, Moncada EG, Khatibzadeh N, Flanagan LA, Berns MW. Phagocytic response of astrocytes to damaged neighboring cells. PLoS One 2018; 13:e0196153. [PMID: 29708987 PMCID: PMC5927416 DOI: 10.1371/journal.pone.0196153] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/07/2018] [Indexed: 11/17/2022] Open
Abstract
This study aims to understand the phagocytic response of astrocytes to the injury of neurons or other astrocytes at the single cell level. Laser nanosurgery was used to damage individual cells in both primary mouse cortical astrocytes and an established astrocyte cell line. In both cases, the release of material/substances from laser-irradiated astrocytes or neurons induced a phagocytic response in near-by astrocytes. Propidium iodide stained DNA originating from irradiated cells was visible in vesicles of neighboring cells, confirming phagocytosis of material from damaged cortical cells. In the presence of an intracellular pH indicator dye, newly formed vesicles correspond to acidic pH fluorescence, thus suggesting lysosome bound degradation of cellular debris. Cells with shared membrane connections prior to laser damage had a significantly higher frequency of induced phagocytosis compared to isolated cells with no shared membrane. The increase in phagocytic response of cells with a shared membrane occurred regardless of the extent of shared membrane (a thin filopodial connection vs. a cell cluster with significant shared membrane). In addition to the presence (or lack) of a membrane connection, variation in phagocytic ability was also observed with differences in injury location within the cell and distance separating isolated astrocytes. These results demonstrate the ability of an astrocyte to respond to the damage of a single cell, be it another astrocyte, or a neuron. This single-cell level of analysis results in a better understanding of the role of astrocytes to maintain homeostasis in the CNS, particularly in the sensing and removal of debris in damaged or pathologic nervous tissue.
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Affiliation(s)
- Nicole M Wakida
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, Irvine, California, United States of America
| | - Gladys Mae S Cruz
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, Irvine, California, United States of America
| | - Clarissa C Ro
- Department of Neurology, University of California, Irvine, Irvine, California, United States of America.,Sue & Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, United States of America
| | - Emmanuel G Moncada
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, Irvine, California, United States of America
| | - Nima Khatibzadeh
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, Irvine, California, United States of America
| | - Lisa A Flanagan
- Department of Neurology, University of California, Irvine, Irvine, California, United States of America.,Sue & Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, United States of America.,Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, California, United States of America.,Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America
| | - Michael W Berns
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, Irvine, California, United States of America.,Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America.,Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, United States of America
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64
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Gaudreau-Lapierre A, Garneau D, Djerir B, Coulombe F, Morin T, Marechal A. Investigation of Protein Recruitment to DNA Lesions Using 405 Nm Laser Micro-irradiation. J Vis Exp 2018. [PMID: 29630045 DOI: 10.3791/57410] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The DNA Damage Response (DDR) uses a plethora of proteins to detect, signal, and repair DNA lesions. Delineating this response is critical to understand genome maintenance mechanisms. Since recruitment and exchange of proteins at lesions are highly dynamic, their study requires the ability to generate DNA damage in a rapid and spatially-delimited manner. Here, we describe procedures to locally induce DNA damage in human cells using a commonly available laser-scanning confocal microscope equipped with a 405 nm laser line. Accumulation of genome maintenance factors at laser stripes can be assessed by immunofluorescence (IF) or in real-time using proteins tagged with fluorescent reporters. Using phosphorylated histone H2A.X (γ-H2A.X) and Replication Protein A (RPA) as markers, the method provides sufficient resolution to discriminate locally-recruited factors from those that spread on adjacent chromatin. We further provide ImageJ-based scripts to efficiently monitor the kinetics of protein relocalization at DNA damage sites. These refinements greatly simplify the study of the DDR dynamics.
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Affiliation(s)
| | | | | | | | - Théo Morin
- Department of Biology, Université de Sherbrooke
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65
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Kong X, Cruz GMS, Silva BA, Wakida NM, Khatibzadeh N, Berns MW, Yokomori K. Laser Microirradiation to Study In Vivo Cellular Responses to Simple and Complex DNA Damage. J Vis Exp 2018. [PMID: 29443023 DOI: 10.3791/56213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
DNA damage induces specific signaling and repair responses in the cell, which is critical for protection of genome integrity. Laser microirradiation became a valuable experimental tool to investigate the DNA damage response (DDR) in vivo. It allows real-time high-resolution single-cell analysis of macromolecular dynamics in response to laser-induced damage confined to a submicrometer region in the cell nucleus. However, various laser conditions have been used without appreciation of differences in the types of damage induced. As a result, the nature of the damage is often not well characterized or controlled, causing apparent inconsistencies in the recruitment or modification profiles. We demonstrated that different irradiation conditions (i.e., different wavelengths as well as different input powers (irradiances) of a femtosecond (fs) near-infrared (NIR) laser) induced distinct DDR and repair protein assemblies. This reflects the type of DNA damage produced. This protocol describes how titration of laser input power allows induction of different amounts and complexities of DNA damage, which can easily be monitored by detection of base and crosslinking damages, differential poly (ADP-ribose) (PAR) signaling, and pathway-specific repair factor assemblies at damage sites. Once the damage conditions are determined, it is possible to investigate the effects of different damage complexity and differential damage signaling as well as depletion of upstream factor(s) on any factor of interest.
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Affiliation(s)
- Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California, Irvine
| | - Gladys M S Cruz
- Beckman Laser Institute and Medical Clinic, University of California, Irvine
| | - Bárbara A Silva
- Beckman Laser Institute and Medical Clinic, University of California, Irvine
| | - Nicole M Wakida
- Beckman Laser Institute and Medical Clinic, University of California, Irvine
| | - Nima Khatibzadeh
- Beckman Laser Institute and Medical Clinic, University of California, Irvine
| | - Michael W Berns
- Beckman Laser Institute and Medical Clinic, University of California, Irvine; Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine; Department of Biomedical Engineering and Surgery, University of California, Irvine
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine;
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66
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Koury E, Harrell K, Smolikove S. Differential RPA-1 and RAD-51 recruitment in vivo throughout the C. elegans germline, as revealed by laser microirradiation. Nucleic Acids Res 2018; 46:748-764. [PMID: 29244155 PMCID: PMC5778493 DOI: 10.1093/nar/gkx1243] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/25/2017] [Accepted: 11/30/2017] [Indexed: 01/12/2023] Open
Abstract
Studies of the repair pathways associated with DNA double strand breaks (DSBs) are numerous, and provide evidence for cell-cycle specific regulation of homologous recombination (HR) by the regulation of its associated proteins. Laser microirradiation is a well-established method to examine in vitro kinetics of repair and allows for live-imaging of DSB repair from the moment of induction. Here we apply this method to whole, live organisms, introducing an effective system to analyze exogenous, microirradiation-induced breaks in the Caenorhabditis elegans germline. Through this method we observed the sequential kinetics of the recruitment of ssDNA binding proteins RPA-1 and RAD-51 in vivo. We analyze these kinetics throughout different regions of the germline, and thus throughout a range of developmental stages of mitotic and meiotic nuclei. Our analysis demonstrates a largely conserved timing of recruitment of ssDNA binding proteins to DSBs throughout the germline, with a delay of RAD-51 recruitment at mid-pachytene nuclei. Microirradiated nuclei are viable and undergo a slow kinetics of resolution. We observe RPA-1 and RAD-51 colocalization for hours post-microirradiation throughout the germline, suggesting that there are mixed RPA-1/RAD-51 filaments. Finally, through live imaging analysis we observed RAD-51 foci movement with low frequency of coalescence.
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Affiliation(s)
- Emily Koury
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Kailey Harrell
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Sarit Smolikove
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
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67
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Smith R, Timinszky G. Monitoring Poly(ADP-Ribosyl)ation in Response to DNA Damage in Live Cells Using Fluorescently Tagged Macrodomains. Methods Mol Biol 2018; 1813:11-24. [PMID: 30097858 DOI: 10.1007/978-1-4939-8588-3_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a dynamic posttranslational modification that is added and removed rapidly at sites of DNA damage. PARylation is important for numerous aspects of DNA repair including chromatin decondensation and protein recruitment. Visualization of PARylation levels after DNA damage induction is generally obtained using traditional immunofluorescent techniques on fixed cells, which results in limited temporal resolution. Here, we describe a microscopy-based method to track ADP-ribosylation at break sites. This method relies on DNA damage induction using a 405 nm FRAP laser on Hoechst-treated cells expressing GFP-tagged PAR-binding proteins, such as macrodomains where the recruitment of the PAR-binder to sites of DNA damage gives an indication of PARylation levels.
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Affiliation(s)
- Rebecca Smith
- Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gyula Timinszky
- Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
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68
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Schneidereit D, Nübler S, Prölß G, Reischl B, Schürmann S, Müller OJ, Friedrich O. Optical prediction of single muscle fiber force production using a combined biomechatronics and second harmonic generation imaging approach. LIGHT, SCIENCE & APPLICATIONS 2018; 7:79. [PMID: 30374401 PMCID: PMC6199289 DOI: 10.1038/s41377-018-0080-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 05/22/2023]
Abstract
Skeletal muscle is an archetypal organ whose structure is tuned to match function. The magnitude of order in muscle fibers and myofibrils containing motor protein polymers determines the directed force output of the summed force vectors and, therefore, the muscle's power performance on the structural level. Structure and function can change dramatically during disease states involving chronic remodeling. Cellular remodeling of the cytoarchitecture has been pursued using noninvasive and label-free multiphoton second harmonic generation (SHG) microscopy. Hereby, structure parameters can be extracted as a measure of myofibrillar order and thus are suggestive of the force output that a remodeled structure can still achieve. However, to date, the parameters have only been an indirect measure, and a precise calibration of optical SHG assessment for an exerted force has been elusive as no technology in existence correlates these factors. We engineered a novel, automated, high-precision biomechatronics system into a multiphoton microscope allows simultaneous isometric Ca2+-graded force or passive viscoelasticity measurements and SHG recordings. Using this MechaMorph system, we studied force and SHG in single EDL muscle fibers from wt and mdx mice; the latter serves as a model for compromised force and abnormal myofibrillar structure. We present Ca2+-graded isometric force, pCa-force curves, passive viscoelastic parameters and 3D structure in the same fiber for the first time. Furthermore, we provide a direct calibration of isometric force to morphology, which allows noninvasive prediction of the force output of single fibers from only multiphoton images, suggesting a potential application in the diagnosis of myopathies.
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Affiliation(s)
- Dominik Schneidereit
- Institute of Medical Biotechnology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), FAU Erlangen-Nürnberg, Paul-Gordan-Str. 7, 91052 Erlangen, Germany
| | - Stefanie Nübler
- Institute of Medical Biotechnology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), FAU Erlangen-Nürnberg, Paul-Gordan-Str. 7, 91052 Erlangen, Germany
| | - Gerhard Prölß
- Institute of Medical Biotechnology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany
| | - Barbara Reischl
- Institute of Medical Biotechnology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany
| | - Sebastian Schürmann
- Institute of Medical Biotechnology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), FAU Erlangen-Nürnberg, Paul-Gordan-Str. 7, 91052 Erlangen, Germany
- Muscle Research Center Erlangen (MURCE), Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Oliver J Müller
- Department of Internal Medicine III, University of Kiel, Arnold-Heller-Str. 3, 24105 Kiel, Germany
- DZHK (German Center for Cardiovascular Research) Partner Site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Oliver Friedrich
- Institute of Medical Biotechnology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), FAU Erlangen-Nürnberg, Paul-Gordan-Str. 7, 91052 Erlangen, Germany
- Muscle Research Center Erlangen (MURCE), Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
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69
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Harrell KE, Koury E, Smolikove S. Microirradiation for Precise, Double-strand Break Induction in vivo in Caenorhabditis elegans. Bio Protoc 2018; 8:e3130. [PMID: 30680294 DOI: 10.21769/bioprotoc.3130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are toxic lesions that every cell must accurately repair in order to survive. The repair of DSBs is an integral part of a cell life cycle and can lead to lethality if repaired incorrectly. Laser microirradiation is an established technique which has been used in yeast, mammalian cell culture, and Drosophila cell culture to study the regulation of DSB repair. Up to our studies, this method has not been adapted for use in a whole, live, multicellular organism to study this repair in vivo. We have recently shown that this system can be used for study of the recruitment of vital repair proteins to microirradiation-induced breaks in the transparent nematode Caenorhabditis elegans. With the integration of microirradiation and imaging technology, we can precisely induce DSBs in target nuclei and study the recruitment of fluorescently tagged repair proteins from the time of damage induction. Whole, live worms are plated and immobilized for targeting of nuclei, and immediately following induction the targeted region can be imaged for up to an hour and a half post-microirradiation. This method is the first that allows for study of DNA repair protein kinetics in vivo in an intact organism, which can be adapted in numerous ways to allow for study of repair kinetics in various aspects of the repair process.
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Affiliation(s)
| | - Emily Koury
- Department of Biology, University of Iowa, Iowa City, USA
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70
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Kochan JA, Desclos EC, Bosch R, Meister L, Vriend LE, van Attikum H, Krawczyk PM. Meta-analysis of DNA double-strand break response kinetics. Nucleic Acids Res 2017; 45:12625-12637. [PMID: 29182755 PMCID: PMC5728399 DOI: 10.1093/nar/gkx1128] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/24/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022] Open
Abstract
Most proteins involved in the DNA double-strand break response (DSBR) accumulate at the damage sites, where they perform functions related to damage signaling, chromatin remodeling and repair. Over the last two decades, studying the accumulation of many DSBR proteins provided information about their functionality and underlying mechanisms of action. However, comparison and systemic interpretation of these data is challenging due to their scattered nature and differing experimental approaches. Here, we extracted, analyzed and compared the available results describing accumulation of 79 DSBR proteins at sites of DNA damage, which can be further explored using Cumulus (http://www.dna-repair.live/cumulus/)-the accompanying interactive online application. Despite large inter-study variability, our analysis revealed that the accumulation of most proteins starts immediately after damage induction, occurs in parallel and peaks within 15-20 min. Various DSBR pathways are characterized by distinct accumulation kinetics with major non-homologous end joining proteins being generally faster than those involved in homologous recombination, and signaling and chromatin remodeling factors accumulating with varying speeds. Our meta-analysis provides, for the first time, comprehensive overview of the temporal organization of the DSBR in mammalian cells and could serve as a reference for future mechanistic studies of this complex process.
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Affiliation(s)
- Jakub A. Kochan
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Emilie C.B. Desclos
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Ruben Bosch
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Luna Meister
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Lianne E.M. Vriend
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Przemek M. Krawczyk
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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71
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Noshadi I, Hong S, Sullivan KE, Sani ES, Portillo-Lara R, Tamayol A, Shin SR, Gao AE, Stoppel WL, Black LD, Khademhosseini A, Annabi N. In vitro and in vivo analysis of visible light crosslinkable gelatin methacryloyl (GelMA) hydrogels. Biomater Sci 2017; 5:2093-2105. [PMID: 28805830 PMCID: PMC5614854 DOI: 10.1039/c7bm00110j] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Photocrosslinkable materials have been frequently used for constructing soft and biomimetic hydrogels for tissue engineering. Although ultraviolet (UV) light is commonly used for photocrosslinking such materials, its use has been associated with several biosafety concerns such as DNA damage, accelerated aging of tissues, and cancer. Here we report an injectable visible light crosslinked gelatin-based hydrogel for myocardium regeneration. Mechanical characterization revealed that the compressive moduli of the engineered hydrogels could be tuned in the range of 5-56 kPa by changing the concentrations of the initiator, co-initiator and co-monomer in the precursor formulation. In addition, the average pore sizes (26-103 μm) and swelling ratios (7-13%) were also shown to be tunable by varying the hydrogel formulation. In vitro studies showed that visible light crosslinked GelMA hydrogels supported the growth and function of primary cardiomyocytes (CMs). In addition, the engineered materials were shown to be biocompatible in vivo, and could be successfully delivered to the heart after myocardial infarction in an animal model to promote tissue healing. The developed visible light crosslinked hydrogel could be used for the repair of various soft tissues such as the myocardium and for the treatment of cardiovascular diseases with enhanced therapeutic functionality.
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Affiliation(s)
- Iman Noshadi
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Seonki Hong
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kelly E. Sullivan
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Ehsan Shirzaei Sani
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115-5000, USA
| | - Roberto Portillo-Lara
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115-5000, USA
- Centro de Biotecnología FEMSA, Tecnológico de Monterrey, Monterrey, NL, 64700, Mexico
| | - Ali Tamayol
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Su Ryon Shin
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Albert E. Gao
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Whitney L. Stoppel
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Lauren D. Black
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
- Cellular, Molecular, and Developmental Biology Program, Sackler School for Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Ali Khademhosseini
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Physics, King Abdulaziz University, Jeddah 21569, Saudi Arabia
| | - Nasim Annabi
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115-5000, USA
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72
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Ramdzan ZM, Ginjala V, Pinder JB, Chung D, Donovan CM, Kaur S, Leduy L, Dellaire G, Ganesan S, Nepveu A. The DNA repair function of CUX1 contributes to radioresistance. Oncotarget 2017; 8:19021-19038. [PMID: 28147323 PMCID: PMC5386666 DOI: 10.18632/oncotarget.14875] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 01/19/2017] [Indexed: 01/19/2023] Open
Abstract
Ionizing radiation generates a broad spectrum of oxidative DNA lesions, including oxidized base products, abasic sites, single-strand breaks and double-strand breaks. The CUX1 protein was recently shown to function as an auxiliary factor that stimulates enzymatic activities of OGG1 through its CUT domains. In the present study, we investigated the requirement for CUX1 and OGG1 in the resistance to radiation. Cancer cell survival following ionizing radiation is reduced by CUX1 knockdown and increased by higher CUX1 expression. However, CUX1 knockdown is sufficient by itself to reduce viability in many cancer cell lines that exhibit high levels of reactive oxygen species (ROS). Consequently, clonogenic results expressed relative to that of non-irradiated cells indicate that CUX1 knockdown confers no or modest radiosensitivity to cancer cells with high ROS. A recombinant protein containing only two CUT domains is sufficient for rapid recruitment to DNA damage, acceleration of DNA repair and increased survival following radiation. In agreement with these findings, OGG1 knockdown and treatment of cells with OGG1 inhibitors sensitize cancer cells to radiation. Together, these results validate CUX1 and more specifically the CUT domains as therapeutic targets.
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Affiliation(s)
- Zubaidah M Ramdzan
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Vasudeva Ginjala
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - Jordan B Pinder
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Dudley Chung
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Caroline M Donovan
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Simran Kaur
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Shridar Ganesan
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - Alain Nepveu
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Medicine, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Oncology, McGill University, Montreal, Quebec, H3A 1A3, Canada
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73
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Holton NW, Andrews JF, Gassman NR. Application of Laser Micro-irradiation for Examination of Single and Double Strand Break Repair in Mammalian Cells. J Vis Exp 2017. [PMID: 28930988 PMCID: PMC5752190 DOI: 10.3791/56265] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Highly coordinated DNA repair pathways exist to detect, excise and replace damaged DNA bases, and coordinate repair of DNA strand breaks. While molecular biology techniques have clarified structure, enzymatic functions, and kinetics of repair proteins, there is still a need to understand how repair is coordinated within the nucleus. Laser micro-irradiation offers a powerful tool for inducing DNA damage and monitoring the recruitment of repair proteins. Induction of DNA damage by laser micro-irradiation can occur with a range of wavelengths, and users can reliably induce single strand breaks, base lesions and double strand breaks with a range of doses. Here, laser micro-irradiation is used to examine repair of single and double strand breaks induced by two common confocal laser wavelengths, 355 nm and 405 nm. Further, proper characterization of the applied laser dose for inducing specific damage mixtures is described, so users can reproducibly perform laser micro-irradiation data acquisition and analysis.
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Affiliation(s)
- Nathaniel W Holton
- Department of Oncologic Sciences, University of South Alabama Mitchell Cancer Institute
| | - Joel F Andrews
- Department of Oncologic Sciences, University of South Alabama Mitchell Cancer Institute
| | - Natalie R Gassman
- Department of Oncologic Sciences, University of South Alabama Mitchell Cancer Institute;
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74
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Annabi N, Rana D, Shirzaei Sani E, Portillo-Lara R, Gifford JL, Fares MM, Mithieux SM, Weiss AS. Engineering a sprayable and elastic hydrogel adhesive with antimicrobial properties for wound healing. Biomaterials 2017; 139:229-243. [PMID: 28579065 PMCID: PMC11110881 DOI: 10.1016/j.biomaterials.2017.05.011] [Citation(s) in RCA: 333] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/25/2017] [Accepted: 05/07/2017] [Indexed: 01/01/2023]
Abstract
Hydrogel-based bioadhesives have emerged as alternatives for sutureless wound closure, since they can mimic the composition and physicochemical properties of the extracellular matrix. However, they are often associated with poor mechanical properties, low adhesion to native tissues, and lack of antimicrobial properties. Herein, a new sprayable, elastic, and biocompatible composite hydrogel, with broad-spectrum antimicrobial activity, for the treatment of chronic wounds is reported. The composite hydrogels were engineered using two ECM-derived biopolymers, gelatin methacryloyl (GelMA) and methacryloyl-substituted recombinant human tropoelastin (MeTro). MeTro/GelMA composite hydrogel adhesives were formed via visible light-induced crosslinking. Additionally, the antimicrobial peptide Tet213 was conjugated to the hydrogels, instilling antimicrobial activity against Gram (+) and (-) bacteria. The physical properties (e.g. porosity, degradability, swellability, mechanical, and adhesive properties) of the engineered hydrogel could be fine-tuned by varying the ratio of MeTro/GelMA and the final polymer concentration. The hydrogels supported in vitro mammalian cellular growth in both two-dimensional and three dimensional cultures. The subcutaneous implantation of the hydrogels in rats confirmed their biocompatibility and biodegradation in vivo. The engineered MeTro/GelMA-Tet213 hydrogels can be used for sutureless wound closure strategies to prevent infection and promote healing of chronic wounds.
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Affiliation(s)
- Nasim Annabi
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA; Biomaterials Innovation Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Devyesh Rana
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Ehsan Shirzaei Sani
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
| | - Roberto Portillo-Lara
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA; Centro de Biotecnología FEMSA, Tecnológico de Monterrey, Monterrey, NL, 64700, Mexico
| | - Jessie L Gifford
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Mohammad M Fares
- Department of Chemical Sciences, Jordan University of Science & Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Suzanne M Mithieux
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, NSW, Australia; Charles Perkins Centre, University of Sydney, NSW, Australia
| | - Anthony S Weiss
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, NSW, Australia; Charles Perkins Centre, University of Sydney, NSW, Australia; Bosch Institute, University of Sydney, NSW, Australia
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75
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Liu C, Vyas A, Kassab MA, Singh AK, Yu X. The role of poly ADP-ribosylation in the first wave of DNA damage response. Nucleic Acids Res 2017; 45:8129-8141. [PMID: 28854736 PMCID: PMC5737498 DOI: 10.1093/nar/gkx565] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 06/15/2017] [Accepted: 06/20/2017] [Indexed: 01/11/2023] Open
Abstract
Poly ADP-ribose polymerases (PARPs) catalyze massive protein poly ADP-ribosylation (PARylation) within seconds after the induction of DNA single- or double-strand breaks. PARylation occurs at or near the sites of DNA damage and promotes the recruitment of DNA repair factors via their poly ADP-ribose (PAR) binding domains. Several novel PAR-binding domains have been recently identified. Here, we summarize these and other recent findings suggesting that PARylation may be the critical event that mediates the first wave of the DNA damage response. We also discuss the potential for functional crosstalk with other DNA damage-induced post-translational modifications.
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Affiliation(s)
- Chao Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Aditi Vyas
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Muzaffer A. Kassab
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Anup K. Singh
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
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76
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Sherry MR, Hay TJM, Gulak MA, Nassiri A, Finnen RL, Banfield BW. The Herpesvirus Nuclear Egress Complex Component, UL31, Can Be Recruited to Sites of DNA Damage Through Poly-ADP Ribose Binding. Sci Rep 2017; 7:1882. [PMID: 28507315 PMCID: PMC5432524 DOI: 10.1038/s41598-017-02109-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/07/2017] [Indexed: 12/20/2022] Open
Abstract
The herpes simplex virus (HSV) UL31 gene encodes a conserved member of the herpesvirus nuclear egress complex that not only functions in the egress of DNA containing capsids from the nucleus, but is also required for optimal replication of viral DNA and its packaging into capsids. Here we report that the UL31 protein from HSV-2 can be recruited to sites of DNA damage by sequences found in its N-terminus. The N-terminus of UL31 contains sequences resembling a poly (ADP-ribose) (PAR) binding motif suggesting that PAR interactions might mediate UL31 recruitment to damaged DNA. Whereas PAR polymerase inhibition prevented UL31 recruitment to damaged DNA, inhibition of signaling through the ataxia telangiectasia mutated DNA damage response pathway had no effect. These findings were further supported by experiments demonstrating direct and specific interaction between HSV-2 UL31 and PAR using purified components. This study reveals a previously unrecognized function for UL31 and may suggest that the recognition of PAR by UL31 is coupled to the nuclear egress of herpesvirus capsids, influences viral DNA replication and packaging, or possibly modulates the DNA damage response mounted by virally infected cells.
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Affiliation(s)
- Maxwell R Sherry
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Thomas J M Hay
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Michael A Gulak
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Arash Nassiri
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Renée L Finnen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Bruce W Banfield
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada.
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77
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Muster B, Rapp A, Cardoso MC. Systematic analysis of DNA damage induction and DNA repair pathway activation by continuous wave visible light laser micro-irradiation. AIMS GENETICS 2017; 4:47-68. [PMID: 31435503 PMCID: PMC6690239 DOI: 10.3934/genet.2017.1.47] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/16/2017] [Indexed: 01/19/2023]
Abstract
Laser micro-irradiation can be used to induce DNA damage with high spatial and temporal resolution, representing a powerful tool to analyze DNA repair in vivo in the context of chromatin. However, most lasers induce a mixture of DNA damage leading to the activation of multiple DNA repair pathways and making it impossible to study individual repair processes. Hence, we aimed to establish and validate micro-irradiation conditions together with inhibition of several key proteins to discriminate different types of DNA damage and repair pathways using lasers commonly available in confocal microscopes. Using time-lapse analysis of cells expressing fluorescently tagged repair proteins and also validation of the DNA damage generated by micro-irradiation using several key damage markers, we show that irradiation with a 405 nm continuous wave laser lead to the activation of all repair pathways even in the absence of exogenous sensitization. In contrast, we found that irradiation with 488 nm laser lead to the selective activation of non-processive short-patch base excision and single strand break repair, which were further validated by PARP inhibition and metoxyamine treatment. We conclude that these low energy conditions discriminated against processive long-patch base excision repair, nucleotide excision repair as well as double strand break repair pathways.
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Affiliation(s)
- Britta Muster
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Alexander Rapp
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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78
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Greulich KO. Manipulation of cells with laser microbeam scissors and optical tweezers: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:026601. [PMID: 28008877 DOI: 10.1088/1361-6633/80/2/026601] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The use of laser microbeams and optical tweezers in a wide field of biological applications from genomic to immunology is discussed. Microperforation is used to introduce a well-defined amount of molecules into cells for genetic engineering and optical imaging. The microwelding of two cells induced by a laser microbeam combines their genetic outfit. Microdissection allows specific regions of genomes to be isolated from a whole set of chromosomes. Handling the cells with optical tweezers supports investigation on the attack of immune systems against diseased or cancerous cells. With the help of laser microbeams, heart infarction can be simulated, and optical tweezers support studies on the heartbeat. Finally, laser microbeams are used to induce DNA damage in living cells for studies on cancer and ageing.
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79
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Kong X, Ball AR, Yokomori K. The Use of Laser Microirradiation to Investigate the Roles of Cohesins in DNA Repair. Methods Mol Biol 2017; 1515:227-242. [PMID: 27797083 DOI: 10.1007/978-1-4939-6545-8_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In addition to their mitotic and transcriptional functions, cohesin plays critical roles in DNA damage response (DDR) and repair. Specifically, cohesin promotes homologous recombination (HR) repair of DNA double-strand breaks (DSBs), which is conserved from yeast to humans, and is a critical effector of ATM/ATR DDR kinase-mediated checkpoint control in mammalian cells. Optical laser microirradiation has been instrumental in revealing the damage site-specific functions of cohesin and, more recently, uncovering the unique role of cohesin-SA2, one of the two cohesin complexes uniquely present in higher eukaryotes, in DNA repair in human cells. In this review, we briefly describe what we know about cohesin function and regulation in response to DNA damage, and discuss the optimized laser microirradiation conditions used to analyze cohesin responses to DNA damage in vivo.
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Affiliation(s)
- Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California-Irvine, 240D Med. Sci I, Irvine, CA, 92697-1700, USA
| | - Alexander R Ball
- Department of Biological Chemistry, School of Medicine, University of California-Irvine, 240D Med. Sci I, Irvine, CA, 92697-1700, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California-Irvine, 240D Med. Sci I, Irvine, CA, 92697-1700, USA.
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80
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Sellou H, Lebeaupin T, Chapuis C, Smith R, Hegele A, Singh HR, Kozlowski M, Bultmann S, Ladurner AG, Timinszky G, Huet S. The poly(ADP-ribose)-dependent chromatin remodeler Alc1 induces local chromatin relaxation upon DNA damage. Mol Biol Cell 2016; 27:3791-3799. [PMID: 27733626 PMCID: PMC5170603 DOI: 10.1091/mbc.e16-05-0269] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/15/2016] [Accepted: 10/05/2016] [Indexed: 11/19/2022] Open
Abstract
PARP1 and its effector, the ATP-dependent chromatin remodeler Alc1/Chd1L, are identified as key players during the rapid chromatin relaxation at DNA damage sites. Chromatin relaxation is one of the earliest cellular responses to DNA damage. However, what determines these structural changes, including their ATP requirement, is not well understood. Using live-cell imaging and laser microirradiation to induce DNA lesions, we show that the local chromatin relaxation at DNA damage sites is regulated by PARP1 enzymatic activity. We also report that H1 is mobilized at DNA damage sites, but, since this mobilization is largely independent of poly(ADP-ribosyl)ation, it cannot solely explain the chromatin relaxation. Finally, we demonstrate the involvement of Alc1, a poly(ADP-ribose)- and ATP-dependent remodeler, in the chromatin-relaxation process. Deletion of Alc1 impairs chromatin relaxation after DNA damage, while its overexpression strongly enhances relaxation. Altogether our results identify Alc1 as an important player in the fast kinetics of the NAD+- and ATP-dependent chromatin relaxation upon DNA damage in vivo.
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Affiliation(s)
- Hafida Sellou
- CNRS, UMR 6290, Institut Génétique et Développement de Rennes, 35043 Rennes, France.,Université de Rennes 1, Structure fédérative de recherche Biosit, 35043 Rennes, France.,Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Théo Lebeaupin
- CNRS, UMR 6290, Institut Génétique et Développement de Rennes, 35043 Rennes, France.,Université de Rennes 1, Structure fédérative de recherche Biosit, 35043 Rennes, France.,Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Catherine Chapuis
- CNRS, UMR 6290, Institut Génétique et Développement de Rennes, 35043 Rennes, France.,Université de Rennes 1, Structure fédérative de recherche Biosit, 35043 Rennes, France
| | - Rebecca Smith
- Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Anna Hegele
- Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Hari R Singh
- Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Marek Kozlowski
- Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Sebastian Bultmann
- Department of Biology II, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Andreas G Ladurner
- Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Biomedical Center Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Gyula Timinszky
- Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Sébastien Huet
- CNRS, UMR 6290, Institut Génétique et Développement de Rennes, 35043 Rennes, France .,Université de Rennes 1, Structure fédérative de recherche Biosit, 35043 Rennes, France
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81
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Sun X, Fu K, Hodgson A, Wier EM, Wen MG, Kamenyeva O, Xia X, Koo LY, Wan F. Sam68 Is Required for DNA Damage Responses via Regulating Poly(ADP-ribosyl)ation. PLoS Biol 2016; 14:e1002543. [PMID: 27635653 PMCID: PMC5026359 DOI: 10.1371/journal.pbio.1002543] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/04/2016] [Indexed: 01/08/2023] Open
Abstract
The rapid and robust synthesis of polymers of adenosine diphosphate (ADP)-ribose (PAR) chains, primarily catalyzed by poly(ADP-ribose) polymerase 1 (PARP1), is crucial for cellular responses to DNA damage. However, the precise mechanisms through which PARP1 is activated and PAR is robustly synthesized are not fully understood. Here, we identified Src-associated substrate during mitosis of 68 kDa (Sam68) as a novel signaling molecule in DNA damage responses (DDRs). In the absence of Sam68, DNA damage-triggered PAR production and PAR-dependent DNA repair signaling were dramatically diminished. With serial cellular and biochemical assays, we demonstrated that Sam68 is recruited to and significantly overlaps with PARP1 at DNA lesions and that the interaction between Sam68 and PARP1 is crucial for DNA damage-initiated and PARP1-conferred PAR production. Utilizing cell lines and knockout mice, we illustrated that Sam68-deleted cells and animals are hypersensitive to genotoxicity caused by DNA-damaging agents. Together, our findings suggest that Sam68 plays a crucial role in DDR via regulating DNA damage-initiated PAR production. The RNA-binding protein Sam68 has unexpected function in the early signaling of DNA damage, and is critical for the activation and regulation of poly(ADP-ribose) polymerase 1 in response to DNA damage. Maintaining genome integrity is crucial for all organisms, and failure to do so can lead to fatal diseases such as cancer. Exposure to challenging environments can induce DNA strand breaks or other lesions; thus, rapid and appropriate DNA damage responses (DDRs) need to be in place to detect and repair the damage. Cellular networks use a variety of signaling molecules and post-translational modifications that are crucial for the signaling of DNA breaks to repair machineries. Poly(adenosine diphosphate [ADP]-ribosyl)ation (PARylation) and activation of the enzyme poly(ADP-ribose) polymerase 1 (PARP1) is a post-translational modification that occurs within seconds upon DNA damage detection and triggers downstream DDR signaling; however, it remains obscure whether other molecules, beyond DNA strand breaks, stimulate or control PARP1 activity. We report here that a novel DDR signaling molecule, Src-associated substrate during mitosis of 68 kDa (Sam68), has a crucial function in governing the DNA damage-initiated PARP1 activation and polymers of ADP-ribose (PAR) production. We show that Sam68 is recruited to and significantly overlaps with PARP1 at DNA lesions and that the Sam68-PARP1 interaction is critical for DNA damage-initiated PARP1 activation and PAR production both in vitro and in vivo. Sam68-deleted cells and animals have a diminished PAR-dependent DNA repair signaling and are hypersensitive to genotoxicity caused by DNA-damaging agents. Hence, our data reveal an unexpected function for Sam68 in DNA damage-initiated early signaling and provide a novel mechanism on the activation and regulation of PARP1 in DDR.
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Affiliation(s)
- Xin Sun
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kai Fu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Andrea Hodgson
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Eric M. Wier
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Matthew G. Wen
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Olena Kamenyeva
- Biological Imaging Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xue Xia
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Lily Y. Koo
- Biological Imaging Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Fengyi Wan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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82
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Discrimination of Kinetic Models by a Combination of Microirradiation and Fluorescence Photobleaching. Biophys J 2016; 109:1551-64. [PMID: 26488646 DOI: 10.1016/j.bpj.2015.08.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 11/23/2022] Open
Abstract
Fluorescence recovery after photobleaching (FRAP) is an excellent tool to measure the chemical rate constants of fluorescently labeled proteins in living cells. Usually FRAP experiments are conducted with the protein concentrations being in a steady state, i.e., when the association and dissociation of the proteins are equilibrated. This is a strong limitation because situations in which rate constants change with time are of great scientific interest. In this study, we present an approach in which FRAP is used shortly after DNA damage introducing laser microirradiation, which results in the recruitment of the DNA clamp protein proliferating cell nuclear antigen (PCNA) to DNA lesions. We establish different kinetic models that are compatible with the observed PCNA recruitment data if FRAP is not used. By using FRAP at different time points during protein accumulation, we can not only exclude two out of three models, but we can also determine the rate constants with increased reliability. This study thus demonstrates the feasibility of using FRAP during protein recruitment and its application in the discrimination of possible kinetic models.
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83
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Dharmadhikari JA, Dharmadhikari AK, Kasuba KC, Bharambe H, D'Souza JS, Rathod KD, Mathur D. Optical control of filamentation-induced damage to DNA by intense, ultrashort, near-infrared laser pulses. Sci Rep 2016; 6:27515. [PMID: 27279565 PMCID: PMC4899723 DOI: 10.1038/srep27515] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 05/20/2016] [Indexed: 11/09/2022] Open
Abstract
We report on damage to DNA in an aqueous medium induced by ultrashort pulses of intense laser light of 800 nm wavelength. Focusing of such pulses, using lenses of various focal lengths, induces plasma formation within the aqueous medium. Such plasma can have a spatial extent that is far in excess of the Rayleigh range. In the case of water, the resulting ionization and dissociation gives rise to in situ generation of low-energy electrons and OH-radicals. Interactions of these with plasmid DNA produce nicks in the DNA backbone: single strand breaks (SSBs) are induced as are, at higher laser intensities, double strand breaks (DSBs). Under physiological conditions, the latter are not readily amenable to repair. Systematic quantification of SSBs and DSBs at different values of incident laser energy and under different external focusing conditions reveals that damage occurs in two distinct regimes. Numerical aperture is the experimental handle that delineates the two regimes, permitting simple optical control over the extent of DNA damage.
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Affiliation(s)
- J A Dharmadhikari
- Centre for Atomic and Molecular Physics, Manipal University, Manipal 576 104, India
| | - A K Dharmadhikari
- Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400 005, India
| | - K C Kasuba
- UM-DAE Centre for Excellence in Basic Sciences, Kalina Campus, Santacruz (East), Mumbai 400 098, India
| | - H Bharambe
- UM-DAE Centre for Excellence in Basic Sciences, Kalina Campus, Santacruz (East), Mumbai 400 098, India
| | - J S D'Souza
- UM-DAE Centre for Excellence in Basic Sciences, Kalina Campus, Santacruz (East), Mumbai 400 098, India
| | - K D Rathod
- Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400 005, India
| | - D Mathur
- Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400 005, India
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84
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Two-photon excited photoconversion of cyanine-based dyes. Sci Rep 2016; 6:23866. [PMID: 27029524 PMCID: PMC4814926 DOI: 10.1038/srep23866] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/15/2016] [Indexed: 12/02/2022] Open
Abstract
The advent of phototransformable fluorescent proteins has led to significant advances in optical imaging, including the unambiguous tracking of cells over large spatiotemporal scales. However, these proteins typically require activating light in the UV-blue spectrum, which limits their in vivo applicability due to poor light penetration and associated phototoxicity on cells and tissue. We report that cyanine-based, organic dyes can be efficiently photoconverted by nonlinear excitation at the near infrared (NIR) window. Photoconversion likely involves singlet-oxygen mediated photochemical cleavage, yielding blue-shifted fluorescent products. Using SYTO62, a biocompatible and cell-permeable dye, we demonstrate photoconversion in a variety of cell lines, including depth-resolved labeling of cells in 3D culture. Two-photon photoconversion of cyanine-based dyes offer several advantages over existing photoconvertible proteins, including use of minimally toxic NIR light, labeling without need for genetic intervention, rapid kinetics, remote subsurface targeting, and long persistence of photoconverted signal. These findings are expected to be useful for applications involving rapid labeling of cells deep in tissue.
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85
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Mistrik M, Vesela E, Furst T, Hanzlikova H, Frydrych I, Gursky J, Majera D, Bartek J. Cells and Stripes: A novel quantitative photo-manipulation technique. Sci Rep 2016; 6:19567. [PMID: 26777522 PMCID: PMC4726120 DOI: 10.1038/srep19567] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/10/2015] [Indexed: 12/17/2022] Open
Abstract
Laser micro-irradiation is a technology widely used in the DNA damage response, checkpoint signaling, chromatin remodeling and related research fields, to assess chromatin modifications and recruitment of diverse DNA damage sensors, mediators and repair proteins to sites of DNA lesions. While this approach has aided numerous discoveries related to cell biology, maintenance of genome integrity, aging and cancer, it has so far been limited by a tedious manual definition of laser-irradiated subcellular regions, with the ensuing restriction to only a small number of cells treated and analyzed in a single experiment. Here, we present an improved and versatile alternative to the micro-irradiation approach: Quantitative analysis of photo-manipulated samples using innovative settings of standard laser-scanning microscopes. Up to 200 cells are simultaneously exposed to a laser beam in a defined pattern of collinear rays. The induced striation pattern is then automatically evaluated by a simple algorithm, which provides a quantitative assessment of various laser-induced phenotypes in live or fixed cells. Overall, this new approach represents a more robust alternative to existing techniques, and provides a versatile tool for a wide range of applications in biomedicine.
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Affiliation(s)
- Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Eva Vesela
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Tomas Furst
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Hana Hanzlikova
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic
| | - Ivo Frydrych
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Jan Gursky
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Dusana Majera
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Jiri Bartek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.,Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic.,Danish Cancer Society Research Center, Copenhagen, Denmark
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86
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Solarczyk KJ, Kordon M, Berniak K, Dobrucki JW. Two stages of XRCC1 recruitment and two classes of XRCC1 foci formed in response to low level DNA damage induced by visible light, or stress triggered by heat shock. DNA Repair (Amst) 2016; 37:12-21. [PMID: 26630398 DOI: 10.1016/j.dnarep.2015.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 12/18/2022]
Abstract
Induction of local photosensitised DNA damage has been used to study recruitment of repair factors, spatial organisation and subsequent stages of the repair processes. However, the damage induced by a focused laser beam interacting with a photosensitiser may not fully reflect the types of damage and repair encountered in cells of an animal under typical conditions in vivo. We report on two characteristic stages of recruitment of XRCC1 (a protein engaged in BER and SSB repair pathways), in response to low level DNA damage induced by visible light. We demonstrate that, when just a few DNA breaks are induced in a small region of the nucleus, the recruited XRCC1 is initially distributed uniformly throughout this region, and rearranges into several small stationary foci within minutes. In contrast, when heavy damage of various types (including oxidative damage) is induced in cells pre-sensitized with a DNA-binding drug ethidium bromide, XRCC1 is also recruited but fails to rearrange from the stage of the uniform distribution to the stage of several small foci, indicating that this heavy damage interferes with the progress and completion of the repair processes. We hypothesize that that first stage may reflect recruitment of XRCC1 to poly(ADP-ribose) moieties in the region surrounding the single-strand break, while the second-binding directly to the DNA lesions. We also show that moderate damage or stress induces formation of two types of XRCC1-containing foci differing in their mobility. A large subset of DNA damage-induced XRCC1 foci is associated with a major component of PML nuclear bodies--the Sp100 protein.
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Affiliation(s)
- Kamil J Solarczyk
- Division of Cell Biophysics Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Magdalena Kordon
- Division of Cell Biophysics Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Krzysztof Berniak
- Division of Cell Biophysics Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Jurek W Dobrucki
- Division of Cell Biophysics Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University ul. Gronostajowa 7, 30-387 Kraków, Poland.
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87
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Dalbosco L, Zanini G, D'Amato E, Tessarolo F, Boi S, Bauer P, Haase A, Antolini R. Photodamage in deep tissue two-photon optical biopsy of human skin. JOURNAL OF BIOPHOTONICS 2015; 8:816-825. [PMID: 25524048 DOI: 10.1002/jbio.201400083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/14/2014] [Accepted: 11/17/2014] [Indexed: 06/04/2023]
Abstract
Photodamage, induced by femtosecond laser radiation, was studied in thick samples of human skin tissue (healthy skin and neoplastic lesions). Photobleaching, photoionization, and thermomechanical damage effects were characterized comparatively. The laser power dependence of the damage rates allowed to connect macroscopic effects to underlying molecular processes. Optical effects were correlated to histopathological changes. Tissue alterations were found only from thermomechanical cavitation and limited to superficial layers of the epidermis. From the depth-dependencies of all damage thresholds a depth-dependent power-compensation scheme was defined allowing for damage-free deep tissue optical biopsy. Damage-induced luminescence pattern for different excitation powers and a corresponding threshold analysis.
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Affiliation(s)
- Luca Dalbosco
- BIOtech Center and Department of Industrial Engineering, University of Trento, via delle Regole 101, 38123, Mattarello, Italy
| | - Giulia Zanini
- Department of Physics, University of Trento, via Sommarive 14, 38123, Povo, Italy
| | - Elvira D'Amato
- Department of Physics, University of Trento, via Sommarive 14, 38123, Povo, Italy
| | - Francesco Tessarolo
- BIOtech Center and Department of Industrial Engineering, University of Trento, via delle Regole 101, 38123, Mattarello, Italy
- Healthcare Research and Innovation Program (IRCS), Bruno Kessler Foundation, via Sommarive 18, 38123, Trento, Italy
| | - Sebastiana Boi
- Department of Pathology, APSS, S. Chiara Hospital, Largo Medaglie d'Oro 9, 38122, Trento, Italy
| | - Paolo Bauer
- Department of Dermatology, APSS, S. Chiara Hospital, Largo Medaglie d'Oro 9, 38122, Trento, Italy
| | - Albrecht Haase
- Department of Physics, University of Trento, via Sommarive 14, 38123, Povo, Italy.
| | - Renzo Antolini
- Department of Physics, University of Trento, via Sommarive 14, 38123, Povo, Italy
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88
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Saquilabon Cruz GM, Kong X, Silva BA, Khatibzadeh N, Thai R, Berns MW, Yokomori K. Femtosecond near-infrared laser microirradiation reveals a crucial role for PARP signaling on factor assemblies at DNA damage sites. Nucleic Acids Res 2015; 44:e27. [PMID: 26424850 PMCID: PMC4756852 DOI: 10.1093/nar/gkv976] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/18/2015] [Indexed: 01/04/2023] Open
Abstract
Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affect the amounts and types of damage and the DDR. We compared different irradiation conditions using a femtosecond near-infrared laser and found distinct damage site recruitment thresholds for 53BP1 and TRF2 correlating with the dose-dependent increase of strand breaks and damage complexity. Low input-power microirradiation that induces relatively simple strand breaks led to robust recruitment of 53BP1 but not TRF2. In contrast, increased strand breaks with complex damage including crosslinking and base damage generated by high input-power microirradiation resulted in TRF2 recruitment to damage sites with no 53BP1 clustering. We found that poly(ADP-ribose) polymerase (PARP) activation distinguishes between the two damage states and that PARP activation is essential for rapid TRF2 recruitment while suppressing 53BP1 accumulation at damage sites. Thus, our results reveal that careful titration of laser irradiation conditions allows induction of varying amounts and complexities of DNA damage that are gauged by differential PARP activation regulating protein assembly at the damage site.
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Affiliation(s)
- Gladys Mae Saquilabon Cruz
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, 1002 Health Sciences Road East, Irvine, CA 92612, USA
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Bárbara Alcaraz Silva
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, 1002 Health Sciences Road East, Irvine, CA 92612, USA Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, CA 92617, USA
| | - Nima Khatibzadeh
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, 1002 Health Sciences Road East, Irvine, CA 92612, USA
| | - Ryan Thai
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Michael W Berns
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, 1002 Health Sciences Road East, Irvine, CA 92612, USA Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, CA 92617, USA Department of Biomedical Engineering and Surgery, University of California, Irvine, CA 92617, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
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89
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Schomaker M, Killian D, Willenbrock S, Heinemann D, Kalies S, Ngezahayo A, Nolte I, Ripken T, Junghanß C, Meyer H, Murua Escobar H, Heisterkamp A. Biophysical effects in off-resonant gold nanoparticle mediated (GNOME) laser transfection of cell lines, primary- and stem cells using fs laser pulses. JOURNAL OF BIOPHOTONICS 2015; 8:646-58. [PMID: 25302483 DOI: 10.1002/jbio.201400065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/29/2014] [Accepted: 09/16/2014] [Indexed: 05/03/2023]
Abstract
Gold nanoparticle mediated (GNOME) laser transfection is a powerful technique to deliver small biologically relevant molecules into cells. However, the transfection of larger and especially negatively charged DNA remains challenging. The efficiency for pDNA was 0.57% using parameter that does not influence the endo- and exogenous DNA. In order to gain a deeper understanding of the actual molecule uptake process, the uptake efficiency was determined using molecules of different sizes. It was evaluated that uncharged dextran molecules (2000 kDa) were delivered with an efficiency of 68%. The intracellular distribution of injected molecules was visualized and larger molecules were primary found in the cytoplasm. Patch clamp measurements suggested a permeabilization time up to 15 minutes. The uptake efficiency depended on the size and charge of the molecule to deliver as well as the cell size. A minor role for transfection plays the cell type since primary stem cells were successfully transfected. The perforation efficiency of semi-adherent and suspension cells is influenced by the cell and molecule size.
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Affiliation(s)
- Markus Schomaker
- Biomedical Optics Department, Laser Zentrum Hannover e. V., Hollerithallee 8, 30419, Hannover, Germany.
| | - Doreen Killian
- Department Hematology, Oncology and Palliative Medicine, University of Rostock, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Saskia Willenbrock
- Small Animal Clinic, University of Veterinary Medicine Hannover, Bünteweg 9, 30559, Hannover, Germany
| | - Dag Heinemann
- Biomedical Optics Department, Laser Zentrum Hannover e. V., Hollerithallee 8, 30419, Hannover, Germany
| | - Stefan Kalies
- Biomedical Optics Department, Laser Zentrum Hannover e. V., Hollerithallee 8, 30419, Hannover, Germany
| | - Anaclet Ngezahayo
- Institute of Biophysics, Leibniz University Hannover, Herrenhaeuserstr. 2, 30419, Hannover, Germany
| | - Ingo Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover, Bünteweg 9, 30559, Hannover, Germany
| | - Tammo Ripken
- Biomedical Optics Department, Laser Zentrum Hannover e. V., Hollerithallee 8, 30419, Hannover, Germany
| | - Christian Junghanß
- Department Hematology, Oncology and Palliative Medicine, University of Rostock, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Heiko Meyer
- Biomedical Optics Department, Laser Zentrum Hannover e. V., Hollerithallee 8, 30419, Hannover, Germany
- Department of Cardiothoracic Transplantation and Vascular Surgery, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Hugo Murua Escobar
- Department Hematology, Oncology and Palliative Medicine, University of Rostock, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
- Small Animal Clinic, University of Veterinary Medicine Hannover, Bünteweg 9, 30559, Hannover, Germany
| | - Alexander Heisterkamp
- Biomedical Optics Department, Laser Zentrum Hannover e. V., Hollerithallee 8, 30419, Hannover, Germany
- Institut für Quantenoptik, Leibniz Universität Hannover, Welfengarten 1, 30167, Hannover, Germany
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90
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Micro-irradiation tools to visualize base excision repair and single-strand break repair. DNA Repair (Amst) 2015; 31:52-63. [PMID: 25996408 DOI: 10.1016/j.dnarep.2015.05.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/30/2015] [Accepted: 05/02/2015] [Indexed: 12/30/2022]
Abstract
Microscopy and micro-irradiation imaging techniques have significantly advanced our knowledge of DNA damage tolerance and the assembly of DNA repair proteins at the sites of damage. While these tools have been extensively applied to the study of nucleotide excision repair and double-strand break repair, their application to the repair of oxidatively-induced base lesions and single-strand breaks is just beginning to yield new insights. This review will focus on examining micro-irradiation techniques reported to create base lesions and single-strand breaks; these lesions are considered to be primarily addressed by proteins involved in the base excision repair (BER) pathway. By examining conditions for generating these DNA lesions and reviewing information on the assembly and dissociation of repair complexes at the induced lesion sites, we hope to promote further investigations into BER and to stimulate further development and enhancement of these techniques for the study of BER.
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91
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Reynolds P, Cooper S, Lomax M, O'Neill P. Disruption of PARP1 function inhibits base excision repair of a sub-set of DNA lesions. Nucleic Acids Res 2015; 43:4028-38. [PMID: 25813046 PMCID: PMC4417162 DOI: 10.1093/nar/gkv250] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 01/18/2023] Open
Abstract
The repair of endogenously induced DNA damage is essential to maintain genomic integrity. It has been shown that XRCC1 and PARP1 are involved in the repair of base lesions and SSBs, although the exact mode of action has yet to be determined. Here we show that XRCC1 is involved in the repair of base lesions and SSBs independent of the cell cycle. However, the rate of repair of damage requiring XRCC1 does reflect the damage complexity. The repair of induced DNA damage occurs by PARP1-dependent and PARP1-independent sub-pathways of BER. It is suggested that the repair of SSBs and purine base damage is by a sub-pathway of BER that requires both XRCC1 and PARP1. Repair of pyrimidine base damage may require XRCC1 but does not require PARP1 activity. Therefore, although BER of simple lesions occurs rapidly, pathway choice and the involvement of PARP1 are highly dependent on the types of lesion induced.
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Affiliation(s)
- Pamela Reynolds
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sarah Cooper
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Martine Lomax
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Peter O'Neill
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
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92
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Lebeaupin T, Sellou H, Timinszky G, Huet S. Chromatin dynamics at DNA breaks: what, how and why? AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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93
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Abdou I, Poirier GG, Hendzel MJ, Weinfeld M. DNA ligase III acts as a DNA strand break sensor in the cellular orchestration of DNA strand break repair. Nucleic Acids Res 2014; 43:875-92. [PMID: 25539916 PMCID: PMC4333375 DOI: 10.1093/nar/gku1307] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In the current model of DNA SSBR, PARP1 is regarded as the sensor of single-strand breaks (SSBs). However, biochemical studies have implicated LIG3 as another possible SSB sensor. Using a laser micro-irradiation protocol that predominantly generates SSBs, we were able to demonstrate that PARP1 is dispensable for the accumulation of different single-strand break repair (SSBR) proteins at sites of DNA damage in live cells. Furthermore, we show in live cells for the first time that LIG3 plays a role in mediating the accumulation of the SSBR proteins XRCC1 and PNKP at sites of DNA damage. Importantly, the accumulation of LIG3 at sites of DNA damage did not require the BRCT domain-mediated interaction with XRCC1. We were able to show that the N-terminal ZnF domain of LIG3 plays a key role in the enzyme's SSB sensing function. Finally, we provide cellular evidence that LIG3 and not PARP1 acts as the sensor for DNA damage caused by the topoisomerase I inhibitor, irinotecan. Our results support the existence of a second damage-sensing mechanism in SSBR involving the detection of nicks in the genome by LIG3.
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Affiliation(s)
- Ismail Abdou
- Department of Oncology, University of Alberta, and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Guy G Poirier
- Cancer Axis, CHUQ Research Center and Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
| | - Michael J Hendzel
- Department of Oncology, University of Alberta, and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, and Cross Cancer Institute, Edmonton, Alberta, Canada
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94
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Ouyang J, Garner E, Hallet A, Nguyen HD, Rickman KA, Gill G, Smogorzewska A, Zou L. Noncovalent interactions with SUMO and ubiquitin orchestrate distinct functions of the SLX4 complex in genome maintenance. Mol Cell 2014; 57:108-22. [PMID: 25533185 DOI: 10.1016/j.molcel.2014.11.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 09/17/2014] [Accepted: 11/04/2014] [Indexed: 11/20/2022]
Abstract
SLX4, a coordinator of multiple DNA structure-specific endonucleases, is important for several DNA repair pathways. Noncovalent interactions of SLX4 with ubiquitin are required for localizing SLX4 to DNA interstrand crosslinks (ICLs), yet how SLX4 is targeted to other functional contexts remains unclear. Here, we show that SLX4 binds SUMO-2/3 chains via SUMO-interacting motifs (SIMs). The SIMs of SLX4 are dispensable for ICL repair but important for processing CPT-induced replication intermediates, suppressing fragile site instability, and localizing SLX4 to ALT telomeres. The localization of SLX4 to laser-induced DNA damage also requires the SIMs, as well as DNA end resection, UBC9, and MDC1. Furthermore, the SUMO binding of SLX4 enhances its interaction with specific DNA-damage sensors or telomere-binding proteins, including RPA, MRE11-RAD50-NBS1, and TRF2. Thus, the interactions of SLX4 with SUMO and ubiquitin increase its affinity for factors recognizing different DNA lesions or telomeres, helping to direct the SLX4 complex in distinct functional contexts.
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Affiliation(s)
- Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Elizabeth Garner
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY 10065, USA
| | - Alexander Hallet
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Hai Dang Nguyen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kimberly A Rickman
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY 10065, USA
| | - Grace Gill
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY 10065, USA.
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.
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95
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Guarino E, Cojoc G, García-Ulloa A, Tolić IM, Kearsey SE. Real-time imaging of DNA damage in yeast cells using ultra-short near-infrared pulsed laser irradiation. PLoS One 2014; 9:e113325. [PMID: 25409521 PMCID: PMC4237433 DOI: 10.1371/journal.pone.0113325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/22/2014] [Indexed: 01/12/2023] Open
Abstract
Analysis of accumulation of repair and checkpoint proteins at repair sites in yeast nuclei has conventionally used chemical agents, ionizing radiation or induction of endonucleases to inflict localized damage. In addition to these methods, similar studies in mammalian cells have used laser irradiation, which has the advantage that damage is inflicted at a specific nuclear region and at a precise time, and this allows accurate kinetic analysis of protein accumulation at DNA damage sites. We show here that it is feasible to use short pulses of near-infrared laser irradiation to inflict DNA damage in subnuclear regions of yeast nuclei by multiphoton absorption. In conjunction with use of fluorescently-tagged proteins, this allows quantitative analysis of protein accumulation at damage sites within seconds of damage induction. PCNA accumulated at damage sites rapidly, such that maximum accumulation was seen approximately 50 s after damage, then levels declined linearly over 200-1000 s after irradiation. RPA accumulated with slower kinetics such that hardly any accumulation was detected within 60 s of irradiation, and levels subsequently increased linearly over the next 900 s, after which levels were approximately constant (up to ca. 2700 s) at the damage site. This approach complements existing methodologies to allow analysis of key damage sensors and chromatin modification changes occurring within seconds of damage inception.
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Affiliation(s)
- Estrella Guarino
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Gheorghe Cojoc
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Iva M. Tolić
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Stephen E. Kearsey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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96
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Dhakal K, Black B, Mohanty S. Introduction of impermeable actin-staining molecules to mammalian cells by optoporation. Sci Rep 2014; 4:6553. [PMID: 25315642 PMCID: PMC4197434 DOI: 10.1038/srep06553] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/02/2014] [Indexed: 12/21/2022] Open
Abstract
The selective insertion of foreign materials, such as fluorescent markers or plasmids, into living cells has been a challenging problem in cell biology due to the cell membrane's selective permeability. However, it is often necessary that researchers insert such materials into cells for various dynamical and/or drug delivery studies. This problem becomes even more challenging if the study is to be limited to specific cells within a larger population, since other transfection methods, such as viral transfection and lipofection, are not realizable with a high degree of spatial selectivity. Here, we have used a focused femtosecond laser beam to create a small transient hole in the cellular membrane (optoporation) in order to inject nanomolar concentrations of rhodamine phalloidin (an impermeable dye molecule for staining filamentous actin) into targeted living mammalian cells (both HEK and primary cortical neurons). Following optoporation, the dye bound to the intracellular actin network and rise in fluorescence intensity was observed. Theoretical dynamics of the dye's diffusion is discussed, and numerical simulations of diffusion time constants are found to match well with experimental values.
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Affiliation(s)
- Kamal Dhakal
- Biophysics and Physiology Lab, Department of Physics, University of Texas at Arlington, Texas, USA
| | - Bryan Black
- Biophysics and Physiology Lab, Department of Physics, University of Texas at Arlington, Texas, USA
| | - Samarendra Mohanty
- Biophysics and Physiology Lab, Department of Physics, University of Texas at Arlington, Texas, USA
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97
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Thomas G, van Voskuilen J, Gerritsen HC, Sterenborg HJCM. Advances and challenges in label-free nonlinear optical imaging using two-photon excitation fluorescence and second harmonic generation for cancer research. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 141:128-38. [PMID: 25463660 DOI: 10.1016/j.jphotobiol.2014.08.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 08/20/2014] [Accepted: 08/23/2014] [Indexed: 11/28/2022]
Abstract
Nonlinear optical imaging (NLOI) has emerged to be a promising tool for bio-medical imaging in recent times. Among the various applications of NLOI, its utility is the most significant in the field of pre-clinical and clinical cancer research. This review begins by briefly covering the core principles involved in NLOI, such as two-photon excitation fluorescence (TPEF) and second harmonic generation (SHG). Subsequently, there is a short description on the various cellular components that contribute to endogenous optical fluorescence. Later on the review deals with its main theme--the challenges faced during label-free NLO imaging in translational cancer research. While this review addresses the accomplishment of various label-free NLOI based studies in cancer diagnostics, it also touches upon the limitations of the mentioned studies. In addition, areas in cancer research that need to be further investigated by label-free NLOI are discussed in a latter segment. The review eventually concludes on the note that label-free NLOI has and will continue to contribute richly in translational cancer research, to eventually provide a very reliable, yet minimally invasive cancer diagnostic tool for the patient.
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Affiliation(s)
- Giju Thomas
- Department of Biomedical Engineering and Physics, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Centre for Optical Diagnostics and Therapy, Erasmus Medical Centre, Post Box 2040, 3000 CA, Rotterdam, the Netherlands.
| | - Johan van Voskuilen
- Department of Molecular Biophysics, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Hans C Gerritsen
- Department of Molecular Biophysics, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - H J C M Sterenborg
- Department of Biomedical Engineering and Physics, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
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98
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Chandsawangbhuwana C, Shi LZ, Zhu Q, Berns MW. Real-time calcium measurements of live optically trapped microorganisms. JOURNAL OF BIOPHOTONICS 2014; 7:571-579. [PMID: 23576396 DOI: 10.1002/jbio.201200209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/06/2013] [Accepted: 03/18/2013] [Indexed: 06/02/2023]
Abstract
A system has been developed that allows for the real-time measurement of calcium dynamics in swimming sperm. Specifically, the ratiometric dye Indo-I is used as a fluorescent indicator of intracellular calcium dynamics. The dual emissions are collected by a high-sensitivity back-illuminated CCD camera coupled to a Dual-View imaging system. From the CCD, the images are sent to a custom developed algorithm which processes the images and outputs the calcium measurements in real-time. Additionally, sperm velocity and position data are processed and outputted in real-time. The velocity and position data are obtained using a separate coupled red light (>670 nm) phase contrast imaging setup that does not optically interfere with the fluorescent imaging. Using this system the effects of optical trapping on calcium dynamics was determined. Optical trapping of sperm with a decaying focused laser power of 510 mW to 3 mW over 8 seconds causes a statistically insignificant change in calcium dynamics between in-trap and out-of-trap conditions. Progesterone, a calcium activator, was added and sperm were trapped under the 8 second power decay conditions. Progesterone treated sperm has a statistically higher average calcium level than untreated sperm, but shows no statistical difference between progesterone treated in-trap and out-of-trap conditions. Trapping at 16 seconds at 510 mW without decay, which have been shown to decrease sperm motility, shows a statistical difference between baseline pre-trap and in-trap intracellular calcium levels.
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Affiliation(s)
- Charlie Chandsawangbhuwana
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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99
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Britton S, Dernoncourt E, Delteil C, Froment C, Schiltz O, Salles B, Frit P, Calsou P. DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal. Nucleic Acids Res 2014; 42:9047-62. [PMID: 25030905 PMCID: PMC4132723 DOI: 10.1093/nar/gku601] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We previously identified the heterogeneous ribonucleoprotein SAF-A/hnRNP U as a substrate for DNA-PK, a protein kinase involved in DNA damage response (DDR). Using laser micro-irradiation in human cells, we report here that SAF-A exhibits a two-phase dynamics at sites of DNA damage, with a rapid and transient recruitment followed by a prolonged exclusion. SAF-A recruitment corresponds to its binding to Poly(ADP-ribose) while its exclusion is dependent on the activity of ATM, ATR and DNA-PK and reflects the dissociation from chromatin of SAF-A associated with ongoing transcription. Having established that SAF-A RNA-binding domain recapitulates SAF-A dynamics, we show that this domain is part of a complex comprising several mRNA biogenesis proteins of which at least two, FUS/TLS and TAFII68/TAF15, exhibit similar biphasic dynamics at sites of damage. Using an original reporter for live imaging of DNA:RNA hybrids (R-loops), we show a transient transcription-dependent accumulation of R-loops at sites of DNA damage that is prolonged upon inhibition of RNA biogenesis factors exclusion. We propose that a new component of the DDR is an active anti-R-loop mechanism operating at damaged transcribed sites which includes the exclusion of mRNA biogenesis factors such as SAF-A, FUS and TAF15.
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Affiliation(s)
- Sébastien Britton
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Emma Dernoncourt
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Christine Delteil
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Carine Froment
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Odile Schiltz
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Bernard Salles
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
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Concerted activities of distinct H4K20 methyltransferases at DNA double-strand breaks regulate 53BP1 nucleation and NHEJ-directed repair. Cell Rep 2014; 8:430-8. [PMID: 25001286 DOI: 10.1016/j.celrep.2014.06.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/04/2014] [Accepted: 06/09/2014] [Indexed: 12/28/2022] Open
Abstract
Although selective binding of 53BP1 to dimethylated histone H4 lysine 20 (H4K20me2) at DNA double-strand breaks (DSBs) is a necessary and pivotal determinant of nonhomologous end joining (NHEJ)-directed repair, the enzymes that generate H4K20me2 at DSBs were unclear. Here, we determined that the PR-Set7 monomethyltransferase (H4K20me1) regulates de novo H4K20 methylation at DSBs. Rapid recruitment of PR-Set7 to DSBs was dependent on the NHEJ Ku70 protein and necessary for NHEJ-directed repair. PR-Set7 monomethyltransferase activity was required, but insufficient, for H4K20me2 and 53BP1 nucleation at DSBs. We determined that PR-Set7-mediated H4K20me1 facilitates Suv4-20 methyltransferase recruitment and catalysis to generate H4K20me2 necessary for 53BP1 binding. The orchestrated and concerted activities of PR-Set7 and Suv4-20 were required for proficient 53BP1 nucleation and DSB repair. This report identifies PR-Set7 as an essential component of NHEJ and implicates PR-Set7 as a central determinant of NHEJ-directed repair early in mammalian DSB repair pathway choice.
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