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Zong D, Jakob B, Lundholm L. Editorial: DNA damage response in the context of chromatin. Front Cell Dev Biol 2023; 10:1095652. [PMID: 36704204 PMCID: PMC9871355 DOI: 10.3389/fcell.2022.1095652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/27/2022] [Indexed: 01/12/2023] Open
Affiliation(s)
- Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Lovisa Lundholm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden,*Correspondence: Lovisa Lundholm,
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Baiocco G, Bartzsch S, Conte V, Friedrich T, Jakob B, Tartas A, Villagrasa C, Prise KM. A matter of space: how the spatial heterogeneity in energy deposition determines the biological outcome of radiation exposure. Radiat Environ Biophys 2022; 61:545-559. [PMID: 36220965 PMCID: PMC9630194 DOI: 10.1007/s00411-022-00989-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/03/2022] [Indexed: 05/10/2023]
Abstract
The outcome of the exposure of living organisms to ionizing radiation is determined by the distribution of the associated energy deposition at different spatial scales. Radiation proceeds through ionizations and excitations of hit molecules with an ~ nm spacing. Approaches such as nanodosimetry/microdosimetry and Monte Carlo track-structure simulations have been successfully adopted to investigate radiation quality effects: they allow to explore correlations between the spatial clustering of such energy depositions at the scales of DNA or chromosome domains and their biological consequences at the cellular level. Physical features alone, however, are not enough to assess the entity and complexity of radiation-induced DNA damage: this latter is the result of an interplay between radiation track structure and the spatial architecture of chromatin, and further depends on the chromatin dynamic response, affecting the activation and efficiency of the repair machinery. The heterogeneity of radiation energy depositions at the single-cell level affects the trade-off between cell inactivation and induction of viable mutations and hence influences radiation-induced carcinogenesis. In radiation therapy, where the goal is cancer cell inactivation, the delivery of a homogenous dose to the tumour has been the traditional approach in clinical practice. However, evidence is accumulating that introducing heterogeneity with spatially fractionated beams (mini- and microbeam therapy) can lead to significant advantages, particularly in sparing normal tissues. Such findings cannot be explained in merely physical terms, and their interpretation requires considering the scales at play in the underlying biological mechanisms, suggesting a systemic response to radiation.
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Affiliation(s)
- Giorgio Baiocco
- Radiation Biophysics and Radiobiology Group, Physics Department, University of Pavia, Pavia, Italy.
| | - Stefan Bartzsch
- Institute for Radiation Medicine, Helmholtz Centre Munich, Munich, Germany
- Department of Radiation Oncology, Technical University of Munich, Munich, Germany
| | - Valeria Conte
- Istituto Nazionale Di Fisica Nucleare INFN, Laboratori Nazionali Di Legnaro, Legnaro, Italy
| | - Thomas Friedrich
- Department of Biophysics, GSI Helmholtz Centre for Heavy Ion Research, Darmstadt, Germany
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtz Centre for Heavy Ion Research, Darmstadt, Germany
| | - Adrianna Tartas
- Biomedical Physics Division, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay aux Roses, France
| | - Kevin M Prise
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
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Averbeck NB, Barent C, Jakob B, Syzonenko T, Durante M, Taucher-Scholz G. The Ubiquitin Ligase RNF138 Cooperates with CtIP to Stimulate Resection of Complex DNA Double-Strand Breaks in Human G1-Phase Cells. Cells 2022; 11:cells11162561. [PMID: 36010636 PMCID: PMC9406464 DOI: 10.3390/cells11162561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Abstract
DNA double-strand breaks (DSBs) represent the molecular origin of ionizing-radiation inflicted biological effects. An increase in the ionization density causes more complex, clustered DSBs that can be processed by resection also in G1 phase, where repair of resected DSBs is considered erroneous and may contribute to the increased biological effectiveness of heavy ions in radiotherapy. To investigate the resection regulation of complex DSBs, we exposed G1 cells depleted for different candidate factors to heavy ions or α-particle radiation. Immunofluorescence microscopy was used to monitor the resection marker RPA, the DSB marker γH2AX and the cell-cycle markers CENP-F and geminin. The Fucci system allowed to select G1 cells, cell survival was measured by clonogenic assay. We show that in G1 phase the ubiquitin ligase RNF138 functions in resection regulation. RNF138 ubiquitinates the resection factor CtIP in a radiation-dependent manner to allow its DSB recruitment in G1 cells. At complex DSBs, RNF138′s participation becomes more relevant, consistent with the observation that also resection is more frequent at these DSBs. Furthermore, deficiency of RNF138 affects both DSB repair and cell survival upon induction of complex DSBs. We conclude that RNF138 is a regulator of resection that is influenced by DSB complexity and can affect the quality of DSB repair in G1 cells.
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Affiliation(s)
- Nicole B. Averbeck
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
- Correspondence:
| | - Carina Barent
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstr. 11, 64287 Darmstadt, Germany
| | - Tatyana Syzonenko
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
| | - Marco Durante
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
- Department of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6–8, 64289 Darmstadt, Germany
| | - Gisela Taucher-Scholz
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291 Darmstadt, Germany
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstr. 11, 64287 Darmstadt, Germany
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Goetting I, Larafa S, Eul K, Kunin M, Jakob B, Matschke J, Jendrossek V. Targeting AKT-Dependent Regulation of Antioxidant Defense Sensitizes AKT-E17K Expressing Cancer Cells to Ionizing Radiation. Front Oncol 2022; 12:920017. [PMID: 35875130 PMCID: PMC9304891 DOI: 10.3389/fonc.2022.920017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Aberrant activation of the phosphatidyl-inositol-3-kinase/protein kinase B (AKT) pathway has clinical relevance to radiation resistance, but the underlying mechanisms are incompletely understood. Protection against reactive oxygen species (ROS) plays an emerging role in the regulation of cell survival upon irradiation. AKT-dependent signaling participates in the regulation of cellular antioxidant defense. Here, we were interested to explore a yet unknown role of aberrant activation of AKT in regulating antioxidant defense in response to IR and associated radiation resistance.We combined genetic and pharmacologic approaches to study how aberrant activation of AKT impacts cell metabolism, antioxidant defense, and radiosensitivity. Therefore, we used TRAMPC1 (TrC1) prostate cancer cells overexpressing the clinically relevant AKT-variant AKT-E17K with increased AKT activity or wildtype AKT (AKT-WT) and analyzed the consequences of direct AKT inhibition (MK2206) and inhibition of AKT-dependent metabolic enzymes on the levels of cellular ROS, antioxidant capacity, metabolic state, short-term and long-term survival without and with irradiation.TrC1 cells expressing the clinically relevant AKT1-E17K variant were characterized by improved antioxidant defense compared to TrC1 AKT-WT cells and this was associated with increased radiation resistance. The underlying mechanisms involved AKT-dependent direct and indirect regulation of cellular levels of reduced glutathione (GSH). Pharmacologic inhibition of specific AKT-dependent metabolic enzymes supporting defense against oxidative stress, e.g., inhibition of glutathione synthase and glutathione reductase, improved eradication of clonogenic tumor cells, particularly of TrC1 cells overexpressing AKT-E17K.We conclude that improved capacity of TrC1 AKT-E17K cells to balance antioxidant defense with provision of energy and other metabolites upon irradiation compared to TrC1 AKT-WT cells contributes to their increased radiation resistance. Our findings on the importance of glutathione de novo synthesis and glutathione regeneration for radiation resistance of TrC1 AKT-E17K cells offer novel perspectives for improving radiosensitivity in cancer cells with aberrant AKT activity by combining IR with inhibitors targeting AKT-dependent regulation of GSH provision.
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Affiliation(s)
- Isabell Goetting
- Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany
| | - Safa Larafa
- Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany
| | - Katharina Eul
- Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany
| | - Mikhail Kunin
- Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Johann Matschke
- Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany
- *Correspondence: Verena Jendrossek, ; Johann Matschke,
| | - Verena Jendrossek
- Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany
- *Correspondence: Verena Jendrossek, ; Johann Matschke,
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Tandl D, Sponagel T, Alansary D, Fuck S, Smit T, Hehlgans S, Jakob B, Fournier C, Niemeyer BA, Rödel F, Roth B, Moroni A, Thiel G. X-ray irradiation triggers immune response in human T-lymphocytes via store-operated Ca2+ entry and NFAT activation. J Gen Physiol 2022; 154:213138. [PMID: 35416945 PMCID: PMC9011325 DOI: 10.1085/jgp.202112865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 09/25/2021] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
Radiation therapy efficiently eliminates cancer cells and reduces tumor growth. To understand collateral agonistic and antagonistic effects of this treatment on the immune system, we examined the impact of x-ray irradiation on human T cells. We find that, in a major population of leukemic Jurkat T cells and peripheral blood mononuclear cells, clinically relevant radiation doses trigger delayed oscillations of the cytosolic Ca2+ concentration. They are generated by store-operated Ca2+ entry (SOCE) following x-ray–induced clustering of Orai1 and STIM1 and formation of a Ca2+ release–activated Ca2+ (CRAC) channel. A consequence of the x-ray–triggered Ca2+ signaling cascade is translocation of the transcription factor nuclear factor of activated T cells (NFAT) from the cytosol into the nucleus, where it elicits the expression of genes required for immune activation. The data imply activation of blood immune cells by ionizing irradiation, with consequences for toxicity and therapeutic effects of radiation therapy.
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Affiliation(s)
- Dominique Tandl
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Tim Sponagel
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Dalia Alansary
- Molecular Biophysics, University of Saarland, Center for Integrative Physiology and Molecular Medicine, Homburg/Saar, Germany
| | - Sebastian Fuck
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Timo Smit
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stephanie Hehlgans
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt am Main, Germany
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany
| | - Claudia Fournier
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany
| | - Barbara A Niemeyer
- Molecular Biophysics, University of Saarland, Center for Integrative Physiology and Molecular Medicine, Homburg/Saar, Germany
| | - Franz Rödel
- Department of Radiotherapy and Oncology, Goethe-University, Frankfurt am Main, Germany
| | - Bastian Roth
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Anna Moroni
- Department of Biosciences and CNR IBF-Mi, Università degli Studi di Milano, Milano, Italy
| | - Gerhard Thiel
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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Averbek S, Jakob B, Durante M, Averbeck NB. O-GlcNAcylation Affects the Pathway Choice of DNA Double-Strand Break Repair. Int J Mol Sci 2021; 22:ijms22115715. [PMID: 34071949 PMCID: PMC8198441 DOI: 10.3390/ijms22115715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/13/2022] Open
Abstract
Exposing cells to DNA damaging agents, such as ionizing radiation (IR) or cytotoxic chemicals, can cause DNA double-strand breaks (DSBs), which are crucial to repair to maintain genetic integrity. O-linked β-N-acetylglucosaminylation (O-GlcNAcylation) is a post-translational modification (PTM), which has been reported to be involved in the DNA damage response (DDR) and chromatin remodeling. Here, we investigated the impact of O-GlcNAcylation on the DDR, DSB repair and chromatin status in more detail. We also applied charged particle irradiation to analyze differences of O-GlcNAcylation and its impact on DSB repair in respect of spatial dose deposition and radiation quality. Various techniques were used, such as the γH2AX foci assay, live cell microscopy and Fluorescence Lifetime Microscopy (FLIM) to detect DSB rejoining, protein accumulation and chromatin states after treating the cells with O-GlcNAc transferase (OGT) or O-GlcNAcase (OGA) inhibitors. We confirmed that O-GlcNAcylation of MDC1 is increased upon irradiation and identified additional repair factors related to Homologous Recombination (HR), CtIP and BRCA1, which were increasingly O-GlcNAcyated upon irradiation. This is consistent with our findings that the function of HR is affected by OGT inhibition. Besides, we found that OGT and OGA activity modulate chromatin compaction states, providing a potential additional level of DNA-repair regulation.
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Affiliation(s)
- Sera Averbek
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany; (S.A.); (B.J.); (M.D.)
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany; (S.A.); (B.J.); (M.D.)
| | - Marco Durante
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany; (S.A.); (B.J.); (M.D.)
- Department of Physics, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Nicole B. Averbeck
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany; (S.A.); (B.J.); (M.D.)
- Correspondence:
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Tonnemacher S, Eltsov M, Jakob B. Correlative Light and Electron Microscopy (CLEM) Analysis of Nuclear Reorganization Induced by Clustered DNA Damage Upon Charged Particle Irradiation. Int J Mol Sci 2020; 21:ijms21061911. [PMID: 32168789 PMCID: PMC7139895 DOI: 10.3390/ijms21061911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 01/12/2023] Open
Abstract
Chromatin architecture plays major roles in gene regulation as well as in the repair of DNA damaged by endogenous or exogenous factors, such as after radiation. Opening up the chromatin might provide the necessary accessibility for the recruitment and binding of repair factors, thus facilitating timely and correct repair. The observed formation of ionizing radiation-induced foci (IRIF) of factors, such as 53BP1, upon induction of DNA double-strand breaks have been recently linked to local chromatin decompaction. Using correlative light and electron microscopy (CLEM) in combination with DNA-specific contrasting for transmission electron microscopy or tomography, we are able to show that at the ultrastructural level, these DNA damage domains reveal a chromatin compaction and organization not distinguishable from regular euchromatin upon irradiation with carbon or iron ions. Low Density Areas (LDAs) at sites of particle-induced DNA damage, as observed after unspecific uranyl acetate (UA)-staining, are thus unlikely to represent pure chromatin decompaction. RNA-specific terbium-citrate (Tb) staining suggests rather a reduced RNA density contributing to the LDA phenotype. Our observations are discussed in the view of liquid-like phase separation as one of the mechanisms of regulating DNA repair.
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Abdollahi E, Taucher-Scholz G, Jakob B. Application of fluorescence lifetime imaging microscopy of DNA binding dyes to assess radiation-induced chromatin compaction changes. Int J Mol Sci 2018; 19:E2399. [PMID: 30110966 PMCID: PMC6121443 DOI: 10.3390/ijms19082399] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/02/2018] [Accepted: 08/10/2018] [Indexed: 01/19/2023] Open
Abstract
In recent years several approaches have been developed to address the chromatin status and its changes in eukaryotic cells under different conditions-but only few are applicable in living cells. Fluorescence lifetime imaging microscopy (FLIM) is a functional tool that can be used for the inspection of the molecular environment of fluorophores in living cells. Here, we present the use of single organic minor groove DNA binder dyes in FLIM for measuring chromatin changes following modulation of chromatin structure in living cells. Treatment with histone deacetylase inhibitors led to an increased fluorescence lifetime indicating global chromatin decompaction, whereas hyperosmolarity decreased the lifetime of the used dyes, thus reflecting the expected compaction. In addition, we demonstrate that time domain FLIM data based on single photon counting should be optimized using pile-up and counting loss correction, which affect the readout even at moderate average detector count rates in inhomogeneous samples. Using these corrections and utilizing Hoechst 34580 as chromatin compaction probe, we measured a pan nuclear increase in the lifetime following irradiation with X-rays in living NIH/3T3 cells thus providing a method to measure radiation-induced chromatin decompaction.
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Affiliation(s)
- Elham Abdollahi
- Department of Biophysics, GSI Helmholzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany.
| | - Gisela Taucher-Scholz
- Department of Biophysics, GSI Helmholzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany.
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany.
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Timm S, Lorat Y, Jakob B, Taucher-Scholz G, Rübe CE. Clustered DNA damage concentrated in particle trajectories causes persistent large-scale rearrangements in chromatin architecture. Radiother Oncol 2018; 129:600-610. [PMID: 30049456 DOI: 10.1016/j.radonc.2018.07.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/07/2018] [Accepted: 07/05/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND PURPOSE High linear-energy-transfer (LET) irradiation (IR) is characterized by unique depth-dose distribution and advantageous biologic effectiveness compared to low-LET-IR, offering promising alternatives for radio-resistant tumors in clinical oncology. While low-LET-IR induces single DNA lesions such as double-strand breaks (DSBs), localized energy deposition along high-LET particle trajectories induces clustered DNA lesions that are more challenging to repair. During DNA damage response (DDR) 53BP1 and ATM are required for Kap1-dependent chromatin relaxation, thereby sustaining heterochromatic DSB repair. Here, spatiotemporal dynamics of chromatin restructuring were visualized during DDR after high-LET and low-LET-IR. MATERIAL AND METHODS Human fibroblasts were irradiated with high-LET carbon/calcium ions or low-LET photons. At 0.1 h, 0.5 h, 5 h and 24 h post-IR fluorophore- and gold-labeled repair factors (53BP1, pATM, pKAP-1, pKu70) were visualized by immunofluorescence and transmission electron microscopy, to monitor formation and repair of DNA damage in chromatin ultrastructure. To track chromatin remodeling at damage sites, decondensed regions (DCR) were delineated based on local chromatin concentration densities. RESULTS Low-LET-IR induced single DNA lesions throughout the nucleus, but nearly all DSBs were efficiently rejoined without visible chromatin decompaction. High-LET-IR induced clustered DNA damage and triggered profound changes in chromatin structure along particle trajectories. In DCR multiple heterochromatic DSBs exhibited delayed repair despite cooperative activity of 53BP1, pATM, pKap-1. These closely localized DSBs may disturb efficient repair and subsequent chromatin restoration, thereby affecting large-scale genome organization. CONCLUSION Clustered damage concentrated in particle trajectories causes persistent rearrangements in chromatin architecture, which may affect structural and functional organization of cell nuclei.
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Affiliation(s)
- Sara Timm
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Yvonne Lorat
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt, Germany
| | - Gisela Taucher-Scholz
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt, Germany
| | - Claudia E Rübe
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany.
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Jakob B, Taucher-Scholz G. Live Cell Imaging to Study Real-Time ATM-Mediated Recruitment of DNA Repair Complexes to Sites of Ionizing Radiation-Induced DNA Damage. Methods Mol Biol 2017; 1599:287-302. [PMID: 28477127 DOI: 10.1007/978-1-4939-6955-5_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Measurements of protein recruitment and the formation of repair complexes at DNA double-strand breaks in real time provide valuable insight into the regulation of the early DNA damage response. Here, we describe the use of live cell microscopy in combination with ionizing radiation as a tool to evaluate the influence of ATM and its site-specific phosphorylation of target proteins on these processes. Recommendations are made for the preparation of the cells and the design of specialized cell chambers for the localized (and/or targeted) irradiation with charged particles at accelerator beamlines as well as the microscopic equipment and protocol to obtain high-resolution, sensitive fluorescence measurements.
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Affiliation(s)
- Burkhard Jakob
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Biophysik, Planckstraße 1, 64291, Darmstadt, Germany.
| | - Gisela Taucher-Scholz
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Biophysik, Planckstraße 1, 64291, Darmstadt, Germany
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Lorat Y, Timm S, Jakob B, Taucher-Scholz G, Rübe CE. Clustered double-strand breaks in heterochromatin perturb DNA repair after high linear energy transfer irradiation. Radiother Oncol 2016; 121:154-161. [PMID: 27637859 DOI: 10.1016/j.radonc.2016.08.028] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/05/2016] [Accepted: 08/18/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND PURPOSE High linear energy transfer (LET) radiotherapy offers superior dose conformity and biological effectiveness compared with low-LET radiotherapy, representing a promising alternative for radioresistant tumours. A prevailing hypothesis is that energy deposition along the high-LET particle trajectories induces DNA lesions that are more complex and clustered and therefore more challenging to repair. The precise molecular mechanisms underlying the differences in radiobiological effects between high-LET and low-LET radiotherapies remain unclear. MATERIAL AND METHODS Human fibroblasts were irradiated with high-LET carbon ions or low-LET photons. At 0.5h and 5h post exposure, the DNA-damage pattern in the chromatin ultrastructure was visualised using gold-labelled DNA-repair factors. The induction and repair of single-strand breaks, double-strand breaks (DSBs), and clustered lesions were analysed in combination with terminal dUTP nick-end labelling of DNA breaks. RESULTS High-LET irradiation induced clustered lesions with multiple DSBs along ion trajectories predominantly in heterochromatic regions. The cluster size increased over time, suggesting inefficient DSB repair. Low-LET irradiation induced many isolated DSBs throughout the nucleus, most of which were efficiently rejoined. CONCLUSIONS The clustering of DSBs in heterochromatin following high-LET irradiation perturbs efficient DNA repair, leading to greater biological effectiveness of high-LET irradiation versus that of low-LET irradiation.
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Affiliation(s)
- Yvonne Lorat
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Sara Timm
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt, Germany
| | - Gisela Taucher-Scholz
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt, Germany
| | - Claudia E Rübe
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany.
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Schweer KE, Jakob B, Liss B, Christ H, Fischer G, Vehreschild MJGT, Cornely OA, Vehreschild JJ. Domestic mould exposure and invasive aspergillosis—air sampling ofAspergillusspp. spores in homes of hematological patients, a pilot study. Med Mycol 2016; 54:576-83. [DOI: 10.1093/mmy/myw007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 11/14/2022] Open
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Lee KJ, Saha J, Sun J, Fattah KR, Wang SC, Jakob B, Chi L, Wang SY, Taucher-Scholz G, Davis AJ, Chen DJ. Phosphorylation of Ku dictates DNA double-strand break (DSB) repair pathway choice in S phase. Nucleic Acids Res 2015; 44:1732-45. [PMID: 26712563 PMCID: PMC4770226 DOI: 10.1093/nar/gkv1499] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/11/2015] [Indexed: 12/16/2022] Open
Abstract
Multiple DNA double-strand break (DSB) repair pathways are active in S phase of the cell cycle; however, DSBs are primarily repaired by homologous recombination (HR) in this cell cycle phase. As the non-homologous end-joining (NHEJ) factor, Ku70/80 (Ku), is quickly recruited to DSBs in S phase, we hypothesized that an orchestrated mechanism modulates pathway choice between HR and NHEJ via displacement of the Ku heterodimer from DSBs to allow HR. Here, we provide evidence that phosphorylation at a cluster of sites in the junction of the pillar and bridge regions of Ku70 mediates the dissociation of Ku from DSBs. Mimicking phosphorylation at these sites reduces Ku's affinity for DSB ends, suggesting that phosphorylation of Ku70 induces a conformational change responsible for the dissociation of the Ku heterodimer from DNA ends. Ablating phosphorylation of Ku70 leads to the sustained retention of Ku at DSBs, resulting in a significant decrease in DNA end resection and HR, specifically in S phase. This decrease in HR is specific as these phosphorylation sites are not required for NHEJ. Our results demonstrate that the phosphorylation-mediated dissociation of Ku70/80 from DSBs frees DNA ends, allowing the initiation of HR in S phase and providing a mechanism of DSB repair pathway choice in mammalian cells.
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Affiliation(s)
- Kyung-Jong Lee
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390, USA
| | - Janapriya Saha
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390, USA
| | - Jingxin Sun
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390, USA
| | - Kazi R Fattah
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390, USA
| | - Shu-Chi Wang
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390, USA
| | - Burkhard Jakob
- Department of Biophysics; GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstraße 1, Darmstadt, Germany
| | - Linfeng Chi
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390, USA
| | - Shih-Ya Wang
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390, USA
| | - Gisela Taucher-Scholz
- Department of Biophysics; GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstraße 1, Darmstadt, Germany
| | - Anthony J Davis
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390, USA
| | - David J Chen
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390, USA
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Averbeck NB, Ringel O, Herrlitz M, Jakob B, Durante M, Taucher-Scholz G. DNA end resection is needed for the repair of complex lesions in G1-phase human cells. Cell Cycle 2015; 13:2509-16. [PMID: 25486192 DOI: 10.4161/15384101.2015.941743] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Repair of DNA double strand breaks (DSBs) is influenced by the chemical complexity of the lesion. Clustered lesions (complex DSBs) are generally considered more difficult to repair and responsible for early and late cellular effects after exposure to genotoxic agents. Resection is commonly used by the cells as part of the homologous recombination (HR) pathway in S- and G2-phase. In contrast, DNA resection in G1-phase may lead to an error-prone microhomology-mediated end joining. We induced DNA lesions with a wide range of complexity by irradiation of mammalian cells with X-rays or accelerated ions of different velocity and mass. We found replication protein A (RPA) foci indicating DSB resection both in S/G2- and G1-cells, and the fraction of resection-positive cells correlates with the severity of lesion complexity throughout the cell cycle. Besides RPA, Ataxia telangiectasia and Rad3-related (ATR) was recruited to complex DSBs both in S/G2- and G1-cells. Resection of complex DSBs is driven by meiotic recombination 11 homolog A (MRE11), CTBP-interacting protein (CtIP), and exonuclease 1 (EXO1) but seems not controlled by the Ku heterodimer or by phosphorylation of H2AX. Reduced resection capacity by CtIP depletion increased cell killing and the fraction of unrepaired DSBs after exposure to densely ionizing heavy ions, but not to X-rays. We conclude that in mammalian cells resection is essential for repair of complex DSBs in all phases of the cell-cycle and targeting this process sensitizes mammalian cells to cytotoxic agents inducing clustered breaks, such as in heavy-ion cancer therapy.
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Key Words
- ATM, Ataxia telangiectasia mutated
- ATR, Ataxia telangiectasia and Rad3-related
- BLM, Bloom syndrome protein
- BRCA1, breast cancer 1, early onset
- CENP-F, centromere protein F
- CtIP
- CtIP, CTBP-interacting protein
- DAPI, 4',6-diamidino-2-phenylindole
- DSB, double strand break
- EXO1
- EXO1, exonuclease 1
- FCS, fetal calf serum
- HR, homologous recombination
- IR, ionizing radiation
- LET, linear energy transfer
- MEF, mouse embryonic fibroblasts
- MMEJ, microhomology-mediated end joining
- MRE11
- MRE11, meiotic recombination 11 homolog A
- NHEJ, none homologous end joining
- PARP, poly (ADP-ribose) polymerase
- RAD51, DNA repair protein RAD51 homolog 1
- RPA, replication protein A
- WRN, Werner syndrome
- complex DNA damage
- double-strand break repair
- kd, knockdown
- resection in G1-phase
- siRNA, small interfering RNA
- ssDNA, single stranded DNA
- wt, wild-type
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Affiliation(s)
- Nicole B Averbeck
- a Department of Biophysics ; GSI Helmholtzzentrum für Schwerionenforschung GmbH ; Planckstraße 1; Darmstadt , Germany
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15
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Kijas AW, Lim YC, Bolderson E, Cerosaletti K, Gatei M, Jakob B, Tobias F, Taucher-Scholz G, Gueven N, Oakley G, Concannon P, Wolvetang E, Khanna KK, Wiesmüller L, Lavin MF. ATM-dependent phosphorylation of MRE11 controls extent of resection during homology directed repair by signalling through Exonuclease 1. Nucleic Acids Res 2015; 43:8352-67. [PMID: 26240375 PMCID: PMC4787824 DOI: 10.1093/nar/gkv754] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/14/2015] [Indexed: 02/07/2023] Open
Abstract
The MRE11/RAD50/NBS1 (MRN) complex plays a central role as a sensor of DNA double strand breaks (DSB) and is responsible for the efficient activation of ataxia-telangiectasia mutated (ATM) kinase. Once activated ATM in turn phosphorylates RAD50 and NBS1, important for cell cycle control, DNA repair and cell survival. We report here that MRE11 is also phosphorylated by ATM at S676 and S678 in response to agents that induce DNA DSB, is dependent on the presence of NBS1, and does not affect the association of members of the complex or ATM activation. A phosphosite mutant (MRE11S676AS678A) cell line showed decreased cell survival and increased chromosomal aberrations after radiation exposure indicating a defect in DNA repair. Use of GFP-based DNA repair reporter substrates in MRE11S676AS678A cells revealed a defect in homology directed repair (HDR) but single strand annealing was not affected. More detailed investigation revealed that MRE11S676AS678A cells resected DNA ends to a greater extent at sites undergoing HDR. Furthermore, while ATM-dependent phosphorylation of Kap1 and SMC1 was normal in MRE11S676AS678A cells, there was no phosphorylation of Exonuclease 1 consistent with the defect in HDR. These results describe a novel role for ATM-dependent phosphorylation of MRE11 in limiting the extent of resection mediated through Exonuclease 1.
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Affiliation(s)
- Amanda W Kijas
- The University of Queensland, UQ Centre for Clinical Research, University of Queensland, Brisbane, Queensland 4029, Australia
| | - Yi Chieh Lim
- Brain Cancer Research Unit, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Emma Bolderson
- Genome Stability Laboratory, Translational Research Institute, Queensland University of Technology, Queensland 4102, Australia
| | - Karen Cerosaletti
- Translational Research Program, Benaroya Research Institute, Seattle, WA 981010, USA
| | - Magtouf Gatei
- The University of Queensland, UQ Centre for Clinical Research, University of Queensland, Brisbane, Queensland 4029, Australia
| | - Burkhard Jakob
- GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt 64291, Germany
| | - Frank Tobias
- GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt 64291, Germany
| | | | - Nuri Gueven
- School of Medicine, Faculty of Health, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Greg Oakley
- University of Nebraska College of Dentistry, Lincoln, NE 68583-0740, USA
| | - Patrick Concannon
- Genetics Institute, University of Florida, Gainesville, Florida, FL 3261, USA
| | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane 4072, Australia
| | - Kum Kum Khanna
- Signal transduction, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynaecology, University of Ulm, Ulm 89075, Germany
| | - Martin F Lavin
- The University of Queensland, UQ Centre for Clinical Research, University of Queensland, Brisbane, Queensland 4029, Australia
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Tommasino F, Friedrich T, Jakob B, Meyer B, Durante M, Scholz M. Induction and Processing of the Radiation-Induced Gamma-H2AX Signal and Its Link to the Underlying Pattern of DSB: A Combined Experimental and Modelling Study. PLoS One 2015; 10:e0129416. [PMID: 26067661 PMCID: PMC4465900 DOI: 10.1371/journal.pone.0129416] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/10/2015] [Indexed: 12/23/2022] Open
Abstract
We present here an analysis of DSB induction and processing after irradiation with X-rays in an extended dose range based on the use of the γH2AX assay. The study was performed by quantitative flow cytometry measurements, since the use of foci counting would result in reasonable accuracy only in a limited dose range of a few Gy. The experimental data are complemented by a theoretical analysis based on the GLOBLE model. In fact, original aim of the study was to test GLOBLE predictions against new experimental data, in order to contribute to the validation of the model. Specifically, the γH2AX signal kinetics has been investigated up to 24 h after exposure to increasing photon doses between 2 and 500 Gy. The prolonged persistence of the signal at high doses strongly suggests dose dependence in DSB processing after low LET irradiation. Importantly, in the framework of our modelling analysis, this is related to a gradually increased fraction of DSB clustering at the micrometre scale. The parallel study of γH2AX dose response curves shows the onset of a pronounced saturation in two cell lines at a dose of about 20 Gy. This dose is much lower than expected according to model predictions based on the values usually adopted for the DSB induction yield (≈ 30 DSB/Gy) and for the γH2AX foci extension of approximately 2 Mbp around the DSB. We show and discuss how theoretical predictions and experimental findings can be in principle reconciled by combining an increased DSB induction yield with the assumption of a larger genomic extension for the single phosphorylated regions. As an alternative approach, we also considered in our model the possibility of a 3D spreading-mechanism of the H2AX phosphorylation around the induced DSB, and applied it to the analysis of both the aspects considered. Our results are found to be supportive for the basic assumptions on which GLOBLE is built. Apart from giving new insights into the H2AX phosphorylation process, experiments performed at high doses are of relevance in the context of radiation therapy, where hypo-fractionated schemes become increasingly popular.
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Affiliation(s)
- Francesco Tommasino
- GSI Helmholtzzentrum für Schwerionenforschung, Department of Biophysics, Darmstadt, Germany
- * E-mail:
| | - Thomas Friedrich
- GSI Helmholtzzentrum für Schwerionenforschung, Department of Biophysics, Darmstadt, Germany
| | - Burkhard Jakob
- GSI Helmholtzzentrum für Schwerionenforschung, Department of Biophysics, Darmstadt, Germany
| | - Barbara Meyer
- GSI Helmholtzzentrum für Schwerionenforschung, Department of Biophysics, Darmstadt, Germany
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Marco Durante
- GSI Helmholtzzentrum für Schwerionenforschung, Department of Biophysics, Darmstadt, Germany
- Technische Universität Darmstadt, Institut für Festkörperphysik, Darmstadt, Germany
| | - Michael Scholz
- GSI Helmholtzzentrum für Schwerionenforschung, Department of Biophysics, Darmstadt, Germany
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17
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Lorat Y, Brunner CU, Schanz S, Jakob B, Taucher-Scholz G, Rübe CE. Nanoscale analysis of clustered DNA damage after high-LET irradiation by quantitative electron microscopy--the heavy burden to repair. DNA Repair (Amst) 2015; 28:93-106. [PMID: 25659339 DOI: 10.1016/j.dnarep.2015.01.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 01/14/2015] [Accepted: 01/20/2015] [Indexed: 12/18/2022]
Abstract
Low- and high-linear energy transfer (LET) ionising radiation are effective cancer therapies, but produce structurally different forms of DNA damage. Isolated DNA damage is repaired efficiently; however, clustered lesions may be more difficult to repair, and are considered as significant biological endpoints. We investigated the formation and repair of DNA double-strand breaks (DSBs) and clustered lesions in human fibroblasts after exposure to sparsely (low-LET; delivered by photons) and densely (high-LET; delivered by carbon ions) ionising radiation. DNA repair factors (pKu70, 53BP1, γH2AX, and pXRCC1) were detected using immunogold-labelling and electron microscopy, and spatiotemporal DNA damage patterns were analysed within the nuclear ultrastructure at the nanoscale level. By labelling activated Ku-heterodimers (pKu70) the number of DSBs was determined in electron-lucent euchromatin and electron-dense heterochromatin. Directly after low-LET exposure (5 min post-irradiation), single pKu70 dimers, which reflect isolated DSBs, were randomly distributed throughout the entire nucleus with a linear dose correlation up to 30 Gy. Most euchromatic DSBs were sensed and repaired within 40 min, whereas heterochromatic DSBs were processed with slower kinetics. Essentially all DNA lesions induced by low-LET irradiation were efficiently rejoined within 24h post-irradiation. High-LET irradiation caused localised energy deposition within the particle tracks, and generated highly clustered DNA lesions with multiple DSBs in close proximity. The dimensions of these clustered lesions along the particle trajectories depended on the chromatin packing density, with huge DSB clusters predominantly localised in condensed heterochromatin. High-LET irradiation-induced clearly higher DSB yields than low-LET irradiation, with up to ∼ 500 DSBs per μm(3) track volume, and large fractions of these heterochromatic DSBs remained unrepaired. Hence, the spacing and quantity of DSBs in clustered lesions influence DNA repair efficiency, and may determine the radiobiological outcome.
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Affiliation(s)
- Yvonne Lorat
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Christina U Brunner
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Stefanie Schanz
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Burkhard Jakob
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt, Germany
| | - Gisela Taucher-Scholz
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt, Germany
| | - Claudia E Rübe
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany.
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18
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Becker A, Durante M, Taucher-Scholz G, Jakob B. ATM alters the otherwise robust chromatin mobility at sites of DNA double-strand breaks (DSBs) in human cells. PLoS One 2014; 9:e92640. [PMID: 24651490 PMCID: PMC3961414 DOI: 10.1371/journal.pone.0092640] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/23/2014] [Indexed: 11/18/2022] Open
Abstract
Ionizing radiation induces DNA double strand breaks (DSBs) which can lead to the formation of chromosome rearrangements through error prone repair. In mammalian cells the positional stability of chromatin contributes to the maintenance of genome integrity. DSBs exhibit only a small, submicron scale diffusive mobility, but a slight increase in the mobility of chromatin domains by the induction of DSBs might influence repair fidelity and the formation of translocations. The radiation-induced local DNA decondensation in the vicinity of DSBs is one factor potentially enhancing the mobility of DSB-containing chromatin domains. Therefore in this study we focus on the influence of different chromatin modifying proteins, known to be activated by the DNA damage response, on the mobility of DSBs. IRIF (ionizing radiation induced foci) in U2OS cells stably expressing 53BP1-GFP were used as a surrogate marker of DSBs. Low angle charged particle irradiation, known to trigger a pronounced DNA decondensation, was used for the defined induction of linear tracks of IRIF. Our results show that movement of IRIF is independent of the investigated chromatin modifying proteins like ACF1 or PARP1 and PARG. Also depletion of proteins that tether DNA strands like MRE11 and cohesin did not alter IRIF dynamics significantly. Inhibition of ATM, a key component of DNA damage response signaling, resulted in a pronounced confinement of DSB mobility, which might be attributed to a diminished radiation induced decondensation. This confinement following ATM inhibition was confirmed using X-rays, proving that this effect is not restricted to densely ionizing radiation. In conclusion, repair sites of DSBs exhibit a limited mobility on a small spatial scale that is mainly unaffected by depletion of single remodeling or DNA tethering proteins. However, it relies on functional ATM kinase which is considered to influence the chromatin structure after irradiation.
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Affiliation(s)
- Annabelle Becker
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
| | - Marco Durante
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
- Technical University of Darmstadt, Darmstadt, Germany
| | - Gisela Taucher-Scholz
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
- Technical University of Darmstadt, Darmstadt, Germany
| | - Burkhard Jakob
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
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20
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Willmott PR, Meister D, Leake SJ, Lange M, Bergamaschi A, Böge M, Calvi M, Cancellieri C, Casati N, Cervellino A, Chen Q, David C, Flechsig U, Gozzo F, Henrich B, Jäggi-Spielmann S, Jakob B, Kalichava I, Karvinen P, Krempasky J, Lüdeke A, Lüscher R, Maag S, Quitmann C, Reinle-Schmitt ML, Schmidt T, Schmitt B, Streun A, Vartiainen I, Vitins M, Wang X, Wullschleger R. The Materials Science beamline upgrade at the Swiss Light Source. J Synchrotron Radiat 2013; 20:667-82. [PMID: 23955029 PMCID: PMC3747948 DOI: 10.1107/s0909049513018475] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 07/03/2013] [Indexed: 05/20/2023]
Abstract
The Materials Science beamline at the Swiss Light Source has been operational since 2001. In late 2010, the original wiggler source was replaced with a novel insertion device, which allows unprecedented access to high photon energies from an undulator installed in a medium-energy storage ring. In order to best exploit the increased brilliance of this new source, the entire front-end and optics had to be redesigned. In this work, the upgrade of the beamline is described in detail. The tone is didactic, from which it is hoped the reader can adapt the concepts and ideas to his or her needs.
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Affiliation(s)
- P R Willmott
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen, Switzerland.
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21
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Müller I, Merk B, Voss KO, Averbeck N, Jakob B, Durante M, Taucher-Scholz G. Species conserved DNA damage response at the inactive human X chromosome. Mutat Res 2013; 756:30-36. [PMID: 23628434 DOI: 10.1016/j.mrgentox.2013.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 04/21/2013] [Indexed: 06/02/2023]
Abstract
Chromatin modifications are long known as an essential part of the orchestrated response resulting in the repair of radiation-induced DNA double-strand breaks (DSBs). Only recently, however, the influence of the chromatin architecture itself on the DNA damage response has been recognised. Thus for heterochromatic DSBs the sensing and early recruitment of repair factors to the lesion occurs within the heterochromatic compartments, but the damage sites are subsequently relocated from the inside to the outside of the heterochromatin. While previous studies were accomplished at the constitutive heterochromatin of centromeric regions in mouse and flies, here we examine the DSB repair at the facultative heterochromatin of the inactive X chromosome (Xi) in humans. Using heavy ion irradiation we show that at later times after irradiation the DSB damage streaks bend around the Xi verifying that the relocation process is conserved between species and not specialised to repetitive sequences only. In addition, to measure chromatin relaxation at rare positions within the genome, we established live cell microscopy at the GSI microbeam thus allowing the aimed irradiation of small nuclear structures like the Xi. Chromatin decondensation at DSBs within the Xi is clearly visible within minutes as a continuous decrease of the DNA staining over time, comparable to the DNA relaxation revealed at DSBs in mouse chromocenters. Furthermore, despite being conserved between species, slight differences in the underlying regulation of these processes in heterochromatic DSBs are apparent.
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Affiliation(s)
- Iris Müller
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, 64291 Darmstadt, Germany.
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22
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Meyer B, Voss KO, Tobias F, Jakob B, Durante M, Taucher-Scholz G. Clustered DNA damage induces pan-nuclear H2AX phosphorylation mediated by ATM and DNA-PK. Nucleic Acids Res 2013; 41:6109-18. [PMID: 23620287 PMCID: PMC3695524 DOI: 10.1093/nar/gkt304] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
DNA double-strand breaks (DSB) are considered as the most deleterious DNA lesions, and their repair is further complicated by increasing damage complexity. However, the molecular effects of clustered lesions are yet not fully understood. As the locally restricted phosphorylation of H2AX to form γH2AX is a key step in facilitating efficient DSB repair, we investigated this process after localized induction of clustered damage by ionizing radiation. We show that in addition to foci at damaged sites, H2AX is also phosphorylated in undamaged chromatin over the whole-cell nucleus in human and rodent cells, but this is not related to apoptosis. This pan-nuclear γH2AX is mediated by the kinases ataxia telangiectasia mutated and DNA-dependent protein kinase (DNA-PK) that also phosphorylate H2AX at DSBs. The pan-nuclear response is dependent on the amount of DNA damage and is transient even under conditions of impaired DSB repair. Using fluorescence recovery after photobleaching (FRAP), we found that MDC1, but not 53BP1, binds to the nuclear-wide γH2AX. Consequently, the accumulation of MDC1 at DSBs is reduced. Altogether, we show that a transient dose-dependent activation of the kinases occurring on complex DNA lesions leads to their nuclear-wide distribution and H2AX phosphorylation, yet without eliciting a full pan-nuclear DNA damage response.
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Affiliation(s)
- Barbara Meyer
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Planckstrasse 1, D-64291 Darmstadt, Germany
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23
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Singh SK, Bencsik-Theilen A, Mladenov E, Jakob B, Taucher-Scholz G, Iliakis G. Reduced contribution of thermally labile sugar lesions to DNA double strand break formation after exposure to heavy ions. Radiat Oncol 2013; 8:77. [PMID: 23547740 PMCID: PMC3627621 DOI: 10.1186/1748-717x-8-77] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/22/2013] [Indexed: 11/10/2022] Open
Abstract
In cells exposed to low linear energy transfer (LET) ionizing-radiation (IR),
double-strand-breaks (DSBs) form within clustered-damage-sites (CDSs) from
lesions disrupting the DNA sugar-phosphate backbone. It is commonly assumed that
all DSBs form promptly and are immediately detected by the cellular
DNA-damage-response (DDR) apparatus. However, there is evidence that the pool of
DSBs detected by physical methods, such as pulsed-field gel electrophoresis
(PFGE), comprises not only promptly forming DSBs (prDSBs) but also DSBs
developing during lysis at high temperatures from thermally-labile sugar-lesions
(TLSLs). We recently demonstrated that conversion of TLSLs to DNA breaks and
ultimately to DSBs also occurs in cells during the first hour of
post-irradiation incubation at physiological temperatures. Thus, TLSL-dependent
DSBs (tlDSBs) are not an avoidable technique-related artifact, but a reality the
cell always faces. The biological consequences of tlDSBs and the dependence of
their formation on LET require in-depth investigation. Heavy-ions (HI) are a
promising high-LET radiation modality used in cancer treatment. HI are also
encountered in space and generate serious radiation protection problems to
prolonged space missions. Here, we study, therefore, the effect of HI on the
yields of tlDSBs and prDSBs. We report a reduction in the yield of tlDBSs
stronger than that earlier reported for neutrons, and with pronounced cell line
dependence. We conclude that with increasing LET the complexity of CDSs
increases resulting in a commensurate increase in the yield prDSBs and a
decrease in tlDSBs. The consequences of these effects to the relative biological
effectiveness are discussed.
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Affiliation(s)
- Satyendra K Singh
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Hufelandstr 55, Essen, 45122, Germany
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Tobias F, Löb D, Lengert N, Durante M, Drossel B, Taucher-Scholz G, Jakob B. Spatiotemporal dynamics of early DNA damage response proteins on complex DNA lesions. PLoS One 2013; 8:e57953. [PMID: 23469115 PMCID: PMC3582506 DOI: 10.1371/journal.pone.0057953] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/29/2013] [Indexed: 11/18/2022] Open
Abstract
The response of cells to ionizing radiation-induced DNA double-strand breaks (DSB) is determined by the activation of multiple pathways aimed at repairing the injury and maintaining genomic integrity. Densely ionizing radiation induces complex damage consisting of different types of DNA lesions in close proximity that are difficult to repair and may promote carcinogenesis. Little is known about the dynamic behavior of repair proteins on complex lesions. In this study we use live-cell imaging for the spatio-temporal characterization of early protein interactions at damage sites of increasing complexity. Beamline microscopy was used to image living cells expressing fluorescently-tagged proteins during and immediately after charged particle irradiation to reveal protein accumulation at damaged sites in real time. Information on the mobility and binding rates of the recruited proteins was obtained from fluorescence recovery after photobleaching (FRAP). Recruitment of the DNA damage sensor protein NBS1 accelerates with increasing lesion density and saturates at very high damage levels. FRAP measurements revealed two different binding modalities of NBS1 to damage sites and a direct impact of lesion complexity on the binding. Faster recruitment with increasing lesion complexity was also observed for the mediator MDC1, but mobility was limited at very high damage densities due to nuclear-wide binding. We constructed a minimal computer model of the initial response to DSB based on known protein interactions only. By fitting all measured data using the same set of parameters, we can reproduce the experimentally characterized steps of the DNA damage response over a wide range of damage densities. The model suggests that the influence of increasing lesion density accelerating NBS1 recruitment is only dependent on the different binding modes of NBS1, directly to DSB and to the surrounding chromatin via MDC1. This elucidates an impact of damage clustering on repair without the need of invoking extra processing steps.
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Affiliation(s)
- Frank Tobias
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
| | - Daniel Löb
- TU Darmstadt, Institut für Festkörperphysik, Darmstadt, Germany
| | - Nicor Lengert
- TU Darmstadt, Institut für Festkörperphysik, Darmstadt, Germany
| | - Marco Durante
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
- TU Darmstadt, Institut für Festkörperphysik, Darmstadt, Germany
| | - Barbara Drossel
- TU Darmstadt, Institut für Festkörperphysik, Darmstadt, Germany
| | | | - Burkhard Jakob
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
- * E-mail:
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Wiese C, Rudolph JH, Jakob B, Fink D, Tobias F, Blattner C, Taucher-Scholz G. PCNA-dependent accumulation of CDKN1A into nuclear foci after ionizing irradiation. DNA Repair (Amst) 2012; 11:511-21. [DOI: 10.1016/j.dnarep.2012.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/04/2012] [Accepted: 02/28/2012] [Indexed: 12/30/2022]
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Abstract
Imaging was one of the earliest techniques to quantify radiation dose. While films and active fluorescent detectors are still commonly used in physical dosimetry, biological imaging is emerging as a new method to visualize and quantify radiation dose in biological targets. Methods for biological imaging are normally based on molecular fluorescent probes, labeling chromatin-conjugated molecules or specific repair proteins. Examples are chromatin-binding coumarin compounds, which become fluorescent under irradiation, or the H2AX histone, which is rapidly phosphorylated at sites of DNA double-strand breaks and can be visualized by immunostaining. Many other DNA repair proteins can be expressed with fluorescent targets, such as green fluorescent protein, thus becoming visible for dose estimation in vivo. The possibility to visualize radiation damage in living biological targets is particularly important for repair kinetic studies, for estimating individual radiation response, and for remote control of living samples exposed to radiation, for instance in robotic space missions. In vivo dose monitoring in particle therapy exploits the production of positron emitters by nuclear interaction of the incident beam in the patient's body. Positron emission tomography (PET) can then be used to visualize and quantify the particle dose in the patient, and it can in principle also be used for radiotherapy with high-energy X rays. Alternatively, prompt γ rays or scattered secondary particles are under study for in vivo dosimetry of ion beams in therapy.
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Affiliation(s)
- B Jakob
- GSI Helmholtzzentrum für Schwerionenforschung, Biophysics Department, Planckstraße 1, 64291 Darmstadt, Germany
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Gatei M, Jakob B, Chen P, Kijas AW, Becherel OJ, Gueven N, Birrell G, Lee JH, Paull TT, Lerenthal Y, Fazry S, Taucher-Scholz G, Kalb R, Schindler D, Waltes R, Dörk T, Lavin MF. ATM protein-dependent phosphorylation of Rad50 protein regulates DNA repair and cell cycle control. J Biol Chem 2011; 286:31542-56. [PMID: 21757780 PMCID: PMC3173097 DOI: 10.1074/jbc.m111.258152] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Revised: 07/12/2011] [Indexed: 02/01/2023] Open
Abstract
The Mre11/Rad50/NBN complex plays a central role in coordinating the cellular response to DNA double-strand breaks. The importance of Rad50 in that response is evident from the recent description of a patient with Rad50 deficiency characterized by chromosomal instability and defective ATM-dependent signaling. We report here that ATM (defective in ataxia-telangiectasia) phosphorylates Rad50 at a single site (Ser-635) that plays an important adaptor role in signaling for cell cycle control and DNA repair. Although a Rad50 phosphosite-specific mutant (S635G) supported normal activation of ATM in Rad50-deficient cells, it was defective in correcting DNA damage-induced signaling through the ATM-dependent substrate SMC1. This mutant also failed to correct radiosensitivity, DNA double-strand break repair, and an S-phase checkpoint defect in Rad50-deficient cells. This was not due to disruption of the Mre11/Rad50/NBN complex revealing for the first time that phosphorylation of Rad50 plays a key regulatory role as an adaptor for specific ATM-dependent downstream signaling through SMC1 for DNA repair and cell cycle checkpoint control in the maintenance of genome integrity.
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Affiliation(s)
- Magtouf Gatei
- From the Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Burkhard Jakob
- Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, 64291 Darmstadt, Germany
| | - Philip Chen
- From the Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Amanda W. Kijas
- From the Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Olivier J. Becherel
- From the Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
- the University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland 4072, Australia
| | - Nuri Gueven
- From the Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Geoff Birrell
- From the Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Ji-Hoon Lee
- The Howard Hughes Medical Institute and the Department of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712
| | - Tanya T. Paull
- The Howard Hughes Medical Institute and the Department of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712
| | - Yaniv Lerenthal
- the Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shazrul Fazry
- From the Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Gisela Taucher-Scholz
- Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, 64291 Darmstadt, Germany
| | - Reinhard Kalb
- the Department of Human Genetics, University of Würzburg, Würzburg 97074, Germany
| | - Detlev Schindler
- the Department of Human Genetics, University of Würzburg, Würzburg 97074, Germany
| | | | - Thilo Dörk
- Gynecology, Hannover Medical School, D-30625 Hannover, Germany, and
| | - Martin F. Lavin
- From the Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
- the University of Queensland Centre for Clinical Research, Brisbane, Queensland 4029, Australia
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Jakob B, Splinter J, Conrad S, Voss KO, Zink D, Durante M, Löbrich M, Taucher-Scholz G. DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin. Nucleic Acids Res 2011; 39:6489-99. [PMID: 21511815 PMCID: PMC3159438 DOI: 10.1093/nar/gkr230] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
DNA double-strand breaks (DSBs) can induce chromosomal aberrations and carcinogenesis and their correct repair is crucial for genetic stability. The cellular response to DSBs depends on damage signaling including the phosphorylation of the histone H2AX (γH2AX). However, a lack of γH2AX formation in heterochromatin (HC) is generally observed after DNA damage induction. Here, we examine γH2AX and repair protein foci along linear ion tracks traversing heterochromatic regions in human or murine cells and find the DSBs and damage signal streaks bending around highly compacted DNA. Given the linear particle path, such bending indicates a relocation of damage from the initial induction site to the periphery of HC. Real-time imaging of the repair protein GFP-XRCC1 confirms fast recruitment to heterochromatic lesions inside murine chromocenters. Using single-ion microirradiation to induce localized DSBs directly within chromocenters, we demonstrate that H2AX is early phosphorylated within HC, but the damage site is subsequently expelled from the center to the periphery of chromocenters within ∼20 min. While this process can occur in the absence of ATM kinase, the repair of DSBs bordering HC requires the protein. Finally, we describe a local decondensation of HC at the sites of ion hits, potentially allowing for DSB movement via physical forces.
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Affiliation(s)
- Burkhard Jakob
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Planckstrasse 1, 64291 Darmstadt, Germany
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Kozlov SV, Graham ME, Jakob B, Tobias F, Kijas AW, Tanuji M, Chen P, Robinson PJ, Taucher-Scholz G, Suzuki K, So S, Chen D, Lavin MF. Autophosphorylation and ATM activation: additional sites add to the complexity. J Biol Chem 2011; 286:9107-19. [PMID: 21149446 PMCID: PMC3059052 DOI: 10.1074/jbc.m110.204065] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Indexed: 12/18/2022] Open
Abstract
The recognition and signaling of DNA double strand breaks involves the participation of multiple proteins, including the protein kinase ATM (mutated in ataxia-telangiectasia). ATM kinase is activated in the vicinity of the break and is recruited to the break site by the Mre11-Rad50-Nbs1 complex, where it is fully activated. In human cells, the activation process involves autophosphorylation on three sites (Ser(367), Ser(1893), and Ser(1981)) and acetylation on Lys(3016). We now describe the identification of a new ATM phosphorylation site, Thr(P)(1885) and an additional autophosphorylation site, Ser(P)(2996), that is highly DNA damage-inducible. We also confirm that human and murine ATM share five identical phosphorylation sites. We targeted the ATM phosphorylation sites, Ser(367) and Ser(2996), for further study by generating phosphospecific antibodies against these sites and demonstrated that phosphorylation of both was rapidly induced by radiation. These phosphorylations were abolished by a specific inhibitor of ATM and were dependent on ATM and the Mre11-Rad50-Nbs1 complex. As found for Ser(P)(1981), ATM phosphorylated at Ser(367) and Ser(2996) localized to sites of DNA damage induced by radiation, but ATM recruitment was not dependent on phosphorylation at these sites. Phosphorylation at Ser(367) and Ser(2996) was functionally important because mutant forms of ATM were defective in correcting the S phase checkpoint defect and restoring radioresistance in ataxia-telangiectasia cells. These data provide further support for the importance of autophosphorylation in the activation and function of ATM in vivo.
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Affiliation(s)
- Sergei V. Kozlov
- From Radiation Biology and Oncology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Mark E. Graham
- the Children's Medical Research Institute, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Burkhard Jakob
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Biophysik, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Frank Tobias
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Biophysik, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Amanda W. Kijas
- From Radiation Biology and Oncology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Marcel Tanuji
- From Radiation Biology and Oncology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Philip Chen
- From Radiation Biology and Oncology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Phillip J. Robinson
- the Children's Medical Research Institute, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Gisela Taucher-Scholz
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Biophysik, Planckstrasse 1, D-64291 Darmstadt, Germany
| | - Keiji Suzuki
- the Department of Molecular Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Sairai So
- the University of Texas Southwestern Medical Center, Dallas, Texas 75390, and
| | - David Chen
- the University of Texas Southwestern Medical Center, Dallas, Texas 75390, and
| | - Martin F. Lavin
- From Radiation Biology and Oncology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
- the University of Queensland Centre for Clinical Research, Brisbane, Queensland 4029, Australia
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Altenbach HJ, Berger M, Jakob B, Ihizane R, Laumen K, Lange K, Machmüller G, Müller S, Schneider M. Lipid modification of amino acids, carbohydrates and polyols. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/lite.201000032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Splinter J, Jakob B, Lang M, Yano K, Engelhardt J, Hell SW, Chen DJ, Durante M, Taucher-Scholz G. Biological dose estimation of UVA laser microirradiation utilizing charged particle-induced protein foci. Mutagenesis 2010; 25:289-97. [PMID: 20167590 DOI: 10.1093/mutage/geq005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The induction of localized DNA damage within a discrete nuclear volume is an important tool in DNA repair studies. Both charged particle irradiation and laser microirradiation (LMI) systems allow for such a localized damage induction, but the results obtained are difficult to compare, as the delivered laser dose cannot be measured directly. Therefore, we revisited the idea of a biological dosimetry based on the microscopic evaluation of irradiation-induced Replication Protein A (RPA) foci numbers. Considering that local dose deposition is characteristic for both LMI and charged particles, we took advantage of the defined dosimetry of particle irradiation to estimate the locally applied laser dose equivalent. Within the irradiated nuclear sub-volumes, the doses were in the range of several hundreds of Gray. However, local dose estimation is limited by the saturation of the RPA foci numbers with increasing particle doses. Even high-resolution 4Pi microscopy did not abrogate saturation as it was not able to resolve single lesions within individual RPA foci. Nevertheless, 4Pi microscopy revealed multiple and distinct 53BP1- and gamma H2AX-stained substructures within the lesion flanking chromatin domains. Monitoring the local recruitment of the telomere repeat-binding factors TRF1 and TRF2 showed that both proteins accumulated at damage sites after UVA-LMI but not after densely ionizing charged particle irradiation. Hence, our results indicate that the local dose delivered by UVA-LMI is extremely high and cannot be accurately translated into an equivalent ionizing radiation dose, despite the sophisticated techniques used in this study.
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Affiliation(s)
- J Splinter
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Planckstrasse 1, D-64291 Darmstadt, Germany
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Costes SV, Chiolo I, Pluth JM, Barcellos-Hoff MH, Jakob B. Spatiotemporal characterization of ionizing radiation induced DNA damage foci and their relation to chromatin organization. Mutat Res 2010; 704:78-87. [PMID: 20060491 DOI: 10.1016/j.mrrev.2009.12.006] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 12/17/2009] [Accepted: 12/22/2009] [Indexed: 11/28/2022]
Abstract
DNA damage sensing proteins have been shown to localize to the sites of DNA double strand breaks (DSB) within seconds to minutes following ionizing radiation (IR) exposure, resulting in the formation of microscopically visible nuclear domains referred to as radiation-induced foci (RIF). This review characterizes the spatiotemporal properties of RIF at physiological doses, minutes to hours following exposure to ionizing radiation, and it proposes a model describing RIF formation and resolution as a function of radiation quality and chromatin territories. Discussion is limited to RIF formed by three interrelated proteins ATM (Ataxia telangiectasia mutated), 53BP1 (p53 binding protein 1) and gammaH2AX (phosphorylated variant histone H2AX), with an emphasis on the later. This review discusses the importance of not equating RIF with DSB in all situations and shows how dose and time dependence of RIF frequency is inconsistent with a one to one equivalence. Instead, we propose that RIF mark regions of the chromatin that would serve as scaffolds rigid enough to keep broken DNA from diffusing away, but open enough to allow the repair machinery to access the damage site. We review data indicating clear kinetic and physical differences between RIF emerging from dense and uncondensed regions of the nucleus. We suggest that persistent RIF observed days following exposure to ionizing radiation are nuclear marks of permanent rearrangement of the chromatin architecture. Such chromatin alterations may not always lead to growth arrest as cells have been shown to replicate these in progeny. Thus, heritable persistent RIF spanning over tens of Mbp may reflect persistent changes in the transcriptome of a large progeny of cells. Such model opens the door to a "non-DNA-centric view" of radiation-induced phenotypes.
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Affiliation(s)
- S V Costes
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Becherel OJ, Jakob B, Cherry AL, Gueven N, Fusser M, Kijas AW, Peng C, Katyal S, McKinnon PJ, Chen J, Epe B, Smerdon SJ, Taucher-Scholz G, Lavin MF. CK2 phosphorylation-dependent interaction between aprataxin and MDC1 in the DNA damage response. Nucleic Acids Res 2009; 38:1489-503. [PMID: 20008512 PMCID: PMC2836575 DOI: 10.1093/nar/gkp1149] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aprataxin, defective in the neurodegenerative disorder ataxia oculomotor apraxia type 1, resolves abortive DNA ligation intermediates during DNA repair. Here, we demonstrate that aprataxin localizes at sites of DNA damage induced by high LET radiation and binds to mediator of DNA-damage checkpoint protein 1 (MDC1/NFBD1) through a phosphorylation-dependent interaction. This interaction is mediated via the aprataxin FHA domain and multiple casein kinase 2 di-phosphorylated S-D-T-D motifs in MDC1. X-ray structural and mutagenic analysis of aprataxin FHA domain, combined with modelling of the pSDpTD peptide interaction suggest an unusual FHA binding mechanism mediated by a cluster of basic residues at and around the canonical pT-docking site. Mutation of aprataxin FHA Arg29 prevented its interaction with MDC1 and recruitment to sites of DNA damage. These results indicate that aprataxin is involved not only in single strand break repair but also in the processing of a subset of double strand breaks presumably through its interaction with MDC1.
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Affiliation(s)
- Olivier J Becherel
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia
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Harris JL, Jakob B, Taucher-Scholz G, Dianov GL, Becherel OJ, Lavin MF. Aprataxin, poly-ADP ribose polymerase 1 (PARP-1) and apurinic endonuclease 1 (APE1) function together to protect the genome against oxidative damage. Hum Mol Genet 2009; 18:4102-17. [PMID: 19643912 DOI: 10.1093/hmg/ddp359] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aprataxin, defective in the neurodegenerative disorder ataxia oculomotor apraxia type 1 (AOA1), is a DNA repair protein that processes the product of abortive ligations, 5' adenylated DNA. In addition to its interaction with the single-strand break repair protein XRCC1, aprataxin also interacts with poly-ADP ribose polymerase 1 (PARP-1), a key player in the detection of DNA single-strand breaks. Here, we reveal reduced expression of PARP-1, apurinic endonuclease 1 (APE1) and OGG1 in AOA1 cells and demonstrate a requirement for PARP-1 in the recruitment of aprataxin to sites of DNA breaks. While inhibition of PARP activity did not affect aprataxin activity in vitro, it retarded its recruitment to sites of DNA damage in vivo. We also demonstrate the presence of elevated levels of oxidative DNA damage in AOA1 cells coupled with reduced base excision and gap filling repair efficiencies indicative of a synergy between aprataxin, PARP-1, APE-1 and OGG1 in the DNA damage response. These data support both direct and indirect modulating functions for aprataxin on base excision repair.
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Affiliation(s)
- Janelle L Harris
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, Queensland 4029, Australia
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Jakob B, Splinter J, Taucher-Scholz G. Positional stability of damaged chromatin domains along radiation tracks in mammalian cells. Radiat Res 2009; 171:405-18. [PMID: 19397441 DOI: 10.1667/rr1520.1] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Irradiation of cell nuclei with charged particles leads to the spatially defined production of DNA damage along the particle trajectories, thus facilitating studies on the dynamics of radiation-induced protein foci associated with lesion processing. Here we used visual inspection and computational analysis of the track morphology after immunodetection to describe the patterns of formation of gamma-H2AX foci and the repair-related proteins 53BP1 and RPA. We addressed the influence of lesion density on gamma-H2AX formation and the mobility of damaged chromatin sites by using low-angle irradiation of cell monolayers with low-energy carbon or uranium ions. We show the discrete formation of gamma-H2AX foci and the recruitment of repair-related proteins along ion trajectories over an LET range from 200 to 14300 keV/microm in human fibroblasts and in HeLa cells. The marked DSBs exhibited a limited mobility that was independent of the LET. The moderate extent of mobility in human fibroblasts pointed to a relatively stable positioning of the damaged chromatin domains during repair, in contrast to HeLa cells, which showed significant changes in the streak patterns in a fraction of cells, suggesting greater mobility in the local processing of DSBs. Our data indicate that the presence of single or multiple DSBs is not associated with an altered potential for movement of damaged chromatin. We infer that the repair of high-LET radiation-induced DSBs in mammalian cells is not coupled to an increased motional activity of lesions enhancing the probability of translocations.
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Affiliation(s)
- B Jakob
- GSI Helmholtzzentrum für Schwerionenforschung, Biophysik, D-64291 Darmstadt, Germany.
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Jakob B, Reinhard PG, Toepffer C, Zwicknagel G. Wave packet simulation of dense hydrogen. Phys Rev E Stat Nonlin Soft Matter Phys 2007; 76:036406. [PMID: 17930350 DOI: 10.1103/physreve.76.036406] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Revised: 05/31/2007] [Indexed: 05/25/2023]
Abstract
Dense hydrogen is studied in the framework of wave packet molecular dynamics. In this semiquantal many-body simulation method the electrons are represented by wave packets which are suitably parametrized. The equilibrium properties and time evolution of the system are obtained with the help of a variational principle. At room temperature the results for the isotherms are in good agreement with anvil experiments. At higher densities beyond the range of the experimental data a transition from a molecular to a metallic state is predicted. The wave packets become delocalized and the electrical conductivity increases sharply. The phase diagram is calculated in a wide range of the pressure-density-temperature space. The observed transition from the molecular to metallic state is accompanied by an increase in density in agreement with recent reverberating shock wave experiments.
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Affiliation(s)
- B Jakob
- Institut für Theoretische Physik II, Universität Erlangen-Nürnberg, Staudtstrasse 7, D-91058 Erlangen, Germany
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Uematsu N, Weterings E, Yano KI, Morotomi-Yano K, Jakob B, Taucher-Scholz G, Mari PO, van Gent DC, Chen BPC, Chen DJ. Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks. ACTA ACUST UNITED AC 2007; 177:219-29. [PMID: 17438073 PMCID: PMC2064131 DOI: 10.1083/jcb.200608077] [Citation(s) in RCA: 307] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PK(CS)) plays an important role during the repair of DNA double-strand breaks (DSBs). It is recruited to DNA ends in the early stages of the nonhomologous end-joining (NHEJ) process, which mediates DSB repair. To study DNA-PK(CS) recruitment in vivo, we used a laser system to introduce DSBs in a specified region of the cell nucleus. We show that DNA-PK(CS) accumulates at DSB sites in a Ku80-dependent manner, and that neither the kinase activity nor the phosphorylation status of DNA-PK(CS) influences its initial accumulation. However, impairment of both of these functions results in deficient DSB repair and the maintained presence of DNA-PK(CS) at unrepaired DSBs. The use of photobleaching techniques allowed us to determine that the kinase activity and phosphorylation status of DNA-PK(CS) influence the stability of its binding to DNA ends. We suggest a model in which DNA-PK(CS) phosphorylation/autophosphorylation facilitates NHEJ by destabilizing the interaction of DNA-PK(CS) with the DNA ends.
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Affiliation(s)
- Naoya Uematsu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Becherel OJ, Gueven N, Birrell GW, Schreiber V, Suraweera A, Jakob B, Taucher-Scholz G, Lavin MF. Nucleolar localization of aprataxin is dependent on interaction with nucleolin and on active ribosomal DNA transcription. Hum Mol Genet 2006; 15:2239-49. [PMID: 16777843 DOI: 10.1093/hmg/ddl149] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The APTX gene, mutated in patients with the neurological disorder ataxia with oculomotor apraxia type 1 (AOA1), encodes a novel protein aprataxin. We describe here, the interaction and interdependence between aprataxin and several nucleolar proteins, including nucleolin, nucleophosmin and upstream binding factor-1 (UBF-1), involved in ribosomal RNA (rRNA) synthesis and cellular stress signalling. Interaction between aprataxin and nucleolin occurred through their respective N-terminal regions. In AOA1 cells lacking aprataxin, the stability of nucleolin was significantly reduced. On the other hand, down-regulation of nucleolin by RNA interference did not affect aprataxin protein levels but abolished its nucleolar localization suggesting that the interaction with nucleolin is involved in its nucleolar targeting. GFP-aprataxin fusion protein co-localized with nucleolin, nucleophosmin and UBF-1 in nucleoli and inhibition of ribosomal DNA transcription altered the distribution of aprataxin in the nucleolus, suggesting that the nature of the nucleolar localization of aprataxin is also dependent on ongoing rRNA synthesis. In vivo rRNA synthesis analysis showed only a minor decrease in AOA1 cells when compared with controls cells. These results demonstrate a cross-dependence between aprataxin and nucleolin in the nucleolus and while aprataxin does not appear to be directly involved in rRNA synthesis its nucleolar localization is dependent on this synthesis.
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Affiliation(s)
- Olivier J Becherel
- Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
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Taucher-Scholz G, Jakob B. Ion Irradiation as a Tool to Reveal the Spatiotemporal Dynamics of DNA Damage Response Processes. Genome Integr 2006. [DOI: 10.1007/7050_015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Abstract
The existing focusing heavy-ion microprobe at the Gesellschaft für Schwerionenforschung in Darmstadt (Germany) has been modified to enable the targeted irradiation of single, selected cells with a defined number of ions. With this setup, ions in the range from helium to uranium with linear energy transfers (LETs) up to approximately 15,000 keV/microm can be positioned with a precision of a few micrometers in the nuclei of single cells that are growing in culture on a thin polypropylene film. To achieve this accuracy, the microbeam traverses a thin vacuum window with minimal scattering. Electron emission from that window is used for particle detection. The cells are kept in a specially designed dish that is mounted directly behind the vacuum window in a setup allowing the precise movement and the imaging of the sample with microscopic methods. The cells are located by an integrated software program that also controls the rapid deflection and switching of the beam. In this paper, the setup is described in detail together with the first experiments showing its performance. We describe the ability of the microprobe to reliably hit randomly positioned etched nuclear tracks in CR-39 with single ions as well as the ability to visualize the ion hits using immunofluorescence staining for 53BP1 as a marker of DNA damage in the targeted cell nuclei.
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Affiliation(s)
- Markus Heiss
- Department of Materials Research, Gesellschaft für Schwerionenforschung, 64291 Darmstadt, Germany.
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41
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Jakob B, Rudolph JH, Gueven N, Lavin MF, Taucher-Scholz G. Live cell imaging of heavy-ion-induced radiation responses by beamline microscopy. Radiat Res 2005; 163:681-90. [PMID: 15913400 DOI: 10.1667/rr3374] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To study the dynamics of protein recruitment to DNA lesions, ion beams can be used to generate extremely localized DNA damage within restricted regions of the nuclei. This inhomogeneous spatial distribution of lesions can be visualized indirectly and rapidly in the form of radiation-induced foci using immunocytochemical detection or GFP-tagged DNA repair proteins. To analyze faster protein translocations and a possible contribution of radiation-induced chromatin movement in DNA damage recognition in live cells, we developed a remote-controlled system to obtain high-resolution fluorescence images of living cells during ion irradiation with a frame rate of the order of seconds. Using scratch replication labeling, only minor chromatin movement at sites of ion traversal was observed within the first few minutes of impact. Furthermore, time-lapse images of the GFP-coupled DNA repair protein aprataxin revealed accumulations within seconds at sites of ion hits, indicating a very fast recruitment to damaged sites. Repositioning of the irradiated cells after fixation allowed the comparison of live cell observation with immunocytochemical staining and retrospective etching of ion tracks. These results demonstrate that heavy-ion radiation-induced changes in subnuclear structures can be used to determine the kinetics of early protein recruitment in living cells and that the changes are not dependent on large-scale chromatin movement at short times postirradiation.
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Affiliation(s)
- B Jakob
- Gesellschaft für Schwerionenforschung, Biophysik, D-64291 Darmstadt, Germany.
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42
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Le HH, Ilisch S, Jakob B, Radusch HJ. Online Characterization of the Effect of Mixing Parameters on Carbon Black Dispersion in Rubber Compounds Using Electrical Conductivity. Rubber Chemistry and Technology 2004. [DOI: 10.5254/1.3547808] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Abstract
The influences of mixing parameters on the carbon black dispersion can be characterized using the electrical conductivity online measured from internal mixer. As a measure for monitoring the development of carbon black dispersion, a normalized conductivity with regard to the conductivity measured at the BIT (black incorporation time) has been suggested. It is observed that in spite of different mixing parameters, the mixtures possessing the same normalized conductivity factor K/KBIT deliver the same carbon black dispersion and the same mechanical properties. Based on normalized conductivity, a deeper insight into the mixing kinetics can be provided to find an optimal mixing regime.
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Affiliation(s)
- H. H. Le
- 1Institute of Materials Science, Martin Luther University Halle Wittenberg D-06099 Halle (Saale), Germany; ThermoElectron, Karlsruhe, Germany;
| | - S. Ilisch
- 1Institute of Materials Science, Martin Luther University Halle Wittenberg D-06099 Halle (Saale), Germany; ThermoElectron, Karlsruhe, Germany;
| | - B. Jakob
- 1Institute of Materials Science, Martin Luther University Halle Wittenberg D-06099 Halle (Saale), Germany; ThermoElectron, Karlsruhe, Germany;
| | - H.-J. Radusch
- 1Institute of Materials Science, Martin Luther University Halle Wittenberg D-06099 Halle (Saale), Germany; ThermoElectron, Karlsruhe, Germany;
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Longin E, Jakob B, Teich M, Schaible T, Lenz T, König S. Herzfrequenzvariabilität bei Frühgeborenen: Normwerte, Reifungsaspekte und physiologische Beobachtungen. KLIN NEUROPHYSIOL 2003. [DOI: 10.1055/s-2003-816482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
The immunocytochemical response to DNA damage induced by low-energy bismuth and carbon ions was investigated in normal human fibroblasts. Inside the nuclei, the traversing charged particles lead to the accumulation of proteins related to DNA lesions and repair along the ion trajectories. Irradiation under a standard geometric setup with the beam direction perpendicular to the cell monolayer generates spots of these proteins as described previously for MRE11B (hMre11), CDKN1A (p21) and PCNA (Jakob et al., Int. J. Radiat. Biol. 78, 75-88, 2002). Here we present data obtained with a new irradiation geometry characterized by a small angle between the beam direction and the monolayer of cells. This new irradiation geometry leads to the formation of protein aggregates in the shape of streaks stretching over several micrometers in the x/y plane, thus facilitating the analysis of the fluorescence distributions along the particle trajectories. Measurements of fluorescence intensity along the ion tracks in double- and triple-stained samples revealed a strict spatial correlation for the occurrence of CDKN1A and MRE11B clusters. In addition, immunostained gamma-H2AX is used as a marker of double-strand breaks (DSBs) to visualize the localized induction of these lesions along the particle paths. A clear coincidence of CDKN1A and gamma-H2AX signals within the ion-induced streaks is observed. Also for PCNA, which mainly associates with lesions processed by excision repair, a strict colocalization with the MRE11B aggregations was found along the ion trajectories, despite the higher estimated yield of this type of lesions compared to DSBs. Strikingly similar patterns of protein clusters are generated not only for the various proteins studied but also using different ion species from carbon to bismuth, covering LET values ranging from about 300 to 13600 keV/microm and producing estimated DSB densities differing by a factor around 45. The patterns of protein clustering along the very heavy-ion trajectories appear far more heterogeneous than expected based on idealized DSB distributions arising from model calculations. The results suggest that additional factors like compaction or confined movement of chromatin are responsible for the observed clustering of proteins.
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Affiliation(s)
- B Jakob
- Gesellschaft für Schwerionenforschung, Biophysik, Planckstrasse 1, D-64291 Darmstadt, Germany.
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Brons S, Jakob B, Taucher-Scholz G, Kraft G. Heavy ion production of single- and double-strand breaks in plasmid DNA in aqueous solution. Phys Med 2002; 17 Suppl 1:217-8. [PMID: 11776277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Preliminary measurements on the production of single- and double-strand breaks in SV40 and phi X174 plasmid DNA by various heavy ions in radioprotective Tris buffer are presented. The dependence of the recorded yields on the LET of the incoming ions is discussed and shown to be comprehensible within the framework of a model based on the X-ray sensitivity of the exposed DNA and the local dose distribution inside the heavy ion track. The question of the influence of the chemical environment is addressed by comparing the measured cross sections to data recorded previously in more radiosensitive TE buffer. The results indicate that also for systems with high scavenging capacity RBE values larger than unity can be achieved with maximum values in the LET range 100-1000 keV micrometers-1.
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Affiliation(s)
- S Brons
- Gesellschaft fur Schwerionenforschung (GSI), D-64291 Darmstadt, Germany
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Jakob B, Scholz M, Taucher-Scholz G. Characterization of CDKN1A (p21) binding to sites of heavy-ion-induced damage: colocalization with proteins involved in DNA repair. Int J Radiat Biol 2002; 78:75-88. [PMID: 11779358 DOI: 10.1080/09553000110090007] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
PURPOSE To determine an association of locally accumulated CDKN1A and DNA repair proteins at the sites of heavy-ion traversals. MATERIALS AND METHODS CDKN1A, PCNA, DNA-PK, hMre11 and Rad50 were investigated for their subnuclear localization after irradiation with heavy-ions using immunocytochemical staining and confocal laser-scanning microscopy. Human fibroblasts (normal diploid or XPA, ATM- or NBS1-deficient lines and HPV16 E6-transfected cells) were used. RESULTS CDKN1A formed nuclear foci in G0/G1 normal human fibroblasts at the sites of particle traversal. Foci were persistent over hours and vanished after treatment with DNase-I. Formation of foci also occurred in NBS1- or ATM-deficient lines and in cells functionally abrogated for TP53. In normal fibroblasts, CDKN1A foci colocalized with particle-induced foci of the hMre11 and Rad50 proteins. However, only CDKN1A relocalization was observed in irradiated NBS1 cells. PCNA foci temporarily colocalizing with CDKN1A were also detected in normal fibroblasts after exposure to heavy-ions. In contrast, no radiation-induced subnuclear relocalization was found for DNA-PK. CONCLUSIONS CDKN1A foci arise rapidly at sites of localized DNA damage induced by heavy-ions and are associated with the chromatin. Evidence is provided that localization of CDKN1A to foci is not dependent on functional TP53 and occurs independently of the formation of the hMre11/Rad50/NBS1 complex. The data support a yet unknown role of CDKN1A in sensing or early processing of radiation-induced DNA lesions.
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Affiliation(s)
- B Jakob
- Gesellschaft für Schwerionenforschung, Biophysik, Planckstrasse 1, D-64291 Darmstadt, Germany
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Scholz M, Jakob B, Taucher-Scholz G. Direct evidence for the spatial correlation between individual particle traversals and localized CDKN1A (p21) response induced by high-LET radiation. Radiat Res 2001; 156:558-63. [PMID: 11604069 DOI: 10.1667/0033-7587(2001)156[0558:deftsc]2.0.co;2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The spatial correlation between individual particle traversals and the nuclear CDKN1A (p21) response after high-LET irradiation of human fibroblasts was investigated. The experiments were based on a technique for the retrospective detection of particle traversals by means of nuclear track detectors, which were used as the cell substratum. This technique requires the precise repositioning of a sample at different steps of the experimental procedure and uses a computerized microscope stage control. The precision of the spatial correlation is further enhanced by means of reference marks in the track etch material that are produced by preirradiation of the plates with charged-particle beams at low fluences. The pattern of the CDKN1A foci that were induced by charged-particle traversals at 1 h postirradiation was found to coincide extremely well with the pattern of particle tracks. This represents direct evidence that CDKN1A foci are located at the sites of particle traversals and thus provides further evidence that the radiation-induced accumulation of the CDKN1A protein takes place at the sites of the primary damage.
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Affiliation(s)
- M Scholz
- Gesellschaft für Schwerionenforschung (GSI)/Biophysik, Planckstrasse 1, D-64291 Darmstadt, Germany.
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Jakob B, Birkholz S, Schneider T, Duchmann R, Zeitz M, Stallmach A. Immune response to autologous and heterologous Helicobacter pylori antigens in humans. Microsc Res Tech 2001; 53:419-24. [PMID: 11525260 DOI: 10.1002/jemt.1111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Infection of humans with Helicobacter pylori results in the development of chronic gastritis and plays an important role in gastric ulcer pathogenesis. Despite the infiltration of the mucosa with specific immunocompetent cells and production of specific antibodies, the infection usually persists for life. This study was performed to investigate if immunologic mechanisms exist which could contribute to the inability of the host to terminate the infection. Therefore, we compared the in vitro immunoreactivity of peripheral blood mononuclear cells (PBMC) from H. pylori-infected patients after stimulation with sonicated H. pylori bacteria from the stomach of the patient (autologous bacterial strain) with stimulation by bacteria from other patients (heterologous bacteria). We measured cell proliferation, expression of T cell activation markers CD25, HLA-DR, and CD71, as well as production ofinterleukin-10 (IL-10), an inhibitory cytokine. We found that the proliferative response of PBMC was significantly lower after autologous than after heterologous stimulation. Furthermore, secretion of IL-10 in the culture supernatants was significantly higher when PBMC were incubated with autologous than with heterologous H. pylori antigens. No significant differences between autologous or heterologous stimulation were observed in the increased expression of T cell activation markers. These data indicate that systemic immunologic response to H. pylori are strain-dependent. For further studies of the immune responses towards H. pylori, the use of an autologous stimulatory system seems necessary.
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Affiliation(s)
- B Jakob
- Department of Internal Medicine II, Saarland University, Homburg/Saar, Germany
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49
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Abstract
Using confocal microscopy on immunofluorescence-stained cells, we have investigated the response of CDKN1A (p21), one of the key proteins involved in the DNA damage response pathway, after irradiation with accelerated lead or chromium ions. Each traversal of an accelerated ion leads to the formation of a single, bright focus of the CDKN1A protein in the nuclei of human fibroblasts within 2 min after irradiation at 4 degrees C. This immediate, localized CDKN1A response is specific for particle irradiation with a high linear energy transfer (LET), whereas X irradiation, after a period of induction, yields a diffusely spread pattern, in line with the differences in the microscopic dose deposition pattern of both radiation types. The particle-induced CDKN1A foci persist for several hours until they become diffuse and vanish. These findings suggest that CDKN1A accumulates at the sites of primary DNA damage, possibly mediated by the interaction with proteins involved in DNA repair. Here, for the first time, an immediate biological response confined to the radial extension of low-energy particle tracks ( approximately 1 micrometer) is directly visualized and correlated to ion traversals. This indicates that particle irradiation represents an ideal tool to study the processing of biological damage induced in defined subnuclear regions.
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Affiliation(s)
- B Jakob
- Gesellschaft für Schwerionenforschung, Biophysik, Planckstrasse 1, D-64291 Darmstadt, Germany
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50
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Abstract
After opening the stomata in CO(2)-free air, darkened leaves of several plant species were titrated with CO(2) at concentrations between 1 and 16%, in air in order to reversibly decrease cellular pH values and to calculate buffer capacities from pH changes and bicarbonate accumulation using both gas-exchange and fluorescence methods for analysis. After equilibration with CO(2) for times ranging between 4.4 and 300 s, fast CO(2) release from bicarbonate indicated catalysis by highly active carbonic anhydrase. Its time constant was below 2.5 s. Additional CO(2) was released with time constants of about 5, 15 and approximately 300 s. With CO(2) as the acidifying agent, calculated buffer capacities depend on assumptions regarding initial pH in the absence of an acid load. At an initial stroma pH of 7.7, the stromal buffer capacity was about 20 mM pH-unit(-1 )in darkened spinach leaves. At an initial pH of 7.5 it would be only 12 mM pH-unit(-1), i.e. not higher than expected solely on the basis of known stromal concentrations of phosphate and phosphate esters, disregarding the contribution of other solutes. At a concentration of 16%, CO(2) reduced the stromal pH by about 1 pH unit. Buffering of the cytosol was measured by the CO(2)-dependent quenching of the fluorescence of pyranine which was fed to spinach leaves via the petiole. Brief exposures to high CO(2) minimized interference by effective cytosolic pH regulation. Cytosolic buffering appeared to be similar to or only somewhat higher than chloroplast buffering if the initial cytosolic pH was assumed to be 7.25, which is in accord with published cytosolic pH values. The difference from chloroplast pH values indicates the existence of a pH gradient across the chloroplast envelope even in darkened leaves. Apoplastic buffering was weak as measured by the CO(2)-dependent quenching of dextran-conjugated fluorescein isothiocyanate which was infiltrated together with sodium vanadate into potato leaves. In the absence of vanadate, the kinetics of apoplastic fluorescence quenching were more complex than in its presence, indicating fast apoplastic pH regulation which strongly interfered with the determination of apoplastic buffering capacities. At an apoplastic pH of 6.1 in potato leaves, apoplastic buffering as determined by CO(2) titration with and without added buffer was somewhat below 4 mM pH-unit(-1). Thus the apoplastic and cytosolic pH responses to additions of CO(2 )indicated that the observed cytoplasmic pH regulation under acid stress involves pumping of protons from the cytosol into the vacuole of leaf cells, but not into the apoplast.
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Affiliation(s)
- V Oja
- Julius-von-Sachs-Institut für Biowissenschaften, Universität Würzburg, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
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