1
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Collins VJ, Ludwig KR, Nelson AE, Rajan SS, Yeung C, Vulikh K, Isanogle KA, Mendoza A, Difilippantonio S, Karim BO, Caplen NJ, Heske CM. Enhancing Standard of Care Chemotherapy Efficacy Using DNA-Dependent Protein Kinase (DNA-PK) Inhibition in Preclinical Models of Ewing Sarcoma. Mol Cancer Ther 2024; 23:1109-1123. [PMID: 38657228 PMCID: PMC11293986 DOI: 10.1158/1535-7163.mct-23-0641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/26/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024]
Abstract
Disruption of DNA damage repair via impaired homologous recombination is characteristic of Ewing sarcoma (EWS) cells. We hypothesize that this disruption results in increased reliance on nonhomologous end joining to repair DNA damage. In this study, we investigated if pharmacologic inhibition of the enzyme responsible for nonhomologous end joining, the DNA-PK holoenzyme, alters the response of EWS cells to genotoxic standard of care chemotherapy. We used analyses of cell viability and proliferation to investigate the effects of clinical DNA-PK inhibitors (DNA-PKi) in combination with six therapeutic or experimental agents for EWS. We performed calculations of synergy using the Loewe additivity model. Immunoblotting evaluated treatment effects on DNA-PK, DNA damage, and apoptosis. Flow cytometric analyses evaluated effects on cell cycle and fate. We used orthotopic xenograft models to interrogate tolerability, drug mechanism, and efficacy in vivo. DNA-PKi demonstrated on-target activity, reducing phosphorylated DNA-PK levels in EWS cells. DNA-PKi sensitized EWS cell lines to agents that function as topoisomerase 2 (TOP2) poisons and enhanced the DNA damage induced by TOP2 poisons. Nanomolar concentrations of single-agent TOP2 poisons induced G2M arrest and little apoptotic response while adding DNA-PKi-mediated apoptosis. In vivo, the combination of AZD7648 and etoposide had limited tolerability but resulted in enhanced DNA damage, apoptosis, and EWS tumor shrinkage. The combination of DNA-PKi with standard of care TOP2 poisons in EWS models is synergistic, enhances DNA damage and cell death, and may form the basis of a promising future therapeutic strategy for EWS.
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Affiliation(s)
- Victor J. Collins
- Translational Sarcoma Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ariana E. Nelson
- Translational Sarcoma Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Choh Yeung
- Translational Sarcoma Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ksenia Vulikh
- Molecular Histopathology Lab, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Kristine A. Isanogle
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Arnulfo Mendoza
- Translational Sarcoma Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Simone Difilippantonio
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Baktiar O. Karim
- Molecular Histopathology Lab, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Christine M. Heske
- Translational Sarcoma Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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2
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Deshpande RA, Marin-Gonzalez A, Barnes HK, Woolley PR, Ha T, Paull TT. Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice. Nat Commun 2023; 14:5759. [PMID: 37717054 PMCID: PMC10505227 DOI: 10.1038/s41467-023-41544-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
The Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5' strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site-a role we postulate is played by DNA-dependent protein kinase (DNA-PK) in mammals. Here we interrogate sites of MRN-dependent processing by identifying sites of CtIP association and by sequencing DNA-PK-bound DNA fragments that are products of MRN cleavage. These intermediates are generated most efficiently when DNA-PK is catalytically blocked, yielding products within 200 bp of the break site, whereas DNA-PK products in the absence of kinase inhibition show greater dispersal. Use of light-activated Cas9 to induce breaks facilitates temporal resolution of DNA-PK and Mre11 binding, showing that both complexes bind to DNA ends before release of DNA-PK-bound products. These results support a sequential model of double-strand break repair involving collaborative interactions between homologous and non-homologous repair complexes.
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Affiliation(s)
| | - Alberto Marin-Gonzalez
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Hannah K Barnes
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Phillip R Woolley
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Tanya T Paull
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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3
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Mokari M, Moeini H, Farazmand S. Computational modeling and a Geant4-DNA study of the rejoining of direct and indirect DNA damage induced by low energy electrons and carbon ions. Int J Radiat Biol 2023; 99:1391-1404. [PMID: 36745857 DOI: 10.1080/09553002.2023.2173824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 02/08/2023]
Abstract
PURPOSE DNA double-strand breaks (DSBs) created by ionizing radiations are considered as the most detrimental lesion, which could result in the cell death or sterilization. As the empirical evidence gathered from the cellular and molecular radiation biology has demonstrated significant correlations between the initial and lasting levels of DSBs, gaining knowledge into the DSB repair mechanisms proves vital. Much effort has been invested into understanding the mechanisms triggering the repair and processes engaged after irradiation of cells. Given a mechanistic model, we performed - to our knowledge - the first Monte Carlo study of the expected repair kinetics of carbon ions and electrons using on the one hand Geant4-DNA simulations of electrons for benchmarking purposes and on the other hand quantifying the influence of direct and indirect damage. Our objective was to calculate the DSB repair rates using a repair mechanism for G1 and early S phases of the cell cycle in conjunction with simulations of the DNA damage. MATERIALS AND METHODS Based on Geant4-DNA simulations of DSB damage caused by electrons and carbon ions - using a B-DNA model and a water sphere of 3 μm radius resembling the mean size of human cells - we derived the kinetics of various biochemical repair processes. RESULTS The overall repair times of carbon ions increased with the DSB complexity. Comparison of the DSB complexity (DSBc) and repair times as a function of carbon-ion energy suggested that the repair time of no specific fraction of DSBs could solely be explained as a function of DSB complexity. CONCLUSION Analysis of the carbon-ion repair kinetics indicated that, given a fraction of DSBs, decreasing the energy would result in an increase of the repair time. The disagreements of the calculated and experimental repair kinetics for electrons could, among others, be due to larger damage complexity predicted by simulations or created actually by electrons of comparable energies to x-rays. They are also due to the employed repair mechanisms, which introduce no inherent dependence on the radiation type but make direct use of the simulated DSBs.
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Affiliation(s)
- Mojtaba Mokari
- Department of Physics, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran
| | - Hossein Moeini
- Department of Physics, School of Science, Shiraz University, Shiraz, Iran
| | - Shahnaz Farazmand
- Department of Physics, Isfahan University of Technology, Isfahan, Iran
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4
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Cekanaviciute E, Tran D, Nguyen H, Lopez Macha A, Pariset E, Langley S, Babbi G, Malkani S, Penninckx S, Schisler JC, Nguyen T, Karpen GH, Costes SV. Mouse genomic associations with in vitro sensitivity to simulated space radiation. LIFE SCIENCES IN SPACE RESEARCH 2023; 36:47-58. [PMID: 36682829 DOI: 10.1016/j.lssr.2022.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 06/17/2023]
Abstract
Exposure to ionizing radiation is considered by NASA to be a major health hazard for deep space exploration missions. Ionizing radiation sensitivity is modulated by both genomic and environmental factors. Understanding their contributions is crucial for designing experiments in model organisms, evaluating the risk of deep space (i.e. high-linear energy transfer, or LET, particle) radiation exposure in astronauts, and also selecting therapeutic irradiation regimes for cancer patients. We identified single nucleotide polymorphisms in 15 strains of mice, including 10 collaborative cross model strains and 5 founder strains, associated with spontaneous and ionizing radiation-induced in vitro DNA damage quantified based on immunofluorescent tumor protein p53 binding protein (53BP1) positive nuclear foci. Statistical analysis suggested an association with pathways primarily related to cellular signaling, metabolism, tumorigenesis and nervous system damage. We observed different genomic associations in early (4 and 8 h) responses to different LET radiation, while later (24 hour) DNA damage responses showed a stronger overlap across all LETs. Furthermore, a subset of pathways was associated with spontaneous DNA damage, suggesting 53BP1 positive foci as a potential biomarker for DNA integrity in mouse models. Our results suggest several mouse strains as new models to further study the impact of ionizing radiation and validate the identified genetic loci. We also highlight the importance of future human in vitro studies to refine the association of genes and pathways with the DNA damage response to ionizing radiation and identify targets for space travel countermeasures.
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Affiliation(s)
- Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Duc Tran
- Department of Computer Science and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Hung Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Alejandra Lopez Macha
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Blue Marble Space Institute of Science, 600 1st Avenue, 1st Floor, Seattle, WA 98104, USA
| | - Eloise Pariset
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Universities Space Research Association, 615 National Avenue, Mountain View, CA 94043, USA
| | - Sasha Langley
- Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA, and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Giulia Babbi
- Bologna Biocomputing Group, FABIT, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Sherina Malkani
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Blue Marble Space Institute of Science, 600 1st Avenue, 1st Floor, Seattle, WA 98104, USA
| | - Sébastien Penninckx
- Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA, and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA; Medical Physics Department, Jules Bordet Institute, Université Libre de Bruxelles, 90 Rue Meylemeersch, 1070 Brussels, Belgium
| | - Jonathan C Schisler
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, NC 27599, USA
| | - Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Gary H Karpen
- Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA, and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
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5
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A rapid multiplex cell-free assay on biochip to evaluate functional aspects of double-strand break repair. Sci Rep 2022; 12:20054. [PMID: 36414637 PMCID: PMC9681732 DOI: 10.1038/s41598-022-23819-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) involves interdependent molecular pathways, of which the choice is crucial for a cell's fate when facing a damage. Growing evidence points toward the fact that DSB repair capacities correlate with disease aggressiveness, treatment response and treatment-related toxicities in cancer. Scientific and medical communities need more easy-to-use and efficient tools to rapidly estimate DSB repair capacities from a tissue, enable routine-accessible treatment personalization, and hopefully, improve survival. Here, we propose a new functional biochip assay (NEXT-SPOT) that characterizes DSB repair-engaged cellular pathways and provides qualitative and quantitative information on the contribution of several pathways in less than 2 h, from 10 mg of cell lysates. We introduce the NEXT-SPOT technology, detail the molecular characterizations of different repair steps occurring on the biochip, and show examples of DSB repair profiling using three cancer cell lines treated or not with a DSB-inducer (doxorubicin) and/or a DNA repair inhibitor (RAD51 inhibitor; DNA-PK inhibitor; PARP inhibitor). Among others, we demonstrate that NEXT-SPOT can accurately detect decreased activities in strand invasion and end-joining mechanisms following DNA-PK or RAD51 inhibition in DNA-PK-proficient cell lines. This approach offers an all-in-one reliable strategy to consider DSB repair capacities as predictive biomarkers easily translatable to the clinic.
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6
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Mairani A, Mein S, Blakely E, Debus J, Durante M, Ferrari A, Fuchs H, Georg D, Grosshans DR, Guan F, Haberer T, Harrabi S, Horst F, Inaniwa T, Karger CP, Mohan R, Paganetti H, Parodi K, Sala P, Schuy C, Tessonnier T, Titt U, Weber U. Roadmap: helium ion therapy. Phys Med Biol 2022; 67. [PMID: 35395649 DOI: 10.1088/1361-6560/ac65d3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/08/2022] [Indexed: 12/16/2022]
Abstract
Helium ion beam therapy for the treatment of cancer was one of several developed and studied particle treatments in the 1950s, leading to clinical trials beginning in 1975 at the Lawrence Berkeley National Laboratory. The trial shutdown was followed by decades of research and clinical silence on the topic while proton and carbon ion therapy made debuts at research facilities and academic hospitals worldwide. The lack of progression in understanding the principle facets of helium ion beam therapy in terms of physics, biological and clinical findings persists today, mainly attributable to its highly limited availability. Despite this major setback, there is an increasing focus on evaluating and establishing clinical and research programs using helium ion beams, with both therapy and imaging initiatives to supplement the clinical palette of radiotherapy in the treatment of aggressive disease and sensitive clinical cases. Moreover, due its intermediate physical and radio-biological properties between proton and carbon ion beams, helium ions may provide a streamlined economic steppingstone towards an era of widespread use of different particle species in light and heavy ion therapy. With respect to the clinical proton beams, helium ions exhibit superior physical properties such as reduced lateral scattering and range straggling with higher relative biological effectiveness (RBE) and dose-weighted linear energy transfer (LETd) ranging from ∼4 keVμm-1to ∼40 keVμm-1. In the frame of heavy ion therapy using carbon, oxygen or neon ions, where LETdincreases beyond 100 keVμm-1, helium ions exhibit similar physical attributes such as a sharp lateral penumbra, however, with reduced radio-biological uncertainties and without potentially spoiling dose distributions due to excess fragmentation of heavier ion beams, particularly for higher penetration depths. This roadmap presents an overview of the current state-of-the-art and future directions of helium ion therapy: understanding physics and improving modeling, understanding biology and improving modeling, imaging techniques using helium ions and refining and establishing clinical approaches and aims from learned experience with protons. These topics are organized and presented into three main sections, outlining current and future tasks in establishing clinical and research programs using helium ion beams-A. Physics B. Biological and C. Clinical Perspectives.
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Affiliation(s)
- Andrea Mairani
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany.,National Centre of Oncological Hadrontherapy (CNAO), Medical Physics, Pavia, Italy.,Division of Molecular and Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital, 69120 Heidelberg, Germany.,National Center for Radiation Research in Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany
| | - Stewart Mein
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital, 69120 Heidelberg, Germany.,National Center for Radiation Research in Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany.,German Cancer Consortium (DKTK) Core-Center Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eleanor Blakely
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Jürgen Debus
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital, 69120 Heidelberg, Germany.,National Center for Radiation Research in Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany.,German Cancer Consortium (DKTK) Core-Center Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Clinical Cooperation Unit Radiation Oncology, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marco Durante
- GSI Helmholtzzentrum für Schwerionenforschung, D-64291 Darmstadt, Germany.,Technische Universität Darmstadt, Institut für Physik Kondensierter Materie, Darmstadt, Germany
| | - Alfredo Ferrari
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hermann Fuchs
- Division of Medical Physics, Department of Radiation Oncology, Medical University of Vienna, Austria.,MedAustron Ion Therapy Center, Wiener Neustadt, Austria
| | - Dietmar Georg
- Division of Medical Physics, Department of Radiation Oncology, Medical University of Vienna, Austria.,MedAustron Ion Therapy Center, Wiener Neustadt, Austria
| | - David R Grosshans
- The University of Texas MD Anderson cancer Center, Houston, Texas, United States of America
| | - Fada Guan
- The University of Texas MD Anderson cancer Center, Houston, Texas, United States of America.,Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, 06510, United States of America
| | - Thomas Haberer
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Semi Harrabi
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany.,National Center for Radiation Research in Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany.,German Cancer Consortium (DKTK) Core-Center Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Clinical Cooperation Unit Radiation Oncology, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Felix Horst
- GSI Helmholtzzentrum für Schwerionenforschung, D-64291 Darmstadt, Germany
| | - Taku Inaniwa
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan.,Medical Physics Laboratory, Division of Health Science, Graduate School of Medicine, Osaka University, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Christian P Karger
- National Center for Radiation Research in Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany.,Department of Medical Physics in Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Radhe Mohan
- The University of Texas MD Anderson cancer Center, Houston, Texas, United States of America
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, United States of America.,Harvard Medical School, Boston, United States of America
| | - Katia Parodi
- Ludwig-Maximilians-Universität München, Department of Experimental Physics-Medical Physics, Munich, Germany
| | - Paola Sala
- Ludwig-Maximilians-Universität München, Department of Experimental Physics-Medical Physics, Munich, Germany
| | - Christoph Schuy
- GSI Helmholtzzentrum für Schwerionenforschung, D-64291 Darmstadt, Germany
| | - Thomas Tessonnier
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Uwe Titt
- The University of Texas MD Anderson cancer Center, Houston, Texas, United States of America
| | - Ulrich Weber
- GSI Helmholtzzentrum für Schwerionenforschung, D-64291 Darmstadt, Germany
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7
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Ingram SP, Warmenhoven JW, Henthorn NT, Chadiwck AL, Santina EE, McMahon SJ, Schuemann J, Kirkby NF, Mackay RI, Kirkby KJ, Merchant MJ. A computational approach to quantifying miscounting of radiation-induced double-strand break immunofluorescent foci. Commun Biol 2022; 5:700. [PMID: 35835982 PMCID: PMC9283546 DOI: 10.1038/s42003-022-03585-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022] Open
Abstract
Immunofluorescent tagging of DNA double-strand break (DSB) markers, such as γ-H2AX and other DSB repair proteins, are powerful tools in understanding biological consequences following irradiation. However, whilst the technique is widespread, there are many uncertainties related to its ability to resolve and reliably deduce the number of foci when counting using microscopy. We present a new tool for simulating radiation-induced foci in order to evaluate microscope performance within in silico immunofluorescent images. Simulations of the DSB distributions were generated using Monte Carlo track-structure simulation. For each DSB distribution, a corresponding DNA repair process was modelled and the un-repaired DSBs were recorded at several time points. Corresponding microscopy images for both a DSB and (γ-H2AX) fluorescent marker were generated and compared for different microscopes, radiation types and doses. Statistically significant differences in miscounting were found across most of the tested scenarios. These inconsistencies were propagated through to repair kinetics where there was a perceived change between radiation-types. These changes did not reflect the underlying repair rate and were caused by inconsistencies in foci counting. We conclude that these underlying uncertainties must be considered when analysing images of DNA damage markers to ensure differences observed are real and are not caused by non-systematic miscounting. PyFoci is a tool that simulates distributions of fluorescently labeled DNA double-strand break marker protein foci and allows the estimation of miscounting under different radiation types, doses and microscopy settings.
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Affiliation(s)
- Samuel P Ingram
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK. .,Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester, M20 4BX, UK.
| | - John-William Warmenhoven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK.,The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Nicholas T Henthorn
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK.,The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Amy L Chadiwck
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK.,The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Elham E Santina
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK.,The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queens University Belfast, 97 Lisburn Rd, Belfast, BT9 7AE, UK
| | - Jan Schuemann
- Massachusetts General Hospital and Harvard Medical School, Department of Radiation Oncology, 30 Fruit Street, Boston, MA, 02114, USA
| | - Norman F Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK.,The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Ranald I Mackay
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK.,Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Karen J Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK.,The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Michael J Merchant
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Rd, Manchester, M13 9PL, UK.,The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Wilmslow Rd, Manchester, M20 4BX, UK
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8
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Ou-Yang H, Yang SH, Chen W, Yang SH, Cidem A, Sung LY, Chen CM. Cruciform DNA Structures Act as Legible Templates for Accelerating Homologous Recombination in Transgenic Animals. Int J Mol Sci 2022; 23:3973. [PMID: 35409332 PMCID: PMC9000021 DOI: 10.3390/ijms23073973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
Inverted repeat (IR) DNA sequences compose cruciform structures. Some genetic disorders are the result of genome inversion or translocation by cruciform DNA structures. The present study examined whether exogenous DNA integration into the chromosomes of transgenic animals was related to cruciform DNA structures. Large imperfect cruciform structures were frequently predicted around predestinated transgene integration sites in host genomes of microinjection-based transgenic (Tg) animals (αLA-LPH Tg goat, Akr1A1eGFP/eGFP Tg mouse, and NFκB-Luc Tg mouse) or CRISPR/Cas9 gene-editing (GE) animals (αLA-AP1 GE mouse). Transgene cassettes were imperfectly matched with their predestinated sequences. According to the analyzed data, we proposed a putative model in which the flexible cruciform DNA structures acted as a legible template for DNA integration into linear DNAs or double-strand break (DSB) alleles. To demonstrate this model, artificial inverted repeat knock-in (KI) reporter plasmids were created to analyze the KI rate using the CRISPR/Cas9 system in NIH3T3 cells. Notably, the KI rate of the 5′ homologous arm inverted repeat donor plasmid (5′IR) with the ROSA gRNA group (31.5%) was significantly higher than the knock-in reporter donor plasmid (KIR) with the ROSA gRNA group (21.3%, p < 0.05). However, the KI rate of the 3′ inverted terminal repeat/inverted repeat donor plasmid (3′ITRIR) group was not different from the KIR group (23.0% vs. 22.0%). These results demonstrated that the legibility of the sequence with the cruciform DNA existing in the transgene promoted homologous recombination (HR) with a higher KI rate. Our findings suggest that flexible cruciform DNAs folded by IR sequences improve the legibility and accelerate DNA 3′-overhang integration into the host genome via homologous recombination machinery.
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Affiliation(s)
- Huan Ou-Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Shiao-Hsuan Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Reproductive Medicine Center, Department of Gynecology, Changhua Christian Hospital, Changhua 515, Taiwan
| | - Wei Chen
- Division of Pulmonary and Critical Care Medicine, Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
| | - Shang-Hsun Yang
- Department of Physiology, National Cheng Kung University, Tainan 701, Taiwan;
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Abdulkadir Cidem
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum 25250, Turkey
| | - Li-Ying Sung
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Chuan-Mu Chen
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Rong-Hsing Translational Medicine Research Center, Taichung Veterans General Hospital, Taichung 407, Taiwan
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9
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Kieffer SR, Lowndes NF. Immediate-Early, Early, and Late Responses to DNA Double Stranded Breaks. Front Genet 2022; 13:793884. [PMID: 35173769 PMCID: PMC8841529 DOI: 10.3389/fgene.2022.793884] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 12/18/2022] Open
Abstract
Loss or rearrangement of genetic information can result from incorrect responses to DNA double strand breaks (DSBs). The cellular responses to DSBs encompass a range of highly coordinated events designed to detect and respond appropriately to the damage, thereby preserving genomic integrity. In analogy with events occurring during viral infection, we appropriate the terms Immediate-Early, Early, and Late to describe the pre-repair responses to DSBs. A distinguishing feature of the Immediate-Early response is that the large protein condensates that form during the Early and Late response and are resolved upon repair, termed foci, are not visible. The Immediate-Early response encompasses initial lesion sensing, involving poly (ADP-ribose) polymerases (PARPs), KU70/80, and MRN, as well as rapid repair by so-called ‘fast-kinetic’ canonical non-homologous end joining (cNHEJ). Initial binding of PARPs and the KU70/80 complex to breaks appears to be mutually exclusive at easily ligatable DSBs that are repaired efficiently by fast-kinetic cNHEJ; a process that is PARP-, ATM-, 53BP1-, Artemis-, and resection-independent. However, at more complex breaks requiring processing, the Immediate-Early response involving PARPs and the ensuing highly dynamic PARylation (polyADP ribosylation) of many substrates may aid recruitment of both KU70/80 and MRN to DSBs. Complex DSBs rely upon the Early response, largely defined by ATM-dependent focal recruitment of many signalling molecules into large condensates, and regulated by complex chromatin dynamics. Finally, the Late response integrates information from cell cycle phase, chromatin context, and type of DSB to determine appropriate pathway choice. Critical to pathway choice is the recruitment of p53 binding protein 1 (53BP1) and breast cancer associated 1 (BRCA1). However, additional factors recruited throughout the DSB response also impact upon pathway choice, although these remain to be fully characterised. The Late response somehow channels DSBs into the appropriate high-fidelity repair pathway, typically either ‘slow-kinetic’ cNHEJ or homologous recombination (HR). Loss of specific components of the DSB repair machinery results in cells utilising remaining factors to effect repair, but often at the cost of increased mutagenesis. Here we discuss the complex regulation of the Immediate-Early, Early, and Late responses to DSBs proceeding repair itself.
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10
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Shademan B, Nourazarian A, Hajazimian S, Isazadeh A, Biray Avci C, Oskouee MA. CRISPR Technology in Gene-Editing-Based Detection and Treatment of SARS-CoV-2. Front Mol Biosci 2022; 8:772788. [PMID: 35087864 PMCID: PMC8787289 DOI: 10.3389/fmolb.2021.772788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023] Open
Abstract
Outbreak and rapid spread of coronavirus disease (COVID-19) caused by coronavirus acute respiratory syndrome (SARS-CoV-2) caused severe acute respiratory syndrome (SARS-CoV-2) that started in Wuhan, and has become a global problem because of the high rate of human-to-human transmission and severe respiratory infections. Because of high prevalence of SARS-CoV-2, which threatens many people worldwide, rapid diagnosis and simple treatment are needed. Genome editing is a nucleic acid-based approach to altering the genome by artificially changes in genetic information and induce irreversible changes in the function of target gene. Clustered, regularly interspaced short palindromic repeats (CRISPR/Cas) could be a practical and straightforward approach to this disease. CRISPR/Cas system contains Cas protein, which is controlled by a small RNA molecule to create a double-stranded DNA gap. Evidence suggested that CRISPR/Cas was also usable for diagnosis and treatment of SARS-CoV-2 infection. In this review study, we discoursed on application of CRISPR technology in detection and treatment of SARS-CoV-2 infection. Another aspect of this study was to introduce potential future problems in use of CRISPR/Cas technology.
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Affiliation(s)
- Behrouz Shademan
- Department of Medical Biology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Alireza Nourazarian
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran
| | - Saba Hajazimian
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Isazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Cigir Biray Avci
- Department of Medical Biology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Mahin Ahangar Oskouee
- Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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11
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Penninckx S, Pariset E, Cekanaviciute E, Costes SV. Quantification of radiation-induced DNA double strand break repair foci to evaluate and predict biological responses to ionizing radiation. NAR Cancer 2021; 3:zcab046. [PMID: 35692378 PMCID: PMC8693576 DOI: 10.1093/narcan/zcab046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/08/2021] [Accepted: 12/17/2021] [Indexed: 08/08/2023] Open
Abstract
Radiation-induced foci (RIF) are nuclear puncta visualized by immunostaining of proteins that regulate DNA double-strand break (DSB) repair after exposure to ionizing radiation. RIF are a standard metric for measuring DSB formation and repair in clinical, environmental and space radiobiology. The time course and dose dependence of their formation has great potential to predict in vivo responses to ionizing radiation, predisposition to cancer and probability of adverse reactions to radiotherapy. However, increasing complexity of experimentally and therapeutically setups (charged particle, FLASH …) is associated with several confounding factors that must be taken into account when interpreting RIF values. In this review, we discuss the spatiotemporal characteristics of RIF development after irradiation, addressing the common confounding factors, including cell proliferation and foci merging. We also describe the relevant endpoints and mathematical models that enable accurate biological interpretation of RIF formation and resolution. Finally, we discuss the use of RIF as a biomarker for quantification and prediction of in vivo radiation responses, including important caveats relating to the choice of the biological endpoint and the detection method. This review intends to help scientific community design radiobiology experiments using RIF as a key metric and to provide suggestions for their biological interpretation.
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Affiliation(s)
- Sébastien Penninckx
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Medical Physics Department, Jules Bordet Institute, Université Libre de Bruxelles, 1 Rue Héger-Bordet, 1000 Brussels, Belgium
| | - Eloise Pariset
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Universities Space Research Association, 615 National Avenue, Mountain View, CA 94043, USA
| | - Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sylvain V Costes
- To whom correspondence should be addressed. Tel: +1 650 604 5343;
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12
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Carlos-Reyes A, Muñiz-Lino MA, Romero-Garcia S, López-Camarillo C, Hernández-de la Cruz ON. Biological Adaptations of Tumor Cells to Radiation Therapy. Front Oncol 2021; 11:718636. [PMID: 34900673 PMCID: PMC8652287 DOI: 10.3389/fonc.2021.718636] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Radiation therapy has been used worldwide for many decades as a therapeutic regimen for the treatment of different types of cancer. Just over 50% of cancer patients are treated with radiotherapy alone or with other types of antitumor therapy. Radiation can induce different types of cell damage: directly, it can induce DNA single- and double-strand breaks; indirectly, it can induce the formation of free radicals, which can interact with different components of cells, including the genome, promoting structural alterations. During treatment, radiosensitive tumor cells decrease their rate of cell proliferation through cell cycle arrest stimulated by DNA damage. Then, DNA repair mechanisms are turned on to alleviate the damage, but cell death mechanisms are activated if damage persists and cannot be repaired. Interestingly, some cells can evade apoptosis because genome damage triggers the cellular overactivation of some DNA repair pathways. Additionally, some surviving cells exposed to radiation may have alterations in the expression of tumor suppressor genes and oncogenes, enhancing different hallmarks of cancer, such as migration, invasion, and metastasis. The activation of these genetic pathways and other epigenetic and structural cellular changes in the irradiated cells and extracellular factors, such as the tumor microenvironment, is crucial in developing tumor radioresistance. The tumor microenvironment is largely responsible for the poor efficacy of antitumor therapy, tumor relapse, and poor prognosis observed in some patients. In this review, we describe strategies that tumor cells use to respond to radiation stress, adapt, and proliferate after radiotherapy, promoting the appearance of tumor radioresistance. Also, we discuss the clinical impact of radioresistance in patient outcomes. Knowledge of such cellular strategies could help the development of new clinical interventions, increasing the radiosensitization of tumor cells, improving the effectiveness of these therapies, and increasing the survival of patients.
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Affiliation(s)
- Angeles Carlos-Reyes
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases “Ismael Cosío Villegas”, Mexico City, Mexico
| | - Marcos A. Muñiz-Lino
- Laboratorio de Patología y Medicina Bucal, Universidad Autónoma Metropolitana Unidad Xochimilco, Mexico City, Mexico
| | - Susana Romero-Garcia
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases “Ismael Cosío Villegas”, Mexico City, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico, Mexico City
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13
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Parisi A, Struelens L, Vanhavere F. Comparison between the results of a recently-developed biological weighting function (V79-RBE 10BWF) and the in vitroclonogenic survival RBE 10of other repair-competent asynchronized normoxic mammalian cell lines and ions not used for the development of the model. Phys Med Biol 2021; 66. [PMID: 34710862 DOI: 10.1088/1361-6560/ac344e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/28/2021] [Indexed: 11/11/2022]
Abstract
728 simulated microdosimetric lineal energy spectra (26 different ions between 1H and 238U, 28 energy points from 1 to 1000 MeV/n) were used in combination with a recently-developed biological weighting function (Parisi et al., 2020) and 571 published in vitro clonogenic survival curves in order to: 1) assess prediction intervals for the in silico results by deriving an empirical indication of the experimental uncertainty from the dispersion in the in vitro hamster lung fibroblast (V79) data used for the development of the biophysical model; 2) explore the possibility of modeling the relative biological effectiveness (RBE) of the 10% clonogenic survival of asynchronized normoxic repair-competent mammalian cell lines other than the one used for the development of the model (V79); 3) investigate the predictive power of the model through a comparison between in silico results and in vitro data for 10 ions not used for the development of the model. At first, different strategies for the assessment of the in silico prediction intervals were compared. The possible sources of uncertainty responsible for the dispersion in the in vitro data were also shortly reviewed. Secondly, also because of the relevant scatter in the in vitro data, no statistically-relevant differences were found between the RBE10 of the investigated different asynchronized normoxic repair-competent mammalian cell lines. The only exception (Chinese Hamster peritoneal fibroblasts, B14FAF28), is likely due to the limited dataset (all in vitro ion data were extracted from a single publication), systematic differences in the linear energy transfer (LET) calculations for the employed very-heavy ions, and the use of reference photon survival curves extracted from a different publication. Finally, the in silico predictions for the 10 ions not used for the model development were in good agreement with the corresponding in vitro data.
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Affiliation(s)
- Alessio Parisi
- Radiation Protection Dosimetry and Calibration, Studiecentrum voor Kernenergie, Boeretang 200, Mol, Belgiun, Mol, 2400, BELGIUM
| | - Lara Struelens
- Radiation Protection, Dosimetry and Calibration, Belgian Nuclear Research Centre SCK.CEN, Boeretang 200, Mol, 2400, BELGIUM
| | - Filip Vanhavere
- Institute of Advanced Nuclear Systems, Belgian Nuclear Research Centre SCK.CEN, Boeretang 200, B-2400 Mol, Mol, BELGIUM
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14
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Cellular functions of the protein kinase ATM and their relevance to human disease. Nat Rev Mol Cell Biol 2021; 22:796-814. [PMID: 34429537 DOI: 10.1038/s41580-021-00394-2] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
The protein kinase ataxia telangiectasia mutated (ATM) is a master regulator of double-strand DNA break (DSB) signalling and stress responses. For three decades, ATM has been investigated extensively to elucidate its roles in the DNA damage response (DDR) and in the pathogenesis of ataxia telangiectasia (A-T), a human neurodegenerative disease caused by loss of ATM. Although hundreds of proteins have been identified as ATM phosphorylation targets and many important roles for this kinase have been identified, it is still unclear how ATM deficiency leads to the early-onset cerebellar degeneration that is common in all individuals with A-T. Recent studies suggest the existence of links between ATM deficiency and other cerebellum-specific neurological disorders, as well as the existence of broader similarities with more common neurodegenerative disorders. In this Review, we discuss recent structural insights into ATM regulation, and possible aetiologies of A-T phenotypes, including reactive oxygen species, mitochondrial dysfunction, alterations in transcription, R-loop metabolism and alternative splicing, defects in cellular proteostasis and metabolism, and potential pathogenic roles for hyper-poly(ADP-ribosyl)ation.
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15
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Paull TT. Reconsidering pathway choice: a sequential model of mammalian DNA double-strand break pathway decisions. Curr Opin Genet Dev 2021; 71:55-62. [PMID: 34293662 DOI: 10.1016/j.gde.2021.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/14/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022]
Abstract
DNA double-strand breaks can be repaired through ligation-based pathways (non-homologous end-joining) or replication-based pathways (homologous recombination) in eukaryotic cells. The decisions that govern these outcomes are widely viewed as a competition between factors that recognize DNA ends and physically promote association of factors specific to each pathway, commonly known as 'pathway choice'. Here I review recent results in the literature and propose that this decision is better described as a sequential set of binding and end processing events, with non-homologous end joining as the first decision point. Physical association and co-localization of end resection factors with non-homologous end-joining factors suggests that ends are transferred between these complexes, thus the ultimate outcome is not the result of a competition but is more akin to a relay race that is determined by the efficiency of the initial end-joining event and the availability of activated DNA end-processing enzymes.
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Affiliation(s)
- Tanya T Paull
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712, United States.
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16
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Ackerson SM, Romney C, Schuck PL, Stewart JA. To Join or Not to Join: Decision Points Along the Pathway to Double-Strand Break Repair vs. Chromosome End Protection. Front Cell Dev Biol 2021; 9:708763. [PMID: 34322492 PMCID: PMC8311741 DOI: 10.3389/fcell.2021.708763] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023] Open
Abstract
The regulation of DNA double-strand breaks (DSBs) and telomeres are diametrically opposed in the cell. DSBs are considered one of the most deleterious forms of DNA damage and must be quickly recognized and repaired. Telomeres, on the other hand, are specialized, stable DNA ends that must be protected from recognition as DSBs to inhibit unwanted chromosome fusions. Decisions to join DNA ends, or not, are therefore critical to genome stability. Yet, the processing of telomeres and DSBs share many commonalities. Accordingly, key decision points are used to shift DNA ends toward DSB repair vs. end protection. Additionally, DSBs can be repaired by two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ). The choice of which repair pathway is employed is also dictated by a series of decision points that shift the break toward HR or NHEJ. In this review, we will focus on these decision points and the mechanisms that dictate end protection vs. DSB repair and DSB repair choice.
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Affiliation(s)
- Stephanie M Ackerson
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Carlan Romney
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - P Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Jason A Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
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17
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Breast Cancer Predisposition Genes and Synthetic Lethality. Int J Mol Sci 2021; 22:ijms22115614. [PMID: 34070674 PMCID: PMC8198377 DOI: 10.3390/ijms22115614] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022] Open
Abstract
BRCA1 and BRCA2 are tumor suppressor genes with pivotal roles in the development of breast and ovarian cancers. These genes are essential for DNA double-strand break repair via homologous recombination (HR), which is a virtually error-free DNA repair mechanism. Following BRCA1 or BRCA2 mutations, HR is compromised, forcing cells to adopt alternative error-prone repair pathways that often result in tumorigenesis. Synthetic lethality refers to cell death caused by simultaneous perturbations of two genes while change of any one of them alone is nonlethal. Therefore, synthetic lethality can be instrumental in identifying new therapeutic targets for BRCA1/2 mutations. PARP is an established synthetic lethal partner of the BRCA genes. Its role is imperative in the single-strand break DNA repair system. Recently, Olaparib (a PARP inhibitor) was approved for treatment of BRCA1/2 breast and ovarian cancer as the first successful synthetic lethality-based therapy, showing considerable success in the development of effective targeted cancer therapeutics. Nevertheless, the possibility of drug resistance to targeted cancer therapy based on synthetic lethality necessitates the development of additional therapeutic options. This literature review addresses cancer predisposition genes, including BRCA1, BRCA2, and PALB2, synthetic lethality in the context of DNA repair machinery, as well as available treatment options.
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18
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Qi Y, Warmenhoven JW, Henthorn NT, Ingram SP, Xu XG, Kirkby KJ, Merchant MJ. Mechanistic Modelling of Slow and Fast NHEJ DNA Repair Pathways Following Radiation for G0/G1 Normal Tissue Cells. Cancers (Basel) 2021; 13:2202. [PMID: 34063683 PMCID: PMC8124137 DOI: 10.3390/cancers13092202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/23/2021] [Accepted: 04/29/2021] [Indexed: 01/12/2023] Open
Abstract
Mechanistic in silico models can provide insight into biological mechanisms and highlight uncertainties for experimental investigation. Radiation-induced double-strand breaks (DSBs) are known to be toxic lesions if not repaired correctly. Non-homologous end joining (NHEJ) is the major DSB-repair pathway available throughout the cell cycle and, recently, has been hypothesised to consist of a fast and slow component in G0/G1. The slow component has been shown to be resection-dependent, requiring the nuclease Artemis to function. However, the pathway is not yet fully understood. This study compares two hypothesised models, simulating the action of individual repair proteins on DSB ends in a step-by-step manner, enabling the modelling of both wild-type and protein-deficient cell systems. Performance is benchmarked against experimental data from 21 cell lines and 18 radiation qualities. A model where resection-dependent and independent pathways are entirely separated can only reproduce experimental repair kinetics with additional restraints on end motion and protein recruitment. However, a model where the pathways are entwined was found to effectively fit without needing additional mechanisms. It has been shown that DaMaRiS is a useful tool when analysing the connections between resection-dependent and independent NHEJ repair pathways and robustly matches with experimental results from several sources.
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Affiliation(s)
- Yaping Qi
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026, China;
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
| | - John William Warmenhoven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Nicholas Thomas Henthorn
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Samuel Peter Ingram
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester M13 9PL, UK
| | - Xie George Xu
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026, China;
| | - Karen Joy Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Michael John Merchant
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
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19
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Liu R, Higley KA, Swat MH, Chaplain MAJ, Powathil GG, Glazier JA. Development of a coupled simulation toolkit for computational radiation biology based on Geant4 and CompuCell3D. Phys Med Biol 2021; 66:045026. [PMID: 33339019 DOI: 10.1088/1361-6560/abd4f9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Understanding and designing clinical radiation therapy is one of the most important areas of state-of-the-art oncological treatment regimens. Decades of research have gone into developing sophisticated treatment devices and optimization protocols for schedules and dosages. In this paper, we presented a comprehensive computational platform that facilitates building of the sophisticated multi-cell-based model of how radiation affects the biology of living tissue. We designed and implemented a coupled simulation method, including a radiation transport model, and a cell biology model, to simulate the tumor response after irradiation. The radiation transport simulation was implemented through Geant4 which is an open-source Monte Carlo simulation platform that provides many flexibilities for users, as well as low energy DNA damage simulation physics, Geant4-DNA. The cell biology simulation was implemented using CompuCell3D (CC3D) which is a cell biology simulation platform. In order to couple Geant4 solver with CC3D, we developed a 'bridging' module, RADCELL, that extracts tumor cellular geometry of the CC3D simulation (including specification of the individual cells) and ported it to the Geant4 for radiation transport simulation. The cell dose and cell DNA damage distribution in multicellular system were obtained using Geant4. The tumor response was simulated using cell-based tissue models based on CC3D, and the cell dose and cell DNA damage information were fed back through RADCELL to CC3D for updating the cell properties. By merging two powerful and widely used modeling platforms, CC3D and Geant4, we delivered a novel tool that can give us the ability to simulate the dynamics of biological tissue in the presence of ionizing radiation, which provides a framework for quantifying the biological consequences of radiation therapy. In this introductory methods paper, we described our modeling platform in detail and showed how it can be applied to study the application of radiotherapy to a vascularized tumor.
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Affiliation(s)
- Ruirui Liu
- School of Nuclear Science and Engineering, Oregon State University, 100 Radiation Center, Corvallis, OR 97331, United States of America.,Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, 63110, United States of America
| | - Kathryn A Higley
- School of Nuclear Science and Engineering, Oregon State University, 100 Radiation Center, Corvallis, OR 97331, United States of America
| | - Maciej H Swat
- Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America
| | - Mark A J Chaplain
- School of Mathematics and Statistics, Mathematical Institute, University of St Andrews, St Andrews KY16 9SS, Fife, United Kingdom
| | - Gibin G Powathil
- Department of Mathematics, College of Science, Swansea University, Swansea, SA2 8PP, United Kingdom
| | - James A Glazier
- Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America
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20
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Falk M, Hausmann M. A Paradigm Revolution or Just Better Resolution-Will Newly Emerging Superresolution Techniques Identify Chromatin Architecture as a Key Factor in Radiation-Induced DNA Damage and Repair Regulation? Cancers (Basel) 2020; 13:E18. [PMID: 33374540 PMCID: PMC7793109 DOI: 10.3390/cancers13010018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023] Open
Abstract
DNA double-strand breaks (DSBs) have been recognized as the most serious lesions in irradiated cells. While several biochemical pathways capable of repairing these lesions have been identified, the mechanisms by which cells select a specific pathway for activation at a given DSB site remain poorly understood. Our knowledge of DSB induction and repair has increased dramatically since the discovery of ionizing radiation-induced foci (IRIFs), initiating the possibility of spatiotemporally monitoring the assembly and disassembly of repair complexes in single cells. IRIF exploration revealed that all post-irradiation processes-DSB formation, repair and misrepair-are strongly dependent on the characteristics of DSB damage and the microarchitecture of the whole affected chromatin domain in addition to the cell status. The microscale features of IRIFs, such as their morphology, mobility, spatiotemporal distribution, and persistence kinetics, have been linked to repair mechanisms. However, the influence of various biochemical and structural factors and their specific combinations on IRIF architecture remains unknown, as does the hierarchy of these factors in the decision-making process for a particular repair mechanism at each individual DSB site. New insights into the relationship between the physical properties of the incident radiation, chromatin architecture, IRIF architecture, and DSB repair mechanisms and repair efficiency are expected from recent developments in optical superresolution microscopy (nanoscopy) techniques that have shifted our ability to analyze chromatin and IRIF architectures towards the nanoscale. In the present review, we discuss this relationship, attempt to correlate still rather isolated nanoscale studies with already better-understood aspects of DSB repair at the microscale, and consider whether newly emerging "correlated multiscale structuromics" can revolutionarily enhance our knowledge in this field.
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Affiliation(s)
- Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany;
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21
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Zhu H, McNamara AL, McMahon SJ, Ramos-Mendez J, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J. Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio. Radiat Res 2020; 194:9-21. [PMID: 32401689 DOI: 10.1667/rr15531.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/11/2020] [Indexed: 12/21/2022]
Abstract
The cellular response to ionizing radiation continues to be of significant research interest in cancer radiotherapy, and DNA is recognized as the critical target for most of the biologic effects of radiation. Incident particles can cause initial DNA damages through physical and chemical interactions within a short time scale. Initial DNA damages can undergo repair via different pathways available at different stages of the cell cycle. The misrepair of DNA damage results in genomic rearrangement and causes mutations and chromosome aberrations, which are drivers of cell death. This work presents an integrated study of simulating cell response after proton irradiation with energies of 0.5-500 MeV (LET of 60-0.2 keV/µm). A model of a whole nucleus with fractal DNA geometry was implemented in TOPAS-nBio for initial DNA damage simulations. The default physics and chemistry models in TOPAS-nBio were used to describe interactions of primary particles, secondary particles, and radiolysis products within the nucleus. The initial DNA double-strand break (DSB) yield was found to increase from 6.5 DSB/Gy/Gbp at low-linear energy transfer (LET) of 0.2 keV/µm to 21.2 DSB/Gy/Gbp at high LET of 60 keV/µm. A mechanistic repair model was applied to predict the characteristics of DNA damage repair and dose response of chromosome aberrations. It was found that more than 95% of the DSBs are repaired within the first 24 h and the misrepaired DSB fraction increases rapidly with LET and reaches 15.8% at 60 keV/µm with an estimated chromosome aberration detection threshold of 3 Mbp. The dicentric and acentric fragment yields and the dose response of micronuclei formation after proton irradiation were calculated and compared with experimental results.
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Affiliation(s)
- Hongyu Zhu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China.,Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, P.R. China
| | - Aimee L McNamara
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Stephen J McMahon
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
| | - Jose Ramos-Mendez
- Department of Radiation Oncology, University of California San Francisco, California 94143
| | - Nicholas T Henthorn
- Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, California 94143
| | - Kathryn D Held
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Joseph Perl
- SLAC National Accelerator Laboratory, Menlo Park, California
| | - Junli Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China.,Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, P.R. China
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
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22
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Kirkby KJ, Kirkby NF, Burnet NG, Owen H, Mackay RI, Crellin A, Green S. Heavy charged particle beam therapy and related new radiotherapy technologies: The clinical potential, physics and technical developments required to deliver benefit for patients with cancer. Br J Radiol 2020; 93:20200247. [PMID: 33021102 PMCID: PMC7715999 DOI: 10.1259/bjr.20200247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 11/05/2022] Open
Abstract
In the UK, one in two people will develop cancer during their lifetimes and radiotherapy (RT) plays a key role in effective treatment. High energy proton beam therapy commenced in the UK National Health Service in 2018. Heavier charged particles have potential advantages over protons by delivering more dose in the Bragg peak, with a sharper penumbra, lower oxygen dependence and increased biological effectiveness. However, they also require more costly equipment including larger gantries to deliver the treatment. There are significant uncertainties in the modelling of relative biological effectiveness and the effects of the fragmentation tail which can deliver dose beyond the Bragg peak. These effects need to be carefully considered especially in relation to long-term outcomes.In 2019, a group of clinicians, clinical scientists, engineers, physical and life scientists from academia and industry, together with funding agency stakeholders, met to consider how the UK should address new technologies for RT, especially the use of heavier charged particles such as helium and carbon and new modes of delivery such as FLASH and spatially fractionated radiotherapy (SFRT).There was unanimous agreement that the UK should develop a facility for heavier charged particle therapy, perhaps constituting a new National Ion Research Centre to enable research using protons and heavier charged particles. Discussion followed on the scale and features, including which ions should be included, from protons through helium, boron, and lithium to carbon, and even oxygen. The consensus view was that any facility intended to treat patients must be located in a hospital setting while providing dedicated research space for physics, preclinical biology and clinical research with beam lines designed for both in vitro and in vivo research. The facility should to be able to investigate and deliver both ultra-high dose rate FLASH RT and SFRT (GRID, minibeams etc.). Discussion included a number of accelerator design options and whether gantries were required. Other potential collaborations might be exploited, including with space agencies, electronics and global communications industries and the nuclear industry.In preparation for clinical delivery, there may be opportunities to send patients overseas (for 12C or 4He ion therapy) using the model of the National Health Service (NHS) Proton Overseas Programme and to look at potential national clinical trials which include heavier ions, FLASH or SFRT. This could be accomplished under the auspices of NCRI CTRad (National Cancer Research Institute, Clinical and Translational Radiotherapy Research Working Group).The initiative should be a community approach, involving all interested parties with a vision that combines discovery science, a translational research capability and a clinical treatment facility. Barriers to the project and ways to overcome them were discussed. Finally, a set of different scenarios of features with different costs and timelines was constructed, with consideration given to the funding environment (prer-Covid-19) and need for cross-funder collaboration.
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Affiliation(s)
| | | | | | - Hywel Owen
- University of Manchester/Cockcroft Institute, Manchester, United Kingdom
| | | | | | - Stuart Green
- Department of Medical Physics, University Hospital Birmingham, Birmingham, Edgbaston, UK
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23
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Ingram SP, Henthorn NT, Warmenhoven JW, Kirkby NF, Mackay RI, Kirkby KJ, Merchant MJ. Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage. PLoS Comput Biol 2020; 16:e1008476. [PMID: 33326415 PMCID: PMC7773326 DOI: 10.1371/journal.pcbi.1008476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/30/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
Developments in the genome organisation field has resulted in the recent methodology to infer spatial conformations of the genome directly from experimentally measured genome contacts (Hi-C data). This provides a detailed description of both intra- and inter-chromosomal arrangements. Chromosomal intermingling is an important driver for radiation-induced DNA mis-repair. Which is a key biological endpoint of relevance to the fields of cancer therapy (radiotherapy), public health (biodosimetry) and space travel. For the first time, we leverage these methods of inferring genome organisation and couple them to nano-dosimetric radiation track structure modelling to predict quantities and distribution of DNA damage within cell-type specific geometries. These nano-dosimetric simulations are highly dependent on geometry and are benefited from the inclusion of experimentally driven chromosome conformations. We show how the changes in Hi-C contract maps impact the inferred geometries resulting in significant differences in chromosomal intermingling. We demonstrate how these differences propagate through to significant changes in the distribution of DNA damage throughout the cell nucleus, suggesting implications for DNA repair fidelity and subsequent cell fate. We suggest that differences in the geometric clustering for the chromosomes between the cell-types are a plausible factor leading to changes in cellular radiosensitivity. Furthermore, we investigate changes in cell shape, such as flattening, and show that this greatly impacts the distribution of DNA damage. This should be considered when comparing in vitro results to in vivo systems. The effect may be especially important when attempting to translate radiosensitivity measurements at the experimental in vitro level to the patient or human level.
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Affiliation(s)
- Samuel P. Ingram
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Nicholas T. Henthorn
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - John W. Warmenhoven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Norman F. Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Ranald I. Mackay
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Karen J. Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Michael J. Merchant
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
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24
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Rzeszutek I, Betlej G. The Role of Small Noncoding RNA in DNA Double-Strand Break Repair. Int J Mol Sci 2020; 21:ijms21218039. [PMID: 33126669 PMCID: PMC7663326 DOI: 10.3390/ijms21218039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 02/01/2023] Open
Abstract
DNA damage is a common phenomenon promoted through a variety of exogenous and endogenous factors. The DNA damage response (DDR) pathway involves a wide range of proteins, and as was indicated, small noncoding RNAs (sncRNAs). These are double-strand break-induced RNAs (diRNAs) and DNA damage response small RNA (DDRNA). Moreover, RNA binding proteins (RBPs) and RNA modifications have also been identified to modulate diRNA and DDRNA function in the DDR process. Several theories have been formulated regarding the synthesis and function of these sncRNAs during DNA repair; nevertheless, these pathways’ molecular details remain unclear. Here, we review the current knowledge regarding the mechanisms of diRNA and DDRNA biosynthesis and discuss the role of sncRNAs in maintaining genome stability.
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Affiliation(s)
- Iwona Rzeszutek
- Institute of Biology and Biotechnology, Department of Biotechnology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
- Correspondence: ; Tel.: +48-17-851-86-20; Fax: +48-17-851-87-64
| | - Gabriela Betlej
- Institute of Physical Culture Studies, College of Medical Sciences, University of Rzeszow, 35-310 Rzeszow, Poland;
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25
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Burnet NG, Mackay RI, Smith E, Chadwick AL, Whitfield GA, Thomson DJ, Lowe M, Kirkby NF, Crellin AM, Kirkby KJ. Proton beam therapy: perspectives on the National Health Service England clinical service and research programme. Br J Radiol 2020; 93:20190873. [PMID: 31860337 PMCID: PMC7066938 DOI: 10.1259/bjr.20190873] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/05/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
The UK has an important role in the evaluation of proton beam therapy (PBT) and takes its place on the world stage with the opening of the first National Health Service (NHS) PBT centre in Manchester in 2018, and the second in London coming in 2020. Systematic evaluation of the role of PBT is a key objective. By September 2019, 108 patients had started treatment, 60 paediatric, 19 teenagers and young adults and 29 adults. Obtaining robust outcome data is vital, if we are to understand the strengths and weaknesses of current treatment approaches. This is important in demonstrating when PBT will provide an advantage and when it will not, and in quantifying the magnitude of benefit.The UK also has an important part to play in translational PBT research, and building a research capability has always been the vision. We are perfectly placed to perform translational pre-clinical biological and physical experiments in the dedicated research room in Manchester. The nature of DNA damage from proton irradiation is considerably different from X-rays and this needs to be more fully explored. A better understanding is needed of the relative biological effectiveness (RBE) of protons, especially at the end of the Bragg peak, and of the effects on tumour and normal tissue of PBT combined with conventional chemotherapy, targeted drugs and immunomodulatory agents. These experiments can be enhanced by deterministic mathematical models of the molecular and cellular processes of DNA damage response. The fashion of ultra-high dose rate FLASH irradiation also needs to be explored.
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Affiliation(s)
| | | | - Ed Smith
- The Christie NHS Foundation Trust, Manchester, and University of Manchester, M20 4BX, UK
| | - Amy L Chadwick
- Division of Cancer Sciences, University of Manchester, Manchester Cancer Research Centre, Manchester Academic Health Science Centre, and The Christie NHS Foundation Trust, Manchester, M20 4BX, UK
| | - Gillian A Whitfield
- The Christie NHS Foundation Trust, Manchester, and University of Manchester, M20 4BX, UK
| | - David J Thomson
- The Christie NHS Foundation Trust, Manchester, and University of Manchester, M20 4BX, UK
| | | | - Norman F Kirkby
- Division of Cancer Sciences, University of Manchester, Manchester Cancer Research Centre, Manchester Academic Health Science Centre, and The Christie NHS Foundation Trust, Manchester, M20 4BX, UK
| | | | - Karen J Kirkby
- Division of Cancer Sciences, University of Manchester, Manchester Cancer Research Centre, Manchester Academic Health Science Centre, and The Christie NHS Foundation Trust, Manchester, M20 4BX, UK
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26
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Abstract
DNA-dependent protein kinase (DNA-PK) is involved in many cellular pathways. It has a key role in the cellular response to DNA damage, in the repair of DNA double-strand break (DNA-DSBs) and as a consequence an important role in maintaining genomic integrity. In addition, DNA-PK has been shown to modulate transcription, to be involved in the development of the immune system and to protect telomeres. These pleotropic involvements and the fact that its expression is de-regulated in cancer have made DNA-PK an intriguing therapeutic target in cancer therapy, especially when combined with agents causing DNA-DSBs such as topoisomerase II inhibitors and ionizing radiation. Different small molecule inhibitors of DNA-PK have been recently synthesized and some are now being tested in clinical trials. This review discusses what is known about DNA-PK, its role in tumor biology, DNA repair and cancer therapy and critically discusses its inhibition as a potential therapeutic approach.
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Affiliation(s)
- Giovanna Damia
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy.
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27
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Margis S, Magouni M, Kyriakou I, Georgakilas AG, Incerti S, Emfietzoglou D. Microdosimetric calculations of the direct DNA damage induced by low energy electrons using the Geant4-DNA Monte Carlo code. Phys Med Biol 2020; 65:045007. [PMID: 31935692 DOI: 10.1088/1361-6560/ab6b47] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To calculate the yield of direct DNA damage induced by low energy electrons using Monte Carlo generated microdosimetric spectra at the nanometer scale and examine the influence of various simulation inputs. The potential of classical microdosimetry to offer a viable and simpler alternative to more elaborate mechanistic approaches for practical applications is discussed. Track-structure simulations with the Geant4-DNA low-energy extension of the Geant4 Monte Carlo toolkit were used for calculating lineal energy spectra in spherical volumes with dimensions relevant to double-strand-break (DSB) induction. The microdosimetric spectra were then used to calculate the yield of simple and clustered DSB based on literature values of the threshold energy of DNA damage. The influence of the different implementations of the dielectric function of liquid water available in Geant4-DNA (Option 2 and Option 4 constructors), as well as the effect of particle tracking cutoff energy and target size are examined. Frequency- and dose-mean lineal energies in liquid-water spheres of 2, 2.3, 2.6, and 3.4 nm diameter, as well as, number of simple and clustered DSB/Gy/cell are presented for electrons over the 100 eV to 100 keV energy range. Results are presented for both the 'default' (Option 2) and 'Ioannina' (Option 4) physics models of Geant4-DNA applying several commonly used tracking cutoff energies (10, 20, 50, 100 eV). Overall, the choice of the physics model and target diameter has a moderate effect (up to ~10%-30%) on the DSB yield whereas the effect of the tracking cutoff energy may be significant (>100%). Importantly, the yield of both simple and clustered DSB was found to vary significantly (by a factor of 2 or more) with electron energy over the examined range. The yields of electron-induced simple and clustered DSB exhibit a strong energy dependence over the 100 eV-100 keV range with implications to radiation quality issues. It is shown that a classical microdosimetry approach for the calculation of DNA damage based on lineal energy spectra in nanometer-size targets predicts comparable results to computationally intensive mechanistic approaches which use detailed atomistic DNA geometries, thus, offering a relatively simple and robust alternative for some practical applications.
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Affiliation(s)
- Stefanos Margis
- Medical Physics Laboratory, University of Ioannina Medical School, 45110 Ioannina, Greece
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28
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Abstract
PARP inhibition (PARPi) kills tumor cells defective in homologous recombination-based repair (HR-) but not their HR+ competent counterparts. In this issue of Cancer Cell, it is shown that, when EZH2 is functionally silenced, HR+, CARM1-high, high-grade serous ovarian cancer cells become PARPi sensitive, undergo mitotic catastrophe, and die.
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Affiliation(s)
- Elodie Hatchi
- Departments of Genetics and Medicine, Harvard Medical School, Department of Cancer Biology Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - David M Livingston
- Departments of Genetics and Medicine, Harvard Medical School, Department of Cancer Biology Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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