Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA

Physica Medica - Tập 105 - Trang 102508 - 2023
Dousatsu Sakata1,2, Ryoichi Hirayama3, Wook-Geun Shin4, Mauro Belli5, Maria A. Tabocchini6, Robert D. Stewart7, Oleg Belov8,9, Mario A. Bernal10, Marie-Claude Bordage11,12, Jeremy M.C. Brown13,14,15, Milos Dordevic16, Dimitris Emfietzoglou17, Ziad Francis18, Susanna Guatelli14, Taku Inaniwa1, Vladimir Ivanchenko19,20, Mathieu Karamitros21, Ioanna Kyriakou17, Nathanael Lampe22, Zhuxin Li23
1Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba 263-8555, Japan
2Division of Health Sciences, Osaka University, Osaka 565-0871, Japan
3Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba 263-8555, Japan
4Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
5Independent Researcher, Rome, Italy
6Istituto Nazionale di Fisica Nucleare (INFN)-Roma 1, Rome, Italy
7Department of Radiation Oncology, University of Washington, WA 98195-6043, USA
8Veksler and Baldin Laboratory of High Energy Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia
9Institute of System Analysis and Management, Dubna State University, 141980 Dubna, Russia
10Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas, Campinas, SP, Brazil
11INSERM, Université Paul Sabatier, UMR 1037, CRCT, Toulouse, France
12Université Toulouse III-Paul Sabatier, UMR 1037, CRCT, Toulouse, France
13Department of Physics and Astronomy, Swinburne University of Technology, Hawthorn, Australia
14Centre for Medical Radiation Physics, University of Wollongong, Wollongong, Australia
15Department of Radiation Science and Technology, Delft University of Technology, The Netherlands
16Vinca Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
17Medical Physics Laboratory, Department of Medicine, University of Ioannina, GR 45110, Ioannina, Greece
18Saint Joseph University of Beirut, UR Mathématiques et Modélisation, Beirut, Lebanon
19Geant4 Associates International Ltd, Hebden Bridge, UK
20Tomsk State University, Tomsk, Russia
21Independent Researcher, Bordeaux, France
22Independent Researcher, Victoria, Australia
23Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France

Tài liệu tham khảo

Nikjoo, 1998, Track structure in radiation biology: theory and applications, Int J Radiat Biol, 73, 355, 10.1080/095530098142176 Nikjoo, 2016, Perspectives in radiation biophysics: From radiation track structure simulation to mechanistic models of DNA damage and repair, Rad Phys Chem, 128, 3, 10.1016/j.radphyschem.2016.05.005 Nikjoo, 2016, Radiation track, DNA damage and response—a review, Rep Progr Phys, 79, 10.1088/0034-4885/79/11/116601 Kyriakou, 2021, Review of the Geant4-DNA simulation toolkit for radiobiological applications at the cellular and DNA level, Cancers, 14, 35, 10.3390/cancers14010035 Hemnani, 1998, Reactive oxygen species and oxidative DNA damage, Ind J Phys Phar, 42, 440 Uehara, 1993, Cross-section of water vapour for the Monte Carlo electrons track structure code from 10 eV to the MeV region, Phys Med Biol, 38, 1841, 10.1088/0031-9155/38/12/010 Nikjoo, 1997, Computational modeling of low-energy electron-induced DNA damage by early physical and chemical events, Int J Radiat Biol, 71, 467, 10.1080/095530097143798 Nikjoo, 2001, Computational approach for determining the spectrum of DNA damage induced by ionizing radiation, Rad Res, 156, 577, 10.1667/0033-7587(2001)156[0577:CAFDTS]2.0.CO;2 Friedl, 1998, Monte Carlo simulation of the production of short DNA fragments by low-linear energy transfer radiation using higher-order DNA models, Rad Res, 150, 170, 10.2307/3579852 Friedl, 2003, Simulation of DNA damage after proton irradiation, Rad Res, 159, 401, 10.1667/0033-7587(2003)159[0401:SODDAP]2.0.CO;2 Friedl, 2011, Track structures, DNA targets and radiation effects in the biophysical Monte Carlo simulation code PARTRAC, Mutat Res, 711, 28, 10.1016/j.mrfmmm.2011.01.003 Friedl, 2017, Comprehensive track-structure based evaluation of DNA damage by light ions from radiotherapy-relevant energies down to stopping, Sci Rep, 7, 45161, 10.1038/srep45161 Plante, 2011, Applications of Monte Carlo methods in biology, 315 Plante, 2016, Radiation physics and chemistry, 157 Incerti, 2009, The Geant4–DNA project, Int J Model Simul Sci Comput, 1, 157, 10.1142/S1793962310000122 Incerti, 2010, Comparison of Geant4 very low energy cross section models with experimental data in water, Med Phys, 37, 4692, 10.1118/1.3476457 Bernal, 2015, Track structure modeling in liquid water: A review of the Geant4–DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit, Phys Med, 31, 157, 10.1016/j.ejmp.2015.10.087 Incerti, 2018, Geant4–DNA example applications for track structure simulations in liquid water: a report from the Geant4–DNA project, Med Phys, 45, e722, 10.1002/mp.13048 Lampe, 2018, Mechanistic DNA damage simulations in Geant4-DNA part 1: A parameter study in a simplified geometry, Phys Med, 48, 135, 10.1016/j.ejmp.2018.02.011 Lampe, 2018, Mechanistic DNA damage simulations in Geant4-DNA part 2: Electron and proton damage in a bacterial cell, Phys Med, 48, 146, 10.1016/j.ejmp.2017.12.008 Sakata, 2019, Evaluation of early radiation DNA damage in a fractal cell nucleus model using Geant4-DNA, Phys Med, 62, 152, 10.1016/j.ejmp.2019.04.010 Sakata, 2020, Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA, Sci Rep, 10, 20788, 10.1038/s41598-020-75982-x Meylan, 2017, Simulation of early DNA damage after the irradiation of a fibroblast cell nucleus using Geant4-DNA, Sci Rep, 7, 11923, 10.1038/s41598-017-11851-4 Perl, 2012, TOPAS: An innovative proton Monte Carlo platform for research and clinical applications, Med Phys, 39, 6818, 10.1118/1.4758060 Schuemann, 2018, TOPAS-nBio: An extension to the TOPAS simulation toolkit for cellular and sub-cellular radiobiology, Rad Res, 191, 125, 10.1667/RR15226.1 McNamara, 2018, Geometrical structures for radiation biology research as implemented in the TOPAS-nbio toolkit, Phys Med Biol, 63, 10.1088/1361-6560/aad8eb Belov, 2015, A quantitative model of the major pathways for radiation-induced DNA double-strand break repair, J Theoret Biol, 366, 115, 10.1016/j.jtbi.2014.09.024 Puck, 1995, Rapid method for viable cell titration and clone production with HeLa cells in tissue culture: the use of X-irradiated cells to supply conditioning factors, Proc Natl Acad Sci, 41, 432, 10.1073/pnas.41.7.432 Puck, 1956, Action of x rays on mammalian cells, J Exp Med, 103, 653, 10.1084/jem.103.5.653 Sørensen, 2011, In vitro RBE-LET dependence for multiple particle types, Acta Oncol, 50, 757, 10.3109/0284186X.2011.582518 Goodhead, 1994, Initial events in the cellular effects of ionizing radiations: clustered damage in DNA, Int J Radiat Biol, 65, 7, 10.1080/09553009414550021 Liamsuwan, 2012, Microdosimetry of low-energy electrons, Int J Radiat Biol, 88, 899, 10.3109/09553002.2012.699136 Sato, 2012, Cell survival fraction estimation based on the probability densities of domain and cell nucleus specific energies using improved microdosimetric kinetic models, Rad Res, 178, 341, 10.1667/RR2842.1 Stewart, 2001, Two-lesion kinetic model of double-strand break rejoining and cell killing, Rad Res, 156, 365, 10.1667/0033-7587(2001)156[0365:TLKMOD]2.0.CO;2 Tang N. évaluation, à partir de modélisations nanodosimétriques, de l’influence de la compaction de la chromatine sur les effets radio-induits précoces et extension aux effets tardifs (réparation des dommages à l’adn et mort cellulaire). [phD thesis], Written in French from the University of Bordeaux France. Belli, 1998, RBE-LET relationships for cell inactivation and mutation induced by low energy protons in V79 cells: further results at the LNL facility, Int J Rad Biol, 74, 501, 10.1080/095530098141375 Belli, 2000, DNA DSB induction and rejoining in V79 cells irradiated with light ions: a constant field gel electrophoresis study, Int J Rad Biol, 76, 1095, 10.1080/09553000050111569 de Lara, 2001, Dependence of the yield of DNA double-strand breaks in Chinese hamster V79-4 cells on the photon energy of ultrasoft X rays, Rad Res, 155, 440, 10.1667/0033-7587(2001)155[0440:DOTYOD]2.0.CO;2 Siragusa, 2018, Radiobiological effects of tritiated water short-term exposure on V79 clonogenic cell survival, Int J Radiat Biol, 94, 157, 10.1080/09553002.2018.1419301 Blöcher, 1990, In CHEF electrophoresis a linear induction of DSB corresponds to a nonlinear fraction of extracted DNA with dose, Int J Radiat Biol, 57, 7, 10.1080/09553009014550291 Belli, 2001, DNA fragmentation in mammalian cells exposed to various light ions, Adv Space Res, 27, 393, 10.1016/S0273-1177(01)00007-2 Emfietzoglou, 2003, Inelastic cross-sections for electron transport in liquid water: a comparison of dielectric models, Radiat Phys Chem, 66, 373, 10.1016/S0969-806X(02)00504-2 Kyriakou, 2016, The impact of new Geant4-DNA cross section models on electron track structure simulations in liquid water, J Appl Phys, 119, 10.1063/1.4950808 Kyriakou, 2015, Technical note: Improvements in Geant4 energy-loss model and the effect on low-energy electron transport in liquid water, Med Phys, 42, 3870, 10.1118/1.4921613 Bordage, 2016, Implementation of new physics models for low energy electrons in liquid water in Geant4–DNA, Phys Med, 32, 1833, 10.1016/j.ejmp.2016.10.006 Kyriakou, 2017, Microdosimetry of electrons in liquid water using the low-energy models of Geant4, J Appl Phys, 122, 10.1063/1.4992076 Green, 1990, Stochastic modeling of fast kinetics in a radiation track, J Phys Chem, 94, 251, 10.1021/j100364a041 McVey, 2008, MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings, Tren Genet, 24, 529, 10.1016/j.tig.2008.08.007 Belli, 1989, RBE–LET relationship for the survival of V79 cells irradiated with low energy protons, Int J Rad Biol, 55, 93, 10.1080/09553008914550101 Kryndushkin, 2003, Yeast [PSI+] prion aggregates are formed by small sup35 polymers fragmented by Hsp104, J Biol Chem, 278, 49636, 10.1074/jbc.M307996200 Iliakis, 1991, Measurement of DNA double strand breaks in CHO cells at various stages of the cell cycle using pulse field gel electrophoresis: Calibrations by means of 125i decay, Int J Radiat Biol, 59, 343, 10.1080/09553009114550321 Contopoulou, 1987, Analysis of DNA double strand breakage and repair using orthogonal field alternation gel electrophoresis, Yeast, 3, 71, 10.1002/yea.320030203 Cook, 1991, A quantitative model of DNA fragments generated by ionizing radiation, and possible experimental applications, Rad Res, 125, 102, 10.2307/3577988 Ito, 2006, Contribution of indirect action to radiation-induced mammalian cell inactivation: Dependence on photon energy and heavy-ion LET, Rad Res, 165, 703, 10.1667/RR3557.1 Hirayama, 2009, Contributions of direct and indirect actions in cell killing by high-LET radiations, Rad Res, 171, 212, 10.1667/RR1490.1 2016, Report 90: Key data for ionizing-radiation dosimetry: Measurement standards and applications, J Int Com Rad Units Meas, 14, 1 McMahon, 2016, Mechanistic modelling of DNA repair and cellular survival following radiation-induced DNA damage, Sci Rep, 6, 33290, 10.1038/srep33290 Cordoni, 2022, Cell survival computation via the generalized stochastic microdosimetric model (GSM2); part I: The theoretical framework, Rad Res, 197, 218 http://ceres-solver.org. Zhiyong, 2008, Comparison of nonhomologous end joining and homologous recombination in human cells, DNA Rep (Amst), 7, 1765, 10.1016/j.dnarep.2008.06.018