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Qiu GH, Fu M, Zheng X, Huang C. Protection of the genome and the central exome by peripheral non-coding DNA against DNA damage in health, ageing and age-related diseases. Biol Rev Camb Philos Soc 2024. [PMID: 39327815 DOI: 10.1111/brv.13151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 09/15/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024]
Abstract
DNA in eukaryotic genomes is under constant assault from both exogenous and endogenous sources, leading to DNA damage, which is considered a major molecular driver of ageing. Fortunately, the genome and the central exome are safeguarded against these attacks by abundant peripheral non-coding DNA. Non-coding DNA codes for small non-coding RNAs that inactivate foreign nucleic acids in the cytoplasm and physically blocks these attacks in the nucleus. Damage to non-coding DNA produced during such blockage is removed in the form of extrachromosomal circular DNA (eccDNA) through nucleic pore complexes. Consequently, non-coding DNA serves as a line of defence for the exome against DNA damage. The total amount of non-coding DNA/heterochromatin declines with age, resulting in a decrease in both physical blockage and eccDNA exclusion, and thus an increase in the accumulation of DNA damage in the nucleus during ageing and in age-related diseases. Here, we summarize recent evidence supporting a protective role of non-coding DNA in healthy and pathological states and argue that DNA damage is the proximate cause of ageing and age-related genetic diseases. Strategies aimed at strengthening the protective role of non-coding DNA/heterochromatin could potentially offer better systematic protection for the dynamic genome and the exome against diverse assaults, reduce the burden of DNA damage to the exome, and thus slow ageing, counteract age-related genetic diseases and promote a healthier life for individuals.
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Affiliation(s)
- Guo-Hua Qiu
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Mingjun Fu
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Xintian Zheng
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Cuiqin Huang
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
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Tuan Anh L, Ngoc Hoang T, Thibaut Y, Chatzipapas K, Sakata D, Incerti S, Villagrasa C, Perrot Y. "dsbandrepair" - An updated Geant4-DNA simulation tool for evaluating the radiation-induced DNA damage and its repair. Phys Med 2024; 124:103422. [PMID: 38981169 DOI: 10.1016/j.ejmp.2024.103422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/07/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024] Open
Abstract
PURPOSE Interdisciplinary scientific communities have shown large interest to achieve a mechanistic description of radiation-induced biological damage, aiming to predict biological results produced by different radiation quality exposures. Monte Carlo track-structure simulations are suitable and reliable for the study of early DNA damage induction used as input for assessing DNA damage. This study presents the most recent improvements of a Geant4-DNA simulation tool named "dsbandrepair". METHODS "dsbandrepair" is a Monte Carlo simulation tool based on a previous code (FullSim) that estimates the induction of early DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). It uses DNA geometries generated by the DNAFabric computational tool for simulating the induction of early single-strand breaks (SSBs) and double-strand breaks (DSBs). Moreover, the new tool includes some published radiobiological models for survival fraction and un-rejoined DSB. Its application for a human fibroblast cell and human umbilical vein endothelial cell containing both heterochromatin and euchromatin was conducted. In addition, this new version offers the possibility of using the new IRT-syn method for computing the chemical stage. RESULTS The direct and indirect strand breaks, SSBs, DSBs, and damage complexity obtained in this work are equivalent to those obtained with the previously published simulation tool when using the same configuration in the physical and chemical stages. Simulation results on survival fraction and un-rejoined DSB are in reasonable agreement with experimental data. CONCLUSIONS "dsbandrepair" is a tool for simulating DNA damage and repair, benchmarked against experimental data. It has been released as an advanced example in Geant4.11.2.
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Affiliation(s)
- Le Tuan Anh
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | - Tran Ngoc Hoang
- CNRS/IN2P3, CENBG, UMR 5797, Bordeaux University, 33170 Gradignan, France
| | - Yann Thibaut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | | | | | - Sébastien Incerti
- CNRS/IN2P3, CENBG, UMR 5797, Bordeaux University, 33170 Gradignan, France
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
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3
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Plante I, West DW, Weeks J, Risca VI. Simulation of Radiation-Induced DNA Damage and Protection by Histones Using the Code RITRACKS. BIOTECH 2024; 13:17. [PMID: 38921049 PMCID: PMC11201919 DOI: 10.3390/biotech13020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/10/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024] Open
Abstract
(1) Background: DNA damage is of great importance in the understanding of the effects of ionizing radiation. Various types of DNA damage can result from exposure to ionizing radiation, with clustered types considered the most important for radiobiological effects. (2) Methods: The code RITRACKS (Relativistic Ion Tracks), a program that simulates stochastic radiation track structures, was used to simulate DNA damage by photons and ions spanning a broad range of linear energy transfer (LET) values. To perform these simulations, the transport code was modified to include cross sections for the interactions of ions or electrons with DNA and amino acids for ionizations, dissociative electron attachment, and elastic collisions. The radiochemistry simulations were performed using a step-by-step algorithm that follows the evolution of all particles in time, including reactions between radicals and DNA structures and amino acids. Furthermore, detailed DNA damage events, such as base pair positions, DNA fragment lengths, and fragment yields, were recorded. (3) Results: We report simulation results using photons and the ions 1H+, 4He2+, 12C6+, 16O8+, and 56Fe26+ at various energies, covering LET values from 0.3 to 164 keV/µm, and performed a comparison with other codes and experimental results. The results show evidence of DNA protection from damage at its points of contacts with histone proteins. (4) Conclusions: RITRACKS can provide a framework for studying DNA damage from a variety of ionizing radiation sources with detailed representations of DNA at the atomic scale, DNA-associated proteins, and resulting DNA damage events and statistics, enabling a broader range of future comparisons with experiments such as those based on DNA sequencing.
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Affiliation(s)
| | - Devany W. West
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY 10065, USA; (D.W.W.); (V.I.R.)
| | - Jason Weeks
- NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY 10065, USA; (D.W.W.); (V.I.R.)
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Rajpurohit YS, Sharma DK, Lal M, Soni I. A perspective on tumor radiation resistance following high-LET radiation treatment. J Cancer Res Clin Oncol 2024; 150:226. [PMID: 38696003 PMCID: PMC11065934 DOI: 10.1007/s00432-024-05757-8] [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: 02/24/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024]
Abstract
High-linear energy transfer (LET) radiation is a promising alternative to conventional low-LET radiation for therapeutic gain against cancer owing to its ability to induce complex and clustered DNA lesions. However, the development of radiation resistance poses a significant barrier. The potential molecular mechanisms that could confer resistance development are translesion synthesis (TLS), replication gap suppression (RGS) mechanisms, autophagy, epithelial-mesenchymal transition (EMT) activation, release of exosomes, and epigenetic changes. This article will discuss various types of complex clustered DNA damage, their repair mechanisms, mutagenic potential, and the development of radiation resistance strategies. Furthermore, it highlights the importance of careful consideration and patient selection when employing high-LET radiotherapy in clinical settings.
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Affiliation(s)
- Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India.
- Homi Bhabha National Institute, DAE- Deemed University, Mumbai, 400094, India.
| | - Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India
| | - Mitu Lal
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India
| | - Ishu Soni
- Homi Bhabha National Institute, DAE- Deemed University, Mumbai, 400094, India
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Thibaut Y, Gonon G, Martinez JS, Petit M, Babut R, Vaurijoux A, Gruel G, Villagrasa C, Incerti S, Perrot Y. Experimental validation in a neutron exposure frame of the MINAS TIRITH for cell damage simulation. Phys Med Biol 2023; 68:225008. [PMID: 37848039 DOI: 10.1088/1361-6560/ad043d] [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: 06/20/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
In the domains of medicine and space exploration, refining risk assessment models for protecting healthy tissue from ionizing radiation is crucial. Understanding radiation-induced effects requires biological experimentations at the cellular population level and the cellular scale modeling using Monte Carlo track structure codes. We present MINAS TIRITH, a tool using Geant4-DNA Monte Carlo-generated databases to study DNA damage distribution at the cell population scale. It introduces a DNA damage location module and proposes a method to convert double-strand breaks (DSB) into DNA Damage Response foci. We evaluate damage location precision and DSB-foci conversion parameters. MINAS TIRITH's accuracy is validated againstγ-H2AX foci distribution from cell population exposed to monoenergetic neutron beams (2.5 or 15.1 MeV) under different configurations, yielding mixed radiation fields. Strong agreement between simulation and experimental results was found demonstrating MINAS TIRITH's predictive precision in radiation-induced DNA damage topology. Additionally, modeling intercellular damage variability within a population subjected to a specific macroscopic dose identifies subpopulations, enhancing realistic fate models. This approach advances our understanding of radiation-induced effects on cellular systems for risk assessment improvement.
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Affiliation(s)
- Y Thibaut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gonon
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - J S Martinez
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - M Petit
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - R Babut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - A Vaurijoux
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gruel
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - C Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, LP2i, UMR 5797, F-33170 Gradignan, France
| | - Y Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
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Liang Y, Wu J, Ding Z, Liu C, Fu Q. Evaluation of the Yield of DNA Double-Strand Breaks for Carbon Ions Using Monte Carlo Simulation and DNA Fragment Distribution. Int J Radiat Oncol Biol Phys 2023; 117:252-261. [PMID: 36966847 DOI: 10.1016/j.ijrobp.2023.03.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023]
Abstract
PURPOSE The aim of this work was to provide a method to evaluate the yield of DNA double-strand breaks (DSBs) for carbon ions, overcoming the bias in existing methods due to the nonrandom distribution of DSBs. METHODS AND MATERIALS A previously established biophysical program based on the radiation track structure and a multilevel chromosome model was used to simulate DNA damage induced by x-rays and carbon ions. The fraction of activity retained (FAR) as a function of absorbed dose or particle fluence was obtained by counting the fraction of DNA fragments larger than 6 Mbp. Simulated FAR curves for the 250 kV x-rays and carbon ions at various energies were compared with measurements using constant-field gel electrophoresis. The doses or fluences at the FAR of 0.7 based on linear interpolation were used to estimate the simulation error for the production of DSBs. RESULTS The relative difference of doses at the FAR of 0.7 between simulation and experiment was -8.5% for the 250 kV x-rays. The relative differences of fluences at the FAR of 0.7 between simulations and experiments were -17.5%, -42.2%, -18.2%, -3.1%, 10.8%, and -14.5% for the 34, 65, 130, 217, 2232, and 3132 MeV carbon ions, respectively. In comparison, the measurement uncertainty was about 20%. Carbon ions produced remarkably more DSBs and DSB clusters per unit dose than x-rays. The yield of DSBs for carbon ions, ranging from 10 to 16 Gbp-1Gy-1, increased with linear energy transfer (LET) but plateaued in the high-LET end. The yield of DSB clusters first increased and then decreased with LET. This pattern was similar to the relative biological effectiveness for cell survival for heavy ions. CONCLUSIONS The estimated yields of DSBs for carbon ions increased from 10 Gbp-1Gy-1 in the low-LET end to 16 Gbp-1Gy-1 in the high-LET end with 20% uncertainty.
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Affiliation(s)
- Ying Liang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.
| | - Jianan Wu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Zhen Ding
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Chenbin Liu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Qibin Fu
- Sino-French Institute of Nuclear Engineering and Technology, Sun Yat-sen University, Zhuhai, China
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Ballisat L, Beck L, De Sio C, Guatelli S, Sakata D, Incerti S, Tran HN, Duan J, Maclean K, Shi Y, Velthuis J, Rosenfeld A. In-silico calculations of DNA damage induced by α-particles in the 224Ra DaRT decay chain for a better understanding of the radiobiological effectiveness of this treatment. Phys Med 2023; 112:102626. [PMID: 37393861 DOI: 10.1016/j.ejmp.2023.102626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 07/04/2023] Open
Abstract
Diffusing alpha-emitters radiation Therapy (DaRT) is an interstitial brachytherapy technique using 224Ra seeds. For accurate treatment planning a good understanding of the early DNA damage due to α-particles is required. Geant4-DNA was used to calculate the initial DNA damage and radiobiological effectiveness due to α-particles with linear energy transfer (LET) values in the range 57.5-225.9 keV/μm from the 224Ra decay chain. The impact of DNA base pair density on DNA damage has been modelled, as this parameter varies between human cell lines. Results show that the quantity and complexity of DNA damage changes with LET as expected. Indirect damage, due to water radical reactions with the DNA, decreases and becomes less significant at higher LET values as shown in previous studies. As expected, the yield of complex double strand breaks (DSBs), which are harder for a cell to repair, increases approximately linearly with LET. The level of complexity of DSBs and radiobiological effectiveness have been found to increase with LET as expected. The quantity of DNA damage has been shown to increase for increased DNA density in the expected base pair density range of human cells. The change in damage yield as a function of base pair density is largest for higher LET α-particles, an increase of over 50% for individual strand breaks between 62.7 and 127.4 keV/μm. This change in yield shows that the DNA base pair density is an important parameter for modelling DNA damage particularly at higher LET where the DNA damage is greatest and most complex.
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Affiliation(s)
| | - Lana Beck
- School of Physics, University of Bristol, Bristol, UK
| | - Chiara De Sio
- School of Physics, University of Bristol, Bristol, UK
| | - Susanna Guatelli
- Centre for Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia
| | - Dousatsu Sakata
- Division of Health Sciences, Osaka University, Osaka 565-0871, Japan
| | - Sébastien Incerti
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - Hoang Ngoc Tran
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - Jinyan Duan
- School of Physics, University of Bristol, Bristol, UK
| | - Katie Maclean
- School of Physics, University of Bristol, Bristol, UK
| | - Yuyao Shi
- School of Physics, University of Bristol, Bristol, UK
| | - Jaap Velthuis
- School of Physics, University of Bristol, Bristol, UK
| | - Anatoly Rosenfeld
- Centre for Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia
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Chatzipapas KP, Tran NH, Dordevic M, Zivkovic S, Zein S, Shin W, Sakata D, Lampe N, Brown JMC, Ristic‐Fira A, Petrovic I, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S. Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application. PRECISION RADIATION ONCOLOGY 2023. [DOI: 10.1002/pro6.1186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Affiliation(s)
| | - Ngoc Hoang Tran
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
| | - Milos Dordevic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Sara Zivkovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Sara Zein
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
| | - Wook‐Geun Shin
- Physics Division, Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School Boston Massachusetts USA
| | | | | | - Jeremy M. C. Brown
- Department of Physics and Astronomy Swinburne University of Technology Melbourne Australia
| | - Aleksandra Ristic‐Fira
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Ivan Petrovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Ioanna Kyriakou
- Medical Physics Laboratory Department of Medicine University of Ioannina Ioannina Greece
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory Department of Medicine University of Ioannina Ioannina Greece
| | - Susanna Guatelli
- Centre for Medical Radiation Physics University of Wollongong Wollongong New South Wales Australia
| | - Sébastien Incerti
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
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Thibaut Y, Gonon G, Martinez JS, Petit M, Vaurijoux A, Gruel G, Villagrasa C, Incerti S, Perrot Y. MINAS TIRITH: a new tool for simulating radiation-induced DNA damage at the cell population level. Phys Med Biol 2023; 68. [PMID: 36623319 DOI: 10.1088/1361-6560/acb196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Objective. The mechanisms of radiation-induced DNA damage can be understood via the fundamental acquisition of knowledge through a combination of experiments and modeling. Currently, most biological experiments are performed by irradiating an entire cell population, whereas modeling of radiation-induced effects is usually performed via Monte Carlo simulations with track structure codes coupled to realistic DNA geometries of a single-cell nucleus. However, the difference in scale between the two methods hinders a direct comparison because the dose distribution in the cell population is not necessarily uniform owing to the stochastic nature of the energy deposition. Thus, this study proposed the MINAS TIRITH tool to model the distribution of radiation-induced DNA damage in a cell population.Approach. The proposed method is based on precomputed databases of microdosimetric parameters and DNA damage distributions generated using the Geant4-DNA Monte Carlo Toolkit. First, a specific energyzwas assigned to each cell of an irradiated population for a particular absorbed doseDabs,following microdosimetric formalism. Then, each cell was assigned a realistic number of DNA damage events according to the specific energyz,respecting the stochastic character of its occurrence.Main results. This study validated the MINAS TIRITH tool by comparing its results with those obtained using the Geant4-DNA track structure code and a Geant4-DNA based simulation chain for DNA damage calculation. The different elements of comparison indicated consistency between MINAS TIRITH and the Monte Carlo simulation in case of the dose distribution in the population and the calculation of the amount of DNA damage.Significance. MINAS TIRITH is a new approach for the calculation of radiation-induced DNA damage at the cell population level that facilitates reasonable simulation times compared to those obtained with track structure codes. Moreover, this tool enables a more direct comparison between modeling and biological experimentation.
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Affiliation(s)
- Y Thibaut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gonon
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - J S Martinez
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - M Petit
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - A Vaurijoux
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gruel
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - C Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, LP2i, UMR 5797, F-33170 Gradignan, France
| | - Y Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
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10
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Lacombe J, Zenhausern F. Effect of mechanical forces on cellular response to radiation. Radiother Oncol 2022; 176:187-198. [PMID: 36228760 DOI: 10.1016/j.radonc.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/08/2022] [Accepted: 10/05/2022] [Indexed: 12/14/2022]
Abstract
While the cellular interactions and biochemical signaling has been investigated for long and showed to play a major role in the cell's fate, it is now also evident that mechanical forces continuously applied to the cells in their microenvironment are as important for tissue homeostasis. Mechanical cues are emerging as key regulators of cellular drug response and we aimed to demonstrate in this review that such effects should also be considered vital for the cellular response to radiation. In order to explore the mechanobiology of the radiation response, we reviewed the main mechanoreceptors and transducers, including integrin-mediated adhesion, YAP/TAZ pathways, Wnt/β-catenin signaling, ion channels and G protein-coupled receptors and showed their implication in the modulation of cellular radiosensitivity. We then discussed the current studies that investigated a direct effect of mechanical stress, including extracellular matrix stiffness, shear stress and mechanical strain, on radiation response of cancer and normal cells and showed through preliminary results that such stress effectively can alter cell response after irradiation. However, we also highlighted the limitations of these studies and emphasized some of the contradictory data, demonstrating that the effect of mechanical cues could involve complex interactions and potential crosstalk with numerous cellular processes also affected by irradiation. Overall, mechanical forces alter radiation response and although additional studies are required to deeply understand the underlying mechanisms, these effects should not be neglected in radiation research as they could reveal new fundamental knowledge for predicting radiosensitivity or understanding resistance to radiotherapy.
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Affiliation(s)
- Jerome Lacombe
- Center for Applied NanoBioscience and Medicine, College of Medicine Phoenix, University of Arizona, 475 North 5th Street, Phoenix, AZ 85004, USA; Department of Basic Medical Sciences, College of Medicine Phoenix, University of Arizona, 425 N 5th St, Phoenix, AZ 85004, USA.
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine, College of Medicine Phoenix, University of Arizona, 475 North 5th Street, Phoenix, AZ 85004, USA; Department of Basic Medical Sciences, College of Medicine Phoenix, University of Arizona, 425 N 5th St, Phoenix, AZ 85004, USA; Department of Biomedical Engineering, College of Engineering, University of Arizona, 1127 E. James E. Rogers Way, Tucson, AZ 85721, USA.
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11
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Bertolet A, Ramos-Méndez J, McNamara A, Yoo D, Ingram S, Henthorn N, Warmenhoven JW, Faddegon B, Merchant M, McMahon SJ, Paganetti H, Schuemann J. Impact of DNA Geometry and Scoring on Monte Carlo Track-Structure Simulations of Initial Radiation-Induced Damage. Radiat Res 2022; 198:207-220. [PMID: 35767729 PMCID: PMC9458623 DOI: 10.1667/rade-21-00179.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/07/2022] [Indexed: 11/03/2022]
Abstract
Track structure Monte Carlo simulations are a useful tool to investigate the damage induced to DNA by ionizing radiation. These simulations usually rely on simplified geometrical representations of the DNA subcomponents. DNA damage is determined by the physical and physicochemical processes occurring within these volumes. In particular, damage to the DNA backbone is generally assumed to result in strand breaks. DNA damage can be categorized as direct (ionization of an atom part of the DNA molecule) or indirect (damage from reactive chemical species following water radiolysis). We also consider quasi-direct effects, i.e., damage originated by charge transfers after ionization of the hydration shell surrounding the DNA. DNA geometries are needed to account for the damage induced by ionizing radiation, and different geometry models can be used for speed or accuracy reasons. In this work, we use the Monte Carlo track structure tool TOPAS-nBio, built on top of Geant4-DNA, for simulation at the nanometer scale to evaluate differences among three DNA geometrical models in an entire cell nucleus, including a sphere/spheroid model specifically designed for this work. In addition to strand breaks, we explicitly consider the direct, quasi-direct, and indirect damage induced to DNA base moieties. We use results from the literature to determine the best values for the relevant parameters. For example, the proportion of hydroxyl radical reactions between base moieties was 80%, and between backbone, moieties was 20%, the proportion of radical attacks leading to a strand break was 11%, and the expected ratio of base damages and strand breaks was 2.5-3. Our results show that failure to update parameters for new geometric models can lead to significant differences in predicted damage yields.
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Affiliation(s)
- Alejandro Bertolet
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Aimee McNamara
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Dohyeon Yoo
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Samuel Ingram
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Nicholas Henthorn
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - John-William Warmenhoven
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Michael Merchant
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, United Kingdom
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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12
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Danforth JM, Provencher L, Goodarzi AA. Chromatin and the Cellular Response to Particle Radiation-Induced Oxidative and Clustered DNA Damage. Front Cell Dev Biol 2022; 10:910440. [PMID: 35912116 PMCID: PMC9326100 DOI: 10.3389/fcell.2022.910440] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Exposure to environmental ionizing radiation is prevalent, with greatest lifetime doses typically from high Linear Energy Transfer (high-LET) alpha particles via the radioactive decay of radon gas in indoor air. Particle radiation is highly genotoxic, inducing DNA damage including oxidative base lesions and DNA double strand breaks. Due to the ionization density of high-LET radiation, the consequent damage is highly clustered wherein ≥2 distinct DNA lesions occur within 1–2 helical turns of one another. These multiply-damaged sites are difficult for eukaryotic cells to resolve either quickly or accurately, resulting in the persistence of DNA damage and/or the accumulation of mutations at a greater rate per absorbed dose, relative to lower LET radiation types. The proximity of the same and different types of DNA lesions to one another is challenging for DNA repair processes, with diverse pathways often confounding or interplaying with one another in complex ways. In this context, understanding the state of the higher order chromatin compaction and arrangements is essential, as it influences the density of damage produced by high-LET radiation and regulates the recruitment and activity of DNA repair factors. This review will summarize the latest research exploring the processes by which clustered DNA damage sites are induced, detected, and repaired in the context of chromatin.
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13
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New damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmid. Sci Rep 2022; 12:11345. [PMID: 35790804 PMCID: PMC9256689 DOI: 10.1038/s41598-022-15521-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
In this work, we proposed a new damage model for estimating radiation-induced direct damage to biomolecular systems and validated its the effectiveness for pBR322 plasmids. The proposed model estimates radiation-induced damage to biomolecular systems by: (1) simulation geometry modeling using the coarse-grained (CG) technique to replace the minimum repeating units of a molecule with a single bead, (2) approximation of the threshold energy for radiation damage through CG potential calculation, (3) calculation of cumulative absorption energy for each radiation event in microscopic regions of CG models using the Monte Carlo track structure (MCTS) code, and (4) estimation of direct radiation damage to biomolecular systems by comparing CG potentials and absorption energy. The proposed model replicated measured data with an average error of approximately 14.2% in the estimation of radiation damage to pBR322 plasmids using the common MCTS code Geant4-DNA. This is similar to the results of previous simulation studies. However, in existing damage models, parameters are adjusted based on experimental data to increase the reliability of simulation results, whereas in the proposed model, they can be determined without using empirical data. Because the proposed model proposed is applicable to DNA and various biomolecular systems with minimal experimental data, it provides a new method that is convenient and effective for predicting damage in living organisms caused by radiation exposure.
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14
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Nanodosimetric Calculations of Radiation-Induced DNA Damage in a New Nucleus Geometrical Model Based on the Isochore Theory. Int J Mol Sci 2022; 23:ijms23073770. [PMID: 35409128 PMCID: PMC8998209 DOI: 10.3390/ijms23073770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Double-strand breaks (DSBs) in nuclear DNA represents radiation-induced damage that has been identified as particularly deleterious. Calculating this damage using Monte Carlo track structure modeling could be a suitable indicator to better assess and anticipate the side-effects of radiation therapy. However, as already demonstrated in previous work, the geometrical description of the nucleus and the DNA content used in the simulation significantly influence damage calculations. Therefore, in order to obtain accurate results, this geometry must be as realistic as possible. In this study, a new geometrical model of an endothelial cell nucleus and DNA distribution according to the isochore theory are presented and used in a Monte Carlo simulation chain based on the Geant4-DNA toolkit. In this theory, heterochromatin and euchromatin compaction are distributed along the genome according to five different families (L1, L2, H1, H2, and H3). Each of these families is associated with a different hetero/euchromatin rate related to its compaction level. In order to compare the results with those obtained using a previous nuclear geometry, simulations were performed for protons with linear energy transfers (LETs) of 4.29 keV/µm, 19.51 keV/µm, and 43.25 keV/µm. The organization of the chromatin fibers at different compaction levels linked to isochore families increased the DSB yield by 6-10%, and it allowed the most affected part of the genome to be identified. These new results indicate that the genome core is more radiosensitive than the genome desert, with a 3-8% increase in damage depending on the LET. This work highlights the importance of using realistic distributions of chromatin compaction levels to calculate radio-induced damage using Monte Carlo simulation methods.
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15
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Review of the Geant4-DNA Simulation Toolkit for Radiobiological Applications at the Cellular and DNA Level. Cancers (Basel) 2021; 14:cancers14010035. [PMID: 35008196 PMCID: PMC8749997 DOI: 10.3390/cancers14010035] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary A brief description of the methodologies to simulate ionizing radiation transport in biologically relevant matter is presented. Emphasis is given to the physical, chemical, and biological models of Geant4-DNA that enable mechanistic radiobiological modeling at the cellular and DNA level, important to improve the efficacy of existing and novel radiotherapeutic modalities for the treatment of cancer. Abstract The Geant4-DNA low energy extension of the Geant4 Monte Carlo (MC) toolkit is a continuously evolving MC simulation code permitting mechanistic studies of cellular radiobiological effects. Geant4-DNA considers the physical, chemical, and biological stages of the action of ionizing radiation (in the form of x- and γ-ray photons, electrons and β±-rays, hadrons, α-particles, and a set of heavier ions) in living cells towards a variety of applications ranging from predicting radiotherapy outcomes to radiation protection both on earth and in space. In this work, we provide a brief, yet concise, overview of the progress that has been achieved so far concerning the different physical, physicochemical, chemical, and biological models implemented into Geant4-DNA, highlighting the latest developments. Specifically, the “dnadamage1” and “molecularDNA” applications which enable, for the first time within an open-source platform, quantitative predictions of early DNA damage in terms of single-strand-breaks (SSBs), double-strand-breaks (DSBs), and more complex clustered lesions for different DNA structures ranging from the nucleotide level to the entire genome. These developments are critically presented and discussed along with key benchmarking results. The Geant4-DNA toolkit, through its different set of models and functionalities, offers unique capabilities for elucidating the problem of radiation quality or the relative biological effectiveness (RBE) of different ionizing radiations which underlines nearly the whole spectrum of radiotherapeutic modalities, from external high-energy hadron beams to internal low-energy gamma and beta emitters that are used in brachytherapy sources and radiopharmaceuticals, respectively.
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16
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Rucinski A, Biernacka A, Schulte R. Applications of nanodosimetry in particle therapy planning and beyond. Phys Med Biol 2021; 66. [PMID: 34731854 DOI: 10.1088/1361-6560/ac35f1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/03/2021] [Indexed: 12/28/2022]
Abstract
This topical review summarizes underlying concepts of nanodosimetry. It describes the development and current status of nanodosimetric detector technology. It also gives an overview of Monte Carlo track structure simulations that can provide nanodosimetric parameters for treatment planning of proton and ion therapy. Classical and modern radiobiological assays that can be used to demonstrate the relationship between the frequency and complexity of DNA lesion clusters and nanodosimetric parameters are reviewed. At the end of the review, existing approaches of treatment planning based on relative biological effectiveness (RBE) models or dose-averaged linear energy transfer are contrasted with an RBE-independent approach based on nandosimetric parameters. Beyond treatment planning, nanodosimetry is also expected to have applications and give new insights into radiation protection dosimetry.
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Affiliation(s)
| | - Anna Biernacka
- University of Gdansk, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdansk, 80-307 Gdansk, Poland
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17
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Zhao X, Liu R, Zhao T, Reynoso FJ. Quantification of gold nanoparticle photon radiosensitization from direct and indirect effects using a complete human genome single cell model based on Geant4. Med Phys 2021; 48:8127-8139. [PMID: 34738643 DOI: 10.1002/mp.15330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 09/22/2021] [Accepted: 10/20/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To investigate the radiosensitization properties of gold nanoparticles (GNPs) and better understand the intricate deoxyribonucleic acid (DNA) damage induction mechanisms involved in GNP-aided radiotherapy, a single cell model with complete human genome based on the Geant4 Monte Carlo toolkit was applied. MATERIALS AND METHODS A Geant4-DNA model was implemented to simulate direct and indirect DNA damage generated in the physical and chemical stages. In the physical stage, a mixed-physics approach was taken by using Geant4-DNA in water and Livermore in gold. Water radiolysis was created posteriorly in the physicochemical and chemical stages to simulate indirect damage from reactions between DNA molecules and OH• radicals. A mono-energetic photon beam (100 keV) and two clinical photon sources (250-kVp, 6-MV flattening-filter free) were simulated for modeling the irradiation of a single cell with or without GNPs. In order to study the effects of GNP size on radiosensitization, 15, 30, and 100 nm GNPs were simulated. The effects of intracellular distribution were simulated using 90-nm GNPs with different characteristics of distribution within the cell. The time dependence of DNA damage enhancement was also studied with chemistry stage simulation end-time no larger than 10 ns. RESULTS Double strand break (DSB) enhancement due to direct and indirect action was quantified under different scenarios. Under realistic cellular uptake condition, the 100-nm GNPs had the most significant increase in DSBs: 40.9% and 28.5% for 100 keV and 250-kVp photon irradiation, respectively. The intracellular localization showed differing levels of radiosensitization with a maximum of 64%, 27%, and 6% DSB enhancements for 100 keV, 250-kVp, and 6-MV respectively, when 90-nm GNPs congregate around the nucleus. CONCLUSION The results indicate that photon energy, GNP size, and intracellular distribution play an important role in the enhancement of DSB from direct and indirect damage under scenarios close to cell experiments. The radiosensitization effects due to indirect damage are significant and should be considered carefully.
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Affiliation(s)
- Xiandong Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ruirui Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tianyu Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Francisco J Reynoso
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
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18
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Montgomery L, Lund CM, Landry A, Kildea J. Towards the characterization of neutron carcinogenesis through direct action simulations of clustered DNA damage. Phys Med Biol 2021; 66. [PMID: 34555818 DOI: 10.1088/1361-6560/ac2998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/23/2021] [Indexed: 11/11/2022]
Abstract
Neutron exposure poses a unique radiation protection concern because neutrons have a large, energy-dependent relative biological effectiveness (RBE) for stochastic effects. Recent computational studies on the microdosimetric properties of neutron dose deposition have implicated clustered DNA damage as a likely contributor to this marked energy dependence. So far, publications have focused solely on neutron RBE for inducing clusters of DNA damage containing two or more DNA double strand breaks (DSBs). In this study, we have conducted a novel assessment of neutron RBE for inducing all types of clustered DNA damage that contain two or more lesions, stratified by whether the clusters contain DSBs (complex DSB clusters) or not (non-DSB clusters). This assessment was conducted for eighteen initial neutron energies between 1 eV and 10 MeV as well as a reference radiation of 250 keV x-rays. We also examined the energy dependence of cluster length and cluster complexity because these factors are believed to impact the DNA repair process. To carry out our investigation, we developed a user-friendly TOPAS-nBio application that includes a custom nuclear DNA model and a novel algorithm for recording clustered DNA damage. We found that neutron RBE for inducing complex DSB clusters exhibited similar energy dependence to the canonical neutron RBE for stochastic radiobiological effects, at multiple depths in human tissue. Qualitatively similar results were obtained for non-DSB clusters, although the quantitative agreement was lower. Additionally we identified a significant neutron energy dependence in the average length and complexity of clustered lesions. These results support the idea that many types of clustered DNA damage contribute to the energy dependence of neutron RBE for stochastic radiobiological effects and imply that the size and constituent lesions of individual clusters should be taken into account when modeling DNA repair. Our results were qualitatively consistent for (i) multiple radiation doses (including a low-dose 0.1 Gy irradiation), (ii) variations in the maximal lesion separation distance used to define a cluster, and (iii) two distinct collections of physics models used to govern particle transport. Our complete TOPAS-nBio application has been released under an open-source license to enable others to independently validate our work and to expand upon it.
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Affiliation(s)
- Logan Montgomery
- Medical Physics Unit, McGill University, Montreal, QC, H4A3J1, Canada
| | | | - Anthony Landry
- Prince Edward Island Cancer Treatment Centre, Charlottetown, PE, C1A8T5, Canada.,Department of Radiation Oncology, Dalhousie University, Halifax, NS, B3H4RZ, Canada
| | - John Kildea
- Medical Physics Unit, McGill University, Montreal, QC, H4A3J1, Canada
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Bertolet A, Ramos-Méndez J, Paganetti H, Schuemann J. The relation between microdosimetry and induction of direct damage to DNA by alpha particles. Phys Med Biol 2021; 66. [PMID: 34280910 DOI: 10.1088/1361-6560/ac15a5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022]
Abstract
In radiopharmaceutical treatmentsα-particles are employed to treat tumor cells. However, the mechanism that drives the biological effect induced is not well known. Being ionizing radiation,α-particles can affect biological organisms by producing damage to the DNA, either directly or indirectly. Following the principle that microdosimetry theory accounts for the stochastic way in which radiation deposits energy in sub-cellular sized volumes via physical collisions, we postulate that microdosimetry represents a reasonable framework to characterize the statistical nature of direct damage induction byα-particles to DNA. We used the TOPAS-nBio Monte Carlo package to simulate direct damage produced by monoenergetic alpha particles to different DNA structures. In separate simulations, we obtained the frequency-mean lineal energy (yF) and dose-mean lineal energy (yD) of microdosimetric distributions sampled with spherical sites of different sizes. The total number of DNA strand breaks, double strand breaks (DSBs) and complex strand breaks per track were quantified and presented as a function of eitheryForyD.The probability of interaction between a track and the DNA depends on how the base pairs are compacted. To characterize this variability on compactness, spherical sites of different size were used to match these probabilities of interaction, correlating the size-dependent specific energy (z) with the damage induced. The total number of DNA strand breaks per track was found to linearly correlate withyFandzFwhen using what we defined an effective volume as microdosimetric site, while the yield of DSB per unit dose linearly correlated withyDorzD,being larger for compacted than for unfolded DNA structures. The yield of complex breaks per unit dose exhibited a quadratic behavior with respect toyDand a greater difference among DNA compactness levels. Microdosimetric quantities correlate with the direct damage imparted on DNA.
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Affiliation(s)
- Alejandro Bertolet
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, United States of America
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, United States of America
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, United States of America
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, United States of America
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20
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Mhamdi-Ghodbani M, Starzonek C, Degenhardt S, Bender M, Said M, Greinert R, Volkmer B. UVB damage response of dermal stem cells as melanocyte precursors compared to keratinocytes, melanocytes, and fibroblasts from human foreskin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 220:112216. [PMID: 34023595 DOI: 10.1016/j.jphotobiol.2021.112216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/21/2021] [Accepted: 05/14/2021] [Indexed: 02/09/2023]
Abstract
Ultraviolet B (UVB) radiation induces mutagenic DNA photolesions in skin cells especially in form of cyclobutane pyrimidine dimers (CPDs). Protection mechanisms as DNA repair and apoptosis are of great importance in order to prevent skin carcinogenesis. In human skin, neural crest-derived precursors of melanocytes, the dermal stem cells (DSCs), are discussed to be at the origin of melanoma. Although they are constantly exposed to solar UV radiation, it is still not investigated how DSCs cope with UV-induced DNA damage. Here, we report a comparative study of the DNA damage response after irradiation with a physiological relevant UVB dose in DSCs in comparison to fibroblasts, melanocytes and keratinocytes isolated from human foreskin. Within our experimental settings, DSCs were able to repair DNA photolesions as efficient as the other skin cell types with solely keratinocytes repairing significantly faster. Interestingly, only fibroblasts showed significant alterations in cell cycle distribution in terms of a transient S phase arrest following irradiation. Moreover, with the applied UVB dose none of the examined cell types was prone to UVB-induced apoptosis. This may cause persistent genomic alterations and in case of DSCs it may have severe consequences for their daughter cells, the differentiated melanocytes. Altogether, this is the first study demonstrating a similar UV response in dermal stem cells compared to differentiated skin cells.
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Affiliation(s)
- Mouna Mhamdi-Ghodbani
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Christin Starzonek
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Sarah Degenhardt
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Marc Bender
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | | | - Rüdiger Greinert
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Beate Volkmer
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany.
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21
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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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22
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Chatzipapas KP, Papadimitroulas P, Loudos G, Papanikolaou N, Kagadis GC. IDDRRA: A novel platform, based on Geant4-DNA to quantify DNA damage by ionizing radiation. Med Phys 2021; 48:2624-2636. [PMID: 33657650 DOI: 10.1002/mp.14817] [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: 09/28/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 01/23/2023] Open
Abstract
PURPOSE This study proposes a novel computational platform that we refer to as IDDRRA (DNA Damage Response to Ionizing RAdiation), which uses Monte Carlo (MC) simulations to score radiation induced DNA damage. MC simulations provide results of high accuracy on the interaction of radiation with matter while scoring the energy deposition based on state-of-the-art physics and chemistry models and probabilistic methods. METHODS The IDDRRA software is based on the Geant4-DNA toolkit together with new tools that were developed for the purpose of this study, including a new algorithm that was developed in Python for the design of the DNA molecules. New classes were developed in C++ to integrate the GUI and produce the simulation's output in text format. An algorithm was also developed to analyze the simulation's output in terms of energy deposition, Single Strand Breaks (SSB), Double Strand Breaks (DSB) and Cluster Damage Sites (CDS). Finally, a new tool was developed to implement probabilistic SSB and DSB repair models using MC techniques. RESULTS This article provides the first benchmarks that the user of the IDDRRA tool can use to validate the functionality of the software as well as to provide a starting point to produce different types of DNA simulations. These benchmarks incorporate different kind of particles (e-, e+, protons, electron spectrum) and DNA molecules. CONCLUSION We have developed the IDDRRA tool and demonstrated its use to study various aspects of the modeling and simulation of a DNA irradiation experiment. The tool is expandable and can be expanded by other users with new benchmarks and applications based on the user's needs and experience. New functionality will be added over time, including the quantification of the indirect damage.
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Affiliation(s)
- Konstantinos P Chatzipapas
- 3dmi Research Group, Department of Medical Physics, School of Medicine, University of Patras, Rion, 26504, Greece
| | | | - George Loudos
- Bioemission Technology Solutions (BIOEMTECH), Athens, 11472, Greece
| | - Niko Papanikolaou
- Health Science Center, University of Texas, San Antonio, TX, 78229, USA
| | - George C Kagadis
- 3dmi Research Group, Department of Medical Physics, School of Medicine, University of Patras, Rion, 26504, Greece
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23
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Peng Q, Weng K, Li S, Xu R, Wang Y, Wu Y. A Perspective of Epigenetic Regulation in Radiotherapy. Front Cell Dev Biol 2021; 9:624312. [PMID: 33681204 PMCID: PMC7930394 DOI: 10.3389/fcell.2021.624312] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Radiation therapy (RT) has been employed as a tumoricidal modality for more than 100 years and on 470,000 patients each year in the United States. The ionizing radiation causes genetic changes and results in cell death. However, since the biological mechanism of radiation remains unclear, there is a pressing need to understand this mechanism to improve the killing effect on tumors and reduce the side effects on normal cells. DNA break and epigenetic remodeling can be induced by radiotherapy. Hence the modulation of histone modification enzymes may tune the radiosensitivity of cancer cells. For instance, histone deacetylase (HDAC) inhibitors sensitize irradiated cancer cells by amplifying the DNA damage signaling and inhibiting double-strand DNA break repair to influence the irradiated cells’ survival. However, the combination of epigenetic drugs and radiotherapy has only been evaluated in several ongoing clinical trials for limited cancer types, partly due to a lack of knowledge on the potential mechanisms on how radiation induces epigenetic regulation and chromatin remodeling. Here, we review recent advances of radiotherapy and radiotherapy-induced epigenetic remodeling and introduce related technologies for epigenetic monitoring. Particularly, we exploit the application of fluorescence resonance energy transfer (FRET) biosensors to visualize dynamic epigenetic regulations in single living cells and tissue upon radiotherapy and drug treatment. We aim to bridge FRET biosensor, epigenetics, and radiotherapy, providing a perspective of using FRET to assess epigenetics and provide guidance for radiotherapy to improve cancer treatment. In the end, we discuss the feasibility of a combination of epigenetic drugs and radiotherapy as new approaches for cancer therapeutics.
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Affiliation(s)
- Qin Peng
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Kegui Weng
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States.,Chongqing Cancer Hospital, Chongqing Cancer Institute, Chongqing University Cancer Hospital, Chongqing, China
| | - Shitian Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Richard Xu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Yingxiao Wang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Yongzhong Wu
- Chongqing Cancer Hospital, Chongqing Cancer Institute, Chongqing University Cancer Hospital, Chongqing, China
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24
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Jones B. Fast neutron energy based modelling of biological effectiveness with implications for proton and ion beams. Phys Med Biol 2021; 66:045028. [PMID: 33472183 DOI: 10.1088/1361-6560/abddd0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A practical neutron energy dependent RBE model has been developed, based on the relationship between a mono-energetic neutron energy and its likely recoil proton energy. Essentially, the linear energy transfer (LET) values of the most appropriate recoil proton energies are then used to modify the linear quadratic model radiosensitivities (α and β) from their reference LET radiation values to provide the RBE estimates. Experimental neutron studies published by Hall (including some mono-energetic beams ranging from 0.2 to 15 MeV), Broerse, Berry, and data from the Clatterbridge and Detroit clinical neutron beams, which all contain some data from a spectrum of neutron energies, are used to derive single effective neutron energies (NEeff) for each spectral beam. These energies yield a recoil proton spectrum, but with an effective mean proton energy (being around 50% of NEeff). The fractional increase in LET is given by the recoil proton LET divided by the proton (LETU) value which provides the highest RBE. This ratio is then used to determine the change in the linear-quadratic model α and β parameters, from those of the reference radiation, to estimate the RBE. The predicted proton recoil RBE is then reasonably close to the experimental neutron RBE values found when taking into account the variation inherent in biological experiments. The work has some important consequences. The data of Hall et al (1975 Radiat. Res. 64 245-55) shows that the highest RBE values are found with neutron energies around 0.3-0.4 MeV, but this energy cannot possibly generate recoil proton energies which are higher, as necessary for a 0.68 MeV proton with a 30.5 keV μm-1 LETU (the LET value which provides the maximum obtainable RBE for a specified ion). For 0.4 MeV neutrons with proton recoil energies of around 0.2 MeV, the latter have a LET of around 62.88 keV μm-1. This could have an impact on proton beam RBE modelling. However, this is compensated by finding that the maximum radiosensitivity for mono-energetic neutrons was around 1.7 times larger than previously suggested from experimental ion beam studies, probably due to the necessary spreading out of Bragg peaks for ion beam experimental purposes, sampling errors and particle range considerations. This semi-empirical model can be used with minimal computer support and could have applications in ionic beams and in radioprotection.
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Affiliation(s)
- Bleddyn Jones
- Gray Laboratory, Department of Oncology, University of Oxford, Old Road Research Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom. Green Templeton College, University of Oxford, 43 Woodstock Road, Oxford, OX2 6HG, United Kingdom. Medical Physics, University College London, United Kingdom
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25
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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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26
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Tran HN, Ramos-Méndez J, Shin WG, Perrot Y, Faddegon B, Okada S, Karamitros M, Davídková M, Štěpán V, Incerti S, Villagrasa C. Assessment of DNA damage with an adapted independent reaction time approach implemented in Geant4-DNA for the simulation of diffusion-controlled reactions between radio-induced reactive species and a chromatin fiber. Med Phys 2020; 48:890-901. [PMID: 33232522 PMCID: PMC7986154 DOI: 10.1002/mp.14612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/11/2023] Open
Abstract
Purpose Simulation of indirect damage originating from the attack of free radical species produced by ionizing radiation on biological molecules based on the independent pair approximation is investigated in this work. In addition, a new approach, relying on the independent pair approximation that is at the origin of the independent reaction time (IRT) method, is proposed in the chemical stage of Geant4‐DNA. Methods This new approach has been designed to respect the current Geant4‐DNA chemistry framework while proposing a variant IRT method. Based on the synchronous algorithm, this implementation allows us to access the information concerning the position of radicals and may make it more convenient for biological damage simulations. Estimates of the evolution of free species as well as biological hits in a segment of DNA chromatin fiber in Geant4‐DNA were compared for the dynamic time step approach of the step‐by‐step (SBS) method, currently used in Geant4‐DNA, and this newly implemented IRT. Results Results show a gain in computation time of a factor of 30 for high LET particle tracks with a better than 10% agreement on the number of DNA hits between the value obtained with the IRT method as implemented in this work and the SBS method currently available in Geant4‐DNA. Conclusion Offering in Geant4‐DNA more efficient methods for the chemical step based on the IRT method is a task in progress. For the calculation of biological damage, information on the position of chemical species is a crucial point. This can be achieved using the method presented in this paper.
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Affiliation(s)
- Hoang Ngoc Tran
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Wook-Geun Shin
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France.,Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea
| | - Yann Perrot
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Mathieu Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, In, 46556, USA
| | - Marie Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Sébastien Incerti
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
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27
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Sakata D, Belov O, Bordage MC, Emfietzoglou D, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, Kyriakou I, Lampe N, Petrovic I, Ristic-Fira A, Shin WG, Incerti S. Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA. Sci Rep 2020; 10:20788. [PMID: 33247225 PMCID: PMC7695857 DOI: 10.1038/s41598-020-75982-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022] Open
Abstract
Ionising radiation induced DNA damage and subsequent biological responses to it depend on the radiation’s track-structure and its energy loss distribution pattern. To investigate the underlying biological mechanisms involved in such complex system, there is need of predicting biological response by integrated Monte Carlo (MC) simulations across physics, chemistry and biology. Hence, in this work, we have developed an application using the open source Geant4-DNA toolkit to propose a realistic “fully integrated” MC simulation to calculate both early DNA damage and subsequent biological responses with time. We had previously developed an application allowing simulations of radiation induced early DNA damage on a naked cell nucleus model. In the new version presented in this work, we have developed three additional important features: (1) modeling of a realistic cell geometry, (2) inclusion of a biological repair model, (3) refinement of DNA damage parameters for direct damage and indirect damage scoring. The simulation results are validated with experimental data in terms of Single Strand Break (SSB) yields for plasmid and Double Strand Break (DSB) yields for plasmid/human cell. In addition, the yields of indirect DSBs are compatible with the experimental scavengeable damage fraction. The simulation application also demonstrates agreement with experimental data of \documentclass[12pt]{minimal}
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\begin{document}$$\gamma$$\end{document}γ-H2AX yields for gamma ray irradiation. Using this application, it is now possible to predict biological response along time through track-structure MC simulations.
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Affiliation(s)
- Dousatsu Sakata
- Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, QST, Chiba, Japan.
| | - Oleg Belov
- Joint Institute for Nuclear Research, Dubna, Russia.,Dubna State University, Dubna, Russia
| | - Marie-Claude Bordage
- INSERM, UMR 1037, CRCT, Université Paul Sabatier, Toulouse, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, Medical School, University of Ioannina, 45110, Ioannina, Greece
| | - Susanna Guatelli
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - Taku Inaniwa
- Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, QST, Chiba, Japan
| | - Vladimir Ivanchenko
- Geant4 Associates International Ltd, Hebden Bridge, UK.,Tomsk State University, Tomsk, Russia
| | | | - Ioanna Kyriakou
- Medical Physics Laboratory, Medical School, University of Ioannina, 45110, Ioannina, Greece
| | | | - Ivan Petrovic
- Vinca Institute of Nuclear Science, University of Belgrade, Belgrade, Serbia
| | | | - Wook-Geun Shin
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, Gradignan, 33170, France
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28
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Ramos-Méndez J, Shin WG, Karamitros M, Domínguez-Kondo J, Tran NH, Incerti S, Villagrasa C, Perrot Y, Štěpán V, Okada S, Moreno-Barbosa E, Faddegon B. Independent reaction times method in Geant4-DNA: Implementation and performance. Med Phys 2020; 47:5919-5930. [PMID: 32970844 DOI: 10.1002/mp.14490] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/07/2020] [Accepted: 09/13/2020] [Indexed: 11/10/2022] Open
Abstract
PURPOSE The simulation of individual particle tracks and the chemical stage following water radiolysis in biological tissue is an effective means of improving our knowledge of the physico-chemical contribution to the biological effect of ionizing radiation. However, the step-by-step simulation of the reaction kinetics of radiolytic species is the most time-consuming task in Monte Carlo track-structure simulations, with long simulation times that are an impediment to research. In this work, we present the implementation of the independent reaction times (IRT) method in Geant4-DNA Monte Carlo toolkit to improve the computational efficiency of calculating G-values, defined as the number of chemical species created or lost per 100 eV of deposited energy. METHODS The computational efficiency of IRT, as implemented, is compared to that from available Geant4-DNA step-by-step simulations for electrons, protons and alpha particles covering a wide range of linear energy transfer (LET). The accuracy of both methods is verified using published measured data from fast electron irradiations for • OH and e aq - for time-dependent G-values. For IRT, simulations in the presence of scavengers irradiated by cobalt-60 γ-ray and 2 MeV protons are compared with measured data for different scavenging capacities. In addition, a qualitative assessment comparing measured LET-dependent G-values with Geant4-DNA calculations in pure liquid water is presented. RESULTS The IRT improved the computational efficiency by three orders of magnitude relative to the step-by-step method while differences in G-values by 3.9% at 1 μs were found. At 7 ps, • OH and e aq - yields calculated with IRT differed from recent published measured data by 5% ± 4% and 2% ± 4%, respectively. At 1 μs, differences were 9% ± 5% and 6% ± 7% for • OH and e aq - , respectively. Uncertainties are one standard deviation. Finally, G-values at different scavenging capacities and LET-dependent G-values reproduced the behavior of measurements for all radiation qualities. CONCLUSION The comprehensive validation of the Geant4-DNA capabilities to accurately simulate the chemistry following water radiolysis is an ongoing work. The implementation presented in this work is a necessary step to facilitate performing such a task.
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Affiliation(s)
- José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Wook-Geun Shin
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France.,Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea
| | - Mathieu Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jorge Domínguez-Kondo
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla PUE, 72000, Mexico
| | - Ngoc Hoang Tran
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France
| | - Sebastien Incerti
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, BP17, Fontenay-aux-Roses, 92262, France
| | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, BP17, Fontenay-aux-Roses, 92262, France
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Eduardo Moreno-Barbosa
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla PUE, 72000, Mexico
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
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29
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Tang J, Xiao Q, Gui Z, Li B, Zhang P. Simulation of Proton-Induced DNA Damage Patterns Using an Improved Clustering Algorithm. Radiat Res 2020; 194:363-378. [PMID: 32931557 DOI: 10.1667/rr15552.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 07/23/2020] [Indexed: 11/03/2022]
Abstract
Simulations of deoxyribonucleic acid (DNA) molecular damage use the traversal algorithm that has the disadvantages of being time-consuming, slowly converging, and requiring high-performance computer clusters. This work presents an improved version of the algorithm, "density-based spatial clustering of applications with noise" (DBSCAN), using a KD-tree approach to find neighbors of each point for calculating clustered DNA damage. The resulting algorithm considers the spatial distributions for sites of energy deposition and hydroxyl radical attack, yielding the statistical probability of (single and double) DNA strand breaks. This work achieves high accuracy and high speed at calculating clustered DNA damage that has been induced by proton treatment at the molecular level while running on an i7 quad-core CPU. The simulations focus on the indirect effect generated by hydroxyl radical attack on DNA. The obtained results are consistent with those of other published experiments and simulations. Due to the array of chemical processes triggered by proton treatment, it is possible to predict the effects that different track structures of various energy protons produce on eliciting direct and indirect damage of DNA.
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Affiliation(s)
- Jing Tang
- Shanxi Provincial Key Laboratory for Biomedical Imaging and Big Data, North University of China, Taiyuan, 030051, P.R. China
| | - Qinfeng Xiao
- School of Computer and Information Technology, Beijing Jiaotong University, Beijing, 100044, P.R. China
| | - Zhiguo Gui
- Shanxi Provincial Key Laboratory for Biomedical Imaging and Big Data, North University of China, Taiyuan, 030051, P.R. China
| | - Baosheng Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, P.R. China
| | - Pengcheng Zhang
- Shanxi Provincial Key Laboratory for Biomedical Imaging and Big Data, North University of China, Taiyuan, 030051, P.R. China
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30
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Zhao X, Liu R, Zhao T, Reynoso FJ. Modeling double-strand breaks from direct and indirect action in a complete human genome single cell Geant4 model. Biomed Phys Eng Express 2020; 6. [PMID: 34035191 DOI: 10.1088/2057-1976/abb4bd] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/02/2020] [Indexed: 11/12/2022]
Abstract
The aim of this work is to develop and validate a computational model to investigate direct and indirect DNA damage by directly quantifying DNA strand breaks. A detailed geometrical target model was created in the Monte Carlo toolkit Geant4 to represent the nucleus of a single human cell with complete human genome. A calculation framework to simulate double-strand breaks (DSBs) was implemented using this single cell model in the Geant4-DNA extension. A detailed ellipsoidal single cell model was implemented using a compacted DNA structure representing the fibroblast cell in the G0/G1 phase of the cycle using a total of 6 Gbp within the nucleus to represent the complete human genome. This geometry was developed from the publicly available Geant4-DNA example (wholeNuclearDNA), and modified to record DNA damage for both the physical and chemical stages. A clustering algorithm was implemented in the analysis process in order to quantify direct, indirect, and mixed DSBs. The model was validated against published experimental and computational results for DSB Gy-1Gbp-1and the relative biological effectiveness (RBE) values for 250 kVp and Co-60 photons, as well as 2-100 MeV mono-energetic protons. A general agreement was observed over the whole simulated proton energy range, Co-60 beam, and 250 kVp in terms of the yield of DSB Gy-1Gbp-1and RBE. The DSB yield was 8.0 ± 0.3 DSB Gy-1Gbp-1for Co-60, and 9.2 ± 0.2 DSB Gy-1Gbp-1for 250 kVp, and between 11.1 ± 0.9 and 8.1 ± 0.5 DSB Gy-1Gbp-1for 2-100 MeV protons. The results also show mixed DSBs composed of direct and indirect SSBs make up more than half of the total DSBs. The results presented indicate that the current model reliably predicts the DSB yield and RBE for proton and photon irradiations, and allows for the detailed computational investigation of direct and indirect effects in DNA damage.
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Affiliation(s)
- Xiandong Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, United States of America
| | - Ruirui Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, United States of America
| | - Tianyu Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, United States of America
| | - Francisco J Reynoso
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, United States of America
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31
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Alpha Radiation as a Way to Target Heterochromatic and Gamma Radiation-Exposed Breast Cancer Cells. Cells 2020; 9:cells9051165. [PMID: 32397212 PMCID: PMC7291130 DOI: 10.3390/cells9051165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/19/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022] Open
Abstract
Compact chromatin is linked to a poor tumour prognosis and resistance to radiotherapy from photons. We investigated DNA damage induction and repair in the context of chromatin structure for densely ionising alpha radiation as well as its therapeutic potential. Chromatin opening by histone deacetylase inhibitor trichostatin A (TSA) pretreatment reduced clonogenic survival and increased γH2AX foci in MDA-MB-231 cells, indicative of increased damage induction by free radicals using gamma radiation. In contrast, TSA pretreatment tended to improve survival after alpha radiation while γH2AX foci were similar or lower; therefore, an increased DNA repair is suggested due to increased access of repair proteins. MDA-MB-231 cells exposed to fractionated gamma radiation (2 Gy × 6) expressed high levels of stem cell markers, elevated heterochromatin H3K9me3 marker, and a trend towards reduced clonogenic survival in response to alpha radiation. There was a higher level of H3K9me3 at baseline, and the ratio of DNA damage induced by alpha vs. gamma radiation was higher in the aggressive MDA-MB-231 cells compared to hormone receptor-positive MCF7 cells. We demonstrate that heterochromatin structure and stemness properties are induced by fractionated radiation exposure. Gamma radiation-exposed cells may be targeted using alpha radiation, and we provide a mechanistic basis for the involvement of chromatin in these effects.
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Zhu H, McNamara AL, Ramos-Mendez J, McMahon SJ, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J. A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio. Phys Med Biol 2020; 65:085015. [PMID: 32101803 DOI: 10.1088/1361-6560/ab7a6b] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Monte Carlo (MC) track structure simulation tools are commonly used for predicting radiation induced DNA damage by modeling the physical and chemical reactions at the nanometer scale. However, the outcome of these MC simulations is particularly sensitive to the adopted parameters which vary significantly across studies. In this study, a previously developed full model of nuclear DNA was used to describe the DNA geometry. The TOPAS-nBio MC toolkit was used to investigate the impact of physics and chemistry models as well as three key parameters (the energy threshold for direct damage, the chemical stage time length, and the probability of damage between hydroxyl radical reactions with DNA) on the induction of DNA damage. Our results show that the difference in physics and chemistry models alone can cause differences up to 34% and 16% in the DNA double strand break (DSB) yield, respectively. Additionally, changing the direct damage threshold, chemical stage length, and hydroxyl damage probability can cause differences of up to 28%, 51%, and 71% in predicted DSB yields, respectively, for the configurations in this study.
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Affiliation(s)
- Hongyu Zhu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, United States of America. Department of Engineering Physics, Tsinghua University, Beijing 100084, People's Republic of China. Key Laboratory of Particle and Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, People's Republic of China
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Ionizing Radiation and Complex DNA Damage: Quantifying the Radiobiological Damage Using Monte Carlo Simulations. Cancers (Basel) 2020; 12:cancers12040799. [PMID: 32225023 PMCID: PMC7226293 DOI: 10.3390/cancers12040799] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023] Open
Abstract
Ionizing radiation is a common tool in medical procedures. Monte Carlo (MC) techniques are widely used when dosimetry is the matter of investigation. The scientific community has invested, over the last 20 years, a lot of effort into improving the knowledge of radiation biology. The present article aims to summarize the understanding of the field of DNA damage response (DDR) to ionizing radiation by providing an overview on MC simulation studies that try to explain several aspects of radiation biology. The need for accurate techniques for the quantification of DNA damage is crucial, as it becomes a clinical need to evaluate the outcome of various applications including both low- and high-energy radiation medical procedures. Understanding DNA repair processes would improve radiation therapy procedures. Monte Carlo simulations are a promising tool in radiobiology studies, as there are clear prospects for more advanced tools that could be used in multidisciplinary studies, in the fields of physics, medicine, biology and chemistry. Still, lot of effort is needed to evolve MC simulation tools and apply them in multiscale studies starting from small DNA segments and reaching a population of cells.
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Dos Santos M, Delorme R, Salmon R, Prezado Y. Minibeam radiation therapy: A micro- and nano-dosimetry Monte Carlo study. Med Phys 2020; 47:1379-1390. [PMID: 31900944 DOI: 10.1002/mp.14009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 12/12/2019] [Accepted: 12/22/2019] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Minibeam radiation therapy (MBRT) is an innovative strategy based on a distinct dose delivery method that is administered using a series of narrow (submillimetric) parallel beams. To shed light on the biological effects of MBRT irradiation, we explored the micro- and nanodosimetric characteristics of three promising MBRT modalities (photon, electron, and proton) using Monte Carlo (MC) calculations. METHODS Irradiation with proton (100 MeV), electron (300 MeV), and photon (effective energy of 69 keV) minibeams were simulated using Geant4 MC code and the Geant4-DNA extension, which allows the simulation of energy transfer points with nanometric accuracy. As the target of the simulations, cells containing spherical nuclei with or without a detailed description of the DNA (deoxyribonucleic acid) geometry were placed at different depths in peak and valley regions in a water phantom. The energy deposition and number of events in the cell nuclei were recorded in the microdosimetry study, and the number of DNA breaks and their complexity were determined in the nanodosimetric study, where a multi-scale simulation approach was used for the latter. For DNA damage assessment, an adapted DBSCAN clustering algorithm was used. To compare the photon MBRT (xMBRT), electron MBRT (eMBRT), and proton MBRT (pMBRT) approaches, we considered the treatment of a brain tumor located at a depth of 75 mm. RESULTS Both mean energy deposition at micrometric scale and DNA damage in the "valley" cell nuclei were very low as compared with these parameters in the peak region at all depths for xMBRT and at depths of 0 to 30 mm and 0 to 50 mm for eMBRT and pMBRT, respectively. Only the charged minibeams were favorable for tumor control by producing similar effects in peak and valley cells after 70 mm. At the micrometer scale, the energy deposited per event pointed to a potential advantage of proton beams for tumor control, as more aggressive events could be expected at the end of their tracks. At the nanometer scale, all three MBRT modalities produced direct clustered DNA breaks, although the majority of damage (>93%) was composed of isolated single strand breaks. The pMBRT led to a significant increase in the proportion of clustered single strand breaks and double-strand breaks at the end of its range as compared to the entrance (7% at 75 mm vs 3% at 10 mm) in contrast to eMBRT and xMBRT. In the latter cases, the proportions of complex breaks remained constant, irrespective of the depth and region (peak or valley). CONCLUSIONS Enhanced normal tissue sparing can be expected with these three MBRT techniques. Among the three modalities, pMBRT offers an additional gain for radioresistant tumors, as it resulted in a higher number of complex DNA damage clusters in the tumor region. These results can aid understanding of the biological mechanisms of MBRT.
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Affiliation(s)
- M Dos Santos
- Department of Radiobiology and regenerative medicine (SERAMED), Laboratory of Radiobiology of Accidental exposures (LRAcc), IRSN, F-92260, Fontenay-aux-Roses, France
| | - R Delorme
- Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC), CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91400, Orsay, France.,Université de Paris, IMNC, F-91400, Orsay, France
| | - R Salmon
- Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC), CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91400, Orsay, France.,Université de Paris, IMNC, F-91400, Orsay, France
| | - Y Prezado
- Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC), CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91400, Orsay, France.,Université de Paris, IMNC, F-91400, Orsay, France
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Assessment of Radio-Induced Damage in Endothelial Cells Irradiated with 40 kVp, 220 kVp, and 4 MV X-rays by Means of Micro and Nanodosimetric Calculations. Int J Mol Sci 2019; 20:ijms20246204. [PMID: 31835321 PMCID: PMC6940891 DOI: 10.3390/ijms20246204] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 01/09/2023] Open
Abstract
The objective of this work was to study the differences in terms of early biological effects that might exist between different X-rays energies by using a mechanistic approach. To this end, radiobiological experiments exposing cell monolayers to three X-ray energies were performed in order to assess the yields of early DNA damage, in particular of double-strand breaks (DSBs). The simulation of these irradiations was set in order to understand the differences in the obtained experimental results. Hence, simulated results in terms of microdosimetric spectra and early DSB induction were analyzed and compared to the experimental data. Human umbilical vein endothelial cells (HUVECs) were irradiated with 40, 220 kVp, and 4 MV X-rays. The Geant4 Monte Carlo simulation toolkit and its extension Geant4-DNA were used for the simulations. Microdosimetric calculations aiming to determine possible differences in the variability of the energy absorbed by the irradiated cell population for those photon spectra were performed on 10,000 endothelial cell nuclei representing a cell monolayer. Nanodosimetric simulations were also carried out using a computation chain that allowed the simulation of physical, physico-chemical, and chemical stages on a single realistic endothelial cell nucleus model including both heterochromatin and euchromatin. DNA damage was scored in terms of yields of prompt DSBs per Gray (Gy) and per giga (109) base pair (Gbp) and DSB complexity was derived in order to be compared to experimental data expressed as numbers of histone variant H2AX (γ-H2AX) foci per cell. The calculated microdosimetric spread in the irradiated cell population was similar when comparing between 40 and 220 kVp X-rays and higher when comparing with 4 MV X-rays. Simulated yields of induced DSB/Gy/Gbp were found to be equivalent to those for 40 and 220 kVp but larger than those for 4 MV, resulting in a relative biological effectiveness (RBE) of 1.3. Additionally, DSB complexity was similar between the considered photon spectra. Simulated results were in good agreement with experimental data obtained by IRSN (Institut de radioprotection et de sûreté nucléaire) radiobiologists. Despite differences in photon energy, few differences were observed when comparing between 40 and 220 kVp X-rays in microdosimetric and nanodosimetric calculations. Nevertheless, variations were observed when comparing between 40/220 kVp and 4 MV X-rays. Thanks to the simulation results, these variations were able to be explained by the differences in the production of secondary electrons with energies below 10 keV.
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