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Hou Z, Yu T, Yi Q, Du Y, Zhou L, Zhao Y, Wu Y, Wu L, Wang T, Bian P. High-complexity of DNA double-strand breaks is key for alternative end-joining choice. Commun Biol 2024; 7:936. [PMID: 39095441 PMCID: PMC11297215 DOI: 10.1038/s42003-024-06640-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
The repair of DNA double-strand breaks (DSBs) through alternative non-homologous end-joining (alt-NHEJ) pathway significantly contributes to genetic instability. However, the mechanism governing alt-NHEJ pathway choice, particularly its association with DSB complexity, remains elusive due to the absence of a suitable reporter system. In this study, we established a unique Escherichia coli reporter system for detecting complex DSB-initiated alternative end-joining (A-EJ), an alt-NHEJ-like pathway. By utilizing various types of ionizing radiation to generate DSBs with varying degrees of complexity, we discovered that high complexity of DSBs might be a determinant for A-EJ choice. To facilitate efficient repair of high-complexity DSBs, A-EJ employs distinct molecular patterns such as longer micro-homologous junctions and non-templated nucleotide addition. Furthermore, the A-EJ choice is modulated by the degree of homology near DSB loci, competing with homologous recombination machinery. These findings further enhance the understanding of A-EJ/alt-NHEJ pathway choice.
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Affiliation(s)
- Zhiyang Hou
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- University of Science and Technology of China, Hefei, China
| | - Tianxiang Yu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- University of Science and Technology of China, Hefei, China
| | - Qiyi Yi
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yan Du
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Libin Zhou
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Ye Zhao
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yuejin Wu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Lijun Wu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Ting Wang
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
| | - Po Bian
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
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Goodhead DT, Weinfeld M. Clustered DNA Damage and its Complexity: Tracking the History. Radiat Res 2024; 202:385-407. [PMID: 38954537 DOI: 10.1667/rade-24-00017.1] [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: 01/16/2024] [Accepted: 03/21/2024] [Indexed: 07/04/2024]
Abstract
The concept of radiation-induced clustered damage in DNA has grown over the past several decades to become a topic of considerable interest across the scientific disciplines involved in studies of the biological effects of ionizing radiation. This paper, prepared for the 70th anniversary issue of Radiation Research, traces historical development of the three main threads of physics, chemistry, and biochemical/cellular responses that led to the hypothesis and demonstration that a key component of the biological effectiveness of ionizing radiation is its characteristic of producing clustered DNA damage of varying complexities. The physics thread has roots that started as early as the 1920s, grew to identify critical nanometre-scale clusterings of ionizations relevant to biological effectiveness, and then, by the turn of the century, had produced an extensive array of quantitative predictions on the complexity of clustered DNA damage from different radiations. Monte Carlo track structure simulation techniques played a key role through these developments, and they are now incorporated into many recent and ongoing studies modelling the effects of radiation. The chemistry thread was seeded by water-radiolysis descriptions of events in water as radical-containing "spurs," demonstration of the important role of the hydroxyl radical in radiation-inactivation of cells and the difficulty of protection by radical scavengers. This led to the concept and description of locally multiply damaged sites (LMDS) for DNA double-strand breaks and other combinations of DNA base damage and strand breakage that could arise from a spur overlapping, or created in very close proximity to, the DNA. In these ways, both the physics and the chemistry threads, largely in parallel, put out the challenge to the experimental research community to verify these predictions of clustered DNA damage from ionizing radiations and to investigate their relevance to DNA repair and subsequent cellular effects. The third thread, biochemical and cell-based research, responded strongly to the challenge by demonstrating the existence and biological importance of clustered DNA damage. Investigations have included repair of a wide variety of defined constructs of clustered damage, evaluation of mutagenic consequences, identification of clustered base-damage within irradiated cells, and identification of co-localization of repair complexes indicative of complex clustered damage after high-LET irradiation, as well as extensive studies of the repair pathways involved in repair of simple double-strand breaks. There remains, however, a great deal more to be learned because of the diversity of clustered DNA damage and of the biological responses.
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Mao H, Zhang H, Luo Y, Yang J, Liu Y, Zhang S, Chen W, Li Q, Dai Z. Primary study of the relative and compound biological effectiveness model for boron neutron capture therapy based on nanodosimetry. Med Phys 2024; 51:3076-3092. [PMID: 38408025 DOI: 10.1002/mp.16998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/31/2023] [Accepted: 02/07/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND The current radiobiological model employed for boron neutron capture therapy (BNCT) treatment planning, which relies on microdosimetry, fails to provide an accurate representation the biological effects of BNCT. The precision in calculating the relative biological effectiveness (RBE) and compound biological effectiveness (CBE) plays a pivotal role in determining the therapeutic efficacy of BNCT. Therefore, this study focuses on how to improve the accuracy of the biological effects of BNCT. PURPOSE The purpose of this study is to propose new radiation biology models based on nanodosimetry to accurately assess RBE and CBE for BNCT. METHODS Nanodosimetry, rooted in ionization cluster size distributions (ICSD), introduces a novel approach to characterize radiation quality by effectively delineating RBE through the ion track structure at the nanoscale. In the context of prior research, this study presents a computational model for the nanoscale assessment of RBE and CBE. We establish a simplified model of DNA chromatin fiber using the Monte Carlo code TOPAS-nBio to evaluate the applicability of ICSD to BNCT and compute nanodosimetric parameters. RESULTS Our investigation reveals that both homogeneous and heterogeneous nanodosimetric parameters, as well as the corresponding biological model coefficients α and β, along with RBE values, exhibit variations in response to varying intracellular 10B concentrations. Notably, the nanodosimetric parameterM 1 C 2 $M_1^{{{\mathrm{C}}}_2}$ effectively captures the fluctuations in model coefficients α and RBE. CONCLUSION Our model facilitates a nanoscale analysis of BNCT, enabling predictions of nanodosimetric quantities for secondary ions as well as RBE, CBE, and other essential biological metrics related to the distribution of boron. This contribution significantly enhances the precision of RBE calculations and holds substantial promise for future applications in treatment planning.
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Affiliation(s)
- Haijun Mao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, China
| | - Hui Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Luo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingfen Yang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yinuo Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Future Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shichao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, China
| | - Weiqiang Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Putian Lanhai Nuclear Medicine Research Center, Putian, China
| | - Qiang Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Putian Lanhai Nuclear Medicine Research Center, Putian, China
| | - Zhongying Dai
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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Derksen L, Adeberg S, Zink K, Baumann KS. Comparison of two methods simulating inter-track interactions using the radiobiological Monte Carlo toolkit TOPAS-nBio. Phys Med Biol 2024; 69:03NT01. [PMID: 38198700 DOI: 10.1088/1361-6560/ad1cf4] [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: 09/19/2023] [Accepted: 01/10/2024] [Indexed: 01/12/2024]
Abstract
Objective.To compare two independently developed methods that enable modelling inter-track interactions in TOPAS-nBio by examining the yield of radiolytic species in radiobiological Monte Carlo track structure simulations. One method uses a phase space file to assign more than one primary to one event, allowing for inter-track interaction between these primary particles. This method has previously been developed by this working group and published earlier. Using the other method, chemical reactions are simulated based on a new version of the independent reaction time approach to allow inter-track interactions.Approach.G-values were calculated and compared using both methods for different numbers of tracks able to undergo inter-track interactions.Main results.Differences in theG-values simulated with the two methods strongly depend on the molecule type, and deviations can range up to 3.9% (H2O2), although, on average, the deviations are smaller than 1.5%.Significance.Both methods seem to be suitable for simulating inter-track interactions, as they provide comparableG-values even though both techniques were developed independently of each other.
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Affiliation(s)
- Larissa Derksen
- University of Applied Sciences, Institute of Medical Physics and Radiation Protection, Giessen, Germany
| | - Sebastian Adeberg
- Marburg University Hospital, Department of Radiotherapy and Radiation Oncology, Marburg, Germany
- Marburg Ion-Beam Therapy Center (MIT), Department of Radiotherapy and Radiation Oncology, Marburg University Hospital, Marburg, Germany
- University Cancer Center, Frankfurt-Marburg, Germany
| | - Klemens Zink
- University of Applied Sciences, Institute of Medical Physics and Radiation Protection, Giessen, Germany
- Marburg University Hospital, Department of Radiotherapy and Radiation Oncology, Marburg, Germany
- Marburg Ion-Beam Therapy Center (MIT), Department of Radiotherapy and Radiation Oncology, Marburg University Hospital, Marburg, Germany
| | - Kilian-Simon Baumann
- University of Applied Sciences, Institute of Medical Physics and Radiation Protection, Giessen, Germany
- Marburg University Hospital, Department of Radiotherapy and Radiation Oncology, Marburg, Germany
- Marburg Ion-Beam Therapy Center (MIT), Department of Radiotherapy and Radiation Oncology, Marburg University Hospital, Marburg, Germany
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Warmenhoven JW, Henthorn NT, McNamara AL, Ingram SP, Merchant MJ, Kirkby KJ, Schuemann J, Paganetti H, Prise KM, McMahon SJ. Effects of Differing Underlying Assumptions in In Silico Models on Predictions of DNA Damage and Repair. Radiat Res 2023; 200:509-522. [PMID: 38014593 DOI: 10.1667/rade-21-00147.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/05/2023] [Indexed: 11/29/2023]
Abstract
The induction and repair of DNA double-strand breaks (DSBs) are critical factors in the treatment of cancer by radiotherapy. To investigate the relationship between incident radiation and cell death through DSB induction many in silico models have been developed. These models produce and use custom formats of data, specific to the investigative aims of the researchers, and often focus on particular pairings of damage and repair models. In this work we use a standard format for reporting DNA damage to evaluate combinations of different, independently developed, models. We demonstrate the capacity of such inter-comparison to determine the sensitivity of models to both known and implicit assumptions. Specifically, we report on the impact of differences in assumptions regarding patterns of DNA damage induction on predicted initial DSB yield, and the subsequent effects this has on derived DNA repair models. The observed differences highlight the importance of considering initial DNA damage on the scale of nanometres rather than micrometres. We show that the differences in DNA damage models result in subsequent repair models assuming significantly different rates of random DSB end diffusion to compensate. This in turn leads to disagreement on the mechanisms responsible for different biological endpoints, particularly when different damage and repair models are combined, demonstrating the importance of inter-model comparisons to explore underlying model assumptions.
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Affiliation(s)
- John W Warmenhoven
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Nicholas T Henthorn
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Aimee L McNamara
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Samuel P Ingram
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Michael J Merchant
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Karen J Kirkby
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Jan Schuemann
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Harald Paganetti
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Kevin M Prise
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
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Rumiantcev M, Li WB, Lindner S, Liubchenko G, Resch S, Bartenstein P, Ziegler SI, Böning G, Delker A. Estimation of relative biological effectiveness of 225Ac compared to 177Lu during [ 225Ac]Ac-PSMA and [ 177Lu]Lu-PSMA radiopharmaceutical therapy using TOPAS/TOPAS-nBio/MEDRAS. EJNMMI Phys 2023; 10:53. [PMID: 37695374 PMCID: PMC10495309 DOI: 10.1186/s40658-023-00567-2] [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: 03/21/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
AIM Over recent years, [225Ac]Ac-PSMA and [177Lu]Lu-PSMA radiopharmaceutical therapy have evolved as a promising treatment option for advanced prostate cancer. Especially for alpha particle emitter treatments, there is still a need for improving dosimetry, which requires accurate values of relative biological effectiveness (RBE). To achieve that, consideration of DNA damages in the cell nucleus and knowledge of the energy deposition in the location of the DNA at the nanometer scale are required. Monte Carlo particle track structure simulations provide access to interactions at this level. The aim of this study was to estimate the RBE of 225Ac compared to 177Lu. The initial damage distribution after radionuclide decay and the residual damage after DNA repair were considered. METHODS This study employed the TOol for PArtcile Simulation (TOPAS) based on the Geant4 simulation toolkit. Simulation of the nuclear DNA and damage scoring were performed using the TOPAS-nBio extension of TOPAS. DNA repair was modeled utilizing the Python-based program MEDRAS (Mechanistic DNA Repair and Survival). Five different cell geometries of equal volume and two radionuclide internalization assumptions as well as two cell arrangement scenarios were investigated. The radionuclide activity (number of source points) was adopted based on SPECT images of patients undergoing the above-mentioned therapies. RESULTS Based on the simulated dose-effect curves, the RBE of 225Ac compared to 177Lu was determined in a wide range of absorbed doses to the nucleus. In the case of spherical geometry, 3D cell arrangement and full radionuclide internalization, the RBE based on the initial damage had a constant value of approximately 2.14. Accounting for damage repair resulted in RBE values ranging between 9.38 and 1.46 for 225Ac absorbed doses to the nucleus between 0 and 50 Gy, respectively. CONCLUSION In this work, the consideration of DNA repair of the damage from [225Ac]Ac-PSMA and [177Lu]Lu-PSMA revealed a dose dependency of the RBE. Hence, this work suggested that DNA repair is an important aspect to understand response to different radiation qualities.
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Affiliation(s)
- Mikhail Rumiantcev
- Department of Nuclear Medicine, LMU University Hospital, LMU Munich, Munich, Germany.
| | - Wei Bo Li
- Federal Office for Radiation Protection, Medical and Occupational Radiation Protection, Oberschleißheim, Germany
| | - Simon Lindner
- Department of Nuclear Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Grigory Liubchenko
- Department of Nuclear Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Sandra Resch
- Department of Nuclear Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Peter Bartenstein
- Department of Nuclear Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Sibylle I Ziegler
- Department of Nuclear Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Guido Böning
- Department of Nuclear Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Astrid Delker
- Department of Nuclear Medicine, LMU University Hospital, LMU Munich, Munich, Germany
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Han Y, Geng C, Liu Y, Wu R, Li M, Yu C, Altieri S, Tang X. Calculation of the DNA damage yield and relative biological effectiveness in boron neutron capture therapy via the Monte Carlo track structure simulation. Phys Med Biol 2023; 68:175028. [PMID: 37524085 DOI: 10.1088/1361-6560/acec2a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023]
Abstract
Objective.Boron neutron capture therapy (BNCT) is an advanced cellular-level hadron therapy that has exhibited remarkable therapeutic efficacy in the treatment of locally invasive malignancies. Despite its clinical success, the intricate nature of relative biological effectiveness (RBE) and mechanisms responsible for DNA damage remains elusive. This work aims to quantify the RBE of compound particles (i.e. alpha and lithium) in BNCT based on the calculation of DNA damage yields via the Monte Carlo track structure (MCTS) simulation.Approach. The TOPAS-nBio toolkit was employed to conduct MCTS simulations. The calculations encompassed four steps: determination of the angle and energy spectra on the nuclear membrane, quantification of the database containing DNA damage yields for ions with specific angle and energy, accumulation of the database and spectra to obtain the DNA damage yields of compound particles, and calculation of the RBE by comparison yields of double-strand break (DSB) with the reference gamma-ray. Furthermore, the impact of cell size and microscopic boron distribution was thoroughly discussed.Main results. The DSB yields induced by compound particles in three types of spherical cells (radius equal to 10, 8, and 6μm) were found to be 13.28, 17.34, 22.15 Gy Gbp-1for boronophenylalanine (BPA), and 1.07, 3.45, 8.32 Gy Gbp-1for sodium borocaptate (BSH). The corresponding DSB-based RBE values were determined to be 1.90, 2.48, 3.16 for BPA and 0.15, 0.49, 1.19 for BSH. The calculated DSB-based RBE showed agreement with experimentally values of compound biological effectiveness for melanoma and gliosarcoma. Besides, the DNA damage yield and DSB-based RBE value exhibited an increasing trend as the cell radius decreased. The impact of the boron concentration ratio on RBE diminished once the drug enrichment surpasses a certain threshold.Significance. This work is potential to provide valuable guidance for accurate biological-weighted dose evaluation in BNCT.
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Affiliation(s)
- Yang Han
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, People's Republic of China
- Department of Physics, University of Pavia, Pavia, Italy
| | - Changran Geng
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, People's Republic of China
| | - Yuanhao Liu
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, People's Republic of China
- Neuboron Medtech. Ltd, Nanjing, People's Republic of China
| | - Renyao Wu
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, People's Republic of China
| | - Mingzhu Li
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, People's Republic of China
| | - Chenxi Yu
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, People's Republic of China
| | - Saverio Altieri
- Department of Physics, University of Pavia, Pavia, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), the section of Pavia, Pavia, Italy
| | - Xiaobin Tang
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, People's Republic of China
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8
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Bui A, Bekerat H, Childress L, Sankey J, Seuntjens J, Enger SA. Effects of incoming particle energy and cluster size on the G-value of hydrated electrons. Phys Med 2023; 107:102540. [PMID: 36804695 DOI: 10.1016/j.ejmp.2023.102540] [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: 05/16/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
In hydrated electron (e-aq) dosimetry, absorbed radiation dose to water is measured by monitoring the concentration of radiation-induced e-aq. However, to obtain accurate dose, the radiation chemical yield of e-aq, G(e-aq), is needed for the radiation quality/setup under investigation. The aim of this study was to investigate the time-evolution of the G-values for the main generated reactive species during water radiolysis using GEANT4-DNA. The effects of cluster size and linear energy transfer (LET) on G(e-aq) were examined. Validity of GEANT4-DNA for calculation of G(e-aq) for clinically relevant energies was studied. Three scenarios were investigated with different phantom sizes and incoming electron energies (1 keV to 1 MeV). The time evolution of G(e-aq) was in good agreement with published data and did not change with decreasing phantom size. The time-evolution of the G-values increases with increasing LET for all radiolytic species. The particle tracks formed with high-energy electrons are separated and the resulting reactive species develop independently in time. With decreasing energy, the mean separation distance between reactive species decreases. The particle tracks might not initially overlap but will overlap shortly thereafter due to diffusion of reactive species, increasing the probability of e-aq recombination with other species. This also explains the decrease of G(e-aq) with cluster size and LET. Finally, if all factors are kept constant, as the incoming electron energy increases to clinically relevant energies, G(e-aq) remains similar to its value at 1 MeV, hence GEANT4-DNA can be used for clinically relevant energies.
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Affiliation(s)
- Alaina Bui
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montréal, Quebec, Canada.
| | - Hamed Bekerat
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montréal, Quebec, Canada; Radiation Oncology Department, Jewish General Hospital, Montréal, Quebec, Canada
| | - Lilian Childress
- Department of Physics, McGill University, Montréal, Quebec, Canada
| | - Jack Sankey
- Department of Physics, McGill University, Montréal, Quebec, Canada
| | - Jan Seuntjens
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montréal, Quebec, Canada; Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
| | - Shirin A Enger
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montréal, Quebec, Canada; Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada; Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Quebec, Canada
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9
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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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10
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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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11
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Monte-Carlo techniques for radiotherapy applications I: introduction and overview of the different Monte-Carlo codes. JOURNAL OF RADIOTHERAPY IN PRACTICE 2023. [DOI: 10.1017/s1460396923000079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Abstract
Introduction:
The dose calculation plays a crucial role in many aspects of contemporary clinical radiotherapy treatment planning process. It therefore goes without saying that the accuracy of the dose calculation is of very high importance. The gold standard for absorbed dose calculation is the Monte-Carlo algorithm.
Methods:
This first of two papers gives an overview of the main openly available and supported codes that have been widely used for radiotherapy simulations.
Results:
The paper aims to provide an overview of Monte-Carlo in the field of radiotherapy and point the reader in the right direction of work that could help them get started or develop their existing understanding and use of Monte-Carlo algorithms in their practice.
Conclusions:
It also serves as a useful companion to a curated collection of papers on Monte-Carlo that have been published in this journal.
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12
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Monte-Carlo techniques for radiotherapy applications II: equipment and source modelling, dose calculations and radiobiology. JOURNAL OF RADIOTHERAPY IN PRACTICE 2023. [DOI: 10.1017/s1460396923000080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Abstract
Introduction:
This is the second of two papers giving an overview of the use of Monte-Carlo techniques for radiotherapy applications.
Methods:
The first paper gave an introduction and introduced some of the codes that are available to the user wishing to model the different aspects of radiotherapy treatment. It also aims to serve as a useful companion to a curated collection of papers on Monte-Carlo that have been published in this journal.
Results and Conclusions:
This paper focuses on the application of Monte-Carlo to specific problems in radiotherapy. These include radiotherapy and imaging beam production, brachytherapy, phantom and patient dosimetry, detector modelling and track structure calculations for micro-dosimetry, nano-dosimetry and radiobiology.
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Zhu K, Wu C, Peng X, Ji X, Luo S, Liu Y, Wang X. Nanoscale Calculation of Proton-Induced DNA Damage Using a Chromatin Geometry Model with Geant4-DNA. Int J Mol Sci 2022; 23:ijms23116343. [PMID: 35683021 PMCID: PMC9181653 DOI: 10.3390/ijms23116343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Monte Carlo simulations can quantify various types of DNA damage to evaluate the biological effects of ionizing radiation at the nanometer scale. This work presents a study simulating the DNA target response after proton irradiation. A chromatin fiber model and new physics constructors with the ELastic Scattering of Electrons and Positrons by neutral Atoms (ELSEPA) model were used to describe the DNA geometry and the physical stage of water radiolysis with the Geant4-DNA toolkit, respectively. Three key parameters (the energy threshold model for strand breaks, the physics model and the maximum distance to distinguish DSB clusters) of scoring DNA damage were studied to investigate the impact on the uncertainties of DNA damage. On the basis of comparison of our results with experimental data and published findings, we were able to accurately predict the yield of various types of DNA damage. Our results indicated that the difference in physics constructor can cause up to 56.4% in the DNA double-strand break (DSB) yields. The DSB yields were quite sensitive to the energy threshold for strand breaks (SB) and the maximum distance to classify the DSB clusters, which were even more than 100 times and four times than the default configurations, respectively.
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Affiliation(s)
- Kun Zhu
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Chun Wu
- School of Nursing, University of South China, Hengyang 421001, China;
| | - Xiaoyu Peng
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Xuantao Ji
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Siyuan Luo
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Yuchen Liu
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Xiaodong Wang
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
- Correspondence:
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14
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Thompson SJ, Rooney A, Prise KM, McMahon SJ. Evaluating Iodine-125 DNA Damage Benchmarks of Monte Carlo DNA Damage Models. Cancers (Basel) 2022; 14:cancers14030463. [PMID: 35158731 PMCID: PMC8833774 DOI: 10.3390/cancers14030463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Simulation of initial radiation-induced DNA damage remains a major area of research, with numerous Monte Carlo models having been developed to model radiation effects on the cellular scale. While many models have been reasonably fit to a range of biological endpoints, there remains a lack of robust benchmarking data. Here, we investigate the application of a dataset on strand breaking in a single DNA strand through incorporation of radioactive Iodine-125 to distinguish between different Monte Carlo nanoscale physics models. We find that, while all models are able to effectively fit this data, they do so using significantly different best-fitting parameters and make substantially different predictions for other endpoints. These observations suggest that most nanoscale models broadly agree on the distribution of energy and can be made to fit to single datasets, but robust, multi-endpoint analysis is required to fully optimize and validate these approaches. Abstract A wide range of Monte Carlo models have been applied to predict yields of DNA damage based on nanoscale track structure calculations. While often similar on the macroscopic scale, these models frequently employ different assumptions which lead to significant differences in nanoscale dose deposition. However, the impact of these differences on key biological readouts remains unclear. A major challenge in this area is the lack of robust datasets which can be used to benchmark models, due to a lack of resolution at the base pair level required to deeply test nanoscale dose deposition. Studies investigating the distribution of strand breakage in short DNA strands following the decay of incorporated 125I offer one of the few benchmarks for model predictions on this scale. In this work, we have used TOPAS-nBio to evaluate the performance of three Geant4-DNA physics models at predicting the distribution and yield of strand breaks in this irradiation scenario. For each model, energy and OH radical distributions were simulated and used to generate predictions of strand breakage, varying energy thresholds for strand breakage and OH interaction rates to fit to the experimental data. All three models could fit well to the observed data, although the best-fitting strand break energy thresholds ranged from 29.5 to 32.5 eV, significantly higher than previous studies. However, despite well describing the resulting DNA fragment distribution, these fit models differed significantly with other endpoints, such as the total yield of breaks, which varied by 70%. Limitations in the underlying data due to inherent normalisation mean it is not possible to distinguish clearly between the models in terms of total yield. This suggests that, while these physics models can effectively fit some biological data, they may not always generalise in the same way to other endpoints, requiring caution in their extrapolation to new systems and the use of multiple different data sources for robust model benchmarking.
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15
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A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast. Cancers (Basel) 2021; 13:cancers13194940. [PMID: 34638425 PMCID: PMC8508455 DOI: 10.3390/cancers13194940] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary DNA damage caused by ionizing radiation in a human fibroblast cell evaluated by the Geant4-DNA Monte Carlo toolkit is presented. A validation study using a computational geometric human DNA model was then carried out, and the calculated DNA damage as a function of particle type and energy is presented. The results of this work showed a significant improvement on past work and were consistent with recent radiobiological experimental data, such as damage yields. This work and the developed methodology could impact a broad number of research fields in which the understanding of radiation effects is crucial, such as cancer radiotherapy, space science, and medical physics. Abstract Accurately modeling the radiobiological mechanisms responsible for the induction of DNA damage remains a major scientific challenge, particularly for understanding the effects of low doses of ionizing radiation on living beings, such as the induction of carcinogenesis. A computational approach based on the Monte Carlo technique to simulate track structures in a biological medium is currently the most reliable method for calculating the early effects induced by ionizing radiation on DNA, the primary cellular target of such effects. The Geant4-DNA Monte Carlo toolkit can simulate not only the physical, but also the physico-chemical and chemical stages of water radiolysis. These stages can be combined with simplified geometric models of biological targets, such as DNA, to assess direct and indirect early DNA damage. In this study, DNA damage induced in a human fibroblast cell was evaluated using Geant4-DNA as a function of incident particle type (gammas, protons, and alphas) and energy. The resulting double-strand break yields as a function of linear energy transfer closely reproduced recent experimental data. Other quantities, such as fragment length distribution, scavengeable damage fraction, and time evolution of damage within an analytical repair model also supported the plausibility of predicting DNA damage using Geant4-DNA.The complete simulation chain application “molecularDNA”, an example for users of Geant4-DNA, will soon be distributed through Geant4.
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16
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Derksen L, Pfuhl T, Engenhart-Cabillic R, Zink K, Baumann KS. Investigating the feasibility of TOPAS-nBio for Monte Carlo track structure simulations by adapting GEANT4-DNA examples application. Phys Med Biol 2021; 66. [PMID: 34384060 DOI: 10.1088/1361-6560/ac1d21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/12/2021] [Indexed: 11/12/2022]
Abstract
Purpose.The purpose of this work is to investigate the feasibility of TOPAS-nBio for track structure simulations using tuple scoring and ROOT/Python-based post-processing.Materials and methods.There are several example applications implemented in GEANT4-DNA demonstrating track structure simulations. These examples are not implemented by default in TOPAS-nBio. In this study, the tuple scorer was used to re-simulate these examples. The simulations contained investigations of different physics lists, calculation of energy-dependent range, stopping power, mean free path andW-value. Additionally, further applications of the TOPAS-nBio tool were investigated, focusing on physical interactions and deposited energies of electrons with initial energies in the range of 10-60 eV, not covered in the recently published GEANT4-DNA simulations. Low-energetic electrons are currently of great interest in the radiobiology research community due to their high effectiveness towards the induction of biological damage.Results.The quantities calculated with TOPAS-nBio show a good agreement with the simulations of GEANT4-DNA with deviations of 5% at maximum. Thus, we have presented a feasible way to implement the example applications included in GEANT4-DNA in TOPAS-nBio. With the extended simulations, an insight could be given, which further tracking information can be gained with the track structure code and how cross sections and physics models influence a particle's fate.Conclusion.With our results, we could show the potentials of applying the tuple scorer in TOPAS-nBio Monte Carlo track structure simulations. Using this scorer, a large amount of information about the track structure can be accessed, which can be analyzed as preferred after the simulation.
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Affiliation(s)
- Larissa Derksen
- University of Applied Sciences, Institute of Medical Physics and Radiation Protection, Giessen, Germany
| | - Tabea Pfuhl
- GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany
| | - Rita Engenhart-Cabillic
- University Medical Center Giessen-Marburg, Department of Radiotherapy and Radiooncology, Marburg, Germany.,Marburg Ion-Beam Therapy Center (MIT), Marburg, Germany
| | - Klemens Zink
- University of Applied Sciences, Institute of Medical Physics and Radiation Protection, Giessen, Germany.,University Medical Center Giessen-Marburg, Department of Radiotherapy and Radiooncology, Marburg, Germany.,Marburg Ion-Beam Therapy Center (MIT), Marburg, Germany
| | - Kilian-Simon Baumann
- University of Applied Sciences, Institute of Medical Physics and Radiation Protection, Giessen, Germany.,University Medical Center Giessen-Marburg, Department of Radiotherapy and Radiooncology, Marburg, Germany.,Marburg Ion-Beam Therapy Center (MIT), Marburg, Germany
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17
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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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18
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Qi J, Geng C, Tang X, Tian F, Han Y, Liu H, Liu Y, Bortolussi S, Guan F. Effect of spatial distribution of boron and oxygen concentration on DNA damage induced from boron neutron capture therapy using Monte Carlo simulations. Int J Radiat Biol 2021; 97:986-996. [PMID: 33970761 DOI: 10.1080/09553002.2021.1928785] [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: 11/20/2020] [Revised: 04/03/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE This paper aims to investigate how the spatial distribution of boron in cells and oxygen concentration affect the DNA damage induced by charged particles in boron neutron capture therapy (BNCT) by Monte Carlo simulations, and further to evaluate the relative biological effectiveness (RBE) of DNA double-strand breaks (DSBs) induction. MATERIALS AND METHODS The kinetic energy spectra of α, 7Li particles in BNCT arriving at the nucleus surface were obtained from GEANT4 (Geant4 10.05.p01). The DNA damage caused by BNCT was then evaluated using MCDS (MCDS 3.10A). RESULTS When α or 7Li particles were distributed in the cytomembrane or cytoplasm, the difference in DNA damage of the same types was less than 0.5%. Taking the 137Cs photons as the reference radiation, when the oxygen concentration varied from 0% to 50%, the RBE of 0.54MeV protons and recoil protons varied from 5 to 2, whereas it decreased from 10 to 3 for α or 7Li particles. CONCLUSION The RBE of DSB induction all charged particles in BNCT decreased with the increase of oxygen concentration. This work indicated that the RBE of different radiation particles of BNCT might be affected by many factors, which should be paid attention to in theoretical research or clinical application.
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Affiliation(s)
- Jie Qi
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Changran Geng
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
- Key Laboratory of Nuclear Technology Application and Radiation Protection in Astronautics, Ministry of Industry and Information Technology, Nanjing, China
- Joint International Research Laboratory on Advanced Particle Therapy, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Xiaobin Tang
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
- Key Laboratory of Nuclear Technology Application and Radiation Protection in Astronautics, Ministry of Industry and Information Technology, Nanjing, China
- Joint International Research Laboratory on Advanced Particle Therapy, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Feng Tian
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Yang Han
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
- Department of Physics, University of Pavia, Pavia, Italy
| | - Huan Liu
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Yuanhao Liu
- Department of Nuclear Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | | | - Fada Guan
- Department of Radiation Physics, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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19
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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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Kyriakou I, Tremi I, Georgakilas AG, Emfietzoglou D. Microdosimetric investigation of the radiation quality of low-medium energy electrons using Geant4-DNA. Appl Radiat Isot 2021; 172:109654. [PMID: 33676082 DOI: 10.1016/j.apradiso.2021.109654] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023]
Abstract
The increasing clinical use of low-energy photon and electron sources (below few tens of keV) has raised concerns on the adequacy of the existing approximation of an energy-independent radiobiological effectiveness. In this work, the variation of the quality factor (Q) and relative biological effectiveness (RBE) of electrons over the low-medium energy range (0.1 keV-1 MeV) is examined using several microdosimetry-based Monte Carlo methodologies with input data obtained from Geant4-DNA track-structure simulations. The sensitivity of the results to the different methodologies, Geant4-DNA physics models, and target sizes is examined. Calculations of Q and RBE are based on the ICRU Report 40 recommendations, the Kellerer-Hahn approximation, the site version of the theory of dual radiation action (TDRA), the microdosimetric kinetic model (MKM) of cell survival, and the calculated yield of DNA double strand breaks (DSB). The stochastic energy deposition spectra needed as input in the above approaches have been calculated for nanometer spherical volumes using the different electron physics models of Geant4-DNA. Results are normalized at 100 keV electrons which is here considered the reference radiation. It is shown that in the energy range ~50 keV-1 MeV, the calculated Q and RBE are approximately unity (to within 1-2%) irrespective of the methodology, Geant4-DNA physics model, and target size. At lower energies, Q and RBE become energy-dependent reaching a maximum value of ~1.5-2.5 between ~200 and 700 eV. The detailed variation of Q and RBE at low energies depends mostly upon the adopted methodology and target size, and less so upon the Geant4-DNA physics model. Overall, the DSB yield predicts the highest RBE values (with RBEmax≈2.5) whereas the MKM the lowest RBE values (with RBEmax≈1.5). The ICRU Report 40, Kellerer-Hahn, and TDRA methods are in excellent agreement (to within 1-2%) over the whole energy range predicting a Qmax≈2. In conclusion, the approximation Q=RBE=1 was found to be valid only above ~50 keV whereas at lower energies both Q and RBE become strongly energy-dependent. It is envisioned that the present work will contribute towards establishing robust methodologies to determine theoretically the energy-dependence of radiation quality of individual electrons which may then be used in subsequent calculations involving practical electron and photon radiation sources.
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Affiliation(s)
- Ioanna Kyriakou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110, Ioannina, Greece.
| | - Ioanna Tremi
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, Athens, Greece
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, Athens, Greece
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110, Ioannina, Greece
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21
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Small KL, Henthorn NT, Angal-Kalinin D, Chadwick AL, Santina E, Aitkenhead A, Kirkby KJ, Smith RJ, Surman M, Jones J, Farabolini W, Corsini R, Gamba D, Gilardi A, Merchant MJ, Jones RM. Evaluating very high energy electron RBE from nanodosimetric pBR322 plasmid DNA damage. Sci Rep 2021; 11:3341. [PMID: 33558553 PMCID: PMC7870938 DOI: 10.1038/s41598-021-82772-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/07/2020] [Indexed: 01/18/2023] Open
Abstract
This paper presents the first plasmid DNA irradiations carried out with Very High Energy Electrons (VHEE) over 100-200 MeV at the CLEAR user facility at CERN to determine the Relative Biological Effectiveness (RBE) of VHEE. DNA damage yields were measured in dry and aqueous environments to determine that ~ 99% of total DNA breaks were caused by indirect effects, consistent with other published measurements for protons and photons. Double-Strand Break (DSB) yield was used as the biological endpoint for RBE calculation, with values found to be consistent with established radiotherapy modalities. Similarities in physical damage between VHEE and conventional modalities gives confidence that biological effects of VHEE will also be similar-key for clinical implementation. Damage yields were used as a baseline for track structure simulations of VHEE plasmid irradiation using GEANT4-DNA. Current models for DSB yield have shown reasonable agreement with experimental values. The growing interest in FLASH radiotherapy motivated a study into DSB yield variation with dose rate following VHEE irradiation. No significant variations were observed between conventional and FLASH dose rate irradiations, indicating that no FLASH effect is seen under these conditions.
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Affiliation(s)
- K L Small
- The University of Manchester, Manchester, UK.
- The Cockcroft Institute, Daresbury, UK.
| | - N T Henthorn
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - D Angal-Kalinin
- The University of Manchester, Manchester, UK
- The Cockcroft Institute, Daresbury, UK
- ASTeC, STFC Daresbury Laboratory, Daresbury, Warrington, UK
| | - A L Chadwick
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - E Santina
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - A Aitkenhead
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, UK
| | - K J Kirkby
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - R J Smith
- The Cockcroft Institute, Daresbury, UK
- ASTeC, STFC Daresbury Laboratory, Daresbury, Warrington, UK
| | - M Surman
- The Cockcroft Institute, Daresbury, UK
- ASTeC, STFC Daresbury Laboratory, Daresbury, Warrington, UK
| | - J Jones
- The Cockcroft Institute, Daresbury, UK
- ASTeC, STFC Daresbury Laboratory, Daresbury, Warrington, UK
| | - W Farabolini
- CERN, Geneva, Switzerland
- CEA Saclay, IRFU-DACM, Saclay, France
| | | | | | - A Gilardi
- CERN, Geneva, Switzerland
- Federico II, DIETI, University of Napoli, Napoli, Italy
| | - M J Merchant
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - R M Jones
- The University of Manchester, Manchester, UK
- The Cockcroft Institute, Daresbury, UK
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22
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Zhu H, McNamara AL, McMahon SJ, Ramos-Mendez J, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J. Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio. Radiat Res 2020; 194:9-21. [PMID: 32401689 DOI: 10.1667/rr15531.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/11/2020] [Indexed: 12/21/2022]
Abstract
The cellular response to ionizing radiation continues to be of significant research interest in cancer radiotherapy, and DNA is recognized as the critical target for most of the biologic effects of radiation. Incident particles can cause initial DNA damages through physical and chemical interactions within a short time scale. Initial DNA damages can undergo repair via different pathways available at different stages of the cell cycle. The misrepair of DNA damage results in genomic rearrangement and causes mutations and chromosome aberrations, which are drivers of cell death. This work presents an integrated study of simulating cell response after proton irradiation with energies of 0.5-500 MeV (LET of 60-0.2 keV/µm). A model of a whole nucleus with fractal DNA geometry was implemented in TOPAS-nBio for initial DNA damage simulations. The default physics and chemistry models in TOPAS-nBio were used to describe interactions of primary particles, secondary particles, and radiolysis products within the nucleus. The initial DNA double-strand break (DSB) yield was found to increase from 6.5 DSB/Gy/Gbp at low-linear energy transfer (LET) of 0.2 keV/µm to 21.2 DSB/Gy/Gbp at high LET of 60 keV/µm. A mechanistic repair model was applied to predict the characteristics of DNA damage repair and dose response of chromosome aberrations. It was found that more than 95% of the DSBs are repaired within the first 24 h and the misrepaired DSB fraction increases rapidly with LET and reaches 15.8% at 60 keV/µm with an estimated chromosome aberration detection threshold of 3 Mbp. The dicentric and acentric fragment yields and the dose response of micronuclei formation after proton irradiation were calculated and compared with experimental results.
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Affiliation(s)
- Hongyu Zhu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China.,Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, P.R. China
| | - Aimee L McNamara
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Stephen J McMahon
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
| | - Jose Ramos-Mendez
- Department of Radiation Oncology, University of California San Francisco, California 94143
| | - Nicholas T Henthorn
- Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, California 94143
| | - Kathryn D Held
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Joseph Perl
- SLAC National Accelerator Laboratory, Menlo Park, California
| | - Junli Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China.,Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, P.R. China
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
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23
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Ingram SP, Henthorn NT, Warmenhoven JW, Kirkby NF, Mackay RI, Kirkby KJ, Merchant MJ. Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage. PLoS Comput Biol 2020; 16:e1008476. [PMID: 33326415 PMCID: PMC7773326 DOI: 10.1371/journal.pcbi.1008476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/30/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
Developments in the genome organisation field has resulted in the recent methodology to infer spatial conformations of the genome directly from experimentally measured genome contacts (Hi-C data). This provides a detailed description of both intra- and inter-chromosomal arrangements. Chromosomal intermingling is an important driver for radiation-induced DNA mis-repair. Which is a key biological endpoint of relevance to the fields of cancer therapy (radiotherapy), public health (biodosimetry) and space travel. For the first time, we leverage these methods of inferring genome organisation and couple them to nano-dosimetric radiation track structure modelling to predict quantities and distribution of DNA damage within cell-type specific geometries. These nano-dosimetric simulations are highly dependent on geometry and are benefited from the inclusion of experimentally driven chromosome conformations. We show how the changes in Hi-C contract maps impact the inferred geometries resulting in significant differences in chromosomal intermingling. We demonstrate how these differences propagate through to significant changes in the distribution of DNA damage throughout the cell nucleus, suggesting implications for DNA repair fidelity and subsequent cell fate. We suggest that differences in the geometric clustering for the chromosomes between the cell-types are a plausible factor leading to changes in cellular radiosensitivity. Furthermore, we investigate changes in cell shape, such as flattening, and show that this greatly impacts the distribution of DNA damage. This should be considered when comparing in vitro results to in vivo systems. The effect may be especially important when attempting to translate radiosensitivity measurements at the experimental in vitro level to the patient or human level.
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Affiliation(s)
- Samuel P. Ingram
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Nicholas T. Henthorn
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - John W. Warmenhoven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Norman F. Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Ranald I. Mackay
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Karen J. Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Michael J. Merchant
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
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24
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Wu J, Xie Y, Wang L, Wang Y. Monte Carlo simulations of energy deposition and DNA damage using TOPAS-nBio. ACTA ACUST UNITED AC 2020; 65:225007. [DOI: 10.1088/1361-6560/abbb73] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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25
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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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26
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Lemelin V, Bass AD, Sanche L. Low energy (6-18 eV) electron scattering from condensed thymidine (dT) III: absolute electronic excitation cross sections. Phys Chem Chem Phys 2020; 22:8364-8372. [PMID: 32266899 DOI: 10.1039/d0cp00198h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Absolute cross sections (CSs) for electronic excitation by low-energy electron (LEE) scattering, from condensed thymidine (dT) in the 6-18 eV incident energy range, were measured by high-resolution electron energy loss spectroscopy (HREELS). Various electron energy loss (EEL) spectra were acquired using 1 ML of dT condensed on a multilayer film of Ar held at about 20 K under ultra-high vacuum (∼1 × 10-11 Torr). dT is one of the most complex DNA constituents to be studied by HREELS and these spectra provide the first LEE energy-loss data for electronic excitation of a nucleoside. CSs for transitions to the states 13A', 13A'', 23A', 21A', 33A', 23A'', 43A', 33A'', 53A' and 51A' of dT were extracted from the EEL spectra. These states correlate to those previously measured for the thymine moiety. Two broad resonances are observed in the energy dependence of the CSs at around 8 and 10 eV; these energies are close to those found in earlier gas- and solid-phase studies on the interaction of LEEs with dT, thymine and related molecules. A quantitative comparison between the electronic CSs of dT and those of thymine and tetrahydrofuran indicates that no variation is induced in the electronic CSs of thymine upon chemically binding to a deoxyribose group.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
| | - A D Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
| | - L Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
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27
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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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28
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Margis S, Magouni M, Kyriakou I, Georgakilas AG, Incerti S, Emfietzoglou D. Microdosimetric calculations of the direct DNA damage induced by low energy electrons using the Geant4-DNA Monte Carlo code. Phys Med Biol 2020; 65:045007. [PMID: 31935692 DOI: 10.1088/1361-6560/ab6b47] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To calculate the yield of direct DNA damage induced by low energy electrons using Monte Carlo generated microdosimetric spectra at the nanometer scale and examine the influence of various simulation inputs. The potential of classical microdosimetry to offer a viable and simpler alternative to more elaborate mechanistic approaches for practical applications is discussed. Track-structure simulations with the Geant4-DNA low-energy extension of the Geant4 Monte Carlo toolkit were used for calculating lineal energy spectra in spherical volumes with dimensions relevant to double-strand-break (DSB) induction. The microdosimetric spectra were then used to calculate the yield of simple and clustered DSB based on literature values of the threshold energy of DNA damage. The influence of the different implementations of the dielectric function of liquid water available in Geant4-DNA (Option 2 and Option 4 constructors), as well as the effect of particle tracking cutoff energy and target size are examined. Frequency- and dose-mean lineal energies in liquid-water spheres of 2, 2.3, 2.6, and 3.4 nm diameter, as well as, number of simple and clustered DSB/Gy/cell are presented for electrons over the 100 eV to 100 keV energy range. Results are presented for both the 'default' (Option 2) and 'Ioannina' (Option 4) physics models of Geant4-DNA applying several commonly used tracking cutoff energies (10, 20, 50, 100 eV). Overall, the choice of the physics model and target diameter has a moderate effect (up to ~10%-30%) on the DSB yield whereas the effect of the tracking cutoff energy may be significant (>100%). Importantly, the yield of both simple and clustered DSB was found to vary significantly (by a factor of 2 or more) with electron energy over the examined range. The yields of electron-induced simple and clustered DSB exhibit a strong energy dependence over the 100 eV-100 keV range with implications to radiation quality issues. It is shown that a classical microdosimetry approach for the calculation of DNA damage based on lineal energy spectra in nanometer-size targets predicts comparable results to computationally intensive mechanistic approaches which use detailed atomistic DNA geometries, thus, offering a relatively simple and robust alternative for some practical applications.
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Affiliation(s)
- Stefanos Margis
- Medical Physics Laboratory, University of Ioannina Medical School, 45110 Ioannina, Greece
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29
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Li WB, Belchior A, Beuve M, Chen YZ, Di Maria S, Friedland W, Gervais B, Heide B, Hocine N, Ipatov A, Klapproth AP, Li CY, Li JL, Multhoff G, Poignant F, Qiu R, Rabus H, Rudek B, Schuemann J, Stangl S, Testa E, Villagrasa C, Xie WZ, Zhang YB. Intercomparison of dose enhancement ratio and secondary electron spectra for gold nanoparticles irradiated by X-rays calculated using multiple Monte Carlo simulation codes. Phys Med 2020; 69:147-163. [PMID: 31918367 DOI: 10.1016/j.ejmp.2019.12.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 11/29/2019] [Accepted: 12/15/2019] [Indexed: 12/22/2022] Open
Abstract
PURPOSE Targeted radiation therapy has seen an increased interest in the past decade. In vitro and in vivo experiments showed enhanced radiation doses due to gold nanoparticles (GNPs) to tumors in mice and demonstrated a high potential for clinical application. However, finding a functionalized molecular formulation for actively targeting GNPs in tumor cells is challenging. Furthermore, the enhanced energy deposition by secondary electrons around GNPs, particularly by short-ranged Auger electrons is difficult to measure. Computational models, such as Monte Carlo (MC) radiation transport codes, have been used to estimate the physical quantities and effects of GNPs. However, as these codes differ from one to another, the reliability of physical and dosimetric quantities needs to be established at cellular and molecular levels, so that the subsequent biological effects can be assessed quantitatively. METHODS In this work, irradiation of single GNPs of 50 nm and 100 nm diameter by X-ray spectra generated by 50 and 100 peak kilovoltages was simulated for a defined geometry setup, by applying multiple MC codes in the EURADOS framework. RESULTS The mean dose enhancement ratio of the first 10 nm-thick water shell around a 100 nm GNP ranges from 400 for 100 kVp X-rays to 600 for 50 kVp X-rays with large uncertainty factors up to 2.3. CONCLUSIONS It is concluded that the absolute dose enhancement effects have large uncertainties and need an inter-code intercomparison for a high quality assurance; relative properties may be a better measure until more experimental data is available to constrain the models.
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Affiliation(s)
- W B Li
- Institute of Radiation Medicine, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
| | - A Belchior
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066 Bobadela LRS, Portugal
| | - M Beuve
- Institut de Physique Nucléaire de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS/IN2P3 UMR 5822, Villeurbanne, France
| | - Y Z Chen
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - S Di Maria
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066 Bobadela LRS, Portugal
| | - W Friedland
- Institute of Radiation Medicine, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - B Gervais
- Normandie University, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, UMR 6252, BP 5133, F-14070 Caen Cedex 05, France
| | - B Heide
- Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - N Hocine
- Institut de Radioprotection et de Sûreté Nucléaire, Fontenay-Aux-Roses, France
| | - A Ipatov
- Alferov Federal State Budgetary Institution of Higher Education and Science Saint Petersburg National Research Academic University of the Russian Academy of Sciences, St. Petersburg, Russia
| | - A P Klapproth
- Institute of Radiation Medicine, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; TranslaTUM, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - C Y Li
- Department of Engineering Physics, Tsinghua University, Beijing, China; Nuctech Company Limited, Beijing, China
| | - J L Li
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - G Multhoff
- TranslaTUM, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - F Poignant
- Institut de Physique Nucléaire de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS/IN2P3 UMR 5822, Villeurbanne, France
| | - R Qiu
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - H Rabus
- Physikalisch-Technische Bundesanstalt, Braunschweig, Germany
| | - B Rudek
- Physikalisch-Technische Bundesanstalt, Braunschweig, Germany; Massachusetts General Hospital & Harvard Medical School, Department of Radiation Oncology, Boston, MA, USA
| | - J Schuemann
- Massachusetts General Hospital & Harvard Medical School, Department of Radiation Oncology, Boston, MA, USA
| | - S Stangl
- TranslaTUM, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - E Testa
- Institut de Physique Nucléaire de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS/IN2P3 UMR 5822, Villeurbanne, France
| | - C Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire, Fontenay-Aux-Roses, France
| | - W Z Xie
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Y B Zhang
- Peking University Cancer Hospital, Beijing, China
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30
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Warmenhoven JW, Henthorn NT, Ingram SP, Chadwick AL, Sotiropoulos M, Korabel N, Fedotov S, Mackay RI, Kirkby KJ, Merchant MJ. Insights into the non-homologous end joining pathway and double strand break end mobility provided by mechanistic in silico modelling. DNA Repair (Amst) 2020; 85:102743. [DOI: 10.1016/j.dnarep.2019.102743] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022]
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31
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Lemelin V, Bass AD, Cloutier P, Sanche L. Low energy (1-19 eV) electron scattering from condensed thymidine (dT) I: absolute vibrational excitation cross sections. Phys Chem Chem Phys 2019; 21:23808-23817. [PMID: 31503266 DOI: 10.1039/c9cp03447a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Absolute cross sections (CSs) for vibrational excitation by electrons of energy between 1-19 eV scattering from condensed thymidine (dT) were measured by means of high-resolution electron energy loss spectroscopy (HREELS). The CSs were extracted from electron energy loss spectra of dT condensed on multilayers film of Ar held at about 20 K under ultra-high vacuum (∼1 × 10-11 Torr). dT is one of the most complex molecules to be studied in condensed phase by HREELS. The magnitudes of the vibrational CSs lie within the 10-17 cm2 range. Structures observed in the energy dependence of the vibrational CSs under 3 eV and around 4 eV were compared with previous results of gas- and solid-phase studies on dT and related molecules (e.g., thymine and tetrahydrofuran). These structures were attributed to the formation of shape resonances.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
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32
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Dai T, Li Q, Liu X, Dai Z, He P, Ma Y, Shen G, Chen W, Zhang H, Meng Q, Zhang X. Nanodosimetric quantities and RBE of a clinically relevant carbon-ion beam. Med Phys 2019; 47:772-780. [PMID: 31705768 DOI: 10.1002/mp.13914] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/09/2019] [Accepted: 11/01/2019] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Although carbon-ion therapy is becoming increasingly attractive to the treatment of tumors, details about the ionization pattern formed by therapeutic carbon-ion beam in tissue have not been fully investigated. In this work, systematic calculations for the nanodosimetric quantities and relative biological effectiveness (RBE) of a clinically relevant carbon-ion beam were studied for the first time. METHODS The method combining both track structure and condensed history Monte Carlo (MC) simulations was adopted to calculate the nanodosimetric quantities. Fragments and energy spectra at different positions of the radiation field of a clinically relevant carbon-ion pencil beam were generated by means of MC simulations in water. Nanodosimetric quantities such as mean ionization cluster size ( M 1 ), the first moment of conditional cluster size ( M 1 C 2 ), cumulative probability ( F 2 ), and conditional cumulative probability ( F 3 C 2 ) at these positions were then acquired based on the spectra and the pre-calculated nanodosimetric database created by track structure MC simulations. What's more, a novel approach to calculate RBE based on the said nanodosimetric quantities was introduced. The RBE calculations were then conducted for the carbon-ion beam at different water-equivalent depths. RESULTS Lateral distributions at various water-equivalent depths of both the nanodosimetric quantities and RBE values were obtained. The values of M 1 , M 1 C 2 , F 2 , and F 3 C 2 were 1.49, 2.67, 0.30, and 0.38 at the plateau at the beam central axis and maximized at 2.79, 5.69, 0.47, and 0.68 at the depths around the Bragg peak, respectively. At a given depth, M 1 and F 2 decreased laterally with increasing the distance to the beam central axis while M 1 C 2 and F 3 C 2 remained nearly unchanged at first and then decreased except for M 1 C 2 at the rising edge of the Bragg peak. The calculated RBE values were 1.07 at the plateau and 3.13 around the Bragg peak. Good agreement between the calculated RBE values and experimental data was obtained. CONCLUSIONS Different nanodosimetric quantities feature the track structure of therapeutic carbon-ion beam in different manners. Detailed ionization patterns generated by carbon-ion beam could be characterized by nanodosimetric quantities. Moreover the combined method adopted in this work to calculate nanodosimetric quantities is not only valid but also convenient. Nanodosimetric quantities are significantly helpful for the RBE calculations in carbon-ion therapy.
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Affiliation(s)
- Tianyuan Dai
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinguo Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongying Dai
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengbo He
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Ma
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guosheng Shen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiqiang Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qianqian Meng
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofang Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 73000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, Lanzhou, 730000, China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Gansu Province, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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Surdutovich E, Solov’yov AV. Science vs. technology in radiation therapy from X-rays to ions. Cancer Nanotechnol 2019. [DOI: 10.1186/s12645-019-0054-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Rudek B, McNamara A, Ramos-Méndez J, Byrne H, Kuncic Z, Schuemann J. Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams. Phys Med Biol 2019; 64:175005. [PMID: 31295730 PMCID: PMC11222020 DOI: 10.1088/1361-6560/ab314c] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Gold nanoparticle (GNP) radio-enhancement is a promising technique to increase the dose deposition in a tumor while sparing neighboring healthy tissue. Previous experimental studies showed effects on cell survival and tumor control for keV x-rays but surprisingly also for MV-photons, proton and carbon-ion beams. In a systematic study, we use the Monte Carlo simulation tool TOPAS-nBio to model the GNP radio-enhancement within a cell as a function of GNP concentration, size and clustering for a wide range of energies for photons, protons and, for the first time, carbon-ions. Moreover, we include water radiolysis, which has been recognized as a major pathway of GNP mediated radio-enhancement. At a GNP concentration of 0.5% and a GNP diameter of 10 nm, the dose enhancement ratio was highest for 50 keV x-rays (1.36) and decreased in the orthovoltage (1.04 at 250 keV) and megavoltage range (1.01 at 1 MeV). The dose enhancement linearly increased with GNP concentration and decreased with GNP size and degree of clustering for all radiation modalities. While the highest physical dose enhancement at 5% concentrations was only 1.003 for 10 MeV protons and 1.004 for 100 MeV carbon-ions, we find the number of hydroxyl ([Formula: see text]) altered by 23% and 3% after 1 [Formula: see text]s at low, clinically-relevant concentrations. For the same concentration and proton-impact, the G-value is most sensitive to the nanoparticle size with 46 times more radical interactions at GNPs for 2 nm than for 50 nm GNP diameter within 1 [Formula: see text]s. Nanoparticle clustering was found to decrease the number of interactions at GNPs, e.g. for a cluster of 25 GNPs by a factor of 3.4. The changes in G-value correlate to the average distance between the chemical species and the GNPs. While the radiochemistry of GNP-loaded water has yet to be fully understood, this work offers a first relative quantification of radiolysis products for a broad parameter-set.
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Affiliation(s)
- Benedikt Rudek
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts, MA, United States of America. Department of Physics, Boston University, Boston, Massachusetts, MA, United States of America. Department of Ionizing Radiation, Physikalisch-Technische Bundesanstalt, Braunschweig, Germany. Author to whom any correspondence should be addressed
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Sakata D, Lampe N, Karamitros M, Kyriakou I, Belov O, Bernal MA, Bolst D, Bordage MC, Breton V, Brown JM, Francis Z, Ivanchenko V, Meylan S, Murakami K, Okada S, Petrovic I, Ristic-Fira A, Santin G, Sarramia D, Sasaki T, Shin WG, Tang N, Tran HN, Villagrasa C, Emfietzoglou D, Nieminen P, Guatelli S, Incerti S. Evaluation of early radiation DNA damage in a fractal cell nucleus model using Geant4-DNA. Phys Med 2019; 62:152-157. [DOI: 10.1016/j.ejmp.2019.04.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/25/2019] [Accepted: 04/13/2019] [Indexed: 11/26/2022] Open
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37
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Mechanistic Modelling of Radiation Responses. Cancers (Basel) 2019; 11:cancers11020205. [PMID: 30744204 PMCID: PMC6406300 DOI: 10.3390/cancers11020205] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 12/30/2022] Open
Abstract
Radiobiological modelling has been a key part of radiation biology and therapy for many decades, and many aspects of clinical practice are guided by tools such as the linear-quadratic model. However, most of the models in regular clinical use are abstract and empirical, and do not provide significant scope for mechanistic interpretation or making predictions in novel cell lines or therapies. In this review, we will discuss the key areas of ongoing mechanistic research in radiation biology, including physical, chemical, and biological steps, and review a range of mechanistic modelling approaches which are being applied in each area, highlighting the possible opportunities and challenges presented by these techniques.
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38
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Petringa G, Romano F, Manti L, Pandola L, Attili A, Cammarata F, Cuttone G, Forte G, Manganaro L, Pipek J, Pisciotta P, Russo G, Cirrone GAP. Radiobiological quantities in proton-therapy: Estimation and validation using Geant4-based Monte Carlo simulations. Phys Med 2019; 58:72-80. [PMID: 30824153 DOI: 10.1016/j.ejmp.2019.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 12/11/2022] Open
Abstract
PURPOSE The Geant4 Monte Carlo simulation toolkit was used to reproduce radiobiological parameters measured by irradiating three different cancerous cell lines with monochromatic and clinical proton beams. METHODS The experimental set-up adopted for irradiations was fully simulated with a dedicated open-source Geant4 application. Cells survival fractions was calculated coupling the Geant4 simulations with two analytical radiobiological models: one based on the LEM (Local Effect Model) approach and the other on a semi-empirical parameterisation. Results was evaluated and compared with experimental data. RESULTS AND CONCLUSIONS The results demonstrated the Geant4 ability to reproduce radiobiological quantities for different cell lines.
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Affiliation(s)
- G Petringa
- INFN-LNS. Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud, Via S. Sofia 62, 95123 Catania, Italy; Dipartimento di Fisica e Astronomia, Universitá degli Studi di Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - F Romano
- INFN-LNS. Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud, Via S. Sofia 62, 95123 Catania, Italy; National Physical Laboratory, Acoustic and Ionizing Radiation Division, Teddington TW11 0LW, Middlesex, UK
| | - L Manti
- Dipartimento di Fisica E. Pancini, Universitá degli Studi Federico II di Napoli, Via Cinthia, I-80126 Napoli, Italy; INFN-NA, Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di M. S. Angelo, Via Cintia, I-80126 Napoli, Italy
| | - L Pandola
- INFN-LNS. Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud, Via S. Sofia 62, 95123 Catania, Italy
| | - A Attili
- INFN-TO, Istituto Nazionale di Fisica Nucleare, Sezione di Torino, Torino, Italy
| | - F Cammarata
- INFN-LNS. Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud, Via S. Sofia 62, 95123 Catania, Italy; IBFM-CNR, Institute of Molecular Bioimaging and Physiology - National Research Council, Cefalù, PA, Italy
| | - G Cuttone
- INFN-LNS. Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud, Via S. Sofia 62, 95123 Catania, Italy
| | - G Forte
- INFN-LNS. Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud, Via S. Sofia 62, 95123 Catania, Italy; IBFM-CNR, Institute of Molecular Bioimaging and Physiology - National Research Council, Cefalù, PA, Italy
| | - L Manganaro
- INFN-TO, Istituto Nazionale di Fisica Nucleare, Sezione di Torino, Torino, Italy
| | - J Pipek
- ELI-Beamline Project, Inst. Physics, ASCR, PALS Center, Prague, Czech Republic
| | - P Pisciotta
- INFN-LNS. Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud, Via S. Sofia 62, 95123 Catania, Italy; Dipartimento di Fisica e Astronomia, Universitá degli Studi di Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - G Russo
- INFN-LNS. Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud, Via S. Sofia 62, 95123 Catania, Italy; IBFM-CNR, Institute of Molecular Bioimaging and Physiology - National Research Council, Cefalù, PA, Italy
| | - G A P Cirrone
- INFN-LNS. Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud, Via S. Sofia 62, 95123 Catania, Italy; ELI-Beamline Project, Inst. Physics, ASCR, PALS Center, Prague, Czech Republic.
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Schuemann J, McNamara AL, Ramos-Méndez J, Perl J, Held KD, Paganetti H, Incerti S, Faddegon B. TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology. Radiat Res 2019; 191:125-138. [PMID: 30609382 DOI: 10.1667/rr15226.1] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The TOPAS Monte Carlo (MC) system is used in radiation therapy and medical imaging research, having played a significant role in making Monte Carlo simulations widely available for proton therapy related research. While TOPAS provides detailed simulations of patient scale properties, the fundamental unit of the biological response to radiation is a cell. Thus, our goal was to develop TOPAS-nBio, an extension of TOPAS dedicated to advance understanding of radiobiological effects at the (sub-)cellular, (i.e., the cellular and sub-cellular) scale. TOPAS-nBio was designed as a set of open source classes that extends TOPAS to model radiobiological experiments. TOPAS-nBio is based on and extends Geant4-DNA, which extends the Geant4 toolkit, the basis of TOPAS, to include very low-energy interactions of particles down to vibrational energies, explicitly simulates every particle interaction (i.e., without using condensed histories) and propagates radiolysis products. To further facilitate the use of TOPAS-nBio, a graphical user interface was developed. TOPAS-nBio offers full track-structure Monte Carlo simulations, integration of chemical reactions within the first millisecond, an extensive catalogue of specialized cell geometries as well as sub-cellular structures such as DNA and mitochondria, and interfaces to mechanistic models of DNA repair kinetics. We compared TOPAS-nBio simulations to measured and published data of energy deposition patterns and chemical reaction rates (G values). Our simulations agreed well within the experimental uncertainties. Additionally, we expanded the chemical reactions and species provided in Geant4-DNA and developed a new method based on independent reaction times (IRT), including a total of 72 reactions classified into 6 types between neutral and charged species. Chemical stage simulations using IRT were a factor of 145 faster than with step-by-step tracking. Finally, we applied the geometric/chemical modeling to obtain initial yields of double-strand breaks (DSBs) in DNA fibers for proton irradiations of 3 and 50 MeV and compared the effect of including chemical reactions on the number and complexity of DSB induction. Over half of the DSBs were found to include chemical reactions with approximately 5% of DSBs caused only by chemical reactions. In conclusion, the TOPAS-nBio extension to the TOPAS MC application offers access to accurate and detailed multiscale simulations, from a macroscopic description of the radiation field to microscopic description of biological outcome for selected cells. TOPAS-nBio offers detailed physics and chemistry simulations of radiobiological experiments on cells simulating the initially induced damage and links to models of DNA repair kinetics.
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Affiliation(s)
- J Schuemann
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - A L McNamara
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - J Ramos-Méndez
- b Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - J Perl
- c SLAC National Accelerator Laboratory, Menlo Park, California
| | - K D Held
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - H Paganetti
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - S Incerti
- d CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France.,e University of Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
| | - B Faddegon
- b Department of Radiation Oncology, University of California San Francisco, San Francisco, California
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Henthorn NT, Warmenhoven JW, Sotiropoulos M, Aitkenhead AH, Smith EAK, Ingram SP, Kirkby NF, Chadwick A, Burnet NG, Mackay RI, Kirkby KJ, Merchant MJ. Clinically relevant nanodosimetric simulation of DNA damage complexity from photons and protons. RSC Adv 2019; 9:6845-6858. [PMID: 35518487 PMCID: PMC9061037 DOI: 10.1039/c8ra10168j] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
Relative Biological Effectiveness (RBE), the ratio of doses between radiation modalities to produce the same biological endpoint, is a controversial and important topic in proton therapy. A number of phenomenological models incorporate variable RBE as a function of Linear Energy Transfer (LET), though a lack of mechanistic description limits their applicability. In this work we take a different approach, using a track structure model employing fundamental physics and chemistry to make predictions of proton and photon induced DNA damage, the first step in the mechanism of radiation-induced cell death. We apply this model to a proton therapy clinical case showing, for the first time, predictions of DNA damage on a patient treatment plan. Our model predictions are for an idealised cell and are applied to an ependymoma case, at this stage without any cell specific parameters. By comparing to similar predictions for photons, we present a voxel-wise RBE of DNA damage complexity. This RBE of damage complexity shows similar trends to the expected RBE for cell kill, implying that damage complexity is an important factor in DNA repair and therefore biological effect. Relative Biological Effectiveness (RBE) is a controversial and important topic in proton therapy. This work uses Monte Carlo simulations of DNA damage for protons and photons to probe this phenomenon, providing a plausible mechanistic understanding.![]()
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Affiliation(s)
- N. T. Henthorn
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - J. W. Warmenhoven
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - M. Sotiropoulos
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - A. H. Aitkenhead
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - E. A. K. Smith
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - S. P. Ingram
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - N. F. Kirkby
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - A. L. Chadwick
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - N. G. Burnet
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - R. I. Mackay
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - K. J. Kirkby
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - M. J. Merchant
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
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Chatzipapas KP, Papadimitroulas P, Obeidat M, McConnell KA, Kirby N, Loudos G, Papanikolaou N, Kagadis GC. Quantification of DNA double-strand breaks using Geant4-DNA. Med Phys 2019; 46:405-413. [PMID: 30418675 PMCID: PMC7379675 DOI: 10.1002/mp.13290] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/30/2018] [Accepted: 11/06/2018] [Indexed: 01/24/2023] Open
Abstract
PURPOSE This study aims to standardize the simulation procedure in measuring DNA double-strand breaks (DSBs), by using advanced Monte Carlo toolkits, and newly introduced experimental methods for DNA DSB measurement. METHODS For the experimental quantification of DNA DSB, an innovative DNA dosimeter was used to produce experimental data. GATE in combination with Geant4-DNA toolkit were exploited to simulate the experimental environment. The PDB4DNA example of Geant4-DNA was upgraded and investigated. Parameters of the simulation such energy threshold (ET) for a strand break and base pair threshold (BPT) for a DSB were evaluated, depending on the dose. RESULTS Simulations resulted to minimum differentiation in comparison to experimental data for ET = 19 ± 1 eV and BPT = 10 bp, and high differentiation for ET<17.5 eV or ET>22.5 eV and BPT = 10 bp. There was also small differentiation for ET = 17.5 eV and BPT = 6 bp. Uncertainty has been kept lower than 3%. CONCLUSIONS This study includes first results on the quantification of DNA double-strand breaks. The energy spectrum of a LINAC was simulated and used for the first time to irradiate DNA molecules. Simulation outcome was validated on experimental data that were produced by a prototype DNA dosimeter.
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Affiliation(s)
| | | | | | | | - Neil Kirby
- University of TexasHealth Science CenterSan AntonioTX78229USA
| | - George Loudos
- University of West AtticaDepartment of Biomedical EngineeringEgaleoGR12243Greece
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Durante M, Paganetti H, Pompos A, Kry SF, Wu X, Grosshans DR. Report of a National Cancer Institute special panel: Characterization of the physical parameters of particle beams for biological research. Med Phys 2018; 46:e37-e52. [PMID: 30506898 DOI: 10.1002/mp.13324] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 10/28/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022] Open
Abstract
PURPOSE To define the physical parameters needed to characterize a particle beam in order to allow intercomparison of different experiments performed using different ions at the same facility and using the same ion at different facilities. METHODS At the request of the National Cancer Institute (NCI), a special panel was convened to review the current status of the field and to provide suggested metrics for reporting the physical parameters of particle beams to be used for biological research. A set of physical parameters and measurements that should be performed by facilities and understood and reported by researchers supported by NCI to perform pre-clinical radiobiology and medical physics of heavy ions were generated. RESULTS Standard measures such as radiation delivery technique, beam modifiers used, nominal energy, field size, physical dose and dose rate should all be reported. However, more advanced physical measurements, including detailed characterization of beam quality by microdosimetric spectrum and fragmentation spectra, should also be established and reported. Details regarding how such data should be incorporated into Monte Carlo simulations and the proper reporting of simulation details are also discussed. CONCLUSIONS In order to allow for a clear relation of physical parameters to biological effects, facilities and researchers should establish and report detailed physical characteristics of the irradiation beams utilized including both standard and advanced measures. Biological researchers are encouraged to actively engage facility staff and physicists in the design and conduct of experiments. Modeling individual experimental setups will allow for the reporting of the uncertainties in the measurement or calculation of physical parameters which should be routinely reported.
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Affiliation(s)
- Marco Durante
- Biophysics Department, GSI Helmholtzzentrum für Schwerionenforschung and Technische Universität Darmstadt, Institute of Condensed Matter Physics, Planckstraße 1, 64291, Darmstadt, Germany
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, 02114, USA
| | - Arnold Pompos
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Stephen F Kry
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaodong Wu
- Department of Medical Physics, Shanghai Proton and Heavy Ion Center, Shanghai, China
| | - David R Grosshans
- Departments of Radiation and Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
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McMahon SJ. The linear quadratic model: usage, interpretation and challenges. ACTA ACUST UNITED AC 2018; 64:01TR01. [DOI: 10.1088/1361-6560/aaf26a] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Ramos-Méndez J, Burigo LN, Schulte R, Chuang C, Faddegon B. Fast calculation of nanodosimetric quantities in treatment planning of proton and ion therapy. ACTA ACUST UNITED AC 2018; 63:235015. [DOI: 10.1088/1361-6560/aaeeee] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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45
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Schuemann J, McNamara AL, Warmenhoven JW, Henthorn NT, Kirkby KJ, Merchant MJ, Ingram S, Paganetti H, Held KD, Ramos-Mendez J, Faddegon B, Perl J, Goodhead DT, Plante I, Rabus H, Nettelbeck H, Friedland W, Kundrát P, Ottolenghi A, Baiocco G, Barbieri S, Dingfelder M, Incerti S, Villagrasa C, Bueno M, Bernal MA, Guatelli S, Sakata D, Brown JMC, Francis Z, Kyriakou I, Lampe N, Ballarini F, Carante MP, Davídková M, Štěpán V, Jia X, Cucinotta FA, Schulte R, Stewart RD, Carlson DJ, Galer S, Kuncic Z, Lacombe S, Milligan J, Cho SH, Sawakuchi G, Inaniwa T, Sato T, Li W, Solov'yov AV, Surdutovich E, Durante M, Prise KM, McMahon SJ. A New Standard DNA Damage (SDD) Data Format. Radiat Res 2018; 191:76-92. [PMID: 30407901 DOI: 10.1667/rr15209.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Our understanding of radiation-induced cellular damage has greatly improved over the past few decades. Despite this progress, there are still many obstacles to fully understand how radiation interacts with biologically relevant cellular components, such as DNA, to cause observable end points such as cell killing. Damage in DNA is identified as a major route of cell killing. One hurdle when modeling biological effects is the difficulty in directly comparing results generated by members of different research groups. Multiple Monte Carlo codes have been developed to simulate damage induction at the DNA scale, while at the same time various groups have developed models that describe DNA repair processes with varying levels of detail. These repair models are intrinsically linked to the damage model employed in their development, making it difficult to disentangle systematic effects in either part of the modeling chain. These modeling chains typically consist of track-structure Monte Carlo simulations of the physical interactions creating direct damages to DNA, followed by simulations of the production and initial reactions of chemical species causing so-called "indirect" damages. After the induction of DNA damage, DNA repair models combine the simulated damage patterns with biological models to determine the biological consequences of the damage. To date, the effect of the environment, such as molecular oxygen (normoxic vs. hypoxic), has been poorly considered. We propose a new standard DNA damage (SDD) data format to unify the interface between the simulation of damage induction in DNA and the biological modeling of DNA repair processes, and introduce the effect of the environment (molecular oxygen or other compounds) as a flexible parameter. Such a standard greatly facilitates inter-model comparisons, providing an ideal environment to tease out model assumptions and identify persistent, underlying mechanisms. Through inter-model comparisons, this unified standard has the potential to greatly advance our understanding of the underlying mechanisms of radiation-induced DNA damage and the resulting observable biological effects when radiation parameters and/or environmental conditions change.
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Affiliation(s)
- J Schuemann
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - A L McNamara
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - J W Warmenhoven
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - N T Henthorn
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - K J Kirkby
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - M J Merchant
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - S Ingram
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - H Paganetti
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - K D Held
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - J Ramos-Mendez
- c Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - B Faddegon
- c Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - J Perl
- d SLAC National Accelerator Laboratory, Menlo Park, California
| | - D T Goodhead
- e Medical Research Council, Harwell, United Kingdom
| | | | - H Rabus
- g Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany.,h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany
| | - H Nettelbeck
- g Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany.,h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany
| | - W Friedland
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - P Kundrát
- i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - A Ottolenghi
- j Physics Department, University of Pavia, Pavia, Italy
| | - G Baiocco
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,j Physics Department, University of Pavia, Pavia, Italy
| | - S Barbieri
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,j Physics Department, University of Pavia, Pavia, Italy
| | - M Dingfelder
- k Department of Physics, East Carolina University, Greenville, North Carolina
| | - S Incerti
- l CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France.,m University of Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
| | - C Villagrasa
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,n Institut de Radioprotection et Sûreté Nucléaire, F-92262 Fontenay aux Roses Cedex, France
| | - M Bueno
- n Institut de Radioprotection et Sûreté Nucléaire, F-92262 Fontenay aux Roses Cedex, France
| | - M A Bernal
- o Applied Physics Department, Gleb Wataghin Institute of Physics, State University of Campinas, Campinas, SP, Brazil
| | - S Guatelli
- p Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW, Australia
| | - D Sakata
- p Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW, Australia
| | - J M C Brown
- q Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
| | - Z Francis
- r Department of Physics, Faculty of Science, Saint Joseph University, Beirut, Lebanon
| | - I Kyriakou
- s Medical Physics Laboratory, University of Ioannina Medical School, Ioannina, Greece
| | - N Lampe
- l CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - F Ballarini
- j Physics Department, University of Pavia, Pavia, Italy.,t Italian National Institute of Nuclear Physics, Section of Pavia, I-27100 Pavia, Italy
| | - M P Carante
- j Physics Department, University of Pavia, Pavia, Italy.,t Italian National Institute of Nuclear Physics, Section of Pavia, I-27100 Pavia, Italy
| | - M Davídková
- u Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Řež, Czech Republic
| | - V Štěpán
- u Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Řež, Czech Republic
| | - X Jia
- v Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - F A Cucinotta
- w Health Physics and Diagnostic Sciences, University of Nevada Las Vegas, Las Vegas, Nevada
| | - R Schulte
- x Division of Biomedical Engineering Sciences, School of Medicine, Loma Linda University, Loma Linda, California
| | - R D Stewart
- y Department of Radiation Oncology, University of Washington, Seattle, Washington
| | - D J Carlson
- z Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut
| | - S Galer
- aa Medical Radiation Science Group, National Physical Laboratory, Teddington, United Kingdom
| | - Z Kuncic
- bb School of Physics, University of Sydney, Sydney, NSW, Australia
| | - S Lacombe
- cc Institut des Sciences Moléculaires d'Orsay (UMR 8214) University Paris-Sud, CNRS, University Paris-Saclay, 91405 Orsay Cedex, France
| | | | - S H Cho
- ee Department of Radiation Physics and Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - G Sawakuchi
- ee Department of Radiation Physics and Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - T Inaniwa
- ff Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, Chiba, Japan
| | - T Sato
- gg Japan Atomic Energy Agency, Nuclear Science and Engineering Center, Tokai 319-1196, Japan
| | - W Li
- i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,hh Task Group 7.7 "Internal Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany
| | - A V Solov'yov
- ii MBN Research Center, 60438 Frankfurt am Main, Germany
| | - E Surdutovich
- jj Department of Physics, Oakland University, Rochester, Michigan
| | - M Durante
- kk GSI Helmholtzzentrum für Schwerionenforschung, Biophysics Department, Darmstadt, Germany
| | - K M Prise
- ll Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
| | - S J McMahon
- ll Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
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McNamara AL, Ramos-Méndez J, Perl J, Held K, Dominguez N, Moreno E, Henthorn NT, Kirkby KJ, Meylan S, Villagrasa C, Incerti S, Faddegon B, Paganetti H, Schuemann J. Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit. Phys Med Biol 2018; 63:175018. [PMID: 30088810 DOI: 10.1088/1361-6560/aad8eb] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Computational simulations, such as Monte Carlo track structure simulations, offer a powerful tool for quantitatively investigating radiation interactions within cells. The modelling of the spatial distribution of energy deposition events as well as diffusion of chemical free radical species, within realistic biological geometries, can help provide a comprehensive understanding of the effects of radiation on cells. Track structure simulations, however, generally require advanced computing skills to implement. The TOPAS-nBio toolkit, an extension to TOPAS (TOol for PArticle Simulation), aims to provide users with a comprehensive framework for radiobiology simulations, without the need for advanced computing skills. This includes providing users with an extensive library of advanced, realistic, biological geometries ranging from the micrometer scale (e.g. cells and organelles) down to the nanometer scale (e.g. DNA molecules and proteins). Here we present the geometries available in TOPAS-nBio.
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Affiliation(s)
- Aimee L McNamara
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, 30 Fruit St, Boston, MA 02114, United States of America
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47
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Sung W, Jeong Y, Kim H, Jeong H, Grassberger C, Jung S, Ahn GO, Kim IH, Schuemann J, Lee K, Ye SJ. Computational Modeling and Clonogenic Assay for Radioenhancement of Gold Nanoparticles Using 3D Live Cell Images. Radiat Res 2018; 190:558-564. [PMID: 30142031 DOI: 10.1667/rr15134.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Radioenhancement of gold nanoparticles (GNPs) has shown great potential for increasing the therapeutic efficiency of radiotherapy. Here we report on a computational model of radiation response, which was developed to predict the survival curves of breast cancer cells incubated with GNPs. The amount of GNP uptake was estimated using inductively coupled plasma-mass spectroscopy, and the three-dimensional (3D) intracellular distribution of GNPs was obtained using optical diffraction tomography. The developed computational model utilized the 3D live cell imaging and recent Monte Carlo techniques to calculate microscopic dose distributions within the cell. Clonogenic assays with and without GNPs were performed to estimate the radioenhancement for 150 kVp X rays in terms of cell survival fractions. Measured cell survival fractions were comparable with the computational model.
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Affiliation(s)
- Wonmo Sung
- Programs in a Biomedical Radiation Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Yoon Jeong
- b Nano Science and Technology, Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyejin Kim
- Programs in a Biomedical Radiation Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Hoibin Jeong
- d Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Clemens Grassberger
- e Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Seongmoon Jung
- Programs in a Biomedical Radiation Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - G-One Ahn
- d Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Il Han Kim
- Programs in a Biomedical Radiation Sciences, Seoul National University College of Medicine, Seoul, Korea.,c Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Korea
| | - Jan Schuemann
- e Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kangwon Lee
- b Nano Science and Technology, Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Joon Ye
- Programs in a Biomedical Radiation Sciences, Seoul National University College of Medicine, Seoul, Korea.,c Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Korea.,f Robotics Research Laboratory for Extreme Environment, Advanced Institutes of Convergence Technology, Seoul National University, Suwon, Korea
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48
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Sung W, Schuemann J. Energy optimization in gold nanoparticle enhanced radiation therapy. Phys Med Biol 2018; 63:135001. [PMID: 29873303 DOI: 10.1088/1361-6560/aacab6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Gold nanoparticles (GNPs) have been demonstrated as radiation dose enhancing agents. Kilovoltage external photon beams have been shown to yield the largest enhancement due to the high interaction probability with gold. While orthovoltage irradiations are feasible and promising, they suffer from a reduced tissue penetrating power. This study quantifies the effect of varying photon beam energies on various beam arrangements, body, tumor, and cellular GNP uptake geometries. Cell survival was modeled based on our previously developed GNP-local effect model with radial doses calculated using the TOPAS-nBio Monte Carlo code. Cell survival curves calculated for tumor sites with GNPs were used to calculate the relative biological effectiveness (RBE)-weighted dose. In order to evaluate the plan quality, the ratio of the mean dose between the tumor and normal tissue for 50-250 kVp beams with GNPs was compared to the standard of care using 6 MV photon beams without GNPs for breast and brain tumors. For breast using a single photon beam, kV + GNP was found to yield up to 2.73 times higher mean RBE-weighted dose to the tumor than two tangential megavoltage beams while delivering the same dose to healthy tissue. For irradiation of brain tumors using multiple photon beams, the GNP dose enhancement was found to be effective for energies above 50 keV. A small tumor at shallow depths was found to be the most effective treatment conditions for GNP enhanced radiation therapy. GNP uptake distributions in the cell (with or without nuclear uptake) and the beam arrangement were found to be important factors in determining the optimal photon beam energy.
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Affiliation(s)
- Wonmo Sung
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
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49
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Toward A variable RBE for proton beam therapy. Radiother Oncol 2018; 128:68-75. [PMID: 29910006 DOI: 10.1016/j.radonc.2018.05.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/09/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022]
Abstract
In the clinic, proton beam therapy (PBT) is based on the use of a generic relative biological effectiveness (RBE) of 1.1 compared to photons in human cancers and normal tissues. However, the experimental basis for this RBE lacks any significant number of representative tumor models and clinically relevant endpoints for dose-limiting organs at risk. It is now increasingly appreciated that much of the variations of treatment responses in cancers are due to inter-tumoral genomic heterogeneity. Indeed, recently it has been shown that defects in certain DNA repair pathways, which are found in subsets of many cancers, are associated with a RBE increase in vitro. However, there currently exist little in vivo or clinical data that confirm the existence of similarly increased RBE values in human cancers. Furthermore, evidence for variable RBE values for normal tissue toxicity has been sparse and conflicting to date. If we could predict variable RBE values in patients, we would be able to optimally use and personalize PBT. For example, predictive tumor biomarkers may facilitate selection of patients with proton-sensitive cancers previously ineligible for PBT. Dose de-escalation may be possible to reduce normal tissue toxicity, especially in pediatric patients. Knowledge of increased tumor RBE may allow us to develop biologically optimized therapies to enhance local control while RBE biomarkers for normal tissues could lead to a better understanding and prevention of unusual PBT-associated toxicity. Here, we will review experimental data on the repair of proton damage to DNA that impact both RBE values and biophysical modeling to predict RBE variations. Experimental approaches for studying proton sensitivity in vitro and in vivo will be reviewed as well and recent clinical findings discussed. Ultimately, therapeutically exploiting the understudied biological advantages of protons and developing approaches to limit treatment toxicity should fundamentally impact the clinical use of PBT.
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50
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Incerti S, Kyriakou I, Bernal MA, Bordage MC, Francis Z, Guatelli S, Ivanchenko V, Karamitros M, Lampe N, Lee SB, Meylan S, Min CH, Shin WG, Nieminen P, Sakata D, Tang N, Villagrasa C, Tran HN, Brown JMC. Geant4-DNA example applications for track structure simulations in liquid water: A report from the Geant4-DNA Project. Med Phys 2018; 45. [PMID: 29901835 DOI: 10.1002/mp.13048] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/03/2018] [Accepted: 06/04/2018] [Indexed: 01/11/2023] Open
Abstract
This Special Report presents a description of Geant4-DNA user applications dedicated to the simulation of track structures (TS) in liquid water and associated physical quantities (e.g., range, stopping power, mean free path…). These example applications are included in the Geant4 Monte Carlo toolkit and are available in open access. Each application is described and comparisons to recent international recommendations are shown (e.g., ICRU, MIRD), when available. The influence of physics models available in Geant4-DNA for the simulation of electron interactions in liquid water is discussed. Thanks to these applications, the authors show that the most recent sets of physics models available in Geant4-DNA (the so-called "option4" and "option 6" sets) enable more accurate simulation of stopping powers, dose point kernels, and W-values in liquid water, than the default set of models ("option 2") initially provided in Geant4-DNA. They also serve as reference applications for Geant4-DNA users interested in TS simulations.
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Affiliation(s)
- S Incerti
- University of Bordeaux, CENBG, UMR 5797, F-33170, Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170, Gradignan, France
| | - I Kyriakou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110, Ioannina, Greece
| | - M A Bernal
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - M C Bordage
- Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Toulouse, France
- Inserm, UMR1037 CRCT, Toulouse, France
| | - Z Francis
- Department of Physics, Faculty of Sciences, Université Saint Joseph, Beirut, Lebanon
| | - S Guatelli
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong, Australia
- Illawarra Health & Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - V Ivanchenko
- Geant4 Associates International Ltd., Hebden Bridge, UK
- Tomsk State University, Tomsk, Russia
| | - M Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - N Lampe
- Vicinity Centres, Data Science & Insights, Office Tower One, 1341 Dandenong Rd, Chadstone, Victoria, 3148, Australia
| | - S B Lee
- Proton Therapy Center, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Korea
| | - S Meylan
- SymAlgo Technologies, 75 rue Léon Frot, 75011, Paris, France
| | - C H Min
- Department of Radiation Convergence Engineering, Yonsei University, Wonju, Korea
| | - W G Shin
- Department of Radiation Convergence Engineering, Yonsei University, Wonju, Korea
| | | | - D Sakata
- University of Bordeaux, CENBG, UMR 5797, F-33170, Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170, Gradignan, France
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - N Tang
- IRSN, Institut de Radioprotection et de Sureté Nucléaire, 92262, Fontenay-aux-Roses, France
| | - C Villagrasa
- IRSN, Institut de Radioprotection et de Sureté Nucléaire, 92262, Fontenay-aux-Roses, France
| | - H N Tran
- Division of Nuclear Physics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - J M C Brown
- Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
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