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Yang J, Liu X, Zhang H, Dai Z, He P, Ma Y, Shen G, Chen W, Li Q. Nanodosimetric quantity-weighted dose optimization for carbon-ion treatment planning. Phys Eng Sci Med 2024; 47:703-715. [PMID: 38416372 DOI: 10.1007/s13246-024-01399-9] [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: 09/20/2023] [Accepted: 02/04/2024] [Indexed: 02/29/2024]
Abstract
Dose verification of treatment plans is an essential step in radiotherapy workflows. In this work, we propose a novel method of treatment planning based on nanodosimetric quantity-weighted dose (NQWD), which could realize biological representation using pure physical quantities for biological-oriented carbon ion-beam treatment plans and their direct verification. The relationship between nanodosimetric quantities and relative biological effectiveness (RBE) was studied with the linear least-squares method for carbon-ion radiation fields. Next, under the framework of the matRad treatment planning platform, NQWD was optimized using the existing RBE-weighted dose (RWD) optimization algorithm. The schemes of NQWD-based treatment planning were compared with the RWD treatment plans in term of the microdosimetric kinetic model (MKM). The results showed that the nanodosimetric quantity F3 - 10 had a good correlation with the radiobiological effect reflected by the relationship between RBE and F3 - 10. Moreover, the NQWD-based treatment plans reproduced the RWD plans generally. Therefore, F3 - 10 could be adopted as a radiation quality descriptor for carbon-ion treatment planning. The novel method proposed herein not only might be helpful for rapid physical verification of biological-oriented ion-beam treatment plans with the development of experimental nanodosimetry, but also makes the direct comparison of ion-beam treatment plans in different institutions possible. Thus, our proposed method might be potentially developed to be a new strategy for carbon-ion treatment planning and improve patient safety for carbon-ion radiotherapy.
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Affiliation(s)
- Jingfen Yang
- Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, 730000, Lanzhou, China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, 730000, Lanzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xinguo Liu
- Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, 730000, Lanzhou, China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, 730000, Lanzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Hui Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, 730000, Lanzhou, China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, 730000, Lanzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhongying Dai
- Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, 730000, Lanzhou, China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, 730000, Lanzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Pengbo He
- Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, 730000, Lanzhou, China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, 730000, Lanzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanyuan Ma
- Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, 730000, Lanzhou, China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, 730000, Lanzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Guosheng Shen
- Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, 730000, Lanzhou, China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, 730000, Lanzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Weiqiang Chen
- Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, 730000, Lanzhou, China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, 730000, Lanzhou, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Qiang Li
- Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China.
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Science, 730000, Lanzhou, China.
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, 730000, Lanzhou, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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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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Faddegon B, Blakely EA, Burigo L, Censor Y, Dokic I, Kondo ND, Ortiz R, Méndez JR, Rucinski A, Schubert K, Wahl N, Schulte R. Ionization detail parameters and cluster dose: a mathematical model for selection of nanodosimetric quantities for use in treatment planning in charged particle radiotherapy. Phys Med Biol 2023; 68:10.1088/1361-6560/acea16. [PMID: 37489619 PMCID: PMC10565507 DOI: 10.1088/1361-6560/acea16] [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: 04/19/2022] [Accepted: 07/24/2023] [Indexed: 07/26/2023]
Abstract
Objective. To propose a mathematical model for applying ionization detail (ID), the detailed spatial distribution of ionization along a particle track, to proton and ion beam radiotherapy treatment planning (RTP).Approach. Our model provides for selection of preferred ID parameters (Ip) for RTP, that associate closest to biological effects. Cluster dose is proposed to bridge the large gap between nanoscopicIpand macroscopic RTP. Selection ofIpis demonstrated using published cell survival measurements for protons through argon, comparing results for nineteenIp:Nk,k= 2, 3, …, 10, the number of ionizations in clusters ofkor more per particle, andFk,k= 1, 2, …, 10, the number of clusters ofkor more per particle. We then describe application of the model to ID-based RTP and propose a path to clinical translation.Main results. The preferredIpwereN4andF5for aerobic cells,N5andF7for hypoxic cells. Significant differences were found in cell survival for beams having the same LET or the preferredNk. Conversely, there was no significant difference forF5for aerobic cells andF7for hypoxic cells, regardless of ion beam atomic number or energy. Further, cells irradiated with the same cluster dose for theseIphad the same cell survival. Based on these preliminary results and other compelling results in nanodosimetry, it is reasonable to assert thatIpexist that are more closely associated with biological effects than current LET-based approaches and microdosimetric RBE-based models used in particle RTP. However, more biological variables such as cell line and cycle phase, as well as ion beam pulse structure and rate still need investigation.Significance. Our model provides a practical means to select preferredIpfrom radiobiological data, and to convertIpto the macroscopic cluster dose for particle RTP.
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Affiliation(s)
- Bruce Faddegon
- University of California San Francisco, Department of Radiation Oncology 1600 Divisadero Street, San Francisco, CA 94143 United States of America
| | - Eleanor A. Blakely
- Loma Linda University School of Medicine, 11175 Campus St, Loma Linda,CA92350, United States of America
| | - Lucas Burigo
- Division of Medical Physics in Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Radiation Research in Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany
| | - Yair Censor
- Department of Mathematics, University of Haifa, 199 Aba Khoushy Ave. Mount Carmel, Haifa, 3498838, Israel
| | - Ivana Dokic
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Consortium (DKTK) Core-Center Heidelberg, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University Hospital and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Naoki Domínguez Kondo
- University of California San Francisco, Department of Radiation Oncology 1600 Divisadero Street, San Francisco, CA 94143 United States of America
| | - Ramon Ortiz
- University of California San Francisco, Department of Radiation Oncology 1600 Divisadero Street, San Francisco, CA 94143 United States of America
| | - José Ramos Méndez
- University of California San Francisco, Department of Radiation Oncology 1600 Divisadero Street, San Francisco, CA 94143 United States of America
| | - Antoni Rucinski
- Institute of Nuclear Physics Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland
| | - Keith Schubert
- Baylor University, 1311 S 5th St, Waco, TX 76706, United States of America
| | - Niklas Wahl
- Division of Medical Physics in Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Radiation Research in Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany
| | - Reinhard Schulte
- Loma Linda University School of Medicine, 11085 Campus St, Loma Linda, CA92350, United States of America
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Ngcezu SA, Rabus H. Investigation into the foundations of the track-event theory of cell survival and the radiation action model based on nanodosimetry. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2021; 60:559-578. [PMID: 34427743 PMCID: PMC8551112 DOI: 10.1007/s00411-021-00936-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 08/14/2021] [Indexed: 06/13/2023]
Abstract
This work aims at elaborating the basic assumptions behind the "track-event theory" (TET) and its derivate "radiation action model based on nanodosimetry" (RAMN) by clearly distinguishing between effects of tracks at the cellular level and the induction of lesions in subcellular targets. It is demonstrated that the model assumptions of Poisson distribution and statistical independence of the frequency of single and clustered DNA lesions are dispensable for multi-event distributions because they follow from the Poisson distribution of the number of tracks affecting the considered target volume. It is also shown that making these assumptions for the single-event distributions of the number of lethal and sublethal lesions within a cell would lead to an essentially exponential dose dependence of survival for practically relevant values of the absorbed dose. Furthermore, it is elucidated that the model equation used for consideration of repair within the TET is based on the assumption that DNA lesions induced by different tracks are repaired independently. Consequently, the model equation is presumably inconsistent with the model assumptions and requires an additional model parameter. Furthermore, the methodology for deriving model parameters from nanodosimetric properties of particle track structure is critically assessed. Based on data from proton track simulations it is shown that the assumption of statistically independent targets leads to the prediction of negligible frequency of clustered DNA damage. An approach is outlined how track structure could be considered in determining the model parameters, and the implications for TET and RAMN are discussed.
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Affiliation(s)
| | - Hans Rabus
- Physikalisch-Technische Bundesanstalt (PTB), 10587, Berlin, Germany.
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Selva A, Colautti P, Conte V. Nanodosimetry of light ions in targets of different size. Radiat Phys Chem Oxf Engl 1993 2020. [DOI: 10.1016/j.radphyschem.2020.108806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Tang N, Bueno M, Meylan S, Incerti S, Clairand I, Villagrasa C. SIMULATION OF EARLY RADIATION-INDUCED DNA DAMAGE ON DIFFERENT TYPES OF CELL NUCLEI. RADIATION PROTECTION DOSIMETRY 2019; 183:26-31. [PMID: 30535369 DOI: 10.1093/rpd/ncy237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This work presents a comparison of simulated early radiation-induced DNA damage represented by yields of double-strand breaks (DSB) in three different human cell nuclei geometries representing fibroblasts, lymphocytes and endothelial cells for protons and alpha particles of different energies and for different irradiation configurations. Each cell nucleus model includes a multi-scale description of the DNA target from the molecular level to the whole human genome representation (6 Gbp) in the G0/G1 phase of the cell cycle and was generated with the DnaFabric software. The three nuclei differ in shape, volume, and therefore DNA density. A calculation chain based on Geant4-DNA that takes into account the physical, physico-chemical and chemical stages was used to simulate the irradiation of the different cell nuclei. Results show an increase of DSB/primary/μm with an increase of DNA density and an increase of DSB/Gy/Gbp with an increase of the cell nucleus volume which indicates that the cell nucleus shape and size have an impact on early DNA damage, which may play a role in latter effects.
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Affiliation(s)
- Nicolas Tang
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay aux Roses, France
| | - Marta Bueno
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay aux Roses, France
| | | | - Sébastien Incerti
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux Gradignan, CENBG, chemin du solarium, Gradignan, France
| | - Isabelle Clairand
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay aux Roses, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay aux Roses, France
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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: 104] [Impact Index Per Article: 20.8] [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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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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10
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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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11
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Rühm W, Bottollier-Depois JF, Gilvin P, Harrison R, Knežević Ž, Lopez MA, Tanner R, Vargas A, Woda C. The work programme of EURADOS on internal and external dosimetry. Ann ICRP 2018; 47:20-34. [PMID: 29664324 DOI: 10.1177/0146645318756224] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Since the early 1980s, the European Radiation Dosimetry Group (EURADOS) has been maintaining a network of institutions interested in the dosimetry of ionising radiation. As of 2017, this network includes more than 70 institutions (research centres, dosimetry services, university institutes, etc.), and the EURADOS database lists more than 500 scientists who contribute to the EURADOS mission, which is to promote research and technical development in dosimetry and its implementation into practice, and to contribute to harmonisation of dosimetry in Europe and its conformance with international practices. The EURADOS working programme is organised into eight working groups dealing with environmental, computational, internal, and retrospective dosimetry; dosimetry in medical imaging; dosimetry in radiotherapy; dosimetry in high-energy radiation fields; and harmonisation of individual monitoring. Results are published as freely available EURADOS reports and in the peer-reviewed scientific literature. Moreover, EURADOS organises winter schools and training courses on various aspects relevant for radiation dosimetry, and formulates the strategic research needs in dosimetry important for Europe. This paper gives an overview on the most important EURADOS activities. More details can be found at www.eurados.org .
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Affiliation(s)
- W Rühm
- a Department of Radiation Sciences, Institute for Radiation Protection, Helmholtz Centre Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | | | | | | | | | - M A Lopez
- f Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Spain
| | | | - A Vargas
- g Universitat Politècnica de Catalunya, Spain
| | - C Woda
- a Department of Radiation Sciences, Institute for Radiation Protection, Helmholtz Centre Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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12
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In Silico Non-Homologous End Joining Following Ion Induced DNA Double Strand Breaks Predicts That Repair Fidelity Depends on Break Density. Sci Rep 2018; 8:2654. [PMID: 29422642 PMCID: PMC5805743 DOI: 10.1038/s41598-018-21111-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/25/2018] [Indexed: 12/19/2022] Open
Abstract
This work uses Monte Carlo simulations to investigate the dependence of residual and misrepaired double strand breaks (DSBs) at 24 hours on the initial damage pattern created during ion therapy. We present results from a nanometric DNA damage simulation coupled to a mechanistic model of Non-Homologous End Joining, capable of predicting the position, complexity, and repair of DSBs. The initial damage pattern is scored by calculating the average number of DSBs within 70 nm from every DSB. We show that this local DSB density, referred to as the cluster density, can linearly predict misrepair regardless of ion species. The models predict that the fraction of residual DSBs is constant, with 7.3% of DSBs left unrepaired following 24 hours of repair. Through simulation over a range of doses and linear energy transfer (LET) we derive simple correlations capable of predicting residual and misrepaired DSBs. These equations are applicable to ion therapy treatment planning where both dose and LET are scored. This is demonstrated by applying the correlations to an example of a clinical proton spread out Bragg peak. Here we see a considerable biological effect past the distal edge, dominated by residual DSBs.
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13
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Henthorn NT, Warmenhoven JW, Sotiropoulos M, Mackay RI, Kirkby KJ, Merchant MJ. Nanodosimetric Simulation of Direct Ion-Induced DNA Damage Using Different Chromatin Geometry Models. Radiat Res 2017; 188:690-703. [PMID: 28792846 DOI: 10.1667/rr14755.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Monte Carlo based simulation has proven useful in investigating the effect of proton-induced DNA damage and the processes through which this damage occurs. Clustering of ionizations within a small volume can be related to DNA damage through the principles of nanodosimetry. For simulation, it is standard to construct a small volume of water and determine spatial clusters. More recently, realistic DNA geometries have been used, tracking energy depositions within DNA backbone volumes. Traditionally a chromatin fiber is built within the simulation and identically replicated throughout a cell nucleus, representing the cell in interphase. However, the in vivo geometry of the chromatin fiber is still unknown within the literature, with many proposed models. In this work, the Geant4-DNA toolkit was used to build three chromatin models: the solenoid, zig-zag and cross-linked geometries. All fibers were built to the same chromatin density of 4.2 nucleosomes/11 nm. The fibers were then irradiated with protons (LET 5-80 keV/μm) or alpha particles (LET 63-226 keV/μm). Nanodosimetric parameters were scored for each fiber after each LET and used as a comparator among the models. Statistically significant differences were observed in the double-strand break backbone size distributions among the models, although nonsignificant differences were noted among the nanodosimetric parameters. From the data presented in this article, we conclude that selection of the solenoid, zig-zag or cross-linked chromatin model does not significantly affect the calculated nanodosimetric parameters. This allows for a simulation-based cell model to make use of any of these chromatin models for the scoring of direct ion-induced DNA damage.
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Affiliation(s)
- N T Henthorn
- a Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - J W Warmenhoven
- a Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - M Sotiropoulos
- a Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - R I Mackay
- b Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom; and
| | - K J Kirkby
- a Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom.,c The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - M J Merchant
- a Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom.,c The Christie NHS Foundation Trust, Manchester, United Kingdom
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14
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Review of Geant4-DNA applications for micro and nanoscale simulations. Phys Med 2016; 32:1187-1200. [PMID: 27659007 DOI: 10.1016/j.ejmp.2016.09.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/01/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022] Open
Abstract
Emerging radiotherapy treatments including targeted particle therapy, hadron therapy or radiosensitisation of cells by high-Z nanoparticles demand the theoretical determination of radiation track structure at the nanoscale. This is essential in order to evaluate radiation damage at the cellular and DNA level. Since 2007, Geant4 offers physics models to describe particle interactions in liquid water at the nanometre level through the Geant4-DNA Package. This package currently provides a complete set of models describing the event-by-event electromagnetic interactions of particles with liquid water, as well as developments for the modelling of water radiolysis. Since its release, Geant4-DNA has been adopted as an investigational tool in kV and MV external beam radiotherapy, hadron therapies using protons and heavy ions, targeted therapies and radiobiology studies. It has been benchmarked with respect to other track structure Monte Carlo codes and, where available, against reference experimental measurements. While Geant4-DNA physics models and radiolysis modelling functionalities have already been described in detail in the literature, this review paper summarises and discusses a selection of representative papers with the aim of providing an overview of a) geometrical descriptions of biological targets down to the DNA size, and b) the full spectrum of current micro- and nano-scale applications of Geant4-DNA.
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