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Beaudier P, Zein SA, Chatzipapas K, Ngoc Tran H, Devès G, Plawinski L, Liénard R, Dupuy D, Barberet P, Incerti S, Gobet F, Seznec H. Quantitative analysis of dose dependent DNA fragmentation in dry pBR322 plasmid using long read sequencing and Monte Carlo simulations. Sci Rep 2024; 14:18650. [PMID: 39134627 PMCID: PMC11319478 DOI: 10.1038/s41598-024-69406-3] [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: 04/08/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
Exposure to ionizing radiation can induce genetic aberrations via unrepaired DNA strand breaks. To investigate quantitatively the dose-effect relationship at the molecular level, we irradiated dry pBR322 plasmid DNA with 3 MeV protons and assessed fragmentation yields at different radiation doses using long-read sequencing from Oxford Nanopore Technologies. This technology applied to a reference DNA model revealed dose-dependent fragmentation, as evidenced by read length distributions, showing no discernible radiation sensitivity in specific genetic sequences. In addition, we propose a method for directly measuring the single-strand break (SSB) yield. Furthermore, through a comparative study with a collection of previous works on dry DNA irradiation, we show that the irradiation protocol leads to biases in the definition of ionizing sources. We support this scenario by discussing the size distributions of nanopore sequencing reads in the light of Geant4 and Geant4-DNA simulation toolkit predictions. We show that integrating long-read sequencing technologies with advanced Monte Carlo simulations paves a promising path toward advancing our comprehension and prediction of radiation-induced DNA fragmentation.
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Affiliation(s)
- Pierre Beaudier
- CNRS, LP2iB, UMR 5797, Univ. Bordeaux, 33170, Gradignan, France
- CNRS, INSERM, ARNA, UMR5320, U1212, Univ. Bordeaux, 33000, Bordeaux, France
| | - Sara A Zein
- CNRS, LP2iB, UMR 5797, Univ. Bordeaux, 33170, Gradignan, France
| | | | - Hoang Ngoc Tran
- CNRS, LP2iB, UMR 5797, Univ. Bordeaux, 33170, Gradignan, France
| | - Guillaume Devès
- CNRS, LP2iB, UMR 5797, Univ. Bordeaux, 33170, Gradignan, France
| | | | - Rémy Liénard
- CNRS, LP2iB, UMR 5797, Univ. Bordeaux, 33170, Gradignan, France
| | - Denis Dupuy
- CNRS, INSERM, ARNA, UMR5320, U1212, Univ. Bordeaux, 33000, Bordeaux, France
| | | | | | - Franck Gobet
- CNRS, LP2iB, UMR 5797, Univ. Bordeaux, 33170, Gradignan, France
| | - Hervé Seznec
- CNRS, LP2iB, UMR 5797, Univ. Bordeaux, 33170, Gradignan, France.
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Tran HN, Archer J, Baldacchino G, Brown JMC, Chappuis F, Cirrone GAP, Desorgher L, Dominguez N, Fattori S, Guatelli S, Ivantchenko V, Méndez JR, Nieminen P, Perrot Y, Sakata D, Santin G, Shin WG, Villagrasa C, Zein S, Incerti S. Review of chemical models and applications in Geant4-DNA: Report from the ESA BioRad III Project. Med Phys 2024. [PMID: 38889367 DOI: 10.1002/mp.17256] [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: 01/19/2024] [Revised: 05/17/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024] Open
Abstract
A chemistry module has been implemented in Geant4-DNA since Geant4 version 10.1 to simulate the radiolysis of water after irradiation. It has been used in a number of applications, including the calculation of G-values and early DNA damage, allowing the comparison with experimental data. Since the first version, numerous modifications have been made to the module to improve the computational efficiency and extend the simulation to homogeneous kinetics in bulk solution. With these new developments, new applications have been proposed and released as Geant4 examples, showing how to use chemical processes and models. This work reviews the models implemented and application developments for modeling water radiolysis in Geant4-DNA as reported in the ESA BioRad III Project.
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Affiliation(s)
| | - Jay Archer
- Centre For Medical and Radiation Physics, University of Wollongong, Wollongong, New South Wales, Australia
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, LIDYL, Gif-sur-Yvette, France
- CY Cergy Paris Université, CEA, LIDYL, Gif-sur-Yvette, France
| | - Jeremy M C Brown
- Optical Sciences Centre, Department of Physics and Astronomy, School of Science, Swinburne University of Technology, Melbourne, Australia
| | - Flore Chappuis
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Antonio Pablo Cirrone
- Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali del Sud (LNS), Catania, Italy
- Centro Siciliano di Fisica Nucleare e Struttura della Materia, Catania, Italy
| | - Laurent Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Naoki Dominguez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - Serena Fattori
- Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali del Sud (LNS), Catania, Italy
| | - Susanna Guatelli
- Centre For Medical and Radiation Physics, University of Wollongong, Wollongong, New South Wales, Australia
| | | | - José-Ramos Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | | | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Fontenay-aux-Roses, France
| | - Dousatsu Sakata
- Centre For Medical and Radiation Physics, University of Wollongong, Wollongong, New South Wales, Australia
- Division of Health Sciences, Osaka University, Osaka, Japan
- School of Physics, University of Bristol, Bristol, UK
| | | | - Wook-Geun Shin
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts, USA
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Fontenay-aux-Roses, France
| | - Sara Zein
- Univ. Bordeaux, CNRS, LP2I, UMR 5797, Gradignan, France
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3
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Ballisat L, De Sio C, Beck L, Guatelli S, Sakata D, Shi Y, Duan J, Velthuis J, Rosenfeld A. Dose and DNA damage modelling of diffusing alpha-emitters radiation therapy using Geant4. Phys Med 2024; 121:103367. [PMID: 38701625 DOI: 10.1016/j.ejmp.2024.103367] [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: 11/08/2023] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 05/05/2024] Open
Abstract
PURPOSE Diffusing alpha-emitters radiation therapy (DaRT) is a brachytherapy technique using α-particles to treat solid tumours. The high linear energy transfer (LET) and short range of α-particles make them good candidates for the targeted treatment of cancer. Treatment planning of DaRT requires a good understanding of the dose from α-particles and the other particles released in the 224Ra decay chain. METHODS The Geant4 Monte Carlo toolkit has been used to simulate a DaRT seed to better understand the dose contribution from all particles and simulate the DNA damage due to this treatment. RESULTS Close to the seed α-particles deliver the majority of dose, however at radial distances greater than 4 mm, the contribution of β-particles is greater. The RBE has been estimated as a function of number of double strand breaks (DSBs) and complex DSBs. A maximum seed spacing of 5.5 mm and 6.5 mm was found to deliver at least 20 Gy RBE weighted dose between the seeds for RBEDSB and RBEcDSB respectively. CONCLUSIONS The DNA damage changes with radial distance from the seed and has been found to become less complex with distance, which is potentially easier for the cell to repair. Close to the seed α-particles contribute the majority of dose, however the contribution from other particles cannot be neglected and may influence the choice of seed spacing.
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Affiliation(s)
| | - Chiara De Sio
- School of Physics, University of Bristol, Bristol, UK
| | - Lana Beck
- School of Physics, University of Bristol, Bristol, UK
| | - Susanna Guatelli
- Centre for Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia
| | - Dousatsu Sakata
- Division of Health Sciences, Osaka University, Osaka 565-0871, Japan
| | - Yuyao Shi
- School of Physics, University of Bristol, Bristol, UK
| | - Jinyan Duan
- School of Physics, University of Bristol, Bristol, UK
| | - Jaap Velthuis
- School of Physics, University of Bristol, Bristol, UK
| | - Anatoly Rosenfeld
- Centre for Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia
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Rafiepour P, Sina S, Amoli ZA, Shekarforoush SS, Farajzadeh E, Mortazavi SMJ. A mechanistic simulation of induced DNA damage in a bacterial cell by X- and gamma rays: a parameter study. Phys Eng Sci Med 2024:10.1007/s13246-024-01424-x. [PMID: 38652348 DOI: 10.1007/s13246-024-01424-x] [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: 08/27/2023] [Accepted: 04/07/2024] [Indexed: 04/25/2024]
Abstract
Mechanistic Monte Carlo simulations calculating DNA damage caused by ionizing radiation are highly dependent on the simulation parameters. In the present study, using the Geant4-DNA toolkit, the impact of different parameters on DNA damage induced in a bacterial cell by X- and gamma-ray irradiation was investigated. Three geometry configurations, including the simple (without DNA details), the random (a random multiplication of identical DNA segments), and the fractal (a regular replication of DNA segments using fractal Hilbert curves), were simulated. Also, three physics constructors implemented in Geant4-DNA, i.e., G4EmDNAPhysics_option2, G4EmDNAPhysics_option4, and G4EmDNAPhysics_option6, with two energy thresholds of 17.5 eV and 5-37.5 eV were compared for direct DNA damage calculations. Finally, a previously developed mathematical model of cell repair called MEDRAS (Mechanistic DNA Repair and Survival) was employed to compare the impact of physics constructors on the cell survival curve. The simple geometry leads to undesirable results compared to the random and fractal ones, highlighting the importance of simulating complex DNA structures in mechanistic simulation studies. Under the same conditions, the DNA damage calculated in the fractal geometry was more consistent with the experimental data. All physics constructors can be used alternatively with the fractal geometry, provided that an energy threshold of 17.5 eV is considered for recording direct DNA damage. All physics constructors represent a similar behavior in generating cell survival curves, although the slopes of the curves are different. Since the inverse of the slope of a bacterial cell survival curve (i.e., the D10-value) is highly sensitive to the simulation parameters, it is not logical to determine an optimal set of parameters for calculating the D10-value by Monte Carlo simulation.
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Affiliation(s)
- Payman Rafiepour
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - Sedigheh Sina
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
- Radiation research center, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
| | - Zahra Alizadeh Amoli
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Seyed Shahram Shekarforoush
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Ebrahim Farajzadeh
- Secondary Standard Dosimetry Laboratory (SSDL), Pars Isotope Co, Karaj, Iran
| | - Seyed Mohammad Javad Mortazavi
- Ionizing and Non-ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
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5
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Mortazavi SMJ, Rafiepour P, Mortazavi SAR, Razavi Toosi SMT, Shomal PR, Sihver L. Radium deposition in human brain tissue: A Geant4-DNA Monte Carlo toolkit study. Z Med Phys 2024; 34:166-174. [PMID: 38420703 PMCID: PMC10919964 DOI: 10.1016/j.zemedi.2023.09.004] [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: 05/21/2023] [Revised: 09/09/2023] [Accepted: 09/28/2023] [Indexed: 03/02/2024]
Abstract
NASA has encouraged studies on 226Ra deposition in the human brain to investigate the effects of exposure to alpha particles with high linear energy transfer, which could mimic some of the exposure astronauts face during space travel. However, this approach was criticized, noting that radium is a bone-seeker and accumulates in the skull, which means that the radiation dose from alpha particles emitted by 226Ra would be heavily concentrated in areas close to cranial bones rather than uniformly distributed throughout the brain. In the high background radiation areas of Ramsar, Iran, extremely high levels of 226Ra in soil contribute to a large proportion of the inhabitants' radiation exposure. A prospective study on Ramsar residents with a calcium-rich diet was conducted to improve the dose uniformity due to 226Ra throughout the cerebral and cerebellar parenchyma. The study found that exposure of the human brain to alpha particles did not significantly affect working memory but was significantly associated with increased reaction times. This finding is crucial because astronauts on deep space missions may face similar cognitive impairments due to exposure to high charge and energy particles. The current study was aimed to evaluate the validity of the terrestrial model using the Geant4 Monte Carlo toolkit to simulate the interactions of alpha particles and representative cosmic ray particles, acknowledging that these radiation types are only a subset of the complete space radiation environment.
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Affiliation(s)
- S M J Mortazavi
- Ionizing and Non-Ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
| | - Payman Rafiepour
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - S A R Mortazavi
- MVLS College, The University of Glasgow, Glasgow Scotland, UK
| | - S M T Razavi Toosi
- Physiology Department, School of Medicine, Guilan University of Medical Sciences, Guilan, Iran
| | - Parya Roshan Shomal
- Physiology Department, School of Medicine, Guilan University of Medical Sciences, Guilan, Iran
| | - Lembit Sihver
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czechia; Technische Universität Wien, Atominstitut, Vienna, Austria.
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Feng H, Li W, Zhang Y, Chang C, Hua L, Feng Y, Lai Y, Geng L. Mechanistic modelling of relative biological effectiveness of carbon ion beams and comparison with experiments. Phys Med Biol 2024; 69:035020. [PMID: 38157549 DOI: 10.1088/1361-6560/ad1998] [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: 08/30/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Objective.Relative biological effectiveness (RBE) plays a vital role in carbon ion radiotherapy, which is a promising treatment method for reducing toxic effects on normal tissues and improving treatment efficacy. It is important to have an effective and precise way of obtaining RBE values to support clinical decisions. A method of calculating RBE from a mechanistic perspective is reported.Approach.Ratio of dose to obtain the same number of double strand breaks (DSBs) between different radiation types was used to evaluate RBE. Package gMicroMC was used to simulate DSB yields. The DSB inductions were then analyzed to calculate RBE. The RBE values were compared with experimental results.Main results.Furusawa's experiment yielded RBE values of 1.27, 2.22, 3.00 and 3.37 for carbon ion beam with dose-averaged LET of 30.3 keVμm-1, 54.5 keVμm-1, 88 keVμm-1and 137 keVμm-1, respectively. RBE values computed from gMicroMC simulations were 1.75, 2.22, 2.87 and 2.97. When it came to a more sophisticated carbon ion beam with 6 cm spread-out Bragg peak, RBE values were 1.61, 1.63, 2.19 and 2.36 for proximal, middle, distal and distal end part, respectively. Values simulated by gMicroMC were 1.50, 1.87, 2.19 and 2.34. The simulated results were in reasonable agreement with the experimental data.Significance.As a mechanistic way for the evaluation of RBE for carbon ion radiotherapy by combining the macroscopic simulation of energy spectrum and microscopic simulation of DNA damages, this work provides a promising tool for RBE calculation supporting clinical applications such as treatment planning.
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Affiliation(s)
- Haonan Feng
- School of Physics, Beihang University, Beijing 102206, People's Republic of China
- Department of Medical Management, Chinese Academy of Science Heavy Ion Medicine (CASHIM) Co. Ltd, Beijing 100083, People's Republic of China
| | - Weiguang Li
- School of Physics, Beihang University, Beijing 102206, People's Republic of China
- Department of Medical Management, Chinese Academy of Science Heavy Ion Medicine (CASHIM) Co. Ltd, Beijing 100083, People's Republic of China
| | - Yibao Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, People's Republic of China
| | - Cheng Chang
- Department of Medical Management, Chinese Academy of Science Heavy Ion Medicine (CASHIM) Co. Ltd, Beijing 100083, People's Republic of China
| | - Ling Hua
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, People's Republic of China
| | - Yiwen Feng
- Beijing University of Posts and Telecommunications, Beijing 100876, People's Republic of China
| | - Youfang Lai
- Department of Medical Management, Chinese Academy of Science Heavy Ion Medicine (CASHIM) Co. Ltd, Beijing 100083, People's Republic of China
| | - LiSheng Geng
- School of Physics, Beihang University, Beijing 102206, People's Republic of China
- Peng Huanwu Collaborative Center for Research and Education, Beihang University, Beijing 100191, People's Republic of China
- Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 102206, People's Republic of China
- Southern Center for Nuclear-Science Theory (SCNT), Institute of Modern Physics, Chinese Academy of Sciences, Huizhou 516000, Guangdong Province, People's Republic of China
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Thibaut Y, Gonon G, Martinez JS, Petit M, Babut R, Vaurijoux A, Gruel G, Villagrasa C, Incerti S, Perrot Y. Experimental validation in a neutron exposure frame of the MINAS TIRITH for cell damage simulation. Phys Med Biol 2023; 68:225008. [PMID: 37848039 DOI: 10.1088/1361-6560/ad043d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
In the domains of medicine and space exploration, refining risk assessment models for protecting healthy tissue from ionizing radiation is crucial. Understanding radiation-induced effects requires biological experimentations at the cellular population level and the cellular scale modeling using Monte Carlo track structure codes. We present MINAS TIRITH, a tool using Geant4-DNA Monte Carlo-generated databases to study DNA damage distribution at the cell population scale. It introduces a DNA damage location module and proposes a method to convert double-strand breaks (DSB) into DNA Damage Response foci. We evaluate damage location precision and DSB-foci conversion parameters. MINAS TIRITH's accuracy is validated againstγ-H2AX foci distribution from cell population exposed to monoenergetic neutron beams (2.5 or 15.1 MeV) under different configurations, yielding mixed radiation fields. Strong agreement between simulation and experimental results was found demonstrating MINAS TIRITH's predictive precision in radiation-induced DNA damage topology. Additionally, modeling intercellular damage variability within a population subjected to a specific macroscopic dose identifies subpopulations, enhancing realistic fate models. This approach advances our understanding of radiation-induced effects on cellular systems for risk assessment improvement.
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Affiliation(s)
- Y Thibaut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gonon
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - J S Martinez
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - M Petit
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - R Babut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - A Vaurijoux
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gruel
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - C Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, LP2i, UMR 5797, F-33170 Gradignan, France
| | - Y Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
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8
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Micheloni M, Petrolli L, Lattanzi G, Potestio R. Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations. Biophys J 2023; 122:3314-3322. [PMID: 37455429 PMCID: PMC10465705 DOI: 10.1016/j.bpj.2023.07.008] [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: 07/11/2022] [Revised: 01/16/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
Double-strand breaks (DSBs), i.e., the covalent cut of the DNA backbone over both strands, are a detrimental outcome of cell irradiation, bearing chromosomal aberrations and leading to cell apoptosis. In the early stages of the evolution of a DSB, the disruption of the residual interactions between the DNA moieties drives the fracture of the helical layout; in spite of its biological significance, the details of this process are still largely uncertain. Here, we address the mechanical rupture of DNA by DSBs via coarse-grained molecular dynamics simulations: the setup involves a 3855-bp DNA filament and diverse DSB motifs, i.e., within a range of distances between strand breaks (or DSB distance). By employing a coarse-grained model of DNA, we access the molecular details and characteristic timescales of the rupturing process. A sequence-nonspecific, linear correlation is observed between the DSB distance and the internal energy contribution to the disruption of the residual (Watson-Crick and stacking) contacts between DNA moieties, which is seemingly driven by an abrupt, cooperative process. Moreover, we infer an exponential dependence of the characteristic rupture times on the DSB distances, which we associate to an Arrhenius-like law of thermally-activated processes. This work lays the foundations of a detailed, mechanistic assessment of DSBs in silico as a benchmark to both numerical simulations and data from single-molecule experiments.
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Affiliation(s)
- Manuel Micheloni
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Lorenzo Petrolli
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Gianluca Lattanzi
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaello Potestio
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy.
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9
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Chatzipapas K, Dordevic M, Zivkovic S, Tran NH, Lampe N, Sakata D, Petrovic I, Ristic-Fira A, Shin WG, Zein S, Brown JMC, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S. Geant4-DNA simulation of human cancer cells irradiation with helium ion beams. Phys Med 2023; 112:102613. [PMID: 37356419 DOI: 10.1016/j.ejmp.2023.102613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/03/2023] [Accepted: 05/30/2023] [Indexed: 06/27/2023] Open
Abstract
PURPOSE This study aimed to develop a computational environment for the accurate simulation of human cancer cell irradiation using Geant4-DNA. New cell geometrical models were developed and irradiated by alpha particle beams to induce DNA damage. The proposed approach may help further investigation of the benefits of external alpha irradiation therapy. METHODS The Geant4-DNA Monte Carlo (MC) toolkit allows the simulation of cancer cell geometries that can be combined with accurate modelling of physical, physicochemical and chemical stages of liquid water irradiation, including radiolytic processes. Geant4-DNA is used to calculate direct and non-direct DNA damage yields, such as single and double strand breaks, produced by the deposition of energy or by the interaction of DNA with free radicals. RESULTS In this study, the "molecularDNA" example application of Geant4-DNA was used to quantify early DNA damage in human cancer cells upon irradiation with alpha particle beams, as a function of linear energy transfer (LET). The MC simulation results are compared to experimental data, as well as previously published simulation data. The simulation results agree well with the experimental data on DSB yields in the lower LET range, while the experimental data on DSB yields are lower than the results obtained with the "molecularDNA" example in the higher LET range. CONCLUSION This study explored and demonstrated the possibilities of the Geant4-DNA toolkit together with the "molecularDNA" example to simulate the helium beam irradiation of cancer cell lines, to quantify the early DNA damage, or even the following DNA damage response.
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Affiliation(s)
| | - Milos Dordevic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovica Alasa 12-14, 11351 Vinca, Belgrade, Serbia.
| | - Sara Zivkovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovica Alasa 12-14, 11351 Vinca, Belgrade, Serbia
| | - Ngoc Hoang Tran
- University of Bordeaux, CNRS, LP2i, UMR5797, F-33170 Gradignan, France
| | | | - Dousatsu Sakata
- Division of Health Sciences, Osaka University, Osaka 565-0871, Japan
| | - Ivan Petrovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovica Alasa 12-14, 11351 Vinca, Belgrade, Serbia
| | - Aleksandra Ristic-Fira
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovica Alasa 12-14, 11351 Vinca, Belgrade, Serbia
| | - Wook-Geun Shin
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, 02114 MA, USA
| | - Sara Zein
- University of Bordeaux, CNRS, LP2i, UMR5797, F-33170 Gradignan, France
| | - Jeremy M C Brown
- Optical Sciences Centre, Department of Physics and Astronomy, Swinburne University of Technology, Hawthorn 3122, Australia
| | - Ioanna Kyriakou
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Susanna Guatelli
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Sebastien Incerti
- University of Bordeaux, CNRS, LP2i, UMR5797, F-33170 Gradignan, France
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10
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Bian J, Duran J, Shin WG, Ramos-Méndez J, Sankey JC, Childress L, Seuntjens J, Enger SA. GEANT4-DNA simulation of temperature-dependent and pH-dependent yields of chemical radiolytic species. Phys Med Biol 2023; 68:124002. [PMID: 37230081 DOI: 10.1088/1361-6560/acd90d] [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: 12/22/2022] [Accepted: 05/25/2023] [Indexed: 05/27/2023]
Abstract
Objective.GEANT4-DNA can simulate radiation chemical yield (G-value) for radiolytic species such as the hydrated electron (eaq-) with the independent reaction times (IRT) method, however, only at room temperature and neutral pH. This work aims to modify the GEANT4-DNA source code to enable the calculation ofG-values for radiolytic species at different temperatures and pH values.Approach.In the GEANT4-DNA source code, values of chemical parameters such as reaction rate constant, diffusion coefficient, Onsager radius, and water density were replaced by corresponding temperature-dependent polynomials. The initial concentration of hydrogen ion (H+)/hydronium ion (H3O+) was scaled for a desired pH using the relationship pH = -log10[H+]. To validate our modifications, two sets of simulations were performed. (A) A water cube with 1.0 km sides and a pH of 7 was irradiated with an isotropic electron source of 1 MeV. The end time was 1μs. The temperatures varied from 25 °C to 150 °C. (B) The same setup as (A) was used, however, the temperature was set to 25 °C while the pH varied from 5 to 9. The results were compared with published experimental and simulated work.Main results.The IRT method in GEANT4-DNA was successfully modified to simulateG-values for radiolytic species at different temperatures and pH values. Our temperature-dependent results agreed with experimental data within 0.64%-9.79%, and with simulated data within 3.52%-12.47%. The pH-dependent results agreed well with experimental data within 0.52% to 3.19% except at a pH of 5 (15.99%) and with simulated data within 4.40%-5.53%. The uncertainties were below ±0.20%. Overall our results agreed better with experimental than simulation data.Significance.Modifications in the GEANT4-DNA code enabled the calculation ofG-values for radiolytic species at different temperatures and pH values.
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Affiliation(s)
- Jingyi Bian
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Juan Duran
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Wook-Geun Shin
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, MA-02114, United States of America
| | - Jose Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, CA, United States of America
| | - Jack C Sankey
- Department of Physics, McGill University, Montreal, Quebec, Canada
| | - Lilian Childress
- Department of Physics, McGill University, Montreal, Quebec, Canada
| | - Jan Seuntjens
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Shirin A Enger
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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11
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Dheyab MA, Aziz AA, Rahman AA, Ashour NI, Musa AS, Braim FS, Jameel MS. Monte Carlo simulation of gold nanoparticles for X-ray enhancement application. Biochim Biophys Acta Gen Subj 2023; 1867:130318. [PMID: 36740000 DOI: 10.1016/j.bbagen.2023.130318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
BACKGROUND Gold nanoparticles (Au NPs) are regarded as potential agents that enhance the radiosensitivity of tumor cells for theranostic applications. To elucidate the biological mechanisms of radiation dose enhancement effects of Au NPs as well as DNA damage attributable to the inclusion of Au NPs, Monte Carlo (MC) simulations have been deployed in a number of studies. SCOPE OF REVIEW This review paper concisely collates and reviews the information reported in the simulation research in terms of MC simulation of radiosensitization and dose enhancement effects caused by the inclusion of Au NPs in tumor cells, simulation mechanisms, benefits and limitations. MAJOR CONCLUSIONS In this review, we first explore the recent advances in MC simulation on Au NPs radiosensitization. The MC methods, physical dose enhancement and enhanced chemical and biological effects is discussed, followed by some results regarding the prediction of dose enhancement. We then review Multi-scale MC simulations of Au NP-induced DNA damages for X-ray irradiation. Moreover, we explain and look at Multi-scale MC simulations of Au NP-induced DNA damages for X-ray irradiation. GENERAL SIGNIFICANCE Using advanced chemical module-implemented MC simulations, there is a need to assess the radiation-induced chemical radicals that contribute to the dose-enhancing and biological effects of multiple Au NPs.
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Affiliation(s)
- Mohammed Ali Dheyab
- School of Physics, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia; Nano-Biotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia.
| | - Azlan Abdul Aziz
- School of Physics, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia; Nano-Biotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia.
| | - Azhar Abdul Rahman
- School of Physics, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | | | - Ahmed Sadeq Musa
- School of Physics, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | - Farhank Saber Braim
- School of Physics, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia; Nano-Biotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | - Mahmood S Jameel
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden 11800, Malaysia
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12
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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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13
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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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14
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Sakata D, Hirayama R, Shin WG, Belli M, Tabocchini MA, Stewart RD, Belov O, Bernal MA, Bordage MC, Brown JMC, Dordevic M, Emfietzoglou D, Francis Z, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, Kyriakou I, Lampe N, Li Z, Meylan S, Michelet C, Nieminen P, Perrot Y, Petrovic I, Ramos-Mendez J, Ristic-Fira A, Santin G, Schuemann J, Tran HN, Villagrasa C, Incerti S. Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA. Phys Med 2023; 105:102508. [PMID: 36549067 PMCID: PMC11221566 DOI: 10.1016/j.ejmp.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Track structure Monte Carlo (MC) codes have achieved successful outcomes in the quantitative investigation of radiation-induced initial DNA damage. The aim of the present study is to extend a Geant4-DNA radiobiological application by incorporating a feature allowing for the prediction of DNA rejoining kinetics and corresponding cell surviving fraction along time after irradiation, for a Chinese hamster V79 cell line, which is one of the most popular and widely investigated cell lines in radiobiology. METHODS We implemented the Two-Lesion Kinetics (TLK) model, originally proposed by Stewart, which allows for simulations to calculate residual DNA damage and surviving fraction along time via the number of initial DNA damage and its complexity as inputs. RESULTS By optimizing the model parameters of the TLK model in accordance to the experimental data on V79, we were able to predict both DNA rejoining kinetics at low linear energy transfers (LET) and cell surviving fraction. CONCLUSION This is the first study to demonstrate the implementation of both the cell surviving fraction and the DNA rejoining kinetics with the estimated initial DNA damage, in a realistic cell geometrical model simulated by full track structure MC simulations at DNA level and for various LET. These simulation and model make the link between mechanistic physical/chemical damage processes and these two specific biological endpoints.
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Affiliation(s)
- Dousatsu Sakata
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba 263-8555, Japan; Division of Health Sciences, Osaka University, Osaka 565-0871, Japan.
| | - Ryoichi Hirayama
- Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba 263-8555, Japan
| | - Wook-Geun Shin
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | | | | | - Robert D Stewart
- Department of Radiation Oncology, University of Washington, WA 98195-6043, USA
| | - Oleg Belov
- Veksler and Baldin Laboratory of High Energy Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia; Institute of System Analysis and Management, Dubna State University, 141980 Dubna, Russia
| | - Mario A Bernal
- Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marie-Claude Bordage
- INSERM, Université Paul Sabatier, UMR 1037, CRCT, Toulouse, France; Université Toulouse III-Paul Sabatier, UMR 1037, CRCT, Toulouse, France
| | - Jeremy M C Brown
- Department of Physics and Astronomy, Swinburne University of Technology, Hawthorn, Australia; Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia; Department of Radiation Science and Technology, Delft University of Technology, The Netherlands
| | - Milos Dordevic
- Vinca Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, GR 45110, Ioannina, Greece
| | - Ziad Francis
- Saint Joseph University of Beirut, UR Mathématiques et Modélisation, Beirut, Lebanon
| | - Susanna Guatelli
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - Taku Inaniwa
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba 263-8555, Japan
| | - Vladimir Ivanchenko
- Geant4 Associates International Ltd, Hebden Bridge, UK; Tomsk State University, Tomsk, Russia
| | | | - Ioanna Kyriakou
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, GR 45110, Ioannina, Greece
| | | | - Zhuxin Li
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | | | - Claire Michelet
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | | | - Yann Perrot
- IRSN, Institut de Radioprotection et de Surete Nucleaire, 92262 Fontenay-aux-Roses, France
| | - Ivan Petrovic
- Vinca Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jose Ramos-Mendez
- Department of Radiation Oncology, University of California San Francisco, San Francisco 94143, CA, USA
| | - Aleksandra Ristic-Fira
- Vinca Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Jan Schuemann
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Hoang N Tran
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Surete Nucleaire, 92262 Fontenay-aux-Roses, France
| | - Sebastien Incerti
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
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15
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Sitmukhambetov S, Dinh B, Lai Y, Banigan EJ, Pan Z, Jia X, Chi Y. Development and implementation of a metaphase DNA model for ionizing radiation induced DNA damage calculation. Phys Med Biol 2022; 68:10.1088/1361-6560/aca5ea. [PMID: 36533598 PMCID: PMC9969557 DOI: 10.1088/1361-6560/aca5ea] [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: 08/02/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022]
Abstract
Objective. To develop a metaphase chromosome model representing the complete genome of a human lymphocyte cell to support microscopic Monte Carlo (MMC) simulation-based radiation-induced DNA damage studies.Approach. We first employed coarse-grained polymer physics simulation to obtain a rod-shaped chromatid segment of 730 nm in diameter and 460 nm in height to match Hi-C data. We then voxelized the segment with a voxel size of 11 nm per side and connected the chromatid with 30 types of pre-constructed nucleosomes and 6 types of linker DNAs in base pair (bp) resolutions. Afterward, we piled different numbers of voxelized chromatid segments to create 23 pairs of chromosomes of 1-5μm long. Finally, we arranged the chromosomes at the cell metaphase plate of 5.5μm in radius to create the complete set of metaphase chromosomes. We implemented the model in gMicroMC simulation by denoting the DNA structure in a four-level hierarchical tree: nucleotide pairs, nucleosomes and linker DNAs, chromatid segments, and chromosomes. We applied the model to compute DNA damage under different radiation conditions and compared the results to those obtained with G0/G1 model and experimental measurements. We also performed uncertainty analysis for relevant simulation parameters.Main results. The chromatid segment was successfully voxelized and connected in bps resolution, containing 26.8 mega bps (Mbps) of DNA. With 466 segments, we obtained the metaphase chromosome containing 12.5 Gbps of DNA. Applying it to compute the radiation-induced DNA damage, the obtained results were self-consistent and agreed with experimental measurements. Through the parameter uncertainty study, we found that the DNA damage ratio between metaphase and G0/G1 phase models was not sensitive to the chemical simulation time. The damage was also not sensitive to the specific parameter settings in the polymer physics simulation, as long as the produced metaphase model followed a similar contact map distribution.Significance. Experimental data reveal that ionizing radiation induced DNA damage is cell cycle dependent. Yet, DNA chromosome models, except for the G0/G1 phase, are not available in the state-of-the-art MMC simulation. For the first time, we successfully built a metaphase chromosome model and implemented it into MMC simulation for radiation-induced DNA damage computation.
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Affiliation(s)
| | - Bryan Dinh
- Department of Physics, the University of Texas at Arlington, Arlington, TX 76019, USA
| | - Youfang Lai
- Department of Physics, the University of Texas at Arlington, Arlington, TX 76019, USA
| | - Edward J. Banigan
- Institute for Medical Engineering & Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zui Pan
- Graduate Nursing, the University of Texas at Arlington, Arlington, TX 76019, USA
| | - Xun Jia
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, MD 21231, USA
| | - Yujie Chi
- Department of Physics, the University of Texas at Arlington, Arlington, TX 76019, USA
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16
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Bertolet A, Ramos-Méndez J, McNamara A, Yoo D, Ingram S, Henthorn N, Warmenhoven JW, Faddegon B, Merchant M, McMahon SJ, Paganetti H, Schuemann J. Impact of DNA Geometry and Scoring on Monte Carlo Track-Structure Simulations of Initial Radiation-Induced Damage. Radiat Res 2022; 198:207-220. [PMID: 35767729 PMCID: PMC9458623 DOI: 10.1667/rade-21-00179.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/07/2022] [Indexed: 11/03/2022]
Abstract
Track structure Monte Carlo simulations are a useful tool to investigate the damage induced to DNA by ionizing radiation. These simulations usually rely on simplified geometrical representations of the DNA subcomponents. DNA damage is determined by the physical and physicochemical processes occurring within these volumes. In particular, damage to the DNA backbone is generally assumed to result in strand breaks. DNA damage can be categorized as direct (ionization of an atom part of the DNA molecule) or indirect (damage from reactive chemical species following water radiolysis). We also consider quasi-direct effects, i.e., damage originated by charge transfers after ionization of the hydration shell surrounding the DNA. DNA geometries are needed to account for the damage induced by ionizing radiation, and different geometry models can be used for speed or accuracy reasons. In this work, we use the Monte Carlo track structure tool TOPAS-nBio, built on top of Geant4-DNA, for simulation at the nanometer scale to evaluate differences among three DNA geometrical models in an entire cell nucleus, including a sphere/spheroid model specifically designed for this work. In addition to strand breaks, we explicitly consider the direct, quasi-direct, and indirect damage induced to DNA base moieties. We use results from the literature to determine the best values for the relevant parameters. For example, the proportion of hydroxyl radical reactions between base moieties was 80%, and between backbone, moieties was 20%, the proportion of radical attacks leading to a strand break was 11%, and the expected ratio of base damages and strand breaks was 2.5-3. Our results show that failure to update parameters for new geometric models can lead to significant differences in predicted damage yields.
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Affiliation(s)
- Alejandro Bertolet
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Aimee McNamara
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Dohyeon Yoo
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Samuel Ingram
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Nicholas Henthorn
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - John-William Warmenhoven
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Michael Merchant
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, United Kingdom
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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17
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New damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmid. Sci Rep 2022; 12:11345. [PMID: 35790804 PMCID: PMC9256689 DOI: 10.1038/s41598-022-15521-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
In this work, we proposed a new damage model for estimating radiation-induced direct damage to biomolecular systems and validated its the effectiveness for pBR322 plasmids. The proposed model estimates radiation-induced damage to biomolecular systems by: (1) simulation geometry modeling using the coarse-grained (CG) technique to replace the minimum repeating units of a molecule with a single bead, (2) approximation of the threshold energy for radiation damage through CG potential calculation, (3) calculation of cumulative absorption energy for each radiation event in microscopic regions of CG models using the Monte Carlo track structure (MCTS) code, and (4) estimation of direct radiation damage to biomolecular systems by comparing CG potentials and absorption energy. The proposed model replicated measured data with an average error of approximately 14.2% in the estimation of radiation damage to pBR322 plasmids using the common MCTS code Geant4-DNA. This is similar to the results of previous simulation studies. However, in existing damage models, parameters are adjusted based on experimental data to increase the reliability of simulation results, whereas in the proposed model, they can be determined without using empirical data. Because the proposed model proposed is applicable to DNA and various biomolecular systems with minimal experimental data, it provides a new method that is convenient and effective for predicting damage in living organisms caused by radiation exposure.
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Pfuhl T, Friedrich T, Scholz M. A double-strand-break model for the relative biological effectiveness of electrons based on ionization clustering. Med Phys 2022; 49:5562-5575. [PMID: 35686448 DOI: 10.1002/mp.15796] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The effectiveness of ionizing radiation regarding DNA damage induction depends on its spatial energy deposition pattern. For electrons an increased effectiveness is observed at low kinetic energies due to the enhanced density of energy deposition events at electron track ends. PURPOSE A model is presented, which enables the calculation of the double-strand-break (DSB) yield and the relative biological effectiveness (RBE) for DSB induction of electrons. METHODS The model applies the mean free path between two ionizations and the assumption that two ionizations within a certain threshold distance are necessary to potentially lead to a DSB. Next to an expression for the electron RBE according to its common definition, a local RBE is determined, which describes the electrons' local effectiveness at a defined point on their track. RESULTS This local RBE allows a better understanding of microscopic processes resulting from radiation and can be used, for instance, to describe the mean effectiveness of the mixed electron radiation field as a function of the radial distance to the center of an ion track. CONCLUSIONS The presented model reflects the experimentally observed increased effectiveness of low-energetic electrons. It will be used in a future work to improve RBE predictions for ions performed with the local effect model.
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Affiliation(s)
- Tabea Pfuhl
- GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany
| | - Thomas Friedrich
- GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany
| | - Michael Scholz
- GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany
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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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20
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Moeini H, Mokari M. DNA damage and microdosimetry for carbon ions: Track structure simulations as the key to quantitative modeling of radiation-induced damage. Med Phys 2022; 49:4823-4836. [PMID: 35596669 DOI: 10.1002/mp.15711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/29/2022] [Accepted: 05/04/2022] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Dose distribution in carbon-ion irradiations is generally envisaged to have therapeutic advantages over protons, primarily due to the carbon-ion's comparatively higher relative biological effectiveness (RBE) in the tumor than in the encompassing healthy tissues. The objective of this work was to simulate the overall physical and chemical reactions of primary carbon ions impinging on liquid water and, as such, to investigate the DNA-damage yields in the form of strand breaks (SBs) and in connection with the expected microdosimetric quantities. MATERIALS AND METHODS Using a B-DNA model and Geant4-DNA, we simulated the primary and secondary interactions in a spherical medium of water. Subsequently, we categorized DNA damages based on their complexity utilizing the concept of μ-randomness. We assumed a threshold of 17.5 eV for a direct SB and a probability of 0.13 for an indirect SB triggered by chemical reactions of hydroxyl radicals. Microdosimetric quantities were extracted for three cylindrical volumes representing typical sub-cellular organisms. RESULTS For fully-ionized carbons of 8 to 256 MeV/u, the yield results appeared to be considerably influenced by the chemical reactions - indicating the important role of secondary electrons in inflicting damage. However, it was mostly the direct-damage spectrum that determined the overall shape of the damage spectrum. At all primary energies, it was more probable to break each DNA strand at one point - the two points being less than 10 bp apart - than to break only one strand at two random points. Unlike proton's mean-specific-energy results, which showed more sensitivity to the volume increase of the smallest cylinder than of the larger ones, carbon-ion results showed no such sensitivity. CONCLUSION The growth of the yield ratio of the single- and double-strand breaks (SSB and DSB) with the particle energy was estimated for protons to be about two times that of alphas and 92 times that of carbon ions. Unlike the proton results, which suggested significant correlations between the DSB yields and mean specific (and lineal) energies, carbon ions exhibited no such correlations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hossein Moeini
- Department of Physics, School of Science, Shiraz University, Shiraz, 71946-84795, Iran
| | - Mojtaba Mokari
- Department of Physics, Behbahan Khatam Alanbia University of Technology, Behbahan, 6361647189, Iran
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21
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Koval NE, Koval P, Da Pieve F, Kohanoff J, Artacho E, Emfietzoglou D. Inelastic scattering of electrons in water from first principles: cross sections and inelastic mean free path for use in Monte Carlo track-structure simulations of biological damage. ROYAL SOCIETY OPEN SCIENCE 2022. [PMID: 35619995 DOI: 10.5061/dryad.d51c5b057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Modelling the inelastic scattering of electrons in water is fundamental, given their crucial role in biological damage. In Monte Carlo track-structure (MC-TS) codes used to assess biological damage, the energy loss function (ELF), from which cross sections are extracted, is derived from different semi-empirical optical models. Only recently have first ab initio results for the ELF and cross sections in water become available. For benchmarking purpose, in this work, we present ab initio linear-response time-dependent density functional theory calculations of the ELF of liquid water. We calculated the inelastic scattering cross sections, inelastic mean free paths, and electronic stopping power and compared our results with recent calculations and experimental data showing a good agreement. In addition, we provide an in-depth analysis of the contributions of different molecular orbitals, species and orbital angular momenta to the total ELF. Moreover, we present single-differential cross sections computed for each molecular orbital channel, which should prove useful for MC-TS simulations.
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Affiliation(s)
| | - Peter Koval
- Simune Atomistics SL, 20018 Donostia-San Sebastián, Spain
| | - Fabiana Da Pieve
- Royal Belgian Institute for Space Aeronomy BIRA-IASB, 1180 Brussels, Belgium
| | - Jorge Kohanoff
- Queen's University Belfast, Belfast BT7 1NN, UK
- Instituto de Fusion Nuclear 'Guillermo Velarde', Universidad Politecnica de Madrid, 28006 Madrid, Spain
| | - Emilio Artacho
- CIC Nanogune BRTA, 20018 Donostia-San Sebastián, Spain
- Donostia International Physics Center DIPC, 20018 Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110 Ioannina, Greece
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22
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Koval NE, Koval P, Da Pieve F, Kohanoff J, Artacho E, Emfietzoglou D. Inelastic scattering of electrons in water from first principles: cross sections and inelastic mean free path for use in Monte Carlo track-structure simulations of biological damage. ROYAL SOCIETY OPEN SCIENCE 2022; 9:212011. [PMID: 35619995 PMCID: PMC9115040 DOI: 10.1098/rsos.212011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/19/2022] [Indexed: 05/03/2023]
Abstract
Modelling the inelastic scattering of electrons in water is fundamental, given their crucial role in biological damage. In Monte Carlo track-structure (MC-TS) codes used to assess biological damage, the energy loss function (ELF), from which cross sections are extracted, is derived from different semi-empirical optical models. Only recently have first ab initio results for the ELF and cross sections in water become available. For benchmarking purpose, in this work, we present ab initio linear-response time-dependent density functional theory calculations of the ELF of liquid water. We calculated the inelastic scattering cross sections, inelastic mean free paths, and electronic stopping power and compared our results with recent calculations and experimental data showing a good agreement. In addition, we provide an in-depth analysis of the contributions of different molecular orbitals, species and orbital angular momenta to the total ELF. Moreover, we present single-differential cross sections computed for each molecular orbital channel, which should prove useful for MC-TS simulations.
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Affiliation(s)
| | - Peter Koval
- Simune Atomistics SL, 20018 Donostia-San Sebastián, Spain
| | - Fabiana Da Pieve
- Royal Belgian Institute for Space Aeronomy BIRA-IASB, 1180 Brussels, Belgium
| | - Jorge Kohanoff
- Queen’s University Belfast, Belfast BT7 1NN, UK
- Instituto de Fusion Nuclear ‘Guillermo Velarde’, Universidad Politecnica de Madrid, 28006 Madrid, Spain
| | - Emilio Artacho
- CIC Nanogune BRTA, 20018 Donostia-San Sebastián, Spain
- Donostia International Physics Center DIPC, 20018 Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110 Ioannina, Greece
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23
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Nanodosimetric Calculations of Radiation-Induced DNA Damage in a New Nucleus Geometrical Model Based on the Isochore Theory. Int J Mol Sci 2022; 23:ijms23073770. [PMID: 35409128 PMCID: PMC8998209 DOI: 10.3390/ijms23073770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Double-strand breaks (DSBs) in nuclear DNA represents radiation-induced damage that has been identified as particularly deleterious. Calculating this damage using Monte Carlo track structure modeling could be a suitable indicator to better assess and anticipate the side-effects of radiation therapy. However, as already demonstrated in previous work, the geometrical description of the nucleus and the DNA content used in the simulation significantly influence damage calculations. Therefore, in order to obtain accurate results, this geometry must be as realistic as possible. In this study, a new geometrical model of an endothelial cell nucleus and DNA distribution according to the isochore theory are presented and used in a Monte Carlo simulation chain based on the Geant4-DNA toolkit. In this theory, heterochromatin and euchromatin compaction are distributed along the genome according to five different families (L1, L2, H1, H2, and H3). Each of these families is associated with a different hetero/euchromatin rate related to its compaction level. In order to compare the results with those obtained using a previous nuclear geometry, simulations were performed for protons with linear energy transfers (LETs) of 4.29 keV/µm, 19.51 keV/µm, and 43.25 keV/µm. The organization of the chromatin fibers at different compaction levels linked to isochore families increased the DSB yield by 6-10%, and it allowed the most affected part of the genome to be identified. These new results indicate that the genome core is more radiosensitive than the genome desert, with a 3-8% increase in damage depending on the LET. This work highlights the importance of using realistic distributions of chromatin compaction levels to calculate radio-induced damage using Monte Carlo simulation methods.
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24
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Sarnelli A, Negrini M, Mezzenga E, Feliciani G, D'Arienzo M, Amato A, Paganelli G. Modelling a new approach for radio-ablation after resection of breast ductal carcinoma in-situ based on the BAT-90 medical device. Sci Rep 2022; 12:14. [PMID: 34996956 PMCID: PMC8741759 DOI: 10.1038/s41598-021-03807-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/03/2021] [Indexed: 11/28/2022] Open
Abstract
The majority of local recurrences, after conservative surgery of breast cancer, occurs in the same anatomical area where the tumour was originally located. For the treatment of ductal carcinoma in situ (DCIS), a new medical device, named BAT-90, (BetaGlue Technologies SpA) has been proposed. BAT-90 is based on the administration of 90Y β-emitting microspheres, embedded in a bio-compatible matrix. In this work, the Geant4 simulation toolkit is used to simulate BAT-90 as a homogenous cylindrical 90Y layer placed in the middle of a bulk material. The activity needed to deliver a 20 Gy isodose at a given distance z from the BAT-90 layer is calculated for different device thicknesses, tumour bed sizes and for water and adipose bulk materials. A radiobiological analysis has been performed using both the Poisson and logistic Tumour Control Probability (TCP) models. A range of radiobiological parameters (α and β), target sizes, and densities of tumour cells were considered. Increasing α values, TCP increases too, while, for a fixed α value, TCP decreases as a function of clonogenic cell density. The models predict very solid results in case of limited tumour burden while the activity/dose ratio could be further optimized in case of larger tumour beds.
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Affiliation(s)
- Anna Sarnelli
- Medical Physics Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Via P. Maroncelli 40, 47014, Meldola, FC, Italy.
| | - Matteo Negrini
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, 40126, Bologna, Italy
| | - Emilio Mezzenga
- Medical Physics Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Giacomo Feliciani
- Medical Physics Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Marco D'Arienzo
- Medical Physics Unit, ASL Roma 6, Via Borgo Garibaldi 12, 00041, Albano Laziale, RM, Italy
| | - Antonino Amato
- BetaGlue Technologies Spa, Lungadige Galtarossa 21, 37133, Verona, Italy
| | - Giovanni Paganelli
- Nuclear Medicine Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST), Dino Amadori", Via P. Maroncelli 40, 47014, Meldola, FC, Italy
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25
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Review of the Geant4-DNA Simulation Toolkit for Radiobiological Applications at the Cellular and DNA Level. Cancers (Basel) 2021; 14:cancers14010035. [PMID: 35008196 PMCID: PMC8749997 DOI: 10.3390/cancers14010035] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary A brief description of the methodologies to simulate ionizing radiation transport in biologically relevant matter is presented. Emphasis is given to the physical, chemical, and biological models of Geant4-DNA that enable mechanistic radiobiological modeling at the cellular and DNA level, important to improve the efficacy of existing and novel radiotherapeutic modalities for the treatment of cancer. Abstract The Geant4-DNA low energy extension of the Geant4 Monte Carlo (MC) toolkit is a continuously evolving MC simulation code permitting mechanistic studies of cellular radiobiological effects. Geant4-DNA considers the physical, chemical, and biological stages of the action of ionizing radiation (in the form of x- and γ-ray photons, electrons and β±-rays, hadrons, α-particles, and a set of heavier ions) in living cells towards a variety of applications ranging from predicting radiotherapy outcomes to radiation protection both on earth and in space. In this work, we provide a brief, yet concise, overview of the progress that has been achieved so far concerning the different physical, physicochemical, chemical, and biological models implemented into Geant4-DNA, highlighting the latest developments. Specifically, the “dnadamage1” and “molecularDNA” applications which enable, for the first time within an open-source platform, quantitative predictions of early DNA damage in terms of single-strand-breaks (SSBs), double-strand-breaks (DSBs), and more complex clustered lesions for different DNA structures ranging from the nucleotide level to the entire genome. These developments are critically presented and discussed along with key benchmarking results. The Geant4-DNA toolkit, through its different set of models and functionalities, offers unique capabilities for elucidating the problem of radiation quality or the relative biological effectiveness (RBE) of different ionizing radiations which underlines nearly the whole spectrum of radiotherapeutic modalities, from external high-energy hadron beams to internal low-energy gamma and beta emitters that are used in brachytherapy sources and radiopharmaceuticals, respectively.
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26
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D-Kondo N, Moreno-Barbosa E, Štěphán V, Stefanová K, Perrot Y, Villagrasa C, Incerti S, De Celis Alonso B, Schuemann J, Faddegon B, Ramos-Méndez J. DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions. Phys Med Biol 2021; 66. [PMID: 34787099 DOI: 10.1088/1361-6560/ac3a22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022]
Abstract
The chemical stage of the Monte Carlo track-structure (MCTS) code Geant4-DNA was extended for its use in DNA strand break (SB) simulations and compared against published experimental data. Geant4-DNA simulations were performed using pUC19 plasmids (2686 base pairs) in a buffered solution of DMSO irradiated by60Co or137Csγ-rays. A comprehensive evaluation of SSB yields was performed considering DMSO, DNA concentration, dose and plasmid supercoiling. The latter was measured using the super helix density value used in a Brownian dynamics plasmid generation algorithm. The Geant4-DNA implementation of the independent reaction times method (IRT), developed to simulate the reaction kinetics of radiochemical species, allowed to score the fraction of supercoiled, relaxed and linearized plasmid fractions as a function of the absorbed dose. The percentage of the number of SB after •OH + DNA and H• + DNA reactions, referred as SSB efficiency, obtained using MCTS were 13.77% and 0.74% respectively. This is in reasonable agreement with published values of 12% and 0.8%. The SSB yields as a function of DMSO concentration, DNA concentration and super helix density recreated the expected published experimental behaviors within 5%, one standard deviation. The dose response of SSB and DSB yields agreed with published measurements within 5%, one standard deviation. We demonstrated that the developed extension of IRT in Geant4-DNA, facilitated the reproduction of experimental conditions. Furthermore, its calculations were strongly in agreement with experimental data. These two facts will facilitate the use of this extension in future radiobiological applications, aiding the study of DNA damage mechanisms with a high level of detail.
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Affiliation(s)
- N D-Kondo
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - E Moreno-Barbosa
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - V Štěphán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Stefanová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - Y Perrot
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - C Villagrasa
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - S Incerti
- Univ. Bordeaux, CNRS/IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - B De Celis Alonso
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - J Schuemann
- Department of Radiation Oncology, Massachusets General Hospital and Hardvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
| | - J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
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Sakata D, Suzuki M, Hirayama R, Abe Y, Muramatsu M, Sato S, Belov O, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S, Inaniwa T. Performance Evaluation for Repair of HSGc-C5 Carcinoma Cell Using Geant4-DNA. Cancers (Basel) 2021; 13:6046. [PMID: 34885155 PMCID: PMC8656964 DOI: 10.3390/cancers13236046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/30/2021] [Accepted: 09/07/2021] [Indexed: 12/27/2022] Open
Abstract
Track-structure Monte Carlo simulations are useful tools to evaluate initial DNA damage induced by irradiation. In the previous study, we have developed a Gean4-DNA-based application to estimate the cell surviving fraction of V79 cells after irradiation, bridging the gap between the initial DNA damage and the DNA rejoining kinetics by means of the two-lesion kinetics (TLK) model. However, since the DNA repair performance depends on cell line, the same model parameters cannot be used for different cell lines. Thus, we extended the Geant4-DNA application with a TLK model for the evaluation of DNA damage repair performance in HSGc-C5 carcinoma cells which are typically used for evaluating proton/carbon radiation treatment effects. For this evaluation, we also performed experimental measurements for cell surviving fractions and DNA rejoining kinetics of the HSGc-C5 cells irradiated by 70 MeV protons at the cyclotron facility at the National Institutes for Quantum and Radiological Science and Technology (QST). Concerning fast- and slow-DNA rejoining, the TLK model parameters were adequately optimized with the simulated initial DNA damage. The optimized DNA rejoining speeds were reasonably agreed with the experimental DNA rejoining speeds. Using the optimized TLK model, the Geant4-DNA simulation is now able to predict cell survival and DNA-rejoining kinetics for HSGc-C5 cells.
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Affiliation(s)
- Dousatsu Sakata
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (Y.A.); (M.M.); (S.S.); (T.I.)
| | - Masao Suzuki
- Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (M.S.); (R.H.)
| | - Ryoichi Hirayama
- Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (M.S.); (R.H.)
| | - Yasushi Abe
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (Y.A.); (M.M.); (S.S.); (T.I.)
| | - Masayuki Muramatsu
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (Y.A.); (M.M.); (S.S.); (T.I.)
| | - Shinji Sato
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (Y.A.); (M.M.); (S.S.); (T.I.)
| | - Oleg Belov
- Veksler and Baldin Laboratory of High Energy Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia;
- Institute of System Analysis and Management, Dubna State University, 141980 Dubna, Russia
| | - Ioanna Kyriakou
- Medical Physics Laboratory, Medical School, University of Ioannina, 45110 Ioannina, Greece; (I.K.); (D.E.)
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, Medical School, University of Ioannina, 45110 Ioannina, Greece; (I.K.); (D.E.)
| | - Susanna Guatelli
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong 2522, Australia;
| | - Sebastien Incerti
- Centre d’Études Nucléaires de Bordeaux Gradignan, CNRS/IN2P3, UMR5797, Université de Bordeaux, F-33170 Gradignan, France;
| | - Taku Inaniwa
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (Y.A.); (M.M.); (S.S.); (T.I.)
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28
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Zhao X, Liu R, Zhao T, Reynoso FJ. Quantification of gold nanoparticle photon radiosensitization from direct and indirect effects using a complete human genome single cell model based on Geant4. Med Phys 2021; 48:8127-8139. [PMID: 34738643 DOI: 10.1002/mp.15330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 09/22/2021] [Accepted: 10/20/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To investigate the radiosensitization properties of gold nanoparticles (GNPs) and better understand the intricate deoxyribonucleic acid (DNA) damage induction mechanisms involved in GNP-aided radiotherapy, a single cell model with complete human genome based on the Geant4 Monte Carlo toolkit was applied. MATERIALS AND METHODS A Geant4-DNA model was implemented to simulate direct and indirect DNA damage generated in the physical and chemical stages. In the physical stage, a mixed-physics approach was taken by using Geant4-DNA in water and Livermore in gold. Water radiolysis was created posteriorly in the physicochemical and chemical stages to simulate indirect damage from reactions between DNA molecules and OH• radicals. A mono-energetic photon beam (100 keV) and two clinical photon sources (250-kVp, 6-MV flattening-filter free) were simulated for modeling the irradiation of a single cell with or without GNPs. In order to study the effects of GNP size on radiosensitization, 15, 30, and 100 nm GNPs were simulated. The effects of intracellular distribution were simulated using 90-nm GNPs with different characteristics of distribution within the cell. The time dependence of DNA damage enhancement was also studied with chemistry stage simulation end-time no larger than 10 ns. RESULTS Double strand break (DSB) enhancement due to direct and indirect action was quantified under different scenarios. Under realistic cellular uptake condition, the 100-nm GNPs had the most significant increase in DSBs: 40.9% and 28.5% for 100 keV and 250-kVp photon irradiation, respectively. The intracellular localization showed differing levels of radiosensitization with a maximum of 64%, 27%, and 6% DSB enhancements for 100 keV, 250-kVp, and 6-MV respectively, when 90-nm GNPs congregate around the nucleus. CONCLUSION The results indicate that photon energy, GNP size, and intracellular distribution play an important role in the enhancement of DSB from direct and indirect damage under scenarios close to cell experiments. The radiosensitization effects due to indirect damage are significant and should be considered carefully.
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Affiliation(s)
- Xiandong Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ruirui Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tianyu Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Francisco J Reynoso
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
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Li WB, Stangl S, Klapproth A, Shevtsov M, Hernandez A, Kimm MA, Schuemann J, Qiu R, Michalke B, Bernal MA, Li J, Hürkamp K, Zhang Y, Multhoff G. Application of High-Z Gold Nanoparticles in Targeted Cancer Radiotherapy-Pharmacokinetic Modeling, Monte Carlo Simulation and Radiobiological Effect Modeling. Cancers (Basel) 2021; 13:5370. [PMID: 34771534 PMCID: PMC8582555 DOI: 10.3390/cancers13215370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 02/05/2023] Open
Abstract
High-Z gold nanoparticles (AuNPs) conjugated to a targeting antibody can help to improve tumor control in radiotherapy while simultaneously minimizing radiotoxicity to adjacent healthy tissue. This paper summarizes the main findings of a joint research program which applied AuNP-conjugates in preclinical modeling of radiotherapy at the Klinikum rechts der Isar, Technical University of Munich and Helmholtz Zentrum München. A pharmacokinetic model of superparamagnetic iron oxide nanoparticles was developed in preparation for a model simulating the uptake and distribution of AuNPs in mice. Multi-scale Monte Carlo simulations were performed on a single AuNP and multiple AuNPs in tumor cells at cellular and molecular levels to determine enhancements in the radiation dose and generation of chemical radicals in close proximity to AuNPs. A biologically based mathematical model was developed to predict the biological response of AuNPs in radiation enhancement. Although simulations of a single AuNP demonstrated a clear dose enhancement, simulations relating to the generation of chemical radicals and the induction of DNA strand breaks induced by multiple AuNPs showed only a minor dose enhancement. The differences in the simulated enhancements at molecular and cellular levels indicate that further investigations are necessary to better understand the impact of the physical, chemical, and biological parameters in preclinical experimental settings prior to a translation of these AuNPs models into targeted cancer radiotherapy.
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Affiliation(s)
- Wei Bo Li
- Institute of Radiation Medicine, Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; (A.K.); (K.H.)
| | - Stefan Stangl
- Center for Translational Cancer Research, Technische Universität München (TranslaTUM), Klinikum Rechts der Isar, Einsteinstr. 25, 81675 Munich, Germany; (S.S.); (M.S.); (A.H.)
- Department of Radiation Oncology, Technishe Universität München (TUM), Klinikum Rechts der Isar, Ismaningerstr. 22, 81675 Munich, Germany
| | - Alexander Klapproth
- Institute of Radiation Medicine, Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; (A.K.); (K.H.)
- Center for Translational Cancer Research, Technische Universität München (TranslaTUM), Klinikum Rechts der Isar, Einsteinstr. 25, 81675 Munich, Germany; (S.S.); (M.S.); (A.H.)
- Department of Radiation Oncology, Technishe Universität München (TUM), Klinikum Rechts der Isar, Ismaningerstr. 22, 81675 Munich, Germany
| | - Maxim Shevtsov
- Center for Translational Cancer Research, Technische Universität München (TranslaTUM), Klinikum Rechts der Isar, Einsteinstr. 25, 81675 Munich, Germany; (S.S.); (M.S.); (A.H.)
- Department of Radiation Oncology, Technishe Universität München (TUM), Klinikum Rechts der Isar, Ismaningerstr. 22, 81675 Munich, Germany
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 Saint Petersburg, Russia
- Laboratory of Biomedical Nanotechnologies, Institute of Cytology of the Russian Academy of Sciences (RAS), Tikhoretsky Ave., 4, 194064 Saint Petersburg, Russia
| | - Alicia Hernandez
- Center for Translational Cancer Research, Technische Universität München (TranslaTUM), Klinikum Rechts der Isar, Einsteinstr. 25, 81675 Munich, Germany; (S.S.); (M.S.); (A.H.)
- Department of Radiation Oncology, Technishe Universität München (TUM), Klinikum Rechts der Isar, Ismaningerstr. 22, 81675 Munich, Germany
| | - Melanie A. Kimm
- Department of Diagnostic and Interventional Radiology, Technische Universität München (TUM), Klinikum Rechts der Isar, 81675 Munich, Germany;
- Department of Radiology, University Hospital, Ludwig-Maximilians-Universität München, 81337 Munich, Germany;
| | - Jan Schuemann
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital (MGH) & Harvard Medical School, Boston, MA 02114, USA;
| | - Rui Qiu
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China;
| | - Bernhard Michalke
- Research Unit Analytical BioGeoChemistry, Helmholz Zentrum München-German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany;
| | - Mario A. Bernal
- Gleb Wataghin Institute of Physics, State University of Campinas, Campinas 13083-859, SP, Brazil;
| | - Junli Li
- Department of Radiology, University Hospital, Ludwig-Maximilians-Universität München, 81337 Munich, Germany;
| | - Kerstin Hürkamp
- Institute of Radiation Medicine, Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; (A.K.); (K.H.)
| | - Yibao Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China;
| | - Gabriele Multhoff
- Center for Translational Cancer Research, Technische Universität München (TranslaTUM), Klinikum Rechts der Isar, Einsteinstr. 25, 81675 Munich, Germany; (S.S.); (M.S.); (A.H.)
- Department of Radiation Oncology, Technishe Universität München (TUM), Klinikum Rechts der Isar, Ismaningerstr. 22, 81675 Munich, Germany
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Klapproth AP, Schuemann J, Stangl S, Xie T, Li WB, Multhoff G. Multi-scale Monte Carlo simulations of gold nanoparticle-induced DNA damages for kilovoltage X-ray irradiation in a xenograft mouse model using TOPAS-nBio. Cancer Nanotechnol 2021; 12:27. [PMID: 35663252 PMCID: PMC9165761 DOI: 10.1186/s12645-021-00099-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/12/2021] [Indexed: 11/10/2022] Open
Abstract
Background Gold nanoparticles (AuNPs) are considered as promising agents to increase the radiosensitivity of tumor cells. However, the biological mechanisms of radiation enhancement effects of AuNPs are still not well understood. We present a multi-scale Monte Carlo simulation framework within TOPAS-nBio to investigate the increase of DNA damage due to the presence of AuNPs in mouse tumor models. Methods A tumor was placed inside a voxel mouse model and irradiated with either 100 kVp or 200 kVp x-ray beams. Phase spaces were employed to transfer particles from the macroscopic (voxel) scale to the microscopic scale, which consists of a cell geometry including a detailed mouse DNA model. Radiosensitizing effects were calculated in the presence and absence of hybrid nanoparticles with a Fe2O3 core surrounded by a gold layer (AuFeNPs). To simulate DNA damage even for very small energy tracks, Geant4-DNA physics and chemistry models were used on microscopic scale. Results An AuFeNP induced enhancement of both dose and DNA strand breaks has been established for different scenarios. Produced chemical radicals including hydroxyl molecules, which were assumed to be responsible for DNA damage through chemical reactions, were found to be significantly increased. We further observed a dependency of the results on the location of the cells within the tumor for 200 kVp x-ray beams. Conclusions Our multi-scale approach allows to study irradiation induced physical and chemical effects on cells. We showed a potential increase in cell radiosensitization caused by relatively small concentrations of AuFeNPs. Our new methodology allows the individual adjustment of parameters in each simulation step and therefore can be used for other studies investigating the radiosensitizing effects of AuFeNPs or AuNPs in living cells.
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Affiliation(s)
- Alexander P. Klapproth
- Center for Translational Cancer Research Technische Universität München (TranslaTUM), Klinikum rechts der Isar, München, Germany
- Institute of Radiation Medicine, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jan Schuemann
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, United States of America
- Harvard Medical School, Boston, MA 02115, United States of America
| | - Stefan Stangl
- Center for Translational Cancer Research Technische Universität München (TranslaTUM), Klinikum rechts der Isar, München, Germany
| | - Tianwu Xie
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
- Institute of Radiation Medicine, Fudan University, Shanghai, China
| | - Wei Bo Li
- Institute of Radiation Medicine, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Gabriele Multhoff
- Center for Translational Cancer Research Technische Universität München (TranslaTUM), Klinikum rechts der Isar, München, Germany
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31
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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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Brosch-Lenz J, Yousefirizi F, Zukotynski K, Beauregard JM, Gaudet V, Saboury B, Rahmim A, Uribe C. Role of Artificial Intelligence in Theranostics:: Toward Routine Personalized Radiopharmaceutical Therapies. PET Clin 2021; 16:627-641. [PMID: 34537133 DOI: 10.1016/j.cpet.2021.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We highlight emerging uses of artificial intelligence (AI) in the field of theranostics, focusing on its significant potential to enable routine and reliable personalization of radiopharmaceutical therapies (RPTs). Personalized RPTs require patient-specific dosimetry calculations accompanying therapy. Additionally we discuss the potential to exploit biological information from diagnostic and therapeutic molecular images to derive biomarkers for absorbed dose and outcome prediction; toward personalization of therapies. We try to motivate the nuclear medicine community to expand and align efforts into making routine and reliable personalization of RPTs a reality.
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Affiliation(s)
- Julia Brosch-Lenz
- Department of Integrative Oncology, BC Cancer Research Institute, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Fereshteh Yousefirizi
- Department of Integrative Oncology, BC Cancer Research Institute, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Katherine Zukotynski
- Department of Medicine and Radiology, McMaster University, 1200 Main Street West, Hamilton, Ontario L9G 4X5, Canada
| | - Jean-Mathieu Beauregard
- Department of Radiology and Nuclear Medicine, Cancer Research Centre, Université Laval, 2325 Rue de l'Université, Québec City, Quebec G1V 0A6, Canada; Department of Medical Imaging, Research Center (Oncology Axis), CHU de Québec - Université Laval, 2325 Rue de l'Université, Québec City, Quebec G1V 0A6, Canada
| | - Vincent Gaudet
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Babak Saboury
- Department of Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA; Department of Computer Science and Electrical Engineering, University of Maryland Baltimore County, Baltimore, MD, USA; Department of Radiology, Hospital of the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Arman Rahmim
- Department of Integrative Oncology, BC Cancer Research Institute, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada; Department of Radiology, University of British Columbia, 11th Floor, 2775 Laurel St, Vancouver, British Columbia V5Z 1M9, Canada; Department of Physics, University of British Columbia, 325 - 6224 Agricultural Road, Vancouver, British Columbia V6T 1Z1, Canada
| | - Carlos Uribe
- Department of Radiology, University of British Columbia, 11th Floor, 2775 Laurel St, Vancouver, British Columbia V5Z 1M9, Canada; Department of Functional Imaging, BC Cancer, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada.
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Ramos-Méndez J, LaVerne JA, Domínguez-Kondo N, Milligan J, Štěpán V, Stefanová K, Perrot Y, Villagrasa C, Shin WG, Incerti S, McNamara A, Paganetti H, Perl J, Schuemann J, Faddegon B. TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation. Phys Med Biol 2021; 66. [PMID: 34412044 DOI: 10.1088/1361-6560/ac1f39] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 11/12/2022]
Abstract
The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependentGvalues in pure liquid water for·OH, e-aq, and H2with published experimental data. For H2O2and H·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by137Csγ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependentGvalues and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for·OH and H·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.
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Affiliation(s)
- J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
| | - J A LaVerne
- Radiation Laboratory and Department of Physics, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - N Domínguez-Kondo
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico
| | - J Milligan
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, United States of America
| | - V Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Stefanová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - Y Perrot
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - C Villagrasa
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - W-G Shin
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - S Incerti
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, F-33170 Gradignan, France
| | - A McNamara
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - H Paganetti
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - J Perl
- SLAC National Accelerator Laboratory, Menlo Park, CA, United States of America
| | - J Schuemann
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
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Lai Y, Jia X, Chi Y. Recent Developments on gMicroMC: Transport Simulations of Proton and Heavy Ions and Concurrent Transport of Radicals and DNA. Int J Mol Sci 2021; 22:ijms22126615. [PMID: 34205577 PMCID: PMC8233829 DOI: 10.3390/ijms22126615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mechanistic Monte Carlo (MC) simulation of radiation interaction with water and DNA is important for the understanding of biological responses induced by ionizing radiation. In our previous work, we employed the Graphical Processing Unit (GPU)-based parallel computing technique to develop a novel, highly efficient, and open-source MC simulation tool, gMicroMC, for simulating electron-induced DNA damages. In this work, we reported two new developments in gMicroMC: the transport simulation of protons and heavy ions and the concurrent transport of radicals in the presence of DNA. We modeled these transports based on electromagnetic interactions between charged particles and water molecules and the chemical reactions between radicals and DNA molecules. Various physical properties, such as Linear Energy Transfer (LET) and particle range, from our simulation agreed with data published by NIST or simulation results from other CPU-based MC packages. The simulation results of DNA damage under the concurrent transport of radicals and DNA agreed with those from nBio-Topas simulation in a comprehensive testing case. GPU parallel computing enabled high computational efficiency. It took 41 s to simultaneously transport 100 protons with an initial kinetic energy of 10 MeV in water and 470 s to transport 105 radicals up to 1 µs in the presence of DNA.
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Affiliation(s)
- Youfang Lai
- Department of Physics, University of Texas at Arlington, Arlington, TX 76019, USA;
- Innovative Technology of Radiotherapy Computation and Hardware (iTORCH) Laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75287, USA
| | - Xun Jia
- Innovative Technology of Radiotherapy Computation and Hardware (iTORCH) Laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75287, USA
- Correspondence: (X.J.); (Y.C.)
| | - Yujie Chi
- Department of Physics, University of Texas at Arlington, Arlington, TX 76019, USA;
- Correspondence: (X.J.); (Y.C.)
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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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Ahmadi Ganjeh Z, Eslami-Kalantari M, Ebrahimi Loushab M, Mowlavi AA. Calculation of direct DNA damages by a new approach for carbon ions and protons using Geant4-DNA. Radiat Phys Chem Oxf Engl 1993 2021. [DOI: 10.1016/j.radphyschem.2020.109249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lai Y, Jia X, Chi Y. Modeling the effect of oxygen on the chemical stage of water radiolysis using GPU-based microscopic Monte Carlo simulations, with an application in FLASH radiotherapy. Phys Med Biol 2021; 66:025004. [PMID: 33171449 DOI: 10.1088/1361-6560/abc93b] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Oxygen plays a critical role in determining the initial DNA damages induced by ionizing radiation. It is important to mechanistically model the oxygen effect in the water radiolysis process. However, due to the computational costs from the many body interaction problem, oxygen is often ignored or treated as a constant continuum radiolysis-scavenger background in the simulations using common microscopic Monte Carlo tools. In this work, we reported our recent progress on the modeling of the chemical stage of the water radiolysis with an explicit consideration of the oxygen effect, based upon our initial development of an open-source graphical processing unit (GPU)-based MC simulation tool, gMicroMC. The inclusion of oxygen mainly reduces the yields of [Formula: see text] and [Formula: see text] chemical radicals, turning them into highly toxic [Formula: see text] and [Formula: see text] species. To demonstrate the practical value of gMicroMC in large scale simulation problems, we applied the oxygen-simulation-enabled gMicroMC to compute the yields of chemical radicals under a high instantaneous dose rate [Formula: see text] to study the oxygen depletion hypothesis in FLASH radiotherapy. A decreased oxygen consumption rate (OCR) was found associated with a reduced initial oxygen concentration level due to reduced probabilities of reactions. With respect to dose rate, for the oxygen concentration of 21% and electron energy of 4.5 [Formula: see text], OCR remained approximately constant (∼0.22 [Formula: see text]) for [Formula: see text]'s of [Formula: see text], [Formula: see text] and reduced to 0.19 [Formula: see text] at [Formula: see text], because the increased dose rate improved the mutual reaction frequencies among radicals, hence reducing their reactions with oxygen. We computed the time evolution of oxygen concentration under the FLASH irradiation setups. At the dose rate of [Formula: see text] and initial oxygen concentrations from 0.01% to 21%, the oxygen is unlikely to be fully depleted with an accumulative dose of 30 Gy, which is a typical dose used in FLASH experiments. The computational efficiency of gMicroMC when considering oxygen molecules in the chemical stage was evaluated through benchmark work to GEANT4-DNA with simulating an equivalent number of radicals. With an initial oxygen concentration of 3% (∼105 molecules), a speedup factor of 1228 was achieved for gMicroMC on a single GPU card when comparing with GEANT4-DNA on a single CPU.
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Affiliation(s)
- Youfang Lai
- Department of Physics, University of Texas at Arlington, Arlington, TX 76019, United States of America. innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75287, United States of America
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Tran HN, Ramos-Méndez J, Shin WG, Perrot Y, Faddegon B, Okada S, Karamitros M, Davídková M, Štěpán V, Incerti S, Villagrasa C. Assessment of DNA damage with an adapted independent reaction time approach implemented in Geant4-DNA for the simulation of diffusion-controlled reactions between radio-induced reactive species and a chromatin fiber. Med Phys 2020; 48:890-901. [PMID: 33232522 PMCID: PMC7986154 DOI: 10.1002/mp.14612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/11/2023] Open
Abstract
Purpose Simulation of indirect damage originating from the attack of free radical species produced by ionizing radiation on biological molecules based on the independent pair approximation is investigated in this work. In addition, a new approach, relying on the independent pair approximation that is at the origin of the independent reaction time (IRT) method, is proposed in the chemical stage of Geant4‐DNA. Methods This new approach has been designed to respect the current Geant4‐DNA chemistry framework while proposing a variant IRT method. Based on the synchronous algorithm, this implementation allows us to access the information concerning the position of radicals and may make it more convenient for biological damage simulations. Estimates of the evolution of free species as well as biological hits in a segment of DNA chromatin fiber in Geant4‐DNA were compared for the dynamic time step approach of the step‐by‐step (SBS) method, currently used in Geant4‐DNA, and this newly implemented IRT. Results Results show a gain in computation time of a factor of 30 for high LET particle tracks with a better than 10% agreement on the number of DNA hits between the value obtained with the IRT method as implemented in this work and the SBS method currently available in Geant4‐DNA. Conclusion Offering in Geant4‐DNA more efficient methods for the chemical step based on the IRT method is a task in progress. For the calculation of biological damage, information on the position of chemical species is a crucial point. This can be achieved using the method presented in this paper.
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Affiliation(s)
- Hoang Ngoc Tran
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Wook-Geun Shin
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France.,Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea
| | - Yann Perrot
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Mathieu Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, In, 46556, USA
| | - Marie Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Sébastien Incerti
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
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Sakata D, Belov O, Bordage MC, Emfietzoglou D, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, Kyriakou I, Lampe N, Petrovic I, Ristic-Fira A, Shin WG, Incerti S. Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA. Sci Rep 2020; 10:20788. [PMID: 33247225 PMCID: PMC7695857 DOI: 10.1038/s41598-020-75982-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022] Open
Abstract
Ionising radiation induced DNA damage and subsequent biological responses to it depend on the radiation’s track-structure and its energy loss distribution pattern. To investigate the underlying biological mechanisms involved in such complex system, there is need of predicting biological response by integrated Monte Carlo (MC) simulations across physics, chemistry and biology. Hence, in this work, we have developed an application using the open source Geant4-DNA toolkit to propose a realistic “fully integrated” MC simulation to calculate both early DNA damage and subsequent biological responses with time. We had previously developed an application allowing simulations of radiation induced early DNA damage on a naked cell nucleus model. In the new version presented in this work, we have developed three additional important features: (1) modeling of a realistic cell geometry, (2) inclusion of a biological repair model, (3) refinement of DNA damage parameters for direct damage and indirect damage scoring. The simulation results are validated with experimental data in terms of Single Strand Break (SSB) yields for plasmid and Double Strand Break (DSB) yields for plasmid/human cell. In addition, the yields of indirect DSBs are compatible with the experimental scavengeable damage fraction. The simulation application also demonstrates agreement with experimental data of \documentclass[12pt]{minimal}
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\begin{document}$$\gamma$$\end{document}γ-H2AX yields for gamma ray irradiation. Using this application, it is now possible to predict biological response along time through track-structure MC simulations.
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Affiliation(s)
- Dousatsu Sakata
- Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, QST, Chiba, Japan.
| | - Oleg Belov
- Joint Institute for Nuclear Research, Dubna, Russia.,Dubna State University, Dubna, Russia
| | - Marie-Claude Bordage
- INSERM, UMR 1037, CRCT, Université Paul Sabatier, Toulouse, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, Medical School, University of Ioannina, 45110, Ioannina, Greece
| | - Susanna Guatelli
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - Taku Inaniwa
- Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, QST, Chiba, Japan
| | - Vladimir Ivanchenko
- Geant4 Associates International Ltd, Hebden Bridge, UK.,Tomsk State University, Tomsk, Russia
| | | | - Ioanna Kyriakou
- Medical Physics Laboratory, Medical School, University of Ioannina, 45110, Ioannina, Greece
| | | | - Ivan Petrovic
- Vinca Institute of Nuclear Science, University of Belgrade, Belgrade, Serbia
| | | | - Wook-Geun Shin
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, Gradignan, 33170, France
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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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42
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Schuemann J, Bagley AF, Berbeco R, Bromma K, Butterworth KT, Byrne HL, Chithrani BD, Cho SH, Cook JR, Favaudon V, Gholami YH, Gargioni E, Hainfeld JF, Hespeels F, Heuskin AC, Ibeh UM, Kuncic Z, Kunjachan S, Lacombe S, Lucas S, Lux F, McMahon S, Nevozhay D, Ngwa W, Payne JD, Penninckx S, Porcel E, Prise KM, Rabus H, Ridwan SM, Rudek B, Sanche L, Singh B, Smilowitz HM, Sokolov KV, Sridhar S, Stanishevskiy Y, Sung W, Tillement O, Virani N, Yantasee W, Krishnan S. Roadmap for metal nanoparticles in radiation therapy: current status, translational challenges, and future directions. Phys Med Biol 2020; 65:21RM02. [PMID: 32380492 DOI: 10.1088/1361-6560/ab9159] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This roadmap outlines the potential roles of metallic nanoparticles (MNPs) in the field of radiation therapy. MNPs made up of a wide range of materials (from Titanium, Z = 22, to Bismuth, Z = 83) and a similarly wide spectrum of potential clinical applications, including diagnostic, therapeutic (radiation dose enhancers, hyperthermia inducers, drug delivery vehicles, vaccine adjuvants, photosensitizers, enhancers of immunotherapy) and theranostic (combining both diagnostic and therapeutic), are being fabricated and evaluated. This roadmap covers contributions from experts in these topics summarizing their view of the current status and challenges, as well as expected advancements in technology to address these challenges.
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Affiliation(s)
- Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, MA 02114, United States of America
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Mahdi SM, Babak SB. Dosimetry study on Auger electron-emitting nuclear medicine radioisotopes in micrometer and nanometer scales using Geant4-DNA simulation. Int J Radiat Biol 2020; 96:1452-1465. [DOI: 10.1080/09553002.2020.1820608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Cellular S values in spindle-shaped cells: a dosimetry study on more realistic cell geometries using Geant4-DNA Monte Carlo simulation toolkit. Ann Nucl Med 2020; 34:742-756. [PMID: 32632563 DOI: 10.1007/s12149-020-01498-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/01/2020] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Cellular dosimetry plays a crucial role in radiobiology and evaluation of the relative merits of radiopharmaceuticals used for targeted radionuclide therapy. The present study aims to investigate the effects of various cell geometries on dosimetric characteristics of several Auger emitters distributed in different subcellular compartments using Monte Carlo simulation. METHODS The Geant4-DNA extension of the Geant4 Monte Carlo simulation toolkit was employed to calculate the mean absorbed dose per unit cumulated activity (S value) for different subcellular distributions of several Auger electron-emitting theranostic radionuclides including 99mTc, 111In, 123I, 125I, and 201Tl. The simulations were carried out in various single-cell models of liquid water including spherical, ellipsoidal, spherical spindle, and ellipsoidal spindle cell models. The latter two models which are generalized from the first two models were inspired by the morphologies of spindle-shaped (fusiform) cells, and were developed to provide more realistic modeling of this common geometry observed in many healthy and cancerous cells. RESULTS Evaluation of the S values calculated for the examined cell models reveals that the differences are small (less than 9%) for the cell ← cell, cell ← cell surface, and nucleus ← nucleus source-target combinations. However, moderate discrepancies are seen (up to 28%) when the nucleus is considered as the target, as well as the radioactivity is either internalized into the cytoplasm or bound to the cell membrane. CONCLUSIONS The findings of the present work suggest that the assumption of spherical cell geometry may provide reasonably accurate estimates of the cellular/nuclear dose for the considered Auger emitters, even for spindle-shaped cells. Of course, this approximation should be used with caution for the nucleus ← cytoplasm and nucleus ← cell surface configurations, since the S-value sensitivity to the cell geometry is somewhat significant in these cases.
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Zhu H, McNamara AL, Ramos-Mendez J, McMahon SJ, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J. A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio. Phys Med Biol 2020; 65:085015. [PMID: 32101803 DOI: 10.1088/1361-6560/ab7a6b] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Monte Carlo (MC) track structure simulation tools are commonly used for predicting radiation induced DNA damage by modeling the physical and chemical reactions at the nanometer scale. However, the outcome of these MC simulations is particularly sensitive to the adopted parameters which vary significantly across studies. In this study, a previously developed full model of nuclear DNA was used to describe the DNA geometry. The TOPAS-nBio MC toolkit was used to investigate the impact of physics and chemistry models as well as three key parameters (the energy threshold for direct damage, the chemical stage time length, and the probability of damage between hydroxyl radical reactions with DNA) on the induction of DNA damage. Our results show that the difference in physics and chemistry models alone can cause differences up to 34% and 16% in the DNA double strand break (DSB) yield, respectively. Additionally, changing the direct damage threshold, chemical stage length, and hydroxyl damage probability can cause differences of up to 28%, 51%, and 71% in predicted DSB yields, respectively, for the configurations in this study.
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Affiliation(s)
- Hongyu Zhu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, United States of America. Department of Engineering Physics, Tsinghua University, Beijing 100084, People's Republic of China. Key Laboratory of Particle and Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, People's Republic of China
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Ionizing Radiation and Complex DNA Damage: Quantifying the Radiobiological Damage Using Monte Carlo Simulations. Cancers (Basel) 2020; 12:cancers12040799. [PMID: 32225023 PMCID: PMC7226293 DOI: 10.3390/cancers12040799] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023] Open
Abstract
Ionizing radiation is a common tool in medical procedures. Monte Carlo (MC) techniques are widely used when dosimetry is the matter of investigation. The scientific community has invested, over the last 20 years, a lot of effort into improving the knowledge of radiation biology. The present article aims to summarize the understanding of the field of DNA damage response (DDR) to ionizing radiation by providing an overview on MC simulation studies that try to explain several aspects of radiation biology. The need for accurate techniques for the quantification of DNA damage is crucial, as it becomes a clinical need to evaluate the outcome of various applications including both low- and high-energy radiation medical procedures. Understanding DNA repair processes would improve radiation therapy procedures. Monte Carlo simulations are a promising tool in radiobiology studies, as there are clear prospects for more advanced tools that could be used in multidisciplinary studies, in the fields of physics, medicine, biology and chemistry. Still, lot of effort is needed to evolve MC simulation tools and apply them in multiscale studies starting from small DNA segments and reaching a population of cells.
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Lai Y, Tsai MY, Tian Z, Qin N, Yan C, Hung SH, Chi Y, Jia X. A new open-source GPU-based microscopic Monte Carlo simulation tool for the calculations of DNA damages caused by ionizing radiation - Part II: sensitivity and uncertainty analysis. Med Phys 2020; 47:1971-1982. [PMID: 31975390 DOI: 10.1002/mp.14036] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/26/2019] [Accepted: 01/13/2020] [Indexed: 11/05/2022] Open
Abstract
PURPOSE Calculations of deoxyribonucleic acid (DNA) damages involve many parameters in the computation process. As these parameters are often subject to uncertainties, it is of central importance to comprehensively quantify their impacts on DNA single-strand break (SSB) and double-strand break (DSB) yields. This has been a challenging task due to the required large number of simulations and the relatively low computational efficiency using CPU-based MC packages. In this study, we present comprehensive evaluations on sensitivities and uncertainties of DNA SSB and DSB yields on 12 parameters using our GPU-based MC tool, gMicroMC. METHODS We sampled one electron at a time in a water sphere containing a human lymphocyte nucleus and transport the electrons and generated radicals until 2 Gy dose was accumulated in the nucleus. We computed DNA damages caused by electron energy deposition events in the physical stage and the hydroxyl radicals at the end of the chemical stage. We repeated the computations by varying 12 parameters: (a) physics cross section, (b) cutoff energy for electron transport, (c)-(e) three branching ratios of hydroxyl radicals in the de-excitation of excited water molecules, (f) temporal length of the chemical stage, (g)-(h) reaction radii for direct and indirect damages, (i) threshold energy defining the threshold damage model to generate a physics damage, (j)-(k) minimum and maximum energy values defining the linear-probability damage model to generate a physics damage, and (l) probability to generate a damage by a radical. We quantified sensitivity of SSB and DSB yields with respect to these parameters for cases with 1.0 and 4.5 keV electrons. We further estimated uncertainty of SSB and DSB yields caused by uncertainties of these parameters. RESULTS Using a threshold of 10% uncertainty as a criterion, threshold energy in the threshold damage model, maximum energy in the linear-probability damage model, and probability for a radical to generate a damage were found to cause large uncertainties in both SSB and DSB yields. The scaling factor of the cross section, cutoff energy, physics reaction radius, and minimum energy in the linear-probability damage model were found to generate large uncertainties in DSB yields. CONCLUSIONS We identified parameters that can generate large uncertainties in the calculations of SSB and DSB yields. Our study could serve as a guidance to reduce uncertainties of parameters and hence uncertainties of the simulation results.
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Affiliation(s)
- Youfang Lai
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA.,Department of Physics, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Min-Yu Tsai
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA.,Department of Computer Science & Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Zhen Tian
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA
| | - Nan Qin
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA
| | - Congchong Yan
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA
| | - Shih-Hao Hung
- Department of Computer Science & Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Yujie Chi
- Department of Physics, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Xun Jia
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA
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Tsai MY, Tian Z, Qin N, Yan C, Lai Y, Hung SH, Chi Y, Jia X. A new open-source GPU-based microscopic Monte Carlo simulation tool for the calculations of DNA damages caused by ionizing radiation --- Part I: Core algorithm and validation. Med Phys 2020; 47:1958-1970. [PMID: 31971258 DOI: 10.1002/mp.14037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/26/2019] [Accepted: 01/13/2020] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Monte Carlo (MC) simulation of radiation interactions with water medium at physical, physicochemical, and chemical stages, as well as the computation of biologically relevant quantities such as DNA damages, are of critical importance for the understanding of microscopic basis of radiation effects. Due to the large problem size and many-body simulation problem in the chemical stage, existing CPU-based computational packages encounter the problem of low computational efficiency. This paper reports our development on a GPU-based microscopic Monte Carlo simulation tool gMicroMC using advanced GPU-acceleration techniques. METHODS gMicroMC simulated electron transport in the physical stage using an interaction-by-interaction scheme to calculate the initial events generating radicals in water. After the physicochemical stage, initial positions of all radicals were determined. Simulation of radicals' diffusion and reactions in the chemical stage was achieved using a step-by-step model using GPU-accelerated parallelization together with a GPU-enabled box-sorting algorithm to reduce the computations of searching for interaction pairs and therefore improve efficiency. A multi-scale DNA model of the whole lymphocyte cell nucleus containing ~6.2 Gbp of DNA was built. RESULTS Accuracy of physical stage simulation was demonstrated by computing stopping power and track length. The results agreed with published data and the data produced by GEANT4-DNA (version 10.3.3) simulations with 10 -20% difference in most cases. Difference of yield values of major radiolytic species from GEANT4-DNA results was within 10%. We computed DNA damages caused by monoenergetic 662 keV photons, approximately representing 137 Cs decay. Single-strand break (SSB) and double-strand break (DSB) yields were 196 ± 8 SSB/Gy/Gbp and 7.3 ± 0.7 DSB/Gy/Gbp, respectively, which agreed with the result of 188 SSB/Gy/Gbp and 8.4 DSB/Gy/Gbp computed by Hsiao et al. Compared to computation using a single CPU, gMicroMC achieved a speedup factor of ~540x using an NVidia TITAN Xp GPU card. CONCLUSIONS The achieved accuracy and efficiency demonstrated that gMicroMC can facilitate research on microscopic radiation transport simulation and DNA damage calculation. gMicroMC is an open-source package available to the research community.
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Affiliation(s)
- Min-Yu Tsai
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA.,Department of Computer Science & Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Zhen Tian
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA
| | - Nan Qin
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA
| | - Congchong Yan
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA
| | - Youfang Lai
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA.,Department of Physics, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Shih-Hao Hung
- Department of Computer Science & Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Yujie Chi
- Department of Physics, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Xun Jia
- Innovative Technology Of Radiotherapy Computation and Hardware (iTORCH) laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75287, USA
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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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Zabihi A, Incerti S, Francis Z, Forozani G, Semsarha F, Moslehi A, Rezaeian P, Bernal MA. Computational approach to determine the relative biological effectiveness of fast neutrons using the Geant4-DNA toolkit and a DNA atomic model from the Protein Data Bank. Phys Rev E 2019; 99:052404. [PMID: 31212425 DOI: 10.1103/physreve.99.052404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 11/07/2022]
Abstract
This study proposes an innovative approach to estimate relative biological effectiveness (RBE) of fast neutrons using the Geant4 toolkit. The Geant4-DNA version cannot track heavy ions below 0.5 MeV/nucleon. In order to explore the impact of this issue, secondary particles are simulated instead of the primary low-energy neutrons. The Evaluated Nuclear Data File library is used to determine the cross sections for the elastic and inelastic interactions of neutrons with water and to find the contribution of each secondary particle spectrum. Two strategies are investigated in order to find the best possible approach and results. The first one takes into account only light particles, protons produced from elastic scattering, and α particles from inelastic scattering. Geantino particles are shot instead of heavy ions; hence all heavy ions are considered in the simulations, though their physical effects on DNA not. The second strategy takes into account all the heavy and light ions, although heavy ions cannot be tracked down to very low energies (E<0.5 MeV/nucleon). Our model is based on the combination of an atomic resolution DNA geometrical model and a Monte Carlo simulation toolkit for tracking particles. The atomic coordinates of the DNA double helix are extracted from the Protein Data Bank. Since secondary particle spectra are used instead of simulating the interaction of neutrons explicitly, this method reduces the computation times dramatically. Double-strand break induction is used as the end point for the estimation of the RBE of fast neutrons. ^{60}Co γ rays are used as the reference radiation quality. Both strategies succeed in reproducing the behavior of the RBE_{max} as a function of the incident neutron energy ranging from 0.1 to 14 MeV, including the position of its peak. A comparison of the behavior of the two strategies shows that for neutrons with energies less than 0.7 MeV, the effect of heavy ions would not be very significant, but above 0.7 MeV, heavy ions have an important role in neutron RBE.
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Affiliation(s)
- Azam Zabihi
- Department of Physics, Faculty of Science, Bu-Ali Sina University, Hamedan 651744161, Iran
| | - Sebastien Incerti
- University of Bordeaux, CENBG, UMR No. 5797, 33170 Gradignan, France CNRS, IN2P3, CENBG, UMR No. 5797, 33170 Gradignan, France
| | - Ziad Francis
- Department of Physics, Faculty of Sciences, Université Saint Joseph, 2020 1104 Beirut, Lebanon
| | - Ghasem Forozani
- Department of Physics, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran
| | - Farid Semsarha
- Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, Tehran, Iran
| | - Amir Moslehi
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, P.O. Box 11365-3486, Tehran, Iran
| | - Peiman Rezaeian
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, P.O. Box 11365-3486, Tehran, Iran
| | - Mario A Bernal
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, Campinas, 13083-859 São Paulo, Brazil
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