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Liu Y, Zhu K, Peng X, Luo S, Zhu J, Xiao W, He L, Wang X. Proton relative biological effectiveness for the induction of DNA double strand breaks based on Geant4. Biomed Phys Eng Express 2024; 10:035018. [PMID: 38181453 DOI: 10.1088/2057-1976/ad1bb9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/05/2024] [Indexed: 01/07/2024]
Abstract
Uncertainties in the relative biological effectiveness (RBE) of proton remains a major barrier to the biological optimization of proton therapy. A large amount of experimental data suggest that proton RBE is variable. As an evolving Monte Carlo code toolkit, Geant4-DNA is able to simulate the initial DNA damage caused by particle beams through physical and chemical interactions at the nanometer scale over a short period of time. This contributes to evaluating the radiobiological effects induced by ionizing radiation. Based on the Geant4-DNA toolkit, this study constructed a DNA geometric model containing 6.32Gbp, simulated the relationship between radiochemical yields (G-values) and their corresponding chemical constructors, and calculated a detailed calculation of the sources of damage and the complexity of damage in DNA strand breaks. The damage model constructed in this study can simulate the relative biological effectiveness (RBE) in the proton Bragg peak region. The results indicate that: (1) When the electron energy is below 400 keV, the yield of OH·account for 18.1% to 25.3% of the total water radiolysis yields. (2) Under the influence of histone clearance function, the yield of indirect damage account for over 72.93% of the yield of DNA strand breaks (SBs). When linear energy transfer (LET) increased from 29.79 (keV/μm) to 64.29 (keV/μm), the yield of double strand breaks (DSB) increased from 17.27% to 32.65%. (3) By investigating the effect of proton Bragg peak depth on the yield of direct DSB (DSBdirect) and total DSB (DSBtotal), theRBEDSBtotandRBEDSBdirlevels of cells show that the RBE value of protons reaches 2.2 in the Bragg peak region.
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Affiliation(s)
- Yuchen Liu
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Kun Zhu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou 215123, People's Republic of China
| | - Xiaoyu Peng
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Siyuan Luo
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Jin Zhu
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Wancheng Xiao
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Lie He
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
| | - Xiaodong Wang
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, People's Republic of China
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2
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Rezaee M, Adhikary A. The Effects of Particle LET and Fluence on the Complexity and Frequency of Clustered DNA Damage. DNA 2024; 4:34-51. [PMID: 38282954 PMCID: PMC10810015 DOI: 10.3390/dna4010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Motivation Clustered DNA-lesions are predominantly induced by ionizing radiation, particularly by high-LET particles, and considered as lethal damage. Quantification of this specific type of damage as a function of radiation parameters such as LET, dose rate, dose, and particle type can be informative for the prediction of biological outcome in radiobiological studies. This study investigated the induction and complexity of clustered DNA damage for three different types of particles at an LET range of 0.5-250 keV/μm. Methods Nanometric volumes (36.0 nm3) of 15 base-pair DNA with its hydration shell was modeled. Electron, proton, and alpha particles at various energies were simulated to irradiate the nanometric volumes. The number of ionization events, low-energy electron spectra, and chemical yields for the formation of °OH, H°, e aq - , and H2O2 were calculated for each particle as a function of LET. Single- and double-strand breaks (SSB and DSB), base release, and clustered DNA-lesions were computed from the Monte-Carlo based quantification of the reactive species and measured yields of the species responsible for the DNA lesion formation. Results The total amount of DNA damage depends on particle type and LET. The number of ionization events underestimates the quantity of DNA damage at LETs higher than 10 keV/μm. Minimum LETs of 9.4 and 11.5 keV/μm are required to induce clustered damage by a single track of proton and alpha particles, respectively. For a given radiation dose, an increase in LET reduces the number of particle tracks, leading to more complex clustered DNA damage, but a smaller number of separated clustered damage sites. Conclusions The dependency of the number and the complexity of clustered DNA damage on LET and fluence suggests that the quantification of this damage can be a useful method for the estimation of the biological effectiveness of radiation. These results also suggest that medium-LET particles are more appropriate for the treatment of bulk targets, whereas high-LET particles can be more effective for small targets.
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Affiliation(s)
- Mohammad Rezaee
- Department of Radiation Oncology and Molecular Radiation Sciences, School of Medicine, Johns Hopkins University, 1550 Orleans St., Baltimore, MD 21231, USA
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309, USA
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3
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Lamghari Y, Lu H, Bentourkia M. DNA damage by radiation as a function of electron energy and interaction at the atomic level with Monte Carlo simulation. Z Med Phys 2023; 33:489-498. [PMID: 35973908 PMCID: PMC10751702 DOI: 10.1016/j.zemedi.2022.07.003] [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: 03/19/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022]
Abstract
In radiotherapy, X-ray or heavy ion beams target tumors to cause damage to their cell DNA. This damage is mainly induced by secondary low energy electrons. In this paper, we report the DNA molecular breaks at the atomic level as a function of electron energy and types of electron interactions using of Monte Carlo simulation. The number of DNA single and double strand breaks are compared to those from experimental results based on electron energies. In recent years, DNA atomistic models were introduced but still the simulations consider energy deposition in volumes of DNA or water equivalent material. We simulated a model of atomistic B-DNA in vacuum, forming 1122 base pairs of 30 nm in length. Each atom has been represented by a sphere whose radius equals the radius of van der Waals. We repeatedly simulated 10 million electrons for each energy from 4 eV to 500 eV and counted each interaction type with its position x, y, z in the volume of DNA. Based on the number and types of interactions at the atomic level, the number of DNA single and double strand breaks were calculated. We found that the dissociative electron attachment has the dominant effect on DNA strand breaks at energies below 10 eV compared to excitation and ionization. In addition, it is straightforward with our simulation to discriminate the strand and base breaks as a function of radiation interaction type and energy. In conclusion, the knowledge of DNA damage at the atomic level helps design direct internal therapeutic agents of cancer treatment.
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Affiliation(s)
- Youssef Lamghari
- Department of Nuclear Medicine and Radiobiology, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Huizhong Lu
- Department of Nuclear Medicine and Radiobiology, University of Sherbrooke, Sherbrooke, QC, Canada
| | - M'hamed Bentourkia
- Department of Nuclear Medicine and Radiobiology, University of Sherbrooke, Sherbrooke, QC, Canada.
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4
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Chen X, Karmaker N, Cloutier P, Bass AD, Zheng Y, Sanche L. Low-Energy Electron Damage to Plasmid DNA in Thin Films: Dependence on Substrates, Surface Density, Charging, Environment, and Uniformity. J Phys Chem B 2022; 126:5443-5457. [PMID: 35834372 DOI: 10.1021/acs.jpcb.2c03664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of low-energy electrons (LEEs) with DNA plays a significant role in the mechanisms leading to biological damage induced by ionizing radiation, particularly in radiotherapy, and its sensitization by chemotherapeutic drugs and nanoparticles. Plasmids constitute the form of DNA found in mitochondria and appear as a suitable model of genomic DNA. In a search for the best LEE targets, damage was induced to plasmids, in thin films in vacuum, by 6, 10, and 100 eV electrons under single collision conditions. The yields of single- and double-strand breaks, other cluster damage, isolated base lesions, and crosslinks were measured by electrophoresis and enzyme treatment. The films were deposited on oriented graphite or polycrystalline tantalum, with or without DNA autoassembly via diaminopropane (Dap) intercalation. Yields were correlated with the influence of vacuum, film uniformity, surface density, substrates, and the DNA environment. Aided by surface potential measurements and scanning electron microscopy and atomic force microscopy images, the lyophilized Dap-DNA films were found to be the most practical high-quality targets. These studies pave the way to the fabrication of LEE target-films composed of plasmids intercalated with biomolecules that could mimic the cellular environment; for example, as a first step, by replacing Dap with an amino acid.
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Affiliation(s)
- Xingju Chen
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P. R. China
| | - Nanda Karmaker
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Pierre Cloutier
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Andrew D Bass
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P. R. China.,Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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5
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Clinical Feasibility Study of Gold Nanoparticles as Theragnostic Agents for Precision Radiotherapy. Biomedicines 2022; 10:biomedicines10051214. [PMID: 35625950 PMCID: PMC9139134 DOI: 10.3390/biomedicines10051214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Gold nanoparticles (AuNP) may be useful in precision radiotherapy and disease monitoring as theragnostic agents. In diagnostics, they can be detected by computerized tomography (CT) because of their higher atomic number. AuNP may also improve the treatment results in radiotherapy due to a higher cross-section, locally improving the physically absorbed dose. Methods: Key parameters values involved in the use of AuNP were imposed to be optimal in the clinical scenario. Mass concentration of AuNP as an efficient contrast agent in clinical CT was found and implemented in a Monte Carlo simulation method for dose calculation under different proposed therapeutic beams. The radiosensitization effect was determined in irradiated cells with AuNP. Results: an AuNP concentration was found for a proper contrast level and enhanced therapeutic effect under a beam typically used for image-guided therapy and monitoring. This lower energetic proposed beam showed potential use for treatment monitoring in addition to absorbed dose enhancement and higher radiosensitization at the cellular level. Conclusion: the results obtained show the use of AuNP concentration around 20 mg Au·mL−1 as an efficient tool for diagnosis, treatment planning, and monitoring treatment. Simultaneously, the delivered prescription dose provides a higher radiobiological effect on the cancer cell for achieving precision radiotherapy.
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Mosley RJ, Hart J, Davis KL, Wower J, Byrne ME. Tailored Nucleic Acid Architectures at Gold Surfaces for Controlled Therapeutic Release. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1698-1704. [PMID: 35073106 DOI: 10.1021/acs.langmuir.1c02718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nucleic acids are versatile materials capable of forming smart nanocarriers with highly controllable therapeutic delivery. DNA-gated release is a mechanism by which DNA oligonucleotides physically block the release of encapsulated drugs from porous nanoparticles. We extend this mechanism to be used with drugs bound to the surface of DNA-capped gold nanoparticles (AuNPs). We investigated DNA monolayers of different thicknesses and hybridization states to determine how DNA surface architecture can affect the release of a template drug bound to the gold surface. DNA layers are investigated on the planar gold surface via quartz crystal microbalance with dissipation and on AuNPs via dynamic light scattering. The resultant layer architectures were studied for their effect on the release rate of drugs. We observed that varying DNA architectures on AuNPs result in different release rates of the drug. The rate of drug release can be slowed using either folded or randomly coiled DNA sequences, which act as a physical barrier to diffusion. DNA monolayers with upright orientation release drugs more quickly. When the longer single-stranded DNA is used, the drug release is slowed even further. However, even upright DNA layers provide a barrier to drug diffusion at longer sequence lengths. We hypothesize that it is the architecture of the DNA layer, influenced by the folded or upright orientation of individual DNA molecules, that affects the free diffusion of the drug away from the AuNP surface. This mechanism may improve the biological availability of many surface-bound drugs on solid, DNA-capped nanoparticles.
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Affiliation(s)
- Robert J Mosley
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, Rowan University, Glassboro, New Jersey 08028, United States
| | - Julia Hart
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, Rowan University, Glassboro, New Jersey 08028, United States
| | - Kadie L Davis
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, Rowan University, Glassboro, New Jersey 08028, United States
| | - Jacek Wower
- RNA Biochemistry Laboratories, Department of Animal Sciences, Auburn University, Auburn, Alabama 36849, United States
| | - Mark E Byrne
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, Rowan University, Glassboro, New Jersey 08028, United States
- Department of Chemical Engineering, Rowan University, Glassboro, New Jersey 08028, United States
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Coudy D, Colotte M, Luis A, Tuffet S, Bonnet J. Long term conservation of DNA at ambient temperature. Implications for DNA data storage. PLoS One 2021; 16:e0259868. [PMID: 34763344 PMCID: PMC8585539 DOI: 10.1371/journal.pone.0259868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/27/2021] [Indexed: 11/18/2022] Open
Abstract
DNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and for DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25°C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.
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Affiliation(s)
- Delphine Coudy
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
| | - Marthe Colotte
- Imagene, plateforme de production, Genopole, Evry, France
| | - Aurélie Luis
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
| | - Sophie Tuffet
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
- Imagene, plateforme de production, Genopole, Evry, France
| | - Jacques Bonnet
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
- Université de Bordeaux, Institut Bergonié, INSERM, Bordeaux, France
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8
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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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Montgomery L, Lund CM, Landry A, Kildea J. Towards the characterization of neutron carcinogenesis through direct action simulations of clustered DNA damage. Phys Med Biol 2021; 66. [PMID: 34555818 DOI: 10.1088/1361-6560/ac2998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/23/2021] [Indexed: 11/11/2022]
Abstract
Neutron exposure poses a unique radiation protection concern because neutrons have a large, energy-dependent relative biological effectiveness (RBE) for stochastic effects. Recent computational studies on the microdosimetric properties of neutron dose deposition have implicated clustered DNA damage as a likely contributor to this marked energy dependence. So far, publications have focused solely on neutron RBE for inducing clusters of DNA damage containing two or more DNA double strand breaks (DSBs). In this study, we have conducted a novel assessment of neutron RBE for inducing all types of clustered DNA damage that contain two or more lesions, stratified by whether the clusters contain DSBs (complex DSB clusters) or not (non-DSB clusters). This assessment was conducted for eighteen initial neutron energies between 1 eV and 10 MeV as well as a reference radiation of 250 keV x-rays. We also examined the energy dependence of cluster length and cluster complexity because these factors are believed to impact the DNA repair process. To carry out our investigation, we developed a user-friendly TOPAS-nBio application that includes a custom nuclear DNA model and a novel algorithm for recording clustered DNA damage. We found that neutron RBE for inducing complex DSB clusters exhibited similar energy dependence to the canonical neutron RBE for stochastic radiobiological effects, at multiple depths in human tissue. Qualitatively similar results were obtained for non-DSB clusters, although the quantitative agreement was lower. Additionally we identified a significant neutron energy dependence in the average length and complexity of clustered lesions. These results support the idea that many types of clustered DNA damage contribute to the energy dependence of neutron RBE for stochastic radiobiological effects and imply that the size and constituent lesions of individual clusters should be taken into account when modeling DNA repair. Our results were qualitatively consistent for (i) multiple radiation doses (including a low-dose 0.1 Gy irradiation), (ii) variations in the maximal lesion separation distance used to define a cluster, and (iii) two distinct collections of physics models used to govern particle transport. Our complete TOPAS-nBio application has been released under an open-source license to enable others to independently validate our work and to expand upon it.
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Affiliation(s)
- Logan Montgomery
- Medical Physics Unit, McGill University, Montreal, QC, H4A3J1, Canada
| | | | - Anthony Landry
- Prince Edward Island Cancer Treatment Centre, Charlottetown, PE, C1A8T5, Canada.,Department of Radiation Oncology, Dalhousie University, Halifax, NS, B3H4RZ, Canada
| | - John Kildea
- Medical Physics Unit, McGill University, Montreal, QC, H4A3J1, Canada
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Zhu H, McNamara AL, McMahon SJ, Ramos-Mendez J, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J. Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio. Radiat Res 2020; 194:9-21. [PMID: 32401689 DOI: 10.1667/rr15531.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/11/2020] [Indexed: 12/21/2022]
Abstract
The cellular response to ionizing radiation continues to be of significant research interest in cancer radiotherapy, and DNA is recognized as the critical target for most of the biologic effects of radiation. Incident particles can cause initial DNA damages through physical and chemical interactions within a short time scale. Initial DNA damages can undergo repair via different pathways available at different stages of the cell cycle. The misrepair of DNA damage results in genomic rearrangement and causes mutations and chromosome aberrations, which are drivers of cell death. This work presents an integrated study of simulating cell response after proton irradiation with energies of 0.5-500 MeV (LET of 60-0.2 keV/µm). A model of a whole nucleus with fractal DNA geometry was implemented in TOPAS-nBio for initial DNA damage simulations. The default physics and chemistry models in TOPAS-nBio were used to describe interactions of primary particles, secondary particles, and radiolysis products within the nucleus. The initial DNA double-strand break (DSB) yield was found to increase from 6.5 DSB/Gy/Gbp at low-linear energy transfer (LET) of 0.2 keV/µm to 21.2 DSB/Gy/Gbp at high LET of 60 keV/µm. A mechanistic repair model was applied to predict the characteristics of DNA damage repair and dose response of chromosome aberrations. It was found that more than 95% of the DSBs are repaired within the first 24 h and the misrepaired DSB fraction increases rapidly with LET and reaches 15.8% at 60 keV/µm with an estimated chromosome aberration detection threshold of 3 Mbp. The dicentric and acentric fragment yields and the dose response of micronuclei formation after proton irradiation were calculated and compared with experimental results.
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Affiliation(s)
- Hongyu Zhu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China.,Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, P.R. China
| | - Aimee L McNamara
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Stephen J McMahon
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
| | - Jose Ramos-Mendez
- Department of Radiation Oncology, University of California San Francisco, California 94143
| | - Nicholas T Henthorn
- Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, California 94143
| | - Kathryn D Held
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Joseph Perl
- SLAC National Accelerator Laboratory, Menlo Park, California
| | - Junli Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China.,Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, P.R. China
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
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11
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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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12
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Yang X, Li Z, Polyakova T, Dejneka A, Zablotskii V, Zhang X. Effect of static magnetic field on DNA synthesis: The interplay between DNA chirality and magnetic field left-right asymmetry. FASEB Bioadv 2020; 2:254-263. [PMID: 32259051 PMCID: PMC7133733 DOI: 10.1096/fba.2019-00045] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 05/26/2019] [Accepted: 02/03/2020] [Indexed: 12/13/2022] Open
Abstract
Interactions between magnetic fields (MFs) and living cells may stimulate a large variety of cellular responses to a MF, while the underlying intracellular mechanisms still remain a great puzzle. On a fundamental level, the MF - cell interaction is affected by the two broken symmetries: (a) left-right (LR) asymmetry of the MF and (b) chirality of DNA molecules carrying electric charges and subjected to the Lorentz force when moving in a MF. Here we report on the chirality-driven effect of static magnetic fields (SMFs) on DNA synthesis. This newly discovered effect reveals how the interplay between two fundamental features of symmetry in living and inanimate nature-DNA chirality and the inherent features of MFs to distinguish the left and right-manifests itself in different DNA synthesis rates in the upward and downward SMFs, consequently resulting in unequal cell proliferation for the two directions of the field. The interplay between DNA chirality and MF LR asymmetry will provide fundamental knowledge for many MF-induced biological phenotypes.
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Affiliation(s)
- Xingxing Yang
- High Magnetic Field LaboratoryKey Laboratory of High Magnetic Field and Ion Beam Physical BiologyHefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- Science Island Branch of Graduate SchoolUniversity of Science and Technology of ChinaHefeiChina
| | - Zhiyuan Li
- High Magnetic Field LaboratoryKey Laboratory of High Magnetic Field and Ion Beam Physical BiologyHefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
| | - Tatyana Polyakova
- Institute of Physics of the Czech Academy of SciencesPragueCzech Republic
| | - Alexandr Dejneka
- Institute of Physics of the Czech Academy of SciencesPragueCzech Republic
| | - Vitalii Zablotskii
- Institute of Physics of the Czech Academy of SciencesPragueCzech Republic
| | - Xin Zhang
- High Magnetic Field LaboratoryKey Laboratory of High Magnetic Field and Ion Beam Physical BiologyHefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- Science Island Branch of Graduate SchoolUniversity of Science and Technology of ChinaHefeiChina
- Institutes of Physical Science and Information TechnologyAnhui UniversityHefeiChina
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13
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Henthorn NT, Warmenhoven JW, Sotiropoulos M, Aitkenhead AH, Smith EAK, Ingram SP, Kirkby NF, Chadwick A, Burnet NG, Mackay RI, Kirkby KJ, Merchant MJ. Clinically relevant nanodosimetric simulation of DNA damage complexity from photons and protons. RSC Adv 2019; 9:6845-6858. [PMID: 35518487 PMCID: PMC9061037 DOI: 10.1039/c8ra10168j] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
Relative Biological Effectiveness (RBE), the ratio of doses between radiation modalities to produce the same biological endpoint, is a controversial and important topic in proton therapy. A number of phenomenological models incorporate variable RBE as a function of Linear Energy Transfer (LET), though a lack of mechanistic description limits their applicability. In this work we take a different approach, using a track structure model employing fundamental physics and chemistry to make predictions of proton and photon induced DNA damage, the first step in the mechanism of radiation-induced cell death. We apply this model to a proton therapy clinical case showing, for the first time, predictions of DNA damage on a patient treatment plan. Our model predictions are for an idealised cell and are applied to an ependymoma case, at this stage without any cell specific parameters. By comparing to similar predictions for photons, we present a voxel-wise RBE of DNA damage complexity. This RBE of damage complexity shows similar trends to the expected RBE for cell kill, implying that damage complexity is an important factor in DNA repair and therefore biological effect. Relative Biological Effectiveness (RBE) is a controversial and important topic in proton therapy. This work uses Monte Carlo simulations of DNA damage for protons and photons to probe this phenomenon, providing a plausible mechanistic understanding.![]()
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Affiliation(s)
- N. T. Henthorn
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - J. W. Warmenhoven
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - M. Sotiropoulos
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - A. H. Aitkenhead
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - E. A. K. Smith
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - S. P. Ingram
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - N. F. Kirkby
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - A. L. Chadwick
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - N. G. Burnet
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - R. I. Mackay
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - K. J. Kirkby
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
| | - M. J. Merchant
- Division of Cancer Sciences
- School of Medical Sciences
- Faculty of Biology, Medicine and Health
- The University of Manchester
- UK
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14
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Brodeur N, Cloutier P, Bass AD, Bertrand G, Hunting DJ, Grandbois M, Sanche L. Absolute cross section for DNA damage induced by low-energy (10 eV) electrons: Experimental refinements and sample characterization by AFM. J Chem Phys 2018; 149:164904. [PMID: 30384690 DOI: 10.1063/1.5041805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This work describes multiple experimental improvements for measuring absolute cross sections of DNA damage induced by low-energy electrons in nanometer-thick films in vacuum. Measurements of such cross sections are particularly sensitive to film thickness and uniformity. Using atomic force microscopy in 70% ethanol, we present a novel and effective method to determine plasmid DNA film thickness and uniformity that combines height histograms and force-distance curves. We also investigate film deposition with DNA intercalated with 1,3-diaminopropane (Dap) on tantalum-coated substrates as a convenient and cost-effective alternative to the previously-used graphite substrate. The tantalum substrate permits deposition of films very similar to those formed on graphite. Using these refinements and further optimizations of the experimental procedure, we measure an absolute cross section of (7.4 ± 2.3) × 10-18 cm2 per nucleotide for conformational damage to a 3197 base-pair plasmid, induced by 10 eV electrons, which we believe should be considered as a reference value.
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Affiliation(s)
- N Brodeur
- Department of Nuclear Medicine and Radiobiology, University of Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - P Cloutier
- Department of Nuclear Medicine and Radiobiology, University of Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - A D Bass
- Department of Nuclear Medicine and Radiobiology, University of Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - G Bertrand
- Department of Pharmacology, University of Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - D J Hunting
- Department of Nuclear Medicine and Radiobiology, University of Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - M Grandbois
- Department of Pharmacology, University of Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - L Sanche
- Department of Nuclear Medicine and Radiobiology, University of Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
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15
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Paulson B, Shin I, Jeong H, Kong B, Khazaeinezhad R, Dugasani SR, Jung W, Joo B, Lee HY, Park S, Oh K. Optical dispersion control in surfactant-free DNA thin films by vitamin B 2 doping. Sci Rep 2018; 8:9358. [PMID: 29921918 PMCID: PMC6008429 DOI: 10.1038/s41598-018-27166-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/15/2018] [Indexed: 02/03/2023] Open
Abstract
A new route to systematically control the optical dispersion properties of surfactant-free deoxyribonucleic acid (DNA) thin solid films was developed by doping them with vitamin B2, also known as riboflavin. Surfactant-free DNA solid films of high optical quality were successfully deposited on various types of substrates by spin coating of aqueous solutions without additional chemical processes, with thicknesses ranging from 18 to 100 nm. Optical properties of the DNA films were investigated by measuring UV-visible-NIR transmission, and their refractive indices were measured using variable-angle spectroscopic ellipsometry. By doping DNA solid films with riboflavin, the refractive index was consistently increased with an index difference Δn ≥ 0.015 in the spectral range from 500 to 900 nm, which is sufficiently large to make an all-DNA optical waveguide. Detailed correlation between the optical dispersion and riboflavin concentration was experimentally investigated and thermo-optic coefficients of the DNA-riboflavin thin solid films were also experimentally measured in the temperature range from 20 to 85 °C, opening the potential to new bio-thermal sensing applications.
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Affiliation(s)
- Bjorn Paulson
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, Seoul, 120-749, South Korea
| | - Inchul Shin
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, Seoul, 120-749, South Korea
- Samsung Electronics, Hwasong, Gyeonggi-do, 18448, South Korea
| | - Hayoung Jeong
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, Seoul, 120-749, South Korea
| | - Byungjoo Kong
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, Seoul, 120-749, South Korea
| | - Reza Khazaeinezhad
- Harvard Medical School, Boston, Massachusetts, 02115, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Sreekantha Reddy Dugasani
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Woohyun Jung
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, Seoul, 120-749, South Korea
| | - Boram Joo
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, Seoul, 120-749, South Korea
| | - Hoi-Youn Lee
- Space Optics Research Center, Korea Research Institute of Standards and Science, Daejeon, 34113, South Korea
| | - Sungha Park
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Kyunghwan Oh
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, Seoul, 120-749, South Korea.
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16
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Li L, Pagilla KR. Biomass density-function relationships in suspended growth biological processes - A critical review. WATER RESEARCH 2017; 111:274-287. [PMID: 28104515 DOI: 10.1016/j.watres.2017.01.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/05/2016] [Accepted: 01/05/2017] [Indexed: 06/06/2023]
Abstract
Good settling performance in suspended growth biomass systems, for example in activated sludge (AS) process, leads to efficient wastewater and sludge treatment. Factors that cause the differences in settleablility of AS include the morphology of bacteria, microbial community structure, and the density of bacteria and flocs. Density of AS at three levels, namely, cell, floc, and process, have been discussed here to explain the variations in AS settleability. Dense materials, inside or outside the cell, significantly increase density of AS bacteria or flocs. Functional bacteria, defined as those performing N and P removal and recovery such as phosphate accumulating organisms, nitrifiers, and anammox contain cellular inclusions that increase their density, and consequently a dense and well-settling biomass results at the process level in those systems. A density based selector of AS can be used to enrich functional bacteria in the process through the wasting and sludge age control operations in AS process. This paper critically reviews the latest literature to elucidate mechanisms of density enhancement from cell to process level, and identifies needs/strategies to improve the AS process through a biomass density selector.
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Affiliation(s)
- Lin Li
- Department of Civil and Environmental Engineering, University of Nevada, Reno, Reno, NV 89557, USA
| | - Krishna R Pagilla
- Department of Civil and Environmental Engineering, University of Nevada, Reno, Reno, NV 89557, USA.
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17
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Souici M, Khalil TT, Muller D, Raffy Q, Barillon R, Belafrites A, Champion C, Fromm M. Single- and Double-Strand Breaks of Dry DNA Exposed to Protons at Bragg-Peak Energies. J Phys Chem B 2017; 121:497-507. [DOI: 10.1021/acs.jpcb.6b11060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mounir Souici
- Université de Bourgogne Franche-Comté, UMR CNRS 6249 Chrono-Environnement, 16 Route de Gray, 25030 Besançon Cedex, France
- Laboratoire
de Physique des Rayonnements et Applications, Université de Jijel, BP 98, Ouled Aissa, Jijel 18000, Algérie
| | - Talat T. Khalil
- Université de Bourgogne Franche-Comté, UMR CNRS 6249 Chrono-Environnement, 16 Route de Gray, 25030 Besançon Cedex, France
| | - Dominique Muller
- Laboratoire
ICube, CNRS-Université de Strasbourg, 23 rue du Loess, 67037 Strasbourg, France
| | - Quentin Raffy
- Institut Pluridisciplinaire Hubert Curien, UMR CNRS 7178, 23 rue du Loess, BP 28, 67037 Strasbourg Cedex 2, France
| | - Rémi Barillon
- Institut Pluridisciplinaire Hubert Curien, UMR CNRS 7178, 23 rue du Loess, BP 28, 67037 Strasbourg Cedex 2, France
| | - Abdelfettah Belafrites
- Laboratoire
de Physique des Rayonnements et Applications, Université de Jijel, BP 98, Ouled Aissa, Jijel 18000, Algérie
| | - Christophe Champion
- Université de Bordeaux, CNRS/IN2P3, Centre d’Etudes Nucléaires de Bordeaux Gradignan, CENBG, Chemin du Solarium, BP 120, 33175 Gradignan, France
| | - Michel Fromm
- Université de Bourgogne Franche-Comté, UMR CNRS 6249 Chrono-Environnement, 16 Route de Gray, 25030 Besançon Cedex, France
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18
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Haume K, Rosa S, Grellet S, Śmiałek MA, Butterworth KT, Solov’yov AV, Prise KM, Golding J, Mason NJ. Gold nanoparticles for cancer radiotherapy: a review. Cancer Nanotechnol 2016; 7:8. [PMID: 27867425 PMCID: PMC5095165 DOI: 10.1186/s12645-016-0021-x] [Citation(s) in RCA: 255] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/14/2016] [Indexed: 12/11/2022] Open
Abstract
Radiotherapy is currently used in around 50% of cancer treatments and relies on the deposition of energy directly into tumour tissue. Although it is generally effective, some of the deposited energy can adversely affect healthy tissue outside the tumour volume, especially in the case of photon radiation (gamma and X-rays). Improved radiotherapy outcomes can be achieved by employing ion beams due to the characteristic energy deposition curve which culminates in a localised, high radiation dose (in form of a Bragg peak). In addition to ion radiotherapy, novel sensitisers, such as nanoparticles, have shown to locally increase the damaging effect of both photon and ion radiation, when both are applied to the tumour area. Amongst the available nanoparticle systems, gold nanoparticles have become particularly popular due to several advantages: biocompatibility, well-established methods for synthesis in a wide range of sizes, and the possibility of coating of their surface with a large number of different molecules to provide partial control of, for example, surface charge or interaction with serum proteins. This gives a full range of options for design parameter combinations, in which the optimal choice is not always clear, partially due to a lack of understanding of many processes that take place upon irradiation of such complicated systems. In this review, we summarise the mechanisms of action of radiation therapy with photons and ions in the presence and absence of nanoparticles, as well as the influence of some of the core and coating design parameters of nanoparticles on their radiosensitisation capabilities.
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Affiliation(s)
- Kaspar Haume
- Department of Physical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA UK
| | - Soraia Rosa
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Lisburn Road, Belfast, BT9 7BL UK
| | - Sophie Grellet
- Department of Life, Health and Chemical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA UK
| | - Małgorzata A. Śmiałek
- Department of Control and Power Engineering, Faculty of Ocean Engineering and Ship Technology, Gdansk University of Technology, 80-233 Gdansk, Poland
| | - Karl T. Butterworth
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Lisburn Road, Belfast, BT9 7BL UK
| | | | - Kevin M. Prise
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Lisburn Road, Belfast, BT9 7BL UK
| | - Jon Golding
- Department of Life, Health and Chemical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA UK
| | - Nigel J. Mason
- Department of Physical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA UK
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19
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Lee S, Wang C, Song J, Kim DG, Oh Y, Ko W, Lee J, Park J, Lee HS, Jo K. Investigation of various fluorescent protein–DNA binding peptides for effectively visualizing large DNA molecules. RSC Adv 2016. [DOI: 10.1039/c6ra08683g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-molecule DNA visualization with fluorescent protein DNA binding peptides.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Cong Wang
- Department of Mechanical Engineering
- Sogang University
- Seoul
- Korea
| | - Junghyun Song
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Do-geun Kim
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Yeeun Oh
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Wooseok Ko
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Jinyong Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Jungyul Park
- Department of Mechanical Engineering
- Sogang University
- Seoul
- Korea
| | - Hyun Soo Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
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20
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Champion C, Quinto MA, Monti JM, Galassi ME, Weck PF, Fojón OA, Hanssen J, Rivarola RD. Water versus DNA: new insights into proton track-structure modelling in radiobiology and radiotherapy. Phys Med Biol 2015; 60:7805-28. [PMID: 26406277 DOI: 10.1088/0031-9155/60/20/7805] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence-expressed in terms of total cross sections-as well as their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.
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Affiliation(s)
- C Champion
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux Gradignan, Gradignan, France
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21
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Vyšín L, Pachnerová Brabcová K, Štěpán V, Moretto-Capelle P, Bugler B, Legube G, Cafarelli P, Casta R, Champeaux JP, Sence M, Vlk M, Wagner R, Štursa J, Zach V, Incerti S, Juha L, Davídková M. Proton-induced direct and indirect damage of plasmid DNA. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2015; 54:343-352. [PMID: 26007308 DOI: 10.1007/s00411-015-0605-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
Clustered DNA damage induced by 10, 20 and 30 MeV protons in pBR322 plasmid DNA was investigated. Besides determination of strand breaks, additional lesions were detected using base excision repair enzymes. The plasmid was irradiated in dry form, where indirect radiation effects were almost fully suppressed, and in water solution containing only minimal residual radical scavenger. Simultaneous irradiation of the plasmid DNA in the dry form and in the solution demonstrated the contribution of the indirect effect as prevalent. The damage composition slightly differed when comparing the results for liquid and dry samples. The obtained data were also subjected to analysis concerning different methodological approaches, particularly the influence of irradiation geometry, models used for calculation of strand break yields and interpretation of the strand breaks detected with the enzymes. It was shown that these parameters strongly affect the results.
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Affiliation(s)
- Luděk Vyšín
- Institute of Physics CAS, Na Slovance 1999/2, 182 21, Prague, Czech Republic
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