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Gardner LL, Thompson SJ, O'Connor JD, McMahon SJ. Modelling radiobiology. Phys Med Biol 2024; 69:18TR01. [PMID: 39159658 DOI: 10.1088/1361-6560/ad70f0] [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: 04/25/2024] [Accepted: 08/19/2024] [Indexed: 08/21/2024]
Abstract
Radiotherapy has played an essential role in cancer treatment for over a century, and remains one of the best-studied methods of cancer treatment. Because of its close links with the physical sciences, it has been the subject of extensive quantitative mathematical modelling, but a complete understanding of the mechanisms of radiotherapy has remained elusive. In part this is because of the complexity and range of scales involved in radiotherapy-from physical radiation interactions occurring over nanometres to evolution of patient responses over months and years. This review presents the current status and ongoing research in modelling radiotherapy responses across these scales, including basic physical mechanisms of DNA damage, the immediate biological responses this triggers, and genetic- and patient-level determinants of response. Finally, some of the major challenges in this field and potential avenues for future improvements are also discussed.
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Affiliation(s)
- Lydia L Gardner
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
| | - Shannon J Thompson
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
| | - John D O'Connor
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
- Ulster University School of Engineering, York Street, Belfast BT15 1AP, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
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2
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Nikjoo H, Rahmanian S, Taleei R. Modelling DNA damage-repair and beyond. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 190:1-18. [PMID: 38754703 DOI: 10.1016/j.pbiomolbio.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/27/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024]
Abstract
The paper presents a review of mechanistic modelling studies of DNA damage and DNA repair, and consequences to follow in mammalian cell nucleus. We hypothesize DNA deletions are consequences of repair of double strand breaks leading to the modifications of genome that play crucial role in long term development of genetic inheritance and diseases. The aim of the paper is to review formation mechanisms underlying naturally occurring DNA deletions in the human genome and their potential relevance for bridging the gap between induced DNA double strand breaks and deletions in damaged human genome from endogenous and exogenous events. The model of the cell nucleus presented enables simulation of DNA damage at molecular level identifying the spectrum of damage induced in all chromosomal territories and loops. Our mechanistic modelling of DNA repair for double stand breaks (DSB), single strand breaks (SSB) and base damage (BD), shows the complexity of DNA damage is responsible for the longer repair times and the reason for the biphasic feature of mammalian cells repair curves. In the absence of experimentally determined data, the mechanistic model of repair predicts the in vivo rate constants for the proteins involved in the repair of DSB, SSB, and of BD.
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Affiliation(s)
- Hooshang Nikjoo
- Department of Physiology, Anatomy and Genetics (DPAG), Oxford University, Oxford, OX1 3PT, UK.
| | | | - Reza Taleei
- Medical Physics Division, Department of Radiation Oncology Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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Taleei R, Rahmanian S, Nikjoo H. Modelling Cellular Response to Ionizing Radiation: Mechanistic, Semi-Mechanistic, and Phenomenological Approaches - A Historical Perspective. Radiat Res 2024; 202:143-160. [PMID: 38916125 DOI: 10.1667/rade-24-00019.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/23/2024] [Indexed: 06/26/2024]
Abstract
Radiation research is a multidisciplinary field, and among its many branches, mathematical and computational modelers have played a significant role in advancing boundaries of knowledge. A fundamental contribution is modelling cellular response to ionizing radiation as that is the key to not only understanding how radiation can kill cancer cells, but also cause cancer and other health issues. The invention of microdosimetry in the 1950s by Harold Rossi paved the way for brilliant scientists to study the mechanism of radiation at cellular and sub-cellular scales. This paper reviews some snippets of ingenious mathematical and computational models published in microdosimetry symposium proceedings and publications of the radiation research community. Among these are simulations of radiation tracks at atomic and molecular levels using Monte Carlo methods, models of cell survival, quantification of the amount of energy required to create a single strand break, and models of DNA-damage-repair. These models can broadly be categorized into mechanistic, semi-mechanistic, and phenomenological approaches, and this review seeks to provide historical context of their development. We salute pioneers of the field and great teachers who supported and educated the younger members of the community and showed them how to build upon their work.
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Affiliation(s)
- Reza Taleei
- Medical Physics Division, Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, 19107
| | | | - Hooshang Nikjoo
- Department of Physiology, Anatomy and Genetics (DPAG) Oxford University, Oxford, OX1 3PT, United Kingdom
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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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Matsuya Y, Kai T, Sato T, Liamsuwan T, Sasaki K, Nikjoo H. Verification of KURBUC-based ion track structure mode for proton and carbon ions in the PHITS code. Phys Med Biol 2021; 66:06NT02. [PMID: 33588391 DOI: 10.1088/1361-6560/abe65e] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The particle and heavy ion transport code system (PHITS) is a general-purpose Monte Carlo radiation transport simulation code. It has the ability to handle diverse particle types over a wide range of energy. The latest PHITS development enables the generation of track structure for proton and carbon ions (1H+, 12C6+) based on the algorithms in the KURBUC code, which is considered as one of the most verified track-structure codes worldwide. This ion track-structure mode is referred to as the PHITS-KURBUC mode. In this study, the range, radial dose distributions, and microdosimetric distributions were calculated using the PHITS-KURBUC mode. Subsequently, they were compared with the corresponding data obtained from the original KURBUC and from other studies. These comparative studies confirm the successful inclusion of the KURBUC code in the PHITS code. As results of the synergistic effect between the macroscopic and microscopic radiation transport codes, this implementation enabled the detailed calculation of the microdosimetric and nanodosimetric quantities under complex radiation fields, such as proton beam therapy with the spread-out Bragg peak.
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Affiliation(s)
- Yusuke Matsuya
- Nuclear Science and Engineering Center, Research Group for Radiation Transport Analysis, Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai, Ibaraki, 319-1195, Japan
| | - Takeshi Kai
- Nuclear Science and Engineering Center, Research Group for Radiation Transport Analysis, Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai, Ibaraki, 319-1195, Japan
| | - Tatsuhiko Sato
- Nuclear Science and Engineering Center, Research Group for Radiation Transport Analysis, Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai, Ibaraki, 319-1195, Japan
| | - Thiansin Liamsuwan
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Kohei Sasaki
- Department of Radiological Technology, Faculty of Health Sciences, Hokkaido University of Science, Maeda 7-15, Teine-ku, Sapporo 006-8585, Japan
| | - Hooshang Nikjoo
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, SE-17176 Stockholm, Sweden
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Baptiste BA, Baringer SL, Kulikowicz T, Sommers JA, Croteau DL, Brosh RM, Bohr VA. DNA polymerase β outperforms DNA polymerase γ in key mitochondrial base excision repair activities. DNA Repair (Amst) 2021; 99:103050. [PMID: 33540226 PMCID: PMC7887074 DOI: 10.1016/j.dnarep.2021.103050] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/13/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022]
Abstract
DNA polymerase beta (POLβ), well known for its role in nuclear DNA base excision repair (BER), has been shown to be present in the mitochondria of several different cell types. Here we present a side-by-side comparison of BER activities of POLβ and POLγ, the mitochondrial replicative polymerase, previously thought to be the only mitochondrial polymerase. We find that POLβ is significantly more proficient at single-nucleotide gap filling, both in substrates with ends that require polymerase processing, and those that do not. We also show that POLβ has a helicase-independent functional interaction with the mitochondrial helicase, TWINKLE. This interaction stimulates strand-displacement synthesis, but not single-nucleotide gap filling. Importantly, we find that purified mitochondrial extracts from cells lacking POLβ are severely deficient in processing BER intermediates, suggesting that mitochondrially localized DNA POLβ may be critical for cells with high energetic demands that produce greater levels of oxidative stress and therefore depend upon efficient BER for mitochondrial health.
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Affiliation(s)
- Beverly A Baptiste
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Stephanie L Baringer
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Tomasz Kulikowicz
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd., Baltimore, MD, 21224, USA.
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Zhu W, Hu J, Chi J, Li Y, Yang B, Hu W, Chen F, Xu C, Chai L, Bao Y. Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in Pleurotus ostreatus. Molecules 2020; 25:molecules25214920. [PMID: 33114310 PMCID: PMC7660624 DOI: 10.3390/molecules25214920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/13/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022] Open
Abstract
Pleurotus ostreatus is one of the widely cultivated edible fungi across the world. Mycelial subculture is an indispensable part in the process of cultivation and production for all kinds of edible fungi. However, successive subcultures usually lead to strain degeneration. The degenerated strains usually have a decrease in stress resistance, yield, and an alteration in fruiting time, which will subsequently result in tremendous economic loss. Through proteomic analysis, we identified the differentially expressed proteins (DEPs) in the mycelium of Pleurotus ostreatus from different subcultured generations. We found that the DNA damage repair system, especially the double-strand breaks (DSBs), repairs via homologous recombination, was impaired in the subcultured mycelium, and gradual accumulation of the DSBs would lead to the strain degeneration after successive subculture. The TUNEL assay further confirmed our finding about the DNA breaks in the subcultured mycelium. Interestingly, the enzyme activity of laccase, carboxylic ester hydrolase, α-galactosidase, and catalase directly related to passage number could be used as the characteristic index for strain degeneration determination. Our results not only reveal for the first time at the molecular level that genomic instability is the cause of degeneration, but also provide an applicable approach for monitoring strain degeneration in process of edible fungi cultivation and production.
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Affiliation(s)
- Weiwei Zhu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China;
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Jinbo Hu
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; (J.H.); (B.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingliang Chi
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Yang Li
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Bing Yang
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; (J.H.); (B.Y.)
| | - Wenli Hu
- Core Facility Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Fei Chen
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Chong Xu
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Linshan Chai
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Yongming Bao
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China;
- School of Ocean Science and Technology, Dalian University of Technology, Panjin 124021, China
- Correspondence: ; Tel.: +86-427-2631777; Fax: +86-411-84706365
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Velegzhaninov IO, Belykh ES, Rasova EE, Pylina YI, Shadrin DM, Klokov DY. Radioresistance, DNA Damage and DNA Repair in Cells With Moderate Overexpression of RPA1. Front Genet 2020; 11:855. [PMID: 32849834 PMCID: PMC7411226 DOI: 10.3389/fgene.2020.00855] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/13/2020] [Indexed: 12/02/2022] Open
Abstract
Molecular responses to genotoxic stress, such as ionizing radiation, are intricately complex and involve hundreds of genes. Whether targeted overexpression of an endogenous gene can enhance resistance to ionizing radiation remains to be explored. In the present study we take an advantage of the CRISPR/dCas9 technology to moderately overexpress the RPA1 gene that encodes a key functional subunit of the replication protein A (RPA). RPA is a highly conserved heterotrimeric single-stranded DNA-binding protein complex involved in DNA replication, recombination, and repair. Dysfunction of RPA1 is detrimental for cells and organisms and can lead to diminished resistance to many stress factors. We demonstrate that HEK293T cells overexpressing RPA1 exhibit enhanced resistance to cell killing by gamma-radiation. Using the alkali comet assay, we show a remarkable acceleration of DNA breaks rejoining after gamma-irradiation in RPA1 overexpressing cells. However, the spontaneous rate of DNA damage was also higher in the presence of RPA1 overexpression, suggesting alterations in the processing of replication errors due to elevated activity of the RPA protein. Additionally, the analysis of the distributions of cells with different levels of DNA damage showed a link between the RPA1 overexpression and the kinetics of DNA repair within differentially damaged cell subpopulations. Our results provide knew knowledge on DNA damage stress responses and indicate that the concept of enhancing radioresistance by targeted alteration of the expression of a single gene is feasible, however undesired consequences should be considered and evaluated.
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Affiliation(s)
- Ilya O Velegzhaninov
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Elena S Belykh
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Elena E Rasova
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Yana I Pylina
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Dmitry M Shadrin
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Dmitry Yu Klokov
- Institut de Radioprotection et de Sureté Nucléaire, PSE-SANTE, SESANE, LRTOX, Fontenay-aux-Roses, France.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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9
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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: 52] [Impact Index Per Article: 13.0] [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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Petri net-based model of the human DNA base excision repair pathway. PLoS One 2019; 14:e0217913. [PMID: 31518347 PMCID: PMC6743755 DOI: 10.1371/journal.pone.0217913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 05/21/2019] [Indexed: 12/14/2022] Open
Abstract
Cellular DNA is daily exposed to several damaging agents causing a plethora of DNA lesions. As a first aid to restore DNA integrity, several enzymes got specialized in damage recognition and lesion removal during the process called base excision repair (BER). A large number of DNA damage types and several different readers of nucleic acids lesions during BER pathway as well as two sub-pathways were considered in the definition of a model using the Petri net framework. The intuitive graphical representation in combination with precise mathematical analysis methods are the strong advantages of the Petri net-based representation of biological processes and make Petri nets a promising approach for modeling and analysis of human BER. The reported results provide new information that will aid efforts to characterize in silico knockouts as well as help to predict the sensitivity of the cell with inactivated repair proteins to different types of DNA damage. The results can also help in identifying the by-passing pathways that may lead to lack of pronounced phenotypes associated with mutations in some of the proteins. This knowledge is very useful when DNA damage-inducing drugs are introduced for cancer therapy, and lack of DNA repair is desirable for tumor cell death.
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Taleei R. MODELLING DSB REPAIR KINETICS FOR DNA DAMAGE INDUCED BY PROTON AND CARBON IONS. RADIATION PROTECTION DOSIMETRY 2019; 183:75-78. [PMID: 30668809 DOI: 10.1093/rpd/ncy304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 12/26/2018] [Indexed: 06/09/2023]
Abstract
Proton and carbon therapy are the main choices of particle therapy for cancer treatment. Particle dose distribution is superior to conventional photon therapy dose distribution due to Bragg peak. However, the basic biology of cellular damage and cell death is not well understood. The aim of this work is to present a mechanistic model of double strand break (DSB) repair that predicts the repair kinetics of damage induced by particles employed in cancer therapy. Monte Carlo Track Damage Simulation (MCDS) was employed to model DNA damage. The frequency of DSB and SSB was computed for proton and carbon ions. DSBs were subjected to repair model to calculate the repair kinetics. Two distinct DSB repair models dependent on the cell cycle were proposed. The DSB repair model contains non-homologous end joining (NHEJ), homologous recombination (HR) and back up non-homologous end joining (B-NHEJ) repair processes. The DSB complexity results in the switch in the repair pathway from NHEJ to a slower process that starts with DSB end resection. DSB end resection in early S and G1 phases of the cell cycle enhances the B-NHEJ repair pathway, while in late S and G2 phases of the cell cycle promotes HR repair pathway. The repair model was transformed to a set of nonlinear differential equations. The model calculates the overall repair kinetics and protein temporal repair activity at the site of damage. The damage and repair model provides a detailed mechanistic understanding of all processes that are involved in the damage induction and repair. The number of DSB and their complexity increase as the particle energy decreases due to the proximity of particle interactions in water. The repair kinetics show a biphasic behaviour that is due to the NHEJ fast repair of simple type DSB and HR slow repair of complex type DSB.
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Affiliation(s)
- Reza Taleei
- Division of Medical Physics, Department of Radiation Oncology, University of Virginia, Charlottesville, VA
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12
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Modeling the interplay between DNA-PK, Artemis, and ATM in non-homologous end-joining repair in G1 phase of the cell cycle. J Biol Phys 2019; 45:127-146. [PMID: 30707386 DOI: 10.1007/s10867-018-9519-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 12/28/2018] [Indexed: 01/02/2023] Open
Abstract
Modeling a biological process equips us with more comprehensive insight into the process and a more advantageous experimental design. Non-homologous end joining (NHEJ) is a major double-strand break (DSB) repair pathway that occurs throughout the cell cycle. The objective of the current work is to model the fast and slow phases of NHEJ in G1 phase of the cell cycle following exposure to ionizing radiation (IR). The fast phase contains the major components of NHEJ; Ku70/80 complex, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and XLF/XRCC4/ligase IV complex (XXL). The slow phase in G1 phase of the cell cycle is associated with more complex lesions and involves ATM and Artemis proteins in addition to the major components. Parameters are mainly obtained from experimental data. The model is successful in predicting the kinetics of DSB foci in 13 normal, ATM-deficient, and Artemis-deficient mammalian fibroblast cell lines in G1 phase of the cell cycle after exposure to low doses of IR. The involvement of ATM provides the model with the potency to be connected to different signaling pathways. Ku70/80 concentration and DNA-binding rate as well as XXL concentration and enzymatic activity are introduced as the best targets for affecting NHEJ DSB repair process. On the basis of the current model, decreasing concentration and DNA binding rate of DNA-PKcs is more effective than inhibiting its activity towards the Artemis protein.
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Cortese F, Klokov D, Osipov A, Stefaniak J, Moskalev A, Schastnaya J, Cantor C, Aliper A, Mamoshina P, Ushakov I, Sapetsky A, Vanhaelen Q, Alchinova I, Karganov M, Kovalchuk O, Wilkins R, Shtemberg A, Moreels M, Baatout S, Izumchenko E, de Magalhães JP, Artemov AV, Costes SV, Beheshti A, Mao XW, Pecaut MJ, Kaminskiy D, Ozerov IV, Scheibye-Knudsen M, Zhavoronkov A. Vive la radiorésistance!: converging research in radiobiology and biogerontology to enhance human radioresistance for deep space exploration and colonization. Oncotarget 2018; 9:14692-14722. [PMID: 29581875 PMCID: PMC5865701 DOI: 10.18632/oncotarget.24461] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/31/2018] [Indexed: 12/12/2022] Open
Abstract
While many efforts have been made to pave the way toward human space colonization, little consideration has been given to the methods of protecting spacefarers against harsh cosmic and local radioactive environments and the high costs associated with protection from the deleterious physiological effects of exposure to high-Linear energy transfer (high-LET) radiation. Herein, we lay the foundations of a roadmap toward enhancing human radioresistance for the purposes of deep space colonization and exploration. We outline future research directions toward the goal of enhancing human radioresistance, including upregulation of endogenous repair and radioprotective mechanisms, possible leeways into gene therapy in order to enhance radioresistance via the translation of exogenous and engineered DNA repair and radioprotective mechanisms, the substitution of organic molecules with fortified isoforms, and methods of slowing metabolic activity while preserving cognitive function. We conclude by presenting the known associations between radioresistance and longevity, and articulating the position that enhancing human radioresistance is likely to extend the healthspan of human spacefarers as well.
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Affiliation(s)
- Franco Cortese
- Biogerontology Research Foundation, London, UK
- Department of Biomedical and Molecular Sciences, Queen's University School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Dmitry Klokov
- Canadian Nuclear Laboratories, Chalk River, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Andreyan Osipov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
- State Research Center - Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Jakub Stefaniak
- Biogerontology Research Foundation, London, UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Alexey Moskalev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
| | - Jane Schastnaya
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
| | - Charles Cantor
- Boston University, Department of Biomedical Engineering, Boston, MA, USA
| | - Alexander Aliper
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
- Laboratory of Bioinformatics, D. Rogachev Federal Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Polina Mamoshina
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
- Computer Science Department, University of Oxford, Oxford, UK
| | - Igor Ushakov
- State Research Center - Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - Alex Sapetsky
- State Research Center - Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - Quentin Vanhaelen
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
| | - Irina Alchinova
- Laboratory of Physicochemical and Ecological Pathophysiology, Institute of General Pathology and Pathophysiology, Moscow, Russia
- Research Institute for Space Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Mikhail Karganov
- Laboratory of Physicochemical and Ecological Pathophysiology, Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - Olga Kovalchuk
- Canada Cancer and Aging Research Laboratories, Ltd., Lethbridge, Alberta, Canada
- University of Lethbridge, Lethbridge, Alberta, Canada
| | - Ruth Wilkins
- Environmental and Radiation and Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Andrey Shtemberg
- Laboratory of Extreme Physiology, Institute of Medical and Biological Problems RAS, Moscow, Russia
| | - Marjan Moreels
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre, (SCK·CEN), Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Interdisciplinary Biosciences, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre, (SCK·CEN), Mol, Belgium
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Evgeny Izumchenko
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
- The Johns Hopkins University, School of Medicine, Department of Otolaryngology, Head and Neck Cancer Research, Baltimore, MD, USA
| | - João Pedro de Magalhães
- Biogerontology Research Foundation, London, UK
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Artem V. Artemov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
| | | | - Afshin Beheshti
- Wyle Laboratories, Space Biosciences Division, NASA Ames Research Center, Mountain View, CA, USA
- Division of Hematology/Oncology, Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA
| | - Xiao Wen Mao
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, USA
| | - Michael J. Pecaut
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, USA
| | - Dmitry Kaminskiy
- Biogerontology Research Foundation, London, UK
- Deep Knowledge Life Sciences, London, UK
| | - Ivan V. Ozerov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
- State Research Center - Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | | | - Alex Zhavoronkov
- Biogerontology Research Foundation, London, UK
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, MD, USA
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14
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Mavragani IV, Nikitaki Z, Souli MP, Aziz A, Nowsheen S, Aziz K, Rogakou E, Georgakilas AG. Complex DNA Damage: A Route to Radiation-Induced Genomic Instability and Carcinogenesis. Cancers (Basel) 2017; 9:cancers9070091. [PMID: 28718816 PMCID: PMC5532627 DOI: 10.3390/cancers9070091] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/06/2017] [Accepted: 07/14/2017] [Indexed: 12/26/2022] Open
Abstract
Cellular effects of ionizing radiation (IR) are of great variety and level, but they are mainly damaging since radiation can perturb all important components of the cell, from the membrane to the nucleus, due to alteration of different biological molecules ranging from lipids to proteins or DNA. Regarding DNA damage, which is the main focus of this review, as well as its repair, all current knowledge indicates that IR-induced DNA damage is always more complex than the corresponding endogenous damage resulting from endogenous oxidative stress. Specifically, it is expected that IR will create clusters of damage comprised of a diversity of DNA lesions like double strand breaks (DSBs), single strand breaks (SSBs) and base lesions within a short DNA region of up to 15–20 bp. Recent data from our groups and others support two main notions, that these damaged clusters are: (1) repair resistant, increasing genomic instability (GI) and malignant transformation and (2) can be considered as persistent “danger” signals promoting chronic inflammation and immune response, causing detrimental effects to the organism (like radiation toxicity). Last but not least, the paradigm shift for the role of radiation-induced systemic effects is also incorporated in this picture of IR-effects and consequences of complex DNA damage induction and its erroneous repair.
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Affiliation(s)
- Ifigeneia V Mavragani
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece.
| | - Zacharenia Nikitaki
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece.
| | - Maria P Souli
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece.
| | - Asef Aziz
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA.
| | - Somaira Nowsheen
- Mayo Medical Scientist Training Program, Mayo Medical School and Mayo Graduate School, Mayo Clinic, Rochester, MN 55905, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.
| | - Khaled Aziz
- Mayo Medical Scientist Training Program, Mayo Medical School and Mayo Graduate School, Mayo Clinic, Rochester, MN 55905, USA.
| | - Emmy Rogakou
- First Department of Pediatrics, "Aghia Sophia" Children's Hospital, Medical School, University of Athens, 11527 Athens, Greece.
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece.
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15
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Emfietzoglou D, Papamichael G, Nikjoo H. Monte Carlo Electron Track Structure Calculations in Liquid Water Using a New Model Dielectric Response Function. Radiat Res 2017. [PMID: 28650774 DOI: 10.1667/rr14705.1] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Monte Carlo track structure codes provide valuable information for understanding radiation effects down to the DNA level, where experimental measurements are most difficult or unavailable. It is well recognized that the performance of such codes, especially at low energies and/or subcellular level, critically depends on the reliability of the interaction cross sections that are used as input in the simulation. For biological media such as liquid water, one of the most challenging issues is the role of condensed-phase effects. For inelastic scattering, such effects can be conveniently accounted for through the complex dielectric response function of the media. However, for this function to be useful it must fulfill some important sum rules and have a simple analytic form for arbitrary energy- and momentum-transfer. The Emfietzoglou-Cucinotta-Nikjoo (ECN) model offers a practical, self-consistent and fully analytic parameterization of the dielectric function of liquid water based on the best available experimental data. An important feature of the ECN model is that it includes, in a phenomenological manner, exchange and correlation effects among the screening electrons, thus, going beyond the random-phase approximation implicit in earlier models. In this work, inelastic cross sections beyond the plane wave Born approximation are calculated for low-energy electrons (10 eV-10 keV) based on the ECN model, and used for Monte Carlo track structure simulations of physical quantities relevant to the microdosimetry of low-energy electrons in liquid water. Important new developments in the physics of inelastic scattering are discussed and their effect on electron track structure is investigated by a comparison against simulations (under otherwise identical conditions) using the Born approximation and a simpler form of the dielectric function based on the Oak Ridge National Laboratory model. The results reveal that both the dielectric function and the corrections to the Born approximation may have a sizeable effect on track structure calculations at the nanometer scale (DNA level), where the details of inelastic scattering and the role of low-energy electrons are most critical.
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Affiliation(s)
- Dimitris Emfietzoglou
- a Medical Physics Laboratory, University of Ioannina Medical School, Ioannina 45110, Greece
| | - George Papamichael
- a Medical Physics Laboratory, University of Ioannina Medical School, Ioannina 45110, Greece.,b Division of Applied Statistics, Institute of Labor (GSEE), Athens 10681, Greece
| | - Hooshang Nikjoo
- c Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, Box 260, SE-171 76 Stockholm, Sweden
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16
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Nikjoo H, Emfietzoglou D, Liamsuwan T, Taleei R, Liljequist D, Uehara S. Radiation track, DNA damage and response-a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:116601. [PMID: 27652826 DOI: 10.1088/0034-4885/79/11/116601] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The purpose of this paper has been to review the current status and progress of the field of radiation biophysics, and draw attention to the fact that physics, in general, and radiation physics in particular, with the aid of mathematical modeling, can help elucidate biological mechanisms and cancer therapies. We hypothesize that concepts of condensed-matter physics along with the new genomic knowledge and technologies and mechanistic mathematical modeling in conjunction with advances in experimental DNA (Deoxyrinonucleic acid molecule) repair and cell signaling have now provided us with unprecedented opportunities in radiation biophysics to address problems in targeted cancer therapy, and genetic risk estimation in humans. Obviously, one is not dealing with 'low-hanging fruit', but it will be a major scientific achievement if it becomes possible to state, in another decade or so, that we can link mechanistically the stages between the initial radiation-induced DNA damage; in particular, at doses of radiation less than 2 Gy and with structural changes in genomic DNA as a precursor to cell inactivation and/or mutations leading to genetic diseases. The paper presents recent development in the physics of radiation track structure contained in the computer code system KURBUC, in particular for low-energy electrons in the condensed phase of water for which we provide a comprehensive discussion of the dielectric response function approach. The state-of-the-art in the simulation of proton and carbon ion tracks in the Bragg peak region is also presented. The paper presents a critical discussion of the models used for elastic scattering, and the validity of the trajectory approach in low-electron transport. Brief discussions of mechanistic and quantitative aspects of microdosimetry, DNA damage and DNA repair are also included as developed by the authors' work.
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Affiliation(s)
- H Nikjoo
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, Box 260, P9-02, Stockholm 17176, Sweden
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17
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18
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Nikjoo H, Taleei R, Liamsuwan T, Liljequist D, Emfietzoglou D. Perspectives in radiation biophysics: From radiation track structure simulation to mechanistic models of DNA damage and repair. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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19
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Martin RF, Feinendegen LE. The quest to exploit the Auger effect in cancer radiotherapy - a reflective review. Int J Radiat Biol 2016; 92:617-632. [PMID: 26926313 DOI: 10.3109/09553002.2015.1136854] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To identify the emergence of the recognition of the potential of the Auger effect for clinical application, and after tracing the salient milestones towards that goal, to evaluate the status quo and future prospects. It was not until 40 years after the discovery of Auger electrons, that the availability of radioactive DNA precursors enabled the biological power, and the clinical potential, of the Auger effect to be appreciated. Important milestones on the path to clinical translation have been identified and reached, but hurdles remain. Nevertheless the potential is still evident, and there is reasonable optimism that the goal of clinical translation is achievable.
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Affiliation(s)
- Roger F Martin
- a Molecular Radiation Biology Laboratory , Peter MacCallum Cancer Centre.,b The Sir Peter MacCallum Department of Oncology , The University of Melbourne.,c School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Melbourne , Australia
| | - Ludwig E Feinendegen
- d Heinrich-Heine-University Düsseldorf , Germany.,e Brookhaven National Laboratory , Upton , NY , USA
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20
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Zhao L, Mi D, Hu B, Sun Y. A generalized target theory and its applications. Sci Rep 2015; 5:14568. [PMID: 26411887 PMCID: PMC4585963 DOI: 10.1038/srep14568] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/03/2015] [Indexed: 12/25/2022] Open
Abstract
Different radiobiological models have been proposed to estimate the cell-killing effects, which are very important in radiotherapy and radiation risk assessment. However, most applied models have their own scopes of application. In this work, by generalizing the relationship between "hit" and "survival" in traditional target theory with Yager negation operator in Fuzzy mathematics, we propose a generalized target model of radiation-induced cell inactivation that takes into account both cellular repair effects and indirect effects of radiation. The simulation results of the model and the rethinking of "the number of targets in a cell" and "the number of hits per target" suggest that it is only necessary to investigate the generalized single-hit single-target (GSHST) in the present theoretical frame. Analysis shows that the GSHST model can be reduced to the linear quadratic model and multitarget model in the low-dose and high-dose regions, respectively. The fitting results show that the GSHST model agrees well with the usual experimental observations. In addition, the present model can be used to effectively predict cellular repair capacity, radiosensitivity, target size, especially the biologically effective dose for the treatment planning in clinical applications.
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Affiliation(s)
- Lei Zhao
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, Liaoning, P.R. China
- Institute of Environmental Systems Biology, Dalian Maritime University, Dalian, Liaoning, P.R. China
| | - Dong Mi
- Department of Physics, Dalian Maritime University, Dalian, Liaoning, P.R. China
| | - Bei Hu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, Liaoning, P.R. China
- Institute of Environmental Systems Biology, Dalian Maritime University, Dalian, Liaoning, P.R. China
| | - Yeqing Sun
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, Liaoning, P.R. China
- Institute of Environmental Systems Biology, Dalian Maritime University, Dalian, Liaoning, P.R. China
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21
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Watanabe R, Rahmanian S, Nikjoo H. Spectrum of Radiation-Induced Clustered Non-DSB Damage - A Monte Carlo Track Structure Modeling and Calculations. Radiat Res 2015; 183:525-40. [PMID: 25909147 DOI: 10.1667/rr13902.1] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The aim of this report is to present the spectrum of initial radiation-induced cellular DNA damage [with particular focus on non-double-strand break (DSB) damage] generated by computer simulations. The radiation types modeled in this study were monoenergetic electrons (100 eV-1.5 keV), ultrasoft X-ray photons Ck, AlK and TiK, as well as some selected ions including 3.2 MeV/u proton; 0.74 and 2.4 MeV/u helium ions; 29 MeV/u nitrogen ions and 950 MeV/u iron ions. Monte Carlo track structure methods were used to simulate damage induction by these radiation types in a cell-mimetic condition from a single-track action. The simulations took into account the action of direct energy deposition events and the reaction of hydroxyl radicals on atomistic linear B-DNA segments of a few helical turns including the water of hydration. Our results permitted the following conclusions: a. The absolute levels of different types of damage [base damage, simple and complex single-strand breaks (SSBs) and DSBs] vary depending on the radiation type; b. Within each damage class, the relative proportions of simple and complex damage vary with radiation type, the latter being higher with high-LET radiations; c. Overall, for both low- and high-LET radiations, the ratios of the yields of base damage to SSBs are similar, being about 3.0 ± 0.2; d. Base damage contributes more to the complexity of both SSBs and DSBs, than additional SSB damage and this is true for both low- and high-LET radiations; and e. The average SSB/DSB ratio for low-LET radiations is about 18, which is about 5 times higher than that for high-LET radiations. The hypothesis that clustered DNA damage is more difficult for cells to repair has gained currency among radiobiologists. However, as yet, there is no direct in vivo experimental method to validate the dependence of kinetics of DNA repair on DNA damage complexity (both DSB and non-DSB types). The data on the detailed spectrum of DNA damage presented here, in particular the non-DSB type, provide a good basis for testing mechanistic models of DNA repair kinetics such as base excision repair.
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Affiliation(s)
- Ritsuko Watanabe
- a Research Group for Radiation Effect Analysis, Japan Atomic Energy Agency, Tokai, Ibaraki, 319-1195, Japan
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22
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Taleei R, Girard PM, Nikjoo H. DSB repair model for mammalian cells in early S and G1 phases of the cell cycle: application to damage induced by ionizing radiation of different quality. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 779:5-14. [PMID: 25813721 DOI: 10.1016/j.mrgentox.2015.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 01/01/2023]
Abstract
The purpose of this work is to test the hypothesis that kinetics of double strand breaks (DSB) repair is governed by complexity of DSB. To test the hypothesis we used our recent published mechanistic mathematical model of DSB repair for DSB induced by selected protons, deuterons, and helium ions of different energies representing radiations of different qualities. In light of recent advances in experimental and computational techniques, the most appropriate method to study cellular responses in radiation therapy, and exposures to low doses of ionizing radiations is using mechanistic approaches. To this end, we proposed a 'bottom-up' approach to study cellular response that starts with the DNA damage. Monte Carlo track structure method was employed to simulate initial damage induced in the genomic DNA by direct and indirect effects. Among the different types of DNA damage, DSB are known to be induced in simple and complex forms. The DSB repair model in G1 and early S phases of the cell cycle was employed to calculate the repair kinetics. The model considers the repair of simple and complex DSB, and the DSB produced in the heterochromatin. The inverse sampling method was used to calculate the repair kinetics for each individual DSB. The overall repair kinetics for 500 DSB induced by single tracks of the radiation under test were compared with experimental results. The results show that the model is capable of predicting the repair kinetics for the DSB induced by radiations of different qualities within an accepted range of uncertainty.
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Affiliation(s)
- Reza Taleei
- Department of Radiation Physics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter M Girard
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institute, Stockholm SE171 76, Sweden
| | - Hooshang Nikjoo
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institute, Stockholm SE171 76, Sweden.
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23
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Hufnagl A, Herr L, Friedrich T, Durante M, Taucher-Scholz G, Scholz M. The link between cell-cycle dependent radiosensitivity and repair pathways: a model based on the local, sister-chromatid conformation dependent switch between NHEJ and HR. DNA Repair (Amst) 2015; 27:28-39. [PMID: 25629437 DOI: 10.1016/j.dnarep.2015.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/24/2014] [Accepted: 01/08/2015] [Indexed: 11/29/2022]
Abstract
The different DNA damage repair pathways like homologous recombination (HR) and non-homologous end joining (NHEJ) have been linked to the variation of radiosensitivity throughout the cell cycle. However, no attempts have been made to test the various hypotheses derived from these studies in a quantitative way e.g. by using modeling approaches. Here we present the first modeling approach that allows predicting the cell cycle dependent radiosensitivity of repair proficient as well as of repair deficient cell lines after photon irradiation based on a small set of parameters and assumptions. A key element of the model is the classification of DNA damage according to its complexity on the level of chromatin loops of about 2Mbp size. Isolated DSB (iDSB), characterized by a single DSB within a chromatin loop, are distinguished from clustered DSB (cDSB), characterized by two or more DSB within a chromatin loop. The class of iDSB is further subdivided into two sub-classes, characterized by the replication status of the corresponding chromatin loop. For iDSB in replicated loops that are in close contact, error-free homologous recombination is assumed to be effective; in unreplicated loops or in replicated loops that have already been separated, iDSB are assumed to be repaired by error-prone non-homologous end joining. cDSB are assumed not to be repairable effectively by neither HR nor NHEJ. Assigning empirically derived lethalities to these three damage classes and pathways, we demonstrate that the model is able to accurately reproduce cell cycle dependent survival probabilities. Notably, the relevant parameters are derived solely from two survival curves for normal, repair proficient cells in G1 and late-S phase. Based on a comparison of model predictions with a large data set reported in the literature, we show that the lethality values for wild type cells are simultaneously predictive for the cell cycle dependent variation of sensitivity observed for HR-deficient and NHEJ-deficient cells.
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Affiliation(s)
- Antonia Hufnagl
- GSI Helmholtzzentrum für Schwerionenforschung (GSI), Department of Biophysics, Darmstadt, Germany
| | - Lisa Herr
- GSI Helmholtzzentrum für Schwerionenforschung (GSI), Department of Biophysics, Darmstadt, Germany
| | - Thomas Friedrich
- GSI Helmholtzzentrum für Schwerionenforschung (GSI), Department of Biophysics, Darmstadt, Germany
| | - Marco Durante
- GSI Helmholtzzentrum für Schwerionenforschung (GSI), Department of Biophysics, Darmstadt, Germany; Technische Universität Darmstadt, Darmstadt, Germany
| | - Gisela Taucher-Scholz
- GSI Helmholtzzentrum für Schwerionenforschung (GSI), Department of Biophysics, Darmstadt, Germany
| | - Michael Scholz
- GSI Helmholtzzentrum für Schwerionenforschung (GSI), Department of Biophysics, Darmstadt, Germany.
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24
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Sankaranarayanan K, Nikjoo H. Genome-based, mechanism-driven computational modeling of risks of ionizing radiation: The next frontier in genetic risk estimation? MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 764:1-15. [PMID: 26041262 DOI: 10.1016/j.mrrev.2014.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/18/2014] [Indexed: 10/24/2022]
Abstract
Research activity in the field of estimation of genetic risks of ionizing radiation to human populations started in the late 1940s and now appears to be passing through a plateau phase. This paper provides a background to the concepts, findings and methods of risk estimation that guided the field through the period of its growth to the beginning of the 21st century. It draws attention to several key facts: (a) thus far, genetic risk estimates have been made indirectly using mutation data collected in mouse radiation studies; (b) important uncertainties and unsolved problems remain, one notable example being that we still do not know the sensitivity of human female germ cells to radiation-induced mutations; and (c) the concept that dominated the field thus far, namely, that radiation exposures to germ cells can result in single gene diseases in the descendants of those exposed has been replaced by the concept that radiation exposure can cause DNA deletions, often involving more than one gene. Genetic risk estimation now encompasses work devoted to studies on DNA deletions induced in human germ cells, their expected frequencies, and phenotypes and associated clinical consequences in the progeny. We argue that the time is ripe to embark on a human genome-based, mechanism-driven, computational modeling of genetic risks of ionizing radiation, and we present a provisional framework for catalyzing research in the field in the 21st century.
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Affiliation(s)
- K Sankaranarayanan
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, Box 260, P9-02, Stockholm SE 17176, Sweden
| | - H Nikjoo
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, Box 260, P9-02, Stockholm SE 17176, Sweden.
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