Ionizing Radiation and Complex DNA Damage: Quantifying the Radiobiological Damage Using Monte Carlo Simulations

Overview

Journal Cancers (Basel)

Publisher MDPI

Specialty Oncology

Date 2020 Apr 1

PMID 32225023

Citations 25

Authors

Konstantinos P Chatzipapas

Panagiotis Papadimitroulas

Dimitris Emfietzoglou

Spyridon A Kalospyros

Megumi Hada

Alexandros G Georgakilas

George C Kagadis

Affiliations

Soon will be listed here.

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.

Citing Articles

In silico analysis of radiation-induced double-strand breaks by internal ex vivo irradiation of lymphocytes for 45 alpha- and beta/gamma-emitting radionuclides.

Salas-Ramirez M, Lassmann M, Eberlein U EJNMMI Res. 2025; 15(1):21.

PMID: 40063302 PMC: 11893945. DOI: 10.1186/s13550-025-01214-w.

Position in proton Bragg curve influences DNA damage complexity and survival in head and neck cancer cells.

Heemskerk T, Groenendijk C, Rovituso M, van der Wal E, van Burik W, Chatzipapas K Clin Transl Radiat Oncol. 2025; 51:100908.

PMID: 39877299 PMC: 11772976. DOI: 10.1016/j.ctro.2024.100908.

Radioprotective Effects of Vitamin C, Cimetidine, and Famotidine on Lipid Peroxidase and Hepatic Glutathione Levels in Mouse Liver.

Gholami M, Ahmadi A, Yusofvand R, Khanchoupan M, Hajimazdarany S, Najibi R Int J Cell Biol. 2025; 2025:1106920.

PMID: 39803629 PMC: 11724733. DOI: 10.1155/ijcb/1106920.

Molecular Insights into Radiation Effects and Protective Mechanisms: A Focus on Cellular Damage and Radioprotectors.

Ibanez B, Melero A, Montoro A, San Onofre N, Soriano J Curr Issues Mol Biol. 2024; 46(11):12718-12732.

PMID: 39590349 PMC: 11592695. DOI: 10.3390/cimb46110755.

Current Insights into Molecular Mechanisms and Potential Biomarkers for Treating Radiation-Induced Liver Damage.

Saha B, Pallatt S, Banerjee A, Banerjee A, Pathak R, Pathak S Cells. 2024; 13(18.

PMID: 39329744 PMC: 11429644. DOI: 10.3390/cells13181560.

References

Michalik V, Begusova M, Bigildeev E . Computer-aided stochastic modeling of the radiolysis of liquid water. Radiat Res. 1998; 149(3):224-36. View

Sedelnikova O, Redon C, Dickey J, Nakamura A, Georgakilas A, Bonner W . Role of oxidatively induced DNA lesions in human pathogenesis. Mutat Res. 2010; 704(1-3):152-9. PMC: 3074954. DOI: 10.1016/j.mrrev.2009.12.005. View

Tsai M, Tian Z, Qin N, Yan C, Lai Y, Hung S . A new open-source GPU-based microscopic Monte Carlo simulation tool for the calculations of DNA damages caused by ionizing radiation --- Part I: Core algorithm and validation. Med Phys. 2020; 47(4):1958-1970. DOI: 10.1002/mp.14037. View

Li W, Belchior A, Beuve M, Chen Y, Di Maria S, Friedland W . Intercomparison of dose enhancement ratio and secondary electron spectra for gold nanoparticles irradiated by X-rays calculated using multiple Monte Carlo simulation codes. Phys Med. 2020; 69:147-163. PMC: 7446940. DOI: 10.1016/j.ejmp.2019.12.011. View

Killock D . Targeted therapies: DNA polymerase θ-a new target for synthetic lethality?. Nat Rev Clin Oncol. 2015; 12(3):125. DOI: 10.1038/nrclinonc.2015.23. View

Plante I, Ponomarev A, Cucinotta F . Calculation of the energy deposition in nanovolumes by protons and HZE particles: geometric patterns of initial distributions of DNA repair foci. Phys Med Biol. 2013; 58(18):6393-405. DOI: 10.1088/0031-9155/58/18/6393. View

Rorvik E, Fjaera L, Dahle T, Dale J, Engeseth G, Stokkevag C . Exploration and application of phenomenological RBE models for proton therapy. Phys Med Biol. 2018; 63(18):185013. DOI: 10.1088/1361-6560/aad9db. View

Nikjoo H, ONeill P, Goodhead D, Terrissol M . Computational modelling of low-energy electron-induced DNA damage by early physical and chemical events. Int J Radiat Biol. 1997; 71(5):467-83. DOI: 10.1080/095530097143798. View

Semenenko V, Stewart R . Fast Monte Carlo simulation of DNA damage formed by electrons and light ions. Phys Med Biol. 2006; 51(7):1693-706. DOI: 10.1088/0031-9155/51/7/004. View

10.

Friedrich T, Scholz U, Elsasser T, Durante M, Scholz M . Systematic analysis of RBE and related quantities using a database of cell survival experiments with ion beam irradiation. J Radiat Res. 2012; 54(3):494-514. PMC: 3650740. DOI: 10.1093/jrr/rrs114. View

11.

Park C, Papiez L, Zhang S, Story M, Timmerman R . Universal survival curve and single fraction equivalent dose: useful tools in understanding potency of ablative radiotherapy. Int J Radiat Oncol Biol Phys. 2008; 70(3):847-52. DOI: 10.1016/j.ijrobp.2007.10.059. View

12.

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(5):525-40. DOI: 10.1667/RR13902.1. View

13.

Friedland W, Dingfelder M, Kundrat P, Jacob P . Track structures, DNA targets and radiation effects in the biophysical Monte Carlo simulation code PARTRAC. Mutat Res. 2011; 711(1-2):28-40. DOI: 10.1016/j.mrfmmm.2011.01.003. View

14.

Karr J, Sanghvi J, Macklin D, Gutschow M, Jacobs J, Bolival Jr B . A whole-cell computational model predicts phenotype from genotype. Cell. 2012; 150(2):389-401. PMC: 3413483. DOI: 10.1016/j.cell.2012.05.044. View

15.

Sakata D, Kyriakou I, Okada S, Tran H, Lampe N, Guatelli S . Geant4-DNA track-structure simulations for gold nanoparticles: The importance of electron discrete models in nanometer volumes. Med Phys. 2018; 45(5):2230-2242. DOI: 10.1002/mp.12827. View

16.

Balasubramanian B, Pogozelski W, Tullius T . DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc Natl Acad Sci U S A. 1998; 95(17):9738-43. PMC: 21406. DOI: 10.1073/pnas.95.17.9738. View

17.

Helleday T . The underlying mechanism for the PARP and BRCA synthetic lethality: clearing up the misunderstandings. Mol Oncol. 2011; 5(4):387-93. PMC: 5528309. DOI: 10.1016/j.molonc.2011.07.001. View

18.

Barnard S, Bouffler S, Rothkamm K . The shape of the radiation dose response for DNA double-strand break induction and repair. Genome Integr. 2013; 4(1):1. PMC: 3616853. DOI: 10.1186/2041-9414-4-1. View

19.

Plante I, Slaba T, Shavers Z, Hada M . A Bi-Exponential Repair Algorithm for Radiation-Induced Double-Strand Breaks: Application to Simulation of Chromosome Aberrations. Genes (Basel). 2019; 10(11). PMC: 6896174. DOI: 10.3390/genes10110936. View

20.

Friedland W, Jacob P, Kundrat P . Stochastic simulation of DNA double-strand break repair by non-homologous end joining based on track structure calculations. Radiat Res. 2010; 173(5):677-88. DOI: 10.1667/RR1965.1. View