Studies of the dose-effect relation

Dose-effect relations and, specifically, cell survival curves are surveyed with emphasis on the interplay of the random factors — biological variability, stochastic reaction of the cell, and the statistics of energy deposition —that co-determine their shape. The global parameters mean inactivation dose, , and coefficient of variance, V, represent this interplay better than conventional parameters. Mechanisms such as lesion interaction, misrepair, repair overload, or repair depletion have been invoked to explain sigmoid dose dependencies, but these notions are partly synonymous and are largely undistinguishable on the basis of observed dose dependencies. All dose dependencies reflect, to varying degree, the microdosimetric fluctuations of energy deposition, and these have certain implications, e.g. the linearity of the dose dependence at small doses, that apply regardless of unresolved molecular mechanisms of cellular radiation action

A molecular dynamics simulation of DNA damage induction by ionizing radiation

We present a multi-scale simulation of early stage of DNA damages by the indirect action of hydroxyl ($^\bullet$OH) free radicals generated by electrons and protons. The computational method comprises of interfacing the Geant4-DNA Monte Carlo with the ReaxFF molecular dynamics software. A clustering method was employed to map the coordinates of $^\bullet$OH-radicals extracted from the ionization track-structures onto nano-meter simulation voxels filled with DNA and water molecules. The molecular dynamics simulation provides the time evolution and chemical reactions in individual simulation voxels as well as the energy-landscape accounted for the DNA-$^\bullet$OH chemical reaction that is essential for the first principle enumeration of hydrogen abstractions, chemical bond breaks, and DNA-lesions induced by collection of ions in clusters less than the critical dimension which is approximately 2-3 \AA. We show that the formation of broken bonds leads to DNA base and backbone damages that collectively propagate to DNA single and double strand breaks. For illustration of the methodology, we focused on particles with initial energy of 1 MeV. Our studies reveal a qualitative difference in DNA damage induced by low energy electrons and protons. Electrons mainly generate small pockets of $^\bullet$OH-radicals, randomly dispersed in the cell volume. In contrast, protons generate larger clusters along a straight-line parallel to the direction of the particle. The ratio of the total DNA double strand breaks induced by a single proton and electron track is determined to be $\approx$ 4 in the linear scaling limit. The tool developed in this work can be used in the future to investigate the relative biological effectiveness of light and heavy ions that are used in radiotherapy.Comment: 7 pages, 7 figures, accepted for publication in Physics in Medicine and Biolog

The p53-MDM2 network: from oscillations to apoptosis

The p53 protein is well-known for its tumour suppressor function. The p53-MDM2 negative feedback loop constitutes the core module of a network of regulatory interactions activated under cellular stress. In normal cells, the level of p53 proteins is kept low by MDM2, i.e. MDM2 negatively regulates the activity of p53. In the case of DNA damage,the p53-mediated pathways are activated leading to cell cycle arrest and repair of the DNA. If repair is not possible due to excessive damage, the p53-mediated apoptotic pathway is activated bringing about cell death. In this paper, we give an overview of our studies on the p53-MDM2 module and the associated pathways from a systems biology perspective. We discuss a number of key predictions, related to some specific aspects of cell cycle arrest and cell death, which could be tested in experiments

Estudo do dano direto e indireto induzido ao DNA pela radiação ionizante usando o método de Monte Carlo

Orientador: Mario Antonio Bernal RodriguezTese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb WataghinResumo: A simulação por Monte Carlo (MC) é uma poderosa ferramenta para estudar os efeitos biológicos induzidos pela radiação ionizante em seres vivos. Vários códigos MC, com diferentes níveis de complexidade, são comumente usados em campos de pesquisa como nanodosimetria, radioterapia, proteção radiológica e areoespacial. Este trabalho apresenta uma ampliação de um modelo existente [1] para fins radiobiológicos, a fim de levar em conta o dano indireto e mixto induzido no DNA por radiações ionizantes. O kit de ferramentas de simulação GEANT4-DNA foi usado para simular a etapa física, pré-química e química do dano inicial no DNA induzidos por prótons e partículas alfa. O meio usado nas simulações foi a água líquida. Foram gerados dois arquivos de saída, um contendo eventos de deposição de energia dentro da região de interesse (ROI), e outro com a posição das espécies químicas produzidas pela radiólise d¿água, de 0,1 ps até 1 ns. As informações contidas nos dois arquivos foram sobrepostas em um modelo de material genético com resolução atômica, consistindo de várias cópias de fibras de cromatina de 30 nm. A configuração do B-DNA foi usada. O foco deste trabalho foi o dano indireto produzido pelo ataque do radical hidroxilo (?OH) ao grupo açucar-fosfato, normalmente através da abstração do hidrogênio. A abordagem seguida para explicar o dano indireto no DNA foi o mesmo usado por outros códigos radiobiológicos [2, 3]. O parâmetro crítico aqui considerado foi o raio de reação, calculado a partir da equação de difusão de Smoluchowski. Os rendimentos de quebra de cadeia simples, dupla e total produzidos por mecanismos diretos, indiretos e mistos são relatados. Resultados consistentes com outros trabalhos de simulações e experimentais foram encontrados, mesmo sem seguir qualquer processo de ajuste. Até aonde nós sabemos, esta é a primeira vez que o código GEANT4-DNA é combinado com um modelo atômico do DNA para estudar o dano químico induzido por radiações ionizantesAbstract: Monte Carlo (MC) simulation is a powerful tool to study biological effects induced by ionizing radiation on living beings. Several MC codes, with different level of complexity, are commonly used in research fields such as nanodosimetry, radiotherapy, radiation protection, and space radiation. This work presents an enhancement of an existing model [1] for radiobiological purposes, in order to account for the indirect and mixed DNA damage induced by ionizing particles. The GEANT4-DNA simulation toolkit was used to simulate physical, pre-chemical and chemical stages of the early DNA damage induced by protons and alpha particles. Liquid water was used as the medium for simulations. Two phase-space files were generated, one containing energy deposition events inside the region of interest (ROI), and another one with the position of chemical species produced by water radiolysis from 0.1 ps up to 1 ns. The information contained in both files was superposed on a genetic material model with atomic-resolution, consisting of several copies of 30-nm chromatin fibers. The B-DNA configuration was used. This work focused on the indirect damage produced by the hydroxyl radical (?OH) attack on the sugar-phosphate, normally through hydrogen abstraction. The approach followed to account for the indirect damage in DNA was the same used by other radiobiological codes [2, 3]. The critical parameter considered here was the reaction radius, which was calculated from the Smoluchowski¿s diffusion equation. Single, double, and total strand break yields produced by direct, indirect and mixed mechanisms are reported. Results consistent with simulated and experimental works were found, even without following any fitting process. To the best of our knowledge, this is the first time the GEANT4-DNA code is used in conjunction with a DNA atomic resolution model for studying the chemical damage induced by ionizing radiationsDoutoradoFísicaDoutora em Ciências190154/2013-6CNP

A Paradigm Shift in Low Dose Radiation Biology

When ionizing radiation traverses biological material, some energy depositions occur and ionize directly deoxyribonucleic acid (DNA) molecules, the critical target. A classical paradigm in radiobiology is that the deposition of energy in the cell nucleus and the resulting damage to DNA are responsible for the detrimental biological effects of radiation. It is presumed that no radiation effect would be expected in cells that receive no direct radiation exposure through nucleus. The risks of exposure to low dose ionizing radiation are estimated by extrapolating from data obtained after exposure to high dose radiation. However, the validity of using this dose-response model is controversial because evidence accumulated over the past decade has indicated that living organisms, including humans, respond differently to low dose radiation than they do to high dose radiation. Moreover, recent experimental evidences from many laboratories reveal the fact that radiation effects also occur in cells that were not exposed to radiation and in the progeny of irradiated cells at delayed times after radiation exposure where cells do not encounter direct DNA damage. Recently, the classical paradigm in radiobiology has been shifted from the nucleus, specifically the DNA, as the principal target for the biological effects of radiation to cells. The universality of target theory has been challenged by phenomena of radiation-induced genomic instability, bystander effect and adaptive response. The new radiation biology paradigm would cover both targeted and non-targeted effects of ionizing radiation. The mechanisms underlying these responses involve biochemical/molecular signals that respond to targeted and non-targeted events. These results brought in understanding that the biological response to low dose radiation at tissue or organism level is a complex process of integrated response of cellular targets as well as extra-cellular factors. Biological understanding of the effects of radiation can be used to improve the assessment of low dose radiation risk. In this article, the mechanisms of targeted and non-targeted responses, and interrelation between the phenomena on cellular injury after exposure to low doses of radiation as they relate to low dose radiation effects will be reviewed. Received:14 October 2014; Revised:1 April 2015; Accepted: 14 April 201

A Paradigm Shift in Low Dose Radiation Biology

When ionizing radiation traverses biological material, some energy depositions occur and ionize directly deoxyribonucleic acid (DNA) molecules, the critical target. A classical paradigm in radiobiology is that the deposition of energy in the cell nucleus and the resulting damage to DNA are responsible for the detrimental biological effects of radiation. It is presumed that no radiation effect would be expected in cells that receive no direct radiation exposure through nucleus. The risks of exposure to low dose ionizing radiation are estimated by extrapolating from data obtained after exposure to high dose radiation. However, the validity of using this dose-response model is controversial because evidence accumulated over the past decade has indicated that living organisms, including humans, respond differently to low dose radiation than they do to high dose radiation. Moreover, recent experimental evidences from many laboratories reveal the fact that radiation effects also occur in cells that were not exposed to radiation and in the progeny of irradiated cells at delayed times after radiation exposure where cells do not encounter direct DNA damage. Recently, the classical paradigm in radiobiology has been shifted from the nucleus, specifically the DNA, as the principal target for the biological effects of radiation to cells. The universality of target theory has been challenged by phenomena of radiation-induced genomic instability, bystander effect and adaptive response. The new radiation biology paradigm would cover both targeted and non-targeted effects of ionizing radiation. The mechanisms underlying these responses involve biochemical/molecular signals that respond to targeted and non-targeted events. These results brought in understanding that the biological response to low dose radiation at tissue or organism level is a complex process of integrated response of cellular targets as well as extra-cellular factors. Biological understanding of the effects of radiation can be used to improve the assessment of low dose radiation risk. In this article, the mechanisms of targeted and non-targeted responses, and interrelation between the phenomena on cellular injury after exposure to low doses of radiation as they relate to low dose radiation effects will be reviewed. Received:14 October 2014; Revised:1 April 2015; Accepted: 14 April 201

Renormalization of radiobiological response functions by energy loss fluctuations and complexities in chromosome aberration induction: deactivation theory for proton therapy from cells to tumor control

We employ a multi-scale mechanistic approach to investigate radiation induced cell toxicities and deactivation mechanisms as a function of linear energy transfer in hadron therapy. Our theoretical model consists of a system of Markov chains in microscopic and macroscopic spatio-temporal landscapes, i.e., stochastic birth-death processes of cells in millimeter-scale colonies that incorporates a coarse-grained driving force to account for microscopic radiation induced damage. The coupling, hence the driving force in this process, stems from a nano-meter scale radiation induced DNA damage that incorporates the enzymatic end-joining repair and mis-repair mechanisms. We use this model for global fitting of the high-throughput and high accuracy clonogenic cell-survival data acquired under exposure of the therapeutic scanned proton beams, the experimental design that considers $\gamma$-H2AX as the biological endpoint and exhibits maximum observed achievable dose and LET, beyond which the majority of the cells undergo collective biological deactivation processes. An estimate to optimal dose and LET calculated from tumor control probability by extension to $~ 10^6$ cells per $mm$-size voxels is presented. We attribute the increase in degree of complexity in chromosome aberration to variabilities in the observed biological responses as the beam linear energy transfer (LET) increases, and verify consistency of the predicted cell death probability with the in-vitro cell survival assay of approximately 100 non-small cell lung cancer (NSCLC) cells

Targeting GLI factors to inhibit the Hedgehog pathway

Hedgehog (Hh) signaling has emerged in recent years as an attractive target for anticancer therapy because its aberrant activation is implicated in several cancers. Major progress has been made in the development of SMOOTHENED (SMO) antagonists, although they have shown several limitations due to downstream SMO pathway activation or the occurrence of drug-resistant SMO mutations. Recently, particular interest has been elicited by the identification of molecules able to hit glioma-associated oncogene (GLI) factors, the final effectors of the Hh pathway, which provide a valid tool to overcome anti-SMO resistance. Here, we review results achieved in developing GLI antagonists, explaining their mechanisms of action and highlighting their therapeutic potential. We also underline the relevance of structural details in their discovery and optimization