scholarly journals Monte Carlo Simulation-Based Calculations of Complex DNA Damage for Incidents of Environmental Ionizing Radiation Exposure

2021 ◽  
Vol 11 (19) ◽  
pp. 8985
Author(s):  
Spyridon A. Kalospyros ◽  
Violeta Gika ◽  
Zacharenia Nikitaki ◽  
Antigoni Kalamara ◽  
Ioanna Kyriakou ◽  
...  
Keyword(s):  
Dna Damage ◽  
Monte Carlo ◽  
Ionizing Radiation ◽  
Mammalian Cells ◽  
Absorbed Dose ◽  
Dna Lesions ◽  
Lifetime Cancer Risk ◽  
Exposed Population ◽  
Exposed Individual ◽  
Risk Of Cancer

In this paper, we present a useful Monte Carlo (MC)-based methodology that can be utilized to calculate the absorbed dose and the initial levels of complex DNA damage (such as double strand breaks-DSBs) in the case of an environmental ionizing radiation (IR) exposure incident (REI) i.e., a nuclear accident. Our objective is to assess the doses and complex DNA damage by isolating only one component of the total radiation released in the environment after a REI that will affect the health of the exposed individual. More specifically, the radiation emitted by radionuclide 137Cs in the ground (under the individual’s feet). We use a merging of the Monte Carlo N-Particle Transport code (MCNP) with the Monte Carlo Damage Simulation (MCDS) code. The DNA lesions have been estimated through simulations for different surface activities of a 137Cs ground-based γ radiation source. The energy spectrum of the emitted secondary electrons and the absorbed dose in typical mammalian cells have been calculated using the MCNP code, and then these data are used as an input in the MCDS code for the estimation of critical DNA damage levels and types. As a realistic application, the calculated dose is also used to assess the Excess Lifetime Cancer Risk (ELCR) for eight hypothetical individuals, living in different zones around the Chernobyl Nuclear Power Plant, exposed to different time periods at the days of the accident in 1986. We conclude that any exposition of an individual in the near zone of Chernobyl increases the risk of cancer at a moderate to high grade, connected also with the induction of complex DNA damage by radiation. Generally, our methodology has proven to be useful for assessing γ rays-induced complex DNA damage levels of the exposed population, in the case of a REI and for better understanding the long-term health effects of exposure of the population to IR.

scholarly journals Discovery and Optimisation of Bacterial Nitroreductases for Use in Anti-Cancer Gene Therapy

2021 ◽  
Author(s):  
◽  
Gareth Adrian Prosser
Keyword(s):  
Dna Damage ◽  
Mammalian Cells ◽  
Excision Repair ◽  
Alkylating Agents ◽  
Dna Lesions ◽  
Site Directed Mutagenesis ◽  
In Vitro Assays ◽  
E Coli ◽  
Anti Cancer

<p>Nitroaromatic prodrugs are biologically inert compounds that are attractive candidates for anti-cancer therapy by virtue of their ability to be converted to potent DNA alkylating agents by nitroreductase (NTR) enzymes. In gene-directed enzyme-prodrug therapy (GDEPT), NTR-encoding therapeutic transgenes are delivered specifically to tumour cells, whereupon their expression confers host cell sensitivity to subsequent systemic administration of a nitroaromatic prodrug. The most well studied NTR-GDEPT system involves reduction of the aziridinyl dinitrobenzamide prodrug CB1954 by the Escherichia coli NTR NfsB. However, low affinity of this enzyme for CB1954 has so far limited the clinical efficacy of this GDEPT combination. The research described in this thesis has primarily sought to address this limitation through identification and optimisation of novel NTR enzymes with improved nitroaromatic prodrug reductase activity. Efficient assessment of NTR activity from large libraries of candidate enzymes requires a rapid and reliable screening system. An E. coli-based assay was developed to permit indirect assessment of relative rates of prodrug reduction by over-expressed NTRs via measurement of SOS response induction resulting from reduced prodrug-induced DNA damage. Using this assay in concert with other in vitro and in vivo tests, more than 50 native bacterial NTRs of diverse sequence and origin were assessed for their ability to reduce a panel of clinically attractive nitroaromatic prodrugs. Significantly, a number of NTRs were identified, particularly in the family of enzymes homologous to the native E. coli NTR NfsA, which displayed substantially improved activity over NfsB with CB1954 and other nitroaromatic prodrugs as substrates. This work also examined the roles of E. coli DNA damage repair pathways in processing of adducts induced by various nitroaromatic prodrugs. Of particular interest, nucleotide excision repair was found to be important in the processing of DNA lesions caused by 4-, but not 2-nitro group reduction products of CB1954, which suggests that there are some parallels in the mechanisms of CB1954 adduct repair in E. coli and mammalian cells. Finally, a lead NTR candidate, YcnD from Bacillus subtilis, was selected for further activity improvement through site-directed mutagenesis of active site residues. Using SOS screening, a double-site mutant was identified with 2.5-fold improved activity over the wildtype enzyme in metabolism of the novel dinitrobenzamide mustard prodrug PR-104A. In conclusion, novel NTRs with substantially improved nitroaromatic prodrug reducing activity over previously documented enzymes were identified and characterised. These results hold significance not only for the field of NTR-GDEPT, but also for other biotechnological applications in which NTRs are becoming increasingly significant, including developmental studies, antibiotic discovery and bioremediation. Furthermore, the in vitro assays developed in this study have potential utility in the discovery and evolution of other GDEPT-relevant enzymes whose prodrug metabolism is associated with genotoxicity.</p>

scholarly journals Discovery and Optimisation of Bacterial Nitroreductases for Use in Anti-Cancer Gene Therapy

2021 ◽  
Author(s):  
◽  
Gareth Adrian Prosser
Keyword(s):  
Dna Damage ◽  
Mammalian Cells ◽  
Excision Repair ◽  
Alkylating Agents ◽  
Dna Lesions ◽  
Site Directed Mutagenesis ◽  
In Vitro Assays ◽  
E Coli ◽  
Anti Cancer

<p>Nitroaromatic prodrugs are biologically inert compounds that are attractive candidates for anti-cancer therapy by virtue of their ability to be converted to potent DNA alkylating agents by nitroreductase (NTR) enzymes. In gene-directed enzyme-prodrug therapy (GDEPT), NTR-encoding therapeutic transgenes are delivered specifically to tumour cells, whereupon their expression confers host cell sensitivity to subsequent systemic administration of a nitroaromatic prodrug. The most well studied NTR-GDEPT system involves reduction of the aziridinyl dinitrobenzamide prodrug CB1954 by the Escherichia coli NTR NfsB. However, low affinity of this enzyme for CB1954 has so far limited the clinical efficacy of this GDEPT combination. The research described in this thesis has primarily sought to address this limitation through identification and optimisation of novel NTR enzymes with improved nitroaromatic prodrug reductase activity. Efficient assessment of NTR activity from large libraries of candidate enzymes requires a rapid and reliable screening system. An E. coli-based assay was developed to permit indirect assessment of relative rates of prodrug reduction by over-expressed NTRs via measurement of SOS response induction resulting from reduced prodrug-induced DNA damage. Using this assay in concert with other in vitro and in vivo tests, more than 50 native bacterial NTRs of diverse sequence and origin were assessed for their ability to reduce a panel of clinically attractive nitroaromatic prodrugs. Significantly, a number of NTRs were identified, particularly in the family of enzymes homologous to the native E. coli NTR NfsA, which displayed substantially improved activity over NfsB with CB1954 and other nitroaromatic prodrugs as substrates. This work also examined the roles of E. coli DNA damage repair pathways in processing of adducts induced by various nitroaromatic prodrugs. Of particular interest, nucleotide excision repair was found to be important in the processing of DNA lesions caused by 4-, but not 2-nitro group reduction products of CB1954, which suggests that there are some parallels in the mechanisms of CB1954 adduct repair in E. coli and mammalian cells. Finally, a lead NTR candidate, YcnD from Bacillus subtilis, was selected for further activity improvement through site-directed mutagenesis of active site residues. Using SOS screening, a double-site mutant was identified with 2.5-fold improved activity over the wildtype enzyme in metabolism of the novel dinitrobenzamide mustard prodrug PR-104A. In conclusion, novel NTRs with substantially improved nitroaromatic prodrug reducing activity over previously documented enzymes were identified and characterised. These results hold significance not only for the field of NTR-GDEPT, but also for other biotechnological applications in which NTRs are becoming increasingly significant, including developmental studies, antibiotic discovery and bioremediation. Furthermore, the in vitro assays developed in this study have potential utility in the discovery and evolution of other GDEPT-relevant enzymes whose prodrug metabolism is associated with genotoxicity.</p>

scholarly journals Multipathway risk assessment of trihalomethane exposure in drinking water of Lebanon

2007 ◽  
Vol 5 (4) ◽  
pp. 511-522 ◽  
Author(s):  
Lucy Semerjian ◽  
John Dennis
Keyword(s):  
Cancer Risk ◽  
Tap Water ◽  
Inhalation Exposure ◽  
Dermal Absorption ◽  
Cancer Risks ◽  
Oral Ingestion ◽  
Lifetime Cancer Risk ◽  
Exposed Population ◽  
Total Cancer ◽  
Risk Of Cancer

The toxicological risks and lifetime cancer risks of trihalomethanes through oral ingestion, dermal absorption, and inhalation exposure from tap water in selected regions in Lebanon are estimated. Existing trihalomethane concentrations do not pose any non-carcinogenic and developmental risks in the exposed population via oral ingestion. Among the three pathways, residents have a higher risk of cancer through oral ingestion than through the other two pathways. The lifetime cancer risk through oral ingestion for dibromochloromethane makes the highest contribution to total risks, followed by bromodichloromethane, bromoform, and chloroform. The total multipathway cancer risk analysis suggests that no cancer risks exist during the summer and winter seasons; however, in the spring the total cancer risks exceeds the USEPA acceptable level of 10−6 by a factor of 10.7.

scholarly journals MORC2 regulates DNA damage response through a PARP1-dependent pathway

2019 ◽  
Vol 47 (16) ◽  
pp. 8502-8520 ◽  
Author(s):  
Lin Zhang ◽  
Da-Qiang Li
Keyword(s):  
Dna Damage ◽  
Zinc Finger ◽  
Chromatin Remodeling ◽  
Dna Damage Response ◽  
Mammalian Cells ◽  
Cellular Response ◽  
Genotoxic Stress ◽  
Underlying Mechanism ◽  
Dna Lesions ◽  
Damage Response

Abstract Microrchidia family CW-type zinc finger 2 (MORC2) is a newly identified chromatin remodeling enzyme with an emerging role in DNA damage response (DDR), but the underlying mechanism remains largely unknown. Here, we show that poly(ADP-ribose) polymerase 1 (PARP1), a key chromatin-associated enzyme responsible for the synthesis of poly(ADP-ribose) (PAR) polymers in mammalian cells, interacts with and PARylates MORC2 at two residues within its conserved CW-type zinc finger domain. Following DNA damage, PARP1 recruits MORC2 to DNA damage sites and catalyzes MORC2 PARylation, which stimulates its ATPase and chromatin remodeling activities. Mutation of PARylation residues in MORC2 results in reduced cell survival after DNA damage. MORC2, in turn, stabilizes PARP1 through enhancing acetyltransferase NAT10-mediated acetylation of PARP1 at lysine 949, which blocks its ubiquitination at the same residue and subsequent degradation by E3 ubiquitin ligase CHFR. Consequently, depletion of MORC2 or expression of an acetylation-defective PARP1 mutant impairs DNA damage-induced PAR production and PAR-dependent recruitment of DNA repair proteins to DNA lesions, leading to enhanced sensitivity to genotoxic stress. Collectively, these findings uncover a previously unrecognized mechanistic link between MORC2 and PARP1 in the regulation of cellular response to DNA damage.

scholarly journals Evaluation of Background Ionizing Radiation Level of Selected Oil Spill Communities of Delta State, Nigeria

2019 ◽  
pp. 1-10
Author(s):  
M. U. Audu ◽  
G. O. Avwiri ◽  
C. P. Ononugbo
Keyword(s):  
Cancer Risk ◽  
Ionizing Radiation ◽  
Effective Dose ◽  
Oil Spill ◽  
Annual Effective Dose ◽  
Absorbed Dose ◽  
Nuclear Radiation ◽  
Lifetime Cancer Risk ◽  
Radiation Level ◽  
Excess Lifetime Cancer Risk

Study of the terrestrial Background Ionizing Radiation levels of selected Oil Spill Communities of Delta State, Nigeria have been carried out using Digilert 200 and Radalert 100 nuclear radiation monitor and a geographical positioning system (Garmin GPSMAP 76S). The exposure rates of the five communities ranges from 0.016 to 0.030  at Jones Creek, 0.014 to 0.034  at Opuwade Community, 0.015 to 0.037   at Okpare community, 0.007 to 0.029  at OtuJeremi community and 0.011to 0.040  at Otor-Edo community. The obtained mean exposures rates were higher than ICRP standard limit of 0.013. The absorbed dose rates calculated ranged from 139.2 to 261 (Jones Creek), 121.8 to 259.8 nGyh-1 (Opuwade Community), 130.5 to 321.9 nGyh-1 (Okpare community), 60.9 to 252.3 nGyh-1 (OtuJeremi community) and 95.9 to 348 nGyh-1 (Otor-Edo community). The estimated annual effective dose equivalent varies from  0.21 to 0.40 , 0.19 to  0.45 , 0.20 to  0.49 , 0.09 to 0.39  and  0.15 to 0.53  for Jones Creek, Opuwade Community, Okpare community, Otu Jeremi community and Otor-Edo community respectively while the excess lifetime cancer risk calculated for Jones Creek varies from (0.75  to 1.40)  x 10-3, Opuwade community (0.65 to 1.59 )×, Okpare community (0.70 to 1.73 ) x , OtuJeremi community (0.33 to 1.35)× and Otor-Edo community (0.51 to 1.87)×. All the mean values of absorbed dose, annual effective dose and excess lifetime cancer risk exceeded their recommended safe values. The results obtained in this work may not constitute any immediate health risk to the residents of the selected oil spill communities but long term exposure in the area may lead to detrimental health risks.

scholarly journals Interaction between Fibroblasts and Immune Cells Following DNA Damage Induced by Ionizing Radiation

2020 ◽  
Author(s):  
Kalaiyarasi Ragunathan ◽  
Nikki Lyn Esnardo Upfold ◽  
Valentyn Oksenych
Keyword(s):  
Dna Damage ◽  
Tumor Microenvironment ◽  
Ionizing Radiation ◽  
Immune Cells ◽  
Mammalian Cells ◽  
Cancer Associated Fibroblasts ◽  
Cell Type ◽  
Dna Damages ◽  
Damage Response ◽  
High Doses

Cancer-associated fibroblasts (CAF) form the basis of tumor microenvironment and possess immunomodulatory functions by interacting with other cells surrounding tumor, including T lymphocytes, macrophages, dendritic cells and natural killer cells. Ionizing radiation is a broadly-used method in radiotherapy to target tumors. In mammalian cells, ionizing radiation induces various types of DNA damages and DNA damage response. Being unspecific, radiotherapy affects all the cells in tumor microenvironment, including the tumor itself, CAFs and immune cells. CAFs are extremely radio-resistant and do not initiate apoptosis even at high doses of radiation. However, following radiation, CAFs become senescent and produce a distinct combination of immunoregulatory molecules. Radiosensitivity of immune cells varies depending on the cell type due to inefficient DNA repair in, for example, monocytes and granulocytes. In this minireview, we are summarizing recent findings on the interaction between CAF, ionizing radiation and immune cells in the tumor microenvironment.

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

Cancers ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 799 ◽  
Author(s):  
Konstantinos P. Chatzipapas ◽  
Panagiotis Papadimitroulas ◽  
Dimitris Emfietzoglou ◽  
Spyridon A. Kalospyros ◽  
Megumi Hada ◽  
...  
Keyword(s):  
Dna Damage ◽  
Monte Carlo ◽  
Ionizing Radiation ◽  
Monte Carlo Simulations ◽  
High Energy ◽  
Radiation Biology ◽  
Medical Procedures ◽  
Promising Tool ◽  
Need To Evaluate ◽  
Mc Simulation

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.

scholarly journals Direct observation of damage clustering in irradiated DNA with atomic force microscopy

2019 ◽  
Vol 48 (3) ◽  
pp. e18-e18 ◽  
Author(s):  
Xu Xu ◽  
Toshiaki Nakano ◽  
Masataka Tsuda ◽  
Ryota Kanamoto ◽  
Ryoichi Hirayama ◽  
...  
Keyword(s):  
Dna Damage ◽  
Atomic Force Microscopy ◽  
Ionizing Radiation ◽  
Ion Beams ◽  
Dna Lesions ◽  
X Rays ◽  
Damage Site ◽  
Force Microscopy ◽  
Atomic Force ◽  
Clustered Dna Damage

Abstract Ionizing radiation produces clustered DNA damage that contains two or more lesions in 10–20 bp. It is believed that the complexity of clustered damage (i.e., the number of lesions per damage site) is related to the biological severity of ionizing radiation. However, only simple clustered damage containing two vicinal lesions has been demonstrated experimentally. Here we developed a novel method to analyze the complexity of clustered DNA damage. Plasmid DNA was irradiated with densely and sparsely ionizing Fe-ion beams and X-rays, respectively. Then, the resulting DNA lesions were labeled with biotin/streptavidin and observed with atomic force microscopy. Fe-ion beams produced complex clustered damage containing 2–4 lesions. Furthermore, they generated two or three clustered damage sites in a single plasmid molecule that resulted from the hit of a single track of Fe-ion beams. Conversely, X-rays produced relatively simple clustered damage. The present results provide the first experimental evidence for complex cluster damage.

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