Statistical analysis of comet assay results

Intratumoral androgen biosynthesis associated with 3β-hydroxysteroid dehydrogenase 1 promotes resistance to radiotherapy in prostate cancer

Half of all men with advanced prostate cancer (PCa) inherit at least 1 copy of an adrenal-permissive HSD3B1 (1245C) allele, which increases levels of 3β-hydroxysteroid dehydrogenase 1 (3βHSD1) and promotes intracellular androgen biosynthesis. Germline inheritance of the adrenally permissive allele confers worse outcomes in men with advanced PCa. We investigated whether HSD3B1 (1245C) drives resistance to combined androgen deprivation and radiotherapy. Adrenally permissive 3βHSD1 enhanced resistance to radiotherapy in PCa cell lines and xenograft models engineered to mimic the human adrenal/gonadal axis during androgen deprivation. The allele-specific effects on radiosensitivity were dependent on availability of DHEA, the substrate for 3βHSD1. In lines expressing the HSD3B1 (1245C) allele, enhanced expression of DNA damage response (DDR) genes and more rapid DNA double-strand break (DSB) resolution were observed. A correlation between androgen receptor (AR) expression and increased DDR gene expression was confirmed in 680 radical prostatectomy specimens. Treatment with the nonsteroidal antiandrogen enzalutamide reversed the resistant phenotype of HSD3B1 (1245C) PCa in vitro and in vivo. In conclusion, 3βHSD1 promotes prostate cancer resistance to combined androgen deprivation and radiotherapy by upregulating DNA DSB repair. This work supports prospective validation of early combined androgen blockade for high-risk men harboring the HSD3B1 (1245C) allele.

Evaluation of Deoxyribonucleic Acid Damage Using Neutral Comet Assay for High Radiation Doses: A Feasibility Study

Purpose

This study aims to investigate the use of the neutral comet assay to assess deoxyribonucleic acid (DNA) damage in lymphocytes exposed to high doses of radiation.

Materials and Methods

The research was conducted by obtaining informed consent, after which blood samples were taken from seven healthy individuals and this study was approved by the institutional ethics committee. At first, for the determination of dose-effect curves, samples obtained from the first five individuals were irradiated for doses ranging from 0 to 35 Gy after which they were processed under neutral comet assay. In order to verify the determined dose-effect curves, a test dose of 15 Gy was delivered to the samples obtained from the sixth and seventh individuals. The amount of DNA damage from the obtained comet assay images was analyzed using four comet assay parameters namely % tail DNA, tail length, tail moment (TM), and Olive TM (OTM). The most suitable comet assay parameter was evaluated based on the obtained dose-effect curves. Furthermore, the distribution of individual cells for each dose point was evaluated for all the four comet assay parameters to find the optimal parameter.

Results

From our results, it was found that from 0 to 25 Gy all the four comet assay parameters fit well into a linear quadratic curve and above 25 Gy saturation was observed. Based on the individual cell distribution data, it was found that % tail DNA could be an optimal choice to evaluate DNA damage while using neutral comet assay for high-dose ionizing radiation.

Conclusion

The neutral comet assay could be a potential tool to assess DNA damage from high doses of ionizing radiation greater than 5 Gy.

Damage to Nuclear and Mitochondrial DNA in Different Organs in Streptozotocin-Induced Diabetes Models in BALB/c Mice

Male BALB/c mice with streptozotocin-induced diabetes mellitus were used to study nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) damage using comet DNA assay and real-time PCR, respectively. In animals receiving single injection of streptozotocin in a dose of 200 mg/kg, severe hyperglycemia was observed on days 10 and 21 of the experiment, while after 5-fold administration of streptozotocin in a dose of 40 mg/kg, it developed on days 14 and 28. DNA damage and the level of atypical DNA comets in the liver increased both on days 10 and 21 after single administration of streptozotocin, and on days 14 and 28 after repeated administrations. The level of atypical DNA comets on day 21 after a single administration of streptozotocin increased in the kidneys, but not in the brain, testes, and pancreas. Real-time PCR revealed mtDNA damage in the liver, kidney, and pancreatic cells of mice with streptozotocin-induced diabetes. Thus, these animal models were found to reproduce pathognomic signs of diabetes, hyperglycemia, and nDNA damage; mtDNA damage was also detected.

Biomarkers of nucleic acid oxidation - A summary state-of-the-art

Oxidatively generated damage to DNA has been implicated in the pathogenesis of a wide variety of diseases. Increasingly, interest is also focusing upon the effects of damage to the other nucleic acids, RNA and the (2′-deoxy-)ribonucleotide pools, and evidence is growing that these too may have an important role in disease. LC-MS/MS has the ability to provide absolute quantification of specific biomarkers, such as 8-oxo-7,8-dihydro-2′-deoxyGuo (8-oxodG), in both nuclear and mitochondrial DNA, and 8-oxoGuo in RNA. However, significant quantities of tissue are needed, limiting its use in human biomonitoring studies. In contrast, the comet assay requires much less material, and as little as 5 μL of blood may be used, offering a minimally invasive means of assessing oxidative stress in vivo, but this is restricted to nuclear DNA damage only. Urine is an ideal matrix in which to non-invasively study nucleic acid-derived biomarkers of oxidative stress, and considerable progress has been made towards robustly validating these measurements, not least through the efforts of the European Standards Committee on Urinary (DNA) Lesion Analysis. For urine, LC-MS/MS is considered the gold standard approach, and although there have been improvements to the ELISA methodology, this is largely limited to 8-oxodG. Emerging DNA adductomics approaches, which either comprehensively assess the totality of adducts in DNA, or map DNA damage across the nuclear and mitochondrial genomes, offer the potential to considerably advance our understanding of the mechanistic role of oxidatively damaged nucleic acids in disease.

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Oxidatively damaged nucleic acids are implicated in the pathogenesis of disease.

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LC-MS/MS, comet assay and ELISA are often used to study oxidatively damaged DNA.

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Urinary oxidatively damaged nucleic acids non-invasively reflect oxidative stress.

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DNA adductomics will aid understanding the role of ROS damaged DNA in disease.

Minimum Information for Reporting on the Comet Assay (MIRCA): recommendations for describing comet assay procedures and results

The comet assay is a widely used test for the detection of DNA damage and repair activity. However, there are interlaboratory differences in reported levels of baseline and induced damage in the same experimental systems. These differences may be attributed to protocol differences, although it is difficult to identify the relevant conditions because detailed comet assay procedures are not always published. Here, we present a Consensus Statement for the Minimum Information for Reporting Comet Assay (MIRCA) providing recommendations for describing comet assay conditions and results. These recommendations differentiate between 'desirable' and 'essential' information: 'essential' information refers to the precise details that are necessary to assess the quality of the experimental work, whereas 'desirable' information relates to technical issues that might be encountered when repeating the experiments. Adherence to MIRCA recommendations should ensure that comet assay results can be easily interpreted and independently verified by other researchers.

Holistic View on Cell Survival and DNA Damage: How Model-Based Data Analysis Supports Exploration of Dynamics in Biological Systems

In this work, a method is established to calibrate a model that describes the basic dynamics of DNA damage and repair. The model can be used to extend planning for radiotherapy and hyperthermia in order to include the biological effects. In contrast to “syntactic” models (e.g., describing molecular kinetics), the model used here describes radiobiological semantics, resulting in a more powerful model but also in a far more challenging calibration. Model calibration is attempted from clonogenic assay data (doses of 0–6 Gy) and from time-resolved comet assay data obtained within 6 h after irradiation with 6 Gy. It is demonstrated that either of those two sources of information alone is insufficient for successful model calibration, and that both sources of information combined in a holistic approach are necessary to find viable model parameters. Approximate Bayesian computation (ABC) with simulated annealing is used for parameter search, revealing two aspects that are beneficial to resolving the calibration problem: (1) assessing posterior parameter distributions instead of point-estimates and (2) combining calibration runs from different assays by joining posterior distributions instead of running a single calibration run with a combined, computationally very expensive objective function.

Exposure to a 50 Hz magnetic field at 100 µT exerts no DNA damage in cardiomyocytes

The effects of exposure to magnetic fields (MFs) at electric frequencies (50-60 Hz) on carcinogenicity are still in debate. Whether exposure to MFs affects the heart is also a debated issue. This study aimed to determine whether exposure to extremely low frequency MFs (ELF-MFs) induced DNA damage in cardiomyocytes both in vitro and in vivo Human ventricular cardiomyocytes were exposed to 50 Hz ELF-MF at 100 µT for 1 h continuously or 75 min intermittently. The effects of the treatments were evaluated by DNA damage, redox status changes and relative signal molecular expression. Moreover, ten male Sprague-Dawley rats were exposed to a 50 Hz MF at 100 µT for 7 days, while another 10 rats were sham exposed. The protein levels of p53 and Hsp70 in heart tissue were analyzed by western blot. The results showed that exposure to ELF-MF did not induce DNA damage, changes to cell cycle distribution or increased reactive oxygen species level. No significant differences were detected in p53 and Hsp70 expression level between the ELF-MF and sham-exposure groups both in vitro and in vivo All these data indicate that MFs at power-frequency may not cause DNA damage in cardiomyocytes.This article has an associated First Person interview with the first author of the paper.

BK Polyomavirus Activates the DNA Damage Response To Prolong S Phase

BK polyomavirus (PyV) is a major source of kidney failure in transplant recipients. The standard treatment for patients with lytic BKPyV infection is to reduce immunosuppressive therapy, which increases the risk of graft rejection. PyVs are DNA viruses that rely upon host replication proteins for viral genome replication. A hallmark of PyV infection is activation of the DNA damage response (DDR) to prevent severe host and viral DNA damage that impairs viral production by an unknown mechanism. Therefore, we sought to better understand why BKPyV activates the DDR through the ATR and ATM pathways and how this prevents DNA damage and leads to increased viral production. When ATR was inhibited in BKPyV-infected primary kidney cells, severe DNA damage occurred due to premature Cdk1 activation, which resulted in mitosis of cells that were actively replicating host DNA in S phase. Conversely, ATM was required for efficient entry into S phase and to prevent normal mitotic entry after G₂ phase. The synergistic activation of these DDR kinases promoted and maintained BKPyV-mediated S phase to enhance viral production. In contrast to BKPyV infection, DDR inhibition did not disrupt cell cycle control in uninfected cells. This suggests that DDR inhibitors may be used to specifically target BKPyV-infected cells.IMPORTANCE BK polyomavirus (BKPyV) is an emerging pathogen that reactivates in immunosuppressed organ transplant patients. We wanted to understand why BKPyV-induced activation of the DNA damage response (DDR) enhances viral titers and prevents host DNA damage. Here, we show that the virus activates the DNA damage response in order to keep the infected cells in S phase to replicate the viral DNA. The source of DNA damage was due to actively replicating cells with uncondensed chromosomes entering directly into mitosis when the DDR was inhibited in BKPyV-infected cells. This study clarifies the previously enigmatic role of the DDR during BKPyV infection by demonstrating that the virus activates the DDR to maintain the cells in S phase in order to promote viral replication and that disruption of this cell cycle arrest can lead to catastrophic DNA damage for the host.

Use of statistical analysis to validate ecogenotoxicology findings arising from various comet assay components

Cirrhinus mrigala, Labeo rohita, and Catla catla are economically important fish for human consumption in Pakistan, but industrial and sewage pollution has drastically reduced their population in the River Chenab. Statistics are an important tool to analyze and interpret comet assay results. The specific aims of the study were to determine the DNA damage in Cirrhinus mrigala, Labeo rohita, and Catla catla due to chemical pollution and to assess the validity of statistical analyses to determine the viability of the comet assay for a possible use with these freshwater fish species as a good indicator of pollution load and habitat degradation. Comet assay results indicated a significant (P < 0.05) degree of DNA fragmentation in Cirrhinus mrigala followed by Labeo rohita and Catla catla in respect to comet head diameter, comet tail length, and % DNA damage. Regression analysis and correlation matrices conducted among the parameters of the comet assay affirmed the precision and the legitimacy of the results. The present study, therefore, strongly recommends that genotoxicological studies conduct appropriate analysis of the various components of comet assays to offer better interpretation of the assay data.

Persistent Organochlorine Pollutants in Placentas Sampled from Women in Croatia and an Evaluation of Their DNA Damaging Potential In Vitro

This study investigated the levels and distribution of 17 polychlorinated biphenyls (PCBs) and organochlorine pesticides (HCB, α-HCH, β-HCH, γ-HCH, p,p'-DDE, p,p'-DDD, and p,p'-DDT) in placenta samples from women living in the coastal area of Croatia. During November 2012 to February 2013, 51 placenta samples were collected from healthy mothers. This study presents the first report about Croatian placenta samples. Each of the analysed compounds were found in all of the samples; all of the maximum values were < 1 ng g^-1 w.w., and the highest median value found for PCB-28 was 11.2 pg g^-1 w.w. PCBs and organochlorine pesticide (OCPs) present in placenta samples were tested for their genotoxic potential using the alkaline comet assay. The alkaline comet assay is one of the most reliable methods in assessing the DNA lesions that occurs in direct interaction of a chemical and the genome. The detected levels of PCBs and OCPs in the placenta did not pose a significant risk to the children's DNA during embryonic and foetal growth following short-term exposure. PCB and OCP concentrations in the placenta samples did not induce any significant primary damage to DNA in terms of DNA strand breaks and changes in the primary chemical structure, which could be detected by the alkaline comet assay.

Evaluating the mechanistic evidence and key data gaps in assessing the potential carcinogenicity of carbon nanotubes and nanofibers in humans

In an evaluation of carbon nanotubes (CNTs) for the IARC Monograph 111, the Mechanisms Subgroup was tasked with assessing the strength of evidence on the potential carcinogenicity of CNTs in humans. The mechanistic evidence was considered to be not strong enough to alter the evaluations based on the animal data. In this paper, we provide an extended, in-depth examination of the in vivo and in vitro experimental studies according to current hypotheses on the carcinogenicity of inhaled particles and fibers. We cite additional studies of CNTs that were not available at the time of the IARC meeting in October 2014, and extend our evaluation to include carbon nanofibers (CNFs). Finally, we identify key data gaps and suggest research needs to reduce uncertainty. The focus of this review is on the cancer risk to workers exposed to airborne CNT or CNF during the production and use of these materials. The findings of this review, in general, affirm those of the original evaluation on the inadequate or limited evidence of carcinogenicity for most types of CNTs and CNFs at this time, and possible carcinogenicity of one type of CNT (MWCNT-7). The key evidence gaps to be filled by research include: investigation of possible associations between in vitro and early-stage in vivo events that may be predictive of lung cancer or mesothelioma, and systematic analysis of dose-response relationships across materials, including evaluation of the influence of physico-chemical properties and experimental factors on the observation of nonmalignant and malignant endpoints.

DNA Damage in Chronic Kidney Disease: Evaluation of Clinical Biomarkers

Patients with chronic kidney disease (CKD) exhibit an increased cancer risk compared to a healthy control population. To be able to estimate the cancer risk of the patients and to assess the impact of interventional therapies thereon, it is of particular interest to measure the patients' burden of genomic damage. Chromosomal abnormalities, reduced DNA repair, and DNA lesions were found indeed in cells of patients with CKD. Biomarkers for DNA damage measurable in easily accessible cells like peripheral blood lymphocytes are chromosomal aberrations, structural DNA lesions, and oxidatively modified DNA bases. In this review the most common methods quantifying the three parameters mentioned above, the cytokinesis-block micronucleus assay, the comet assay, and the quantification of 8-oxo-7,8-dihydro-2′-deoxyguanosine, are evaluated concerning the feasibility of the analysis and regarding the marker's potential to predict clinical outcomes.