Statistics of the Comet assay: a key to discriminate between genotoxic effects

Application of public-domain statistical analysis software for evaluation and comparison of comet assay data

A novel approach for statistical analysis of comet assay data (i.e.: tail moment) is proposed, employing public-domain statistical software, the R system. The analytical strategy takes into account that the distribution of comet assay data, like the tail moment, is usually skewed and do not follow a normal distribution. Probability distributions used to model comet assay data included: the Weibull, the exponential, the logistic, the normal, the log normal and log-logistic distribution. In this approach it was also considered that heterogeneity observed among experimental units is a random feature of the comet assay data. This statistical model can be characterized with a location parameter m(ij), a scale parameter r and a between experimental units variability parameter theta. In the logarithmic scale, the parameter m(ij) depends additively on treatment and random effects, as follows: log(m(ij)) = a0 + a1x(ij) + b(i), where exp(a0) represents approximately the mean value of the control group, exp(a1) can be interpreted as the relative risk of damage with respect to the control group, x(ij) is an indicator of experimental group and exp(b(i)) is the individual risk effects assume to follows a Gamma distribution with mean 1 and variance theta. Model selection is based on Akaike's information criteria (AIC). Real data coming from comet analysis of blood samples taken from the flounder Paralichtys orbignyanus (Teleostei: Paralichtyidae) and from samples of cells suspension obtained from the estuarine polychaeta Laeonereis acuta (Nereididae) were employed. This statistical approach showed that the comet assay data should be analyzed under a modeling framework that take into account the important features of these measurements. Model selection and heterogeneity between experimental units play central points in the analysis of these data.

Interindividual variability in response to sodium dichromate-induced oxidative DNA damage: role of the Ser326Cys polymorphism in the DNA-repair protein of 8-oxo-7,8-dihydro-2'-deoxyguanosine DNA glycosylase 1

Although the genotoxic mechanism(s) of hexavalent chromium (CrVI) carcinogenicity remain to be fully elucidated, intracellular reduction of CrVI and concomitant generation of reactive intermediates including reactive oxygen species and subsequent oxidative damage to DNA is believed to contribute to the process of carcinogenesis. In the current study, substantial interindividual variation (7.19-25.84% and 8.79-34.72% tail DNA as assessed by conventional and FPG-modified comet assay, respectively) in levels of DNA strand breaks after in vitro treatment of WBC with sodium dichromate (100 micromol/L, 1 hour) was shown within a group of healthy adult volunteers (n = 72) as assessed by both comet and formamidopyrimidine glycosylase-modified comet assays. No statistically significant correlation between glutathione S-transferases M1 or T1, NADPH quinone oxidoreductase 1 (codon 187) and X-ray repair cross complementation factor 1 (codon 194) genotypes and individual levels of DNA damage were observed. However, individuals homozygous for the Cys(326) 8-oxo 7,8-dihydro-2'-deoxyguanosine glycosylase 1 (OGG1) polymorphism had a statistically significant elevation of formamidopyrimidine glycosylase-dependent oxidative DNA damage after treatment with sodium dichromate when compared with either Ser(326)/Ser(326) or Ser(326)/Cys(326) individuals (P = 0.008 and P = 0.003, respectively). In contrast, no effect of OGG1 genotype on background levels of oxidative DNA damage was observed. When individuals were divided on the basis of OGG1 genotype, Cys(326)/Cys(326) individuals had a statistically significant (P < 0.05, one-way ANOVA followed by Tukey test) higher ratio of oxidative DNA damage to plasma antioxidant capacity than either Ser(326)/Ser(326) or Ser(326)/Cys(326) individuals. The results of this study suggest that the Cys(326)/Cys(326) OGG1 genotype may represent a phenotype that is deficient in the repair of 8-oxo-7,8-dihydro-2'-deoxyguanosine, but only under conditions of cellular oxidative stress. We hypothesize that this may be due to oxidation of the Cys(326) residue. In conclusion, the homozygous Cys(326) genotype may represent a biomarker of individual susceptibility of lung cancer risk in individuals that are occupationally exposed to CrVI.

A comparative investigation of DNA strand breaks, sister chromatid exchanges and K-ras gene mutations induced by cadmium salts in cultured human cells

Cadmium (Cd) is a toxic heavy metal of continuing occupational and environmental concern with a wide variety of adverse effects. Several studies have shown that cadmium produces DNA strand breaks, DNA-protein cross-links, oxidative DNA damage, chromosomal aberrations, dysregulation of gene expression resulting in enhanced proliferation, depressed apoptosis and/or altered DNA repair. This study was undertaken to investigate the ability of cadmium chloride (CdCl(2)) and cadmium sulphate (CdSO(4)) to induce point mutations in codon 12 of the K-ras protooncogene assessed by polymerase chain reaction-single strand conformation polymorphisms (PCR-SSCP) and RFLP-enriched PCR methods. Also their genotoxic effects were analyzed by the comet assay and sister chromatid exchanges test. The human lung fibroblast cell line MRC-5 was used for the experiments. Sister chromatid exchanges assay (SCEs) frequencies were significantly increased in cells exposed to cadmium salts in relation to controls (p<0.001). Despite the slow increment observed in the three comet parameters considered when cells were treated with cadmium chloride, significant differences between groups were only found in the variable comet moment (CM) (p<0.005). On the other hand, when cells were exposed to cadmium sulphate, the Kruskal-Wallis test showed highly significant differences between groups for migration, tail moment and comet moment parameters (p<0.001). Nevertheless, a null or weak point mutation induction in K-ras protooncogene was detected using polymerase chain reaction-low ionic strength-single strand conformation polymorphisms (PCR-LIS-SSCP) and RFLP-enriched PCR methods when cells were treated with cadmium salts. Thus, inorganic cadmium produces genotoxicity in human lung fibroblast MRC-5 cells, in the absence of significant point mutation of the K-ras gene.

Modulation of enzymes involved in folate dependent one-carbon metabolism by gamma-radiation stress in mice

The role of various enzymes in folate dependent one-carbon metabolism, which are involved in mobilizing the folate pool for DNA synthesis and the DNA methylation reaction, was investigated. Male Swiss mice (6 weeks old) were subjected to 2, 5 and 7 Gy total body gamma-irradiation. The animals were killed at intervals of 24, 48, 72, 96, 120 and 192 h and the livers were removed. Using a 12000 x g supernatant of 10% tissue homogenate, the activities of dihydrofolate reductase, thymidylate synthase and methylenetetrahydrofolate reductase were determined. The profiles of these folate enzymes were correlated to DNA damage by monitoring p53 protein profile and by comet tail moment analysis. A significant increase in activity of dihydrofolate reductase and thymidylate synthase was observed up to 96 h post-irradiation and the activity subsided thereafter, reaching control value after 192 h. A sharp decline in methylenetetrahydrofolate reductase activity was observed until 192 h after irradiation. Total folates declined by 54% after 96 h following irradiation, and p53 protein concentration in nuclei increased after irradiation, proportionate to radiation dose, and subsided slowly. Thus results indicate a significant drop in total folate levels and rise in p53 protein concentration in the liver after total body gamma-irradiation. It may appear that, under radiation stress conditions, levels of enzymes involved in one-carbon metabolism for DNA repair, are modulated up to a certain time interval, in a dose specific manner. It may also appear that the requirements of folate for nucleotide base synthesis seem to be met at the expense of other one-carbon transfer reactions.

Use of primary blood cells for the assessment of exposure to occupational genotoxicants in human biomonitoring studies

The Comet assay is an often used approach for the assessment of genetic damage in primary cells of exposed populations. In the majority of these studies lymphocytes are used. Therefore, we reviewed human biomonitoring studies of occupational exposure using the Comet assay with lymphocytes. We also tried to elucidate the strengths of the studies, which were that (i) data could be obtained in a fast and cost-effective manner, (ii) the ease at which these cells can be collected and (iii) a remarkable concordance between Comet assay and cytogenetic assays. However, the analysis also revealed some shortcomings: (i) the low number of study participants, (ii) the bias in the distribution of gender, (iii) lack of qualitative and quantitative exposure data, (iv) omission to consider differences in physical activity and diet between control and exposed groups, (v) lack of uniformity in the Comet assay procedures, and (vi) controversy in the sensitivity of Comet assay since it picked up DNA damage caused by agents which were found to be weak genotoxicants or non-genotoxicants in other tests, but gave inconsistent results with known mutagens/carcinogens such as cigarette smoke.

DNA damage produced in HaCaT cells by combined fluoranthene exposure and ultraviolet A irradiation

Fluoranthene is a polycyclic aromatic hydrocarbon (PAH) and a principal constituent of PAH-contaminated aquatic systems. In the present study, fluorescein diacetate uptake and the Comet assay were used to assess the cytotoxicity and genotoxicity of fluoranthene in HaCaT (human adult low calcium high temperature) cells in the presence or absence of ultraviolet A (UVA) irradiation. Exposure of cells to 0.1, 0.25, 0.75, 2, and 5 microM fluoranthene alone for 30 min or to 6.1 +/- 0.07 J/cm2 UVA alone did not cause cytotoxicity or cellular DNA damage. However, concomitant exposure to both caused a nonlinear dose-response in cytotoxicity to HaCat cells. The same exposure conditions also resulted in a dose-responsive DNA damage in HaCaT cells. Because DNA damage mainly was detected at relatively high levels of cytotoxicity, we cannot rule out the possibility that it occurred as a consequence of cellular toxicity mechanisms.