Genomic damage as an independent predictor marker of mortality in hemodialysis patients.

AIM: Hemodialysis (HD) patients present an enhanced mortality. Since oxidative DNA damage can be considered a biomarker of genomic instability our aim was to evaluate the influence of this genetic biomarker in all-cause mortality in a group of HD patients followed for 4 years. MATERIAL AND METHODS: 123 chronic HD patients were included. Overall genomic damage was analyzed using the Comet assay. Oxidative DNA damage was measured using the Comet assay complemented with the use of Endo-III and FPG enzymes. Follow-up was carried out from January 2007 to July 2011. RESULTS: Selected HD patients had a mean age of 62 ± 15 years. During the follow-up 36% of patients died (48% due to cardiovascular disease) and 23% were transplanted. Older patients, with high CRP levels, low levels of cholesterol-HDL and albumin, and higher genetic damage at the beginning of the study showed an increased risk for mortality. Multivariate analysis showed that only genomic damage, age and CRP were independently associated with mortality. CONCLUSIONS: Our study shows for the first time that, in HD patients, the presence of high levels of genomic damage is a strong predictor of all-cause mortality. This association remains significant after adjustment for relevant covariates.

Genetic damage in chronic renal failure patients is associated with the glomerular filtration rate index.

Chronic renal failure (CRF) patients are considered to present genomic instability and, as a consequence, elevated levels of genetic damage. An open question is whether this damage is related to the stage of the pathology. To determine the background levels of genetic damage, a large population of 258 Caucasian adults (201 CRF patients and 57 controls) was analysed using the micronucleus (MN) assay. The frequency of MN in CRF patients was significantly higher than in controls and correlated with the progression of the disease, according to the glomerular filtration rate. In addition, a significant association was observed between genetic damage and serum creatinine levels. Genetic damage, measured as frequency of MN, increases when renal function decreases. The fact that an increased level of MN is already observed in patients' Stage 2 seems to indicate a genetic predisposition on these patients. Nevertheless, part of the observed damage can be attributed to the uraemic state itself.

Oxidative DNA damage in chronic renal failure patients.

BACKGROUND: Chronic renal failure (CRF) patients present a high incidence of cardiovascular pathologies and cancer. This has been attributed to the existence of genomic instability in these patients, and consequently they should present elevated levels of genetic damage. METHODS: To determine the background levels of genetic damage and its specific levels of oxidative damage, a large population of 253 CRF patients (77 in dialysis) was analysed using the comet assay. The percentage of DNA in the tail was used as a measure of basal genetic damage. In addition, the use of endo III and FPG enzymes allowed us to determine the levels of specific oxidative damage in DNA bases. RESULTS: This is the first study that uses endo III and FPG enzymes to measure oxidative damage in CRF patients. Overall genetic damage, as well as specific oxidative damage, was higher in dialysis patients than in the CRF patients with different stages of uraemic state; genetic damage increased when serum creatinine levels increased. Genomic damage in dialysis patients decreased in those patients submitted to dialysis for a long time. CONCLUSIONS: Genetic damage increases when renal function decreases, being maximum in haemodialysis patients. Although part of the observed damage can be attributed to the uraemic state itself, other individual genetic factors can influence a state of genomic instability responsible for the observed genomic damage.

The Comet Assay as a Tool to Detect the Genotoxic Potential of Nanomaterials.

The interesting physicochemical characteristics of nanomaterials (NMs) has brought about their increasing use and, consequently, their increasing presence in the environment. As emergent contaminants, there is an urgent need for new data about their potential side-effects on human health. Among their potential effects, the potential for DNA damage is of paramount relevance. Thus, in the context of the EU project NANoREG, the establishment of common robust protocols for detecting genotoxicity of NMs became an important aim. One of the developed protocols refers to the use of the comet assay, as a tool to detect the induction of DNA strand breaks. In this study, eight different NMs-TiO2NP (2), SiO2NP (2), ZnONP, CeO2NP, AgNP, and multi-walled carbon nanotubes (MWCNT)-were tested using two different human lung epithelial cell lines (A549 and BEAS-2B). The comet assay was carried out with and without the use of the formamidopyrimidine glycosylase (FPG) enzyme to detect the induction of oxidatively damaged DNA bases. As a high throughput approach, we have used GelBond films (GBF) instead of glass slides, allowing the fitting of 48 microgels on the same GBF. The results confirmed the suitability of the comet assay as a powerful tool to detect the genotoxic potential of NMs. Specifically, our results indicate that most of the selected nanomaterials showed mild to significant genotoxic effects, at least in the A549 cell line, reflecting the relevance of the cell line used to determine the genotoxic ability of a defined NM.

Role of the Met(287)Thr polymorphism in the AS3MT gene on the metabolic arsenic profile.

Chronic exposure to arsenic involves a biotransformation process leading to the excretion of methylated metabolites, such as monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA), as well as the parental inorganic species (As(III) and As(V)). Inter-individual variations in arsenic biotransformation have been reported and polymorphisms affecting the genes involved in arsenic biotransformation have been considered as one of the plausible explanations for this variation. Coding and flanking regions of the human arsenic methyltransferase (AS3MT) gene have been analysed in 50 Chilean men exposed to arsenic. Nine polymorphisms were found, including one non-synonymous SNP at exon 9 (Met(287)Thr) with an allele frequency of 0.14. Other four changes occurred at potentially regulatory regions: a variable number of tandem repeats (VNTR) at the 5'-untranslated region (UTR5'), a G/C substitution at the promoter region, a GC/AT substitution inside the VNTR, and a G/A substitution at the 3'-untranslated region (UTR3'). The rest of polymorphisms were located in non-coding regions: a T/G substitution in intron 1, a CTC deletion in intron 2 and a TTT and ATT insertions in intron 5. In addition, the individual urinary arsenic profiles were analysed. Our results indicate that genetic polymorphisms in AS3MT contribute to inter-individual variation in arsenic biotransformation and, therefore, may contribute to inter-individual variations in risk of arsenic toxicity and arsenic carcinogenesis. Individuals with the Met(287)Thr polymorphism displayed increased arsenic methylation and might be at increased risk for toxic and genotoxic effects of arsenic exposure if, as the classical arsenic metabolic pathway indicates, methylation enhances toxicity.

Effects of cerium oxide nanoparticles on differentiated/undifferentiated human intestinal Caco-2 cells.

Since ingestion constitute one of the main routes of nanoparticles (NPs) exposure, intestinal cells seems to be a suitable choice to evaluate their potential harmful effects. Caco-2 cells, derived from a human colon adenocarcinoma, have the ability to differentiate forming consistent cell monolayer structures. For these reasons Caco-2 cells, both in their undifferentiated or differentiated state, are extendedly used. We have used well-structured monolayers of differentiated Caco-2 cells, as a model of intestinal barrier, to evaluate potential harmful effects associated to CeO2NPs exposure via ingestion. Different parameters such as cell toxicity, monolayer integrity and permeability, cell internalization, translocation through the monolayer, and induction of DNA damage were evaluated. No toxic effects of CeO2NPs were observed, independently of the differentiated state of the Caco-2 cells. In the same way, no effects on the monolayer integrity/permeability were observed. Although important cell uptake was demonstrated in undifferentiated cells (by using confocal microscopy), CeO2NPs remained mostly attached to the apical membrane in the differentiated cells. In spite of this apparent lack of uptake in differentiated cells, translocation of CeO2NPs to the basolateral chamber was observed by using confocal microscopy. Finally no genotoxic effects were observed when the comet assay was used, although decreases in the levels of oxidized bases were observed, supporting the antioxidant role of CeO2NPs.

Molecular and bioinformatic analysis of the FB-NOF transposable element.

The Drosophila melanogaster transposable element FB-NOF is known to play a role in genome plasticity through the generation of all sort of genomic rearrangements. Moreover, several insertional mutants due to FB mobilizations have been reported. Its structure and sequence, however, have been poorly studied mainly as a consequence of the long, complex and repetitive sequence of FB inverted repeats. This repetitive region is composed of several 154 bp blocks, each with five almost identical repeats. In this paper, we report the sequencing process of 2 kb long FB inverted repeats of a complete FB-NOF element, with high precision and reliability. This achievement has been possible using a new map of the FB repetitive region, which identifies unambiguously each repeat with new features that can be used as landmarks. With this new vision of the element, a list of FB-NOF in the D. melanogaster genomic clones has been done, improving previous works that used only bioinformatic algorithms. The availability of many FB and FB-NOF sequences allowed an analysis of the FB insertion sequences that showed no sequence specificity, but a preference for A/T rich sequences. The position of NOF into FB is also studied, revealing that it is always located after a second repeat in a random block. With the results of this analysis, we propose a model of transposition in which NOF jumps from FB to FB, using an unidentified transposase enzyme that should specifically recognize the second repeat end of the FB blocks.

Basal and induced micronucleus frequencies in human lymphocytes with different GST and NAT2 genetic backgrounds.

Basal and induced frequencies of genetic damage can be modulated by different host factors, including genes involved in phase II metabolism. Since polymorphic variants in the glutathione S-transferase (GST) and N-acetyl transferase (NAT) genes have been associated with cancer risk, we explored the possible links between GSTM1, GSTP1, GSTT1 and NAT2 variants and the frequency of micronuclei (MN) in human lymphocytes. This exploratory study was carried out in 30 thyroid cancer patients, before and after receiving an average dose of 109.9+/-1.3 mCi radioactive iodine as a co-adjuvant therapy. The results indicate that none of the polymorphisms studied show any kind of association with the basal level of micronuclei. When the same patients were followed after radioiodine exposure, a significant increase in the frequency of MN was observed in practically all of them (28/30), indicating the genotoxic activity of the ionising radiation exposure. The increase in MN frequency was not associated with any of the GST polymorphisms evaluated. Nevertheless, the presence of slow acetylator phenotypes and, in particular, the presence of the NAT2*7 allele was significantly associated with a lower increase of the MN frequency after radioiodine treatment.

Germline genomic instability in PCNA mutants of Drosophila: DNA fingerprinting and microsatellite analysis.

PCNA participates in multiple processes of DNA metabolism with an essential role in DNA replication and intervening in DNA repair. Temperature-sensitive PCNA mutants of Drosophila (mus209) are sensitive to mutagens, impair developmental processes and suppress positional-effect variegation. To investigate the role of proliferating cell nuclear antigen (PCNA) in germline genomic stability, independent mus209-defective and mus209-normal lines were established and maintained over six generations. A time course study was carried out and general genomic alterations were analyzed in the progeny by using arbitrarily primed PCR (AP-PCR) and microsatellite analysis. The AP-PCR analysis has shown that a dysfunctional PCNA leads to germline genomic instability, being the amount of genomic alterations transmitted to the progeny directly related to the number of mus209B1 mutant alleles. In addition, we have found that the frequency of genomic alterations tends to increase over successive generations. Surprisingly, the highest microsatellite instability was found in the heterozygous mus209-defective lines, suggesting a greater mutation rate in these individuals, in comparison with the homozygous mus209-defective lines. In conclusion, our results clearly indicate that PCNA is an important factor to maintain genomic stability in germinal cells, both in the overall genome and in simple repeated sequences. The implication of PCNA mutations in transgenerational genomic instability and related to cancer susceptibility is also discussed.

Glutathione S-transferase polymorphisms in thyroid cancer patients.

Glutathione S-transferases (GST) are enzymes involved in the metabolism of many carcinogens and mutagens, also acting as important free-radical scavengers. The existence of different genetic polymorphisms in human populations has proven to be a susceptibility factor for different tumours. Nevertheless, as far as we know, for thyroid cancer no study has been conducted until now linking its incidence to genetic susceptibility biomarkers. The present investigation has been conducted to detect the possible association between polymorphism at the GSTM1, GSTT1 and GSTP1 genes and thyroid cancer incidence. Thus, 134 thyroid cancer patients and 116 controls, all from the urban district of Barcelona (Spain), have been included in this study. The results indicate that, according to the calculated odds ratio, the frequencies of the different genotypes found in the group of cancer patients do not significantly differ from those values obtained in the controls. This is true for the overall data as well as for the tumour characterization as follicular and papillar types. In addition, none of the possible combinations of mutant genotypes were shown to be risk factors. Finally, when the sex of the patients, the age of tumour onset, and life-style habits were also taken into account, no influence was observed related to the different genotypes. In conclusion, the results obtained in this study clearly suggest that those susceptibility factors related to the different GST polymorphic enzymes are not a predisposing factor in thyroid cancer disease.

Occupational exposure to pesticides and cytogenetic damage: results of a Hungarian population study using the micronucleus assay in lymphocytes and buccal cells.

The frequency of micronuclei (MN) in peripheral blood lymphocytes and in buccal epithelial cells was used as a biomarker of genotoxic effects resulting from occupational exposure to pesticides. In addition, the cytokinesis-block proliferation index (CBPI) was calculated to detect possible variations in the proliferative kinetics of lymphocytes due to pesticide exposure. This study was performed on 84 pesticide-exposed workers and 65 unexposed controls from Hungary. The pesticide-exposed workers, classified as moderately and highly exposed, were also evaluated separately. Statistical evaluation of the cytogenetic biomarkers indicated that there were no significant differences between pesticide-exposed workers and controls, nor between moderately and highly exposed workers. Nevertheless, the statistical analysis revealed that additional factors such as age, sex, ingestion of raw vegetables, and working as a pesticide applicator affected lymphocyte MN frequency. In addition, age, sex, and smoking affected the frequency of MN in buccal cells. Results from the CBPI analysis showed that the proliferation index decreased with pesticide exposure and that this parameter was also affected by smoking and by the gender of individuals. The results of this study indicate no significant increase in MN in this group of Hungarian workers; however, the reduced CBPI in the highly exposed population suggests a possible genotoxic effect of pesticide exposure.

Influence of sodium arsenite on the genotoxicity of potassium dichromate and ethyl methanesulfonate: studies with the wing spot test in Drosophila.

The wing spot test in Drosophila melanogaster was used to investigate the genotoxicity of arsenic and its effects on the action of two clearly genotoxic agents: potassium dichromate (PDC) and ethyl methanesulfonate (EMS). This assay is based on the principle that the loss of heterozygosity of the suitable recessive markers multiple wing hairs (mwh) and flare-3 (flr(3)) can lead to the formation of mutant clones of larval cells, which are then expressed as spots on the wings of adult flies. These spots can be attributed to different genotoxic events: either mitotic recombination or mutation (deletion, point mutation, and specific types of translocation). Pretreatments and chronic cotreatments were comparatively used for combined treatments. From the results obtained it is evident that sodium arsenite (SA) does not increase the frequency of any of the three categories of spots recorded (small, large, and twin spots) at the concentrations tested. The effects of SA in combination with PDC, in both cotreatments and pretreatments, indicate that SA almost suppressed the clones induced by PDC. Nevertheless, no effects of arsenic were observed with respect to the pre- and cotreatments with EMS. Thus, SA does not modify the frequencies of mutant clones induced by EMS.

FB-NOF is a non-autonomous transposable element, expressed in Drosophila melanogaster and present only in the melanogaster group.

Most foldback elements are defective due to the lack of coding sequences but some are associated with coding sequences and may represent the entire element. This is the case of the NOF sequences found in the FB of Drosophila melanogaster, formerly considered as an autonomous TE and currently proposed as part of the so-called FB-NOF element, the transposon that would be complete and fully functional. NOF is always associated with FB and never seen apart from the FB inverted repeats (IR). This is the reason why the FB-NOF composite element can be considered the complete element. At least one of its ORFs encodes a protein that has always been considered its transposase, but no detailed studies have been carried out to verify this. In this work we test the hypothesis that FB-NOF is an active transposon nowadays. We search for its expression product, obtaining its cDNA, and propose the ORF and the sequence of its potential protein. We found that the NOF protein is not a transposase as it lacks any of the motifs of known transposases and also shows structural homology with hydrolases, therefore FB-NOF cannot belong to the superfamily MuDR/foldback, as up to now it has been classified, and can be considered as a non-autonomous transposable element. The alignment with the published genomes of 12 Drosophila species shows that NOF presence is restricted only to the 6 Drosophila species belonging to the melanogaster group.

High arsenic metabolic efficiency in AS3MT287Thr allele carriers.

OBJECTIVES: Epidemiological data indicate the existence of wide interindividual differences in arsenic metabolism. It has recently been shown that arsenic(III)methyltransferase (AS3MT) enzyme catalyses the methylation of arsenite and monomethylarsonous acid (MMA). Thus, genetic variations in the AS3MT gene could explain, at least partly, the interindividual variation in the response to arsenic exposure. In an earlier study, we have demonstrated that the AS3MT Met(287)Thr (C/T) polymorphism affected the urinary arsenic profile in a Chilean group of men (n=50) occupationally exposed to arsenic. METHODS: To confirm, the influence of the Met(287)Thr polymorphism in the metabolism of arsenic, a total of 207 Chilean men working at the copper industry were genotyped and their urinary profiles determined. RESULTS: The results confirm that Met(287)Thr polymorphism does influence arsenic metabolism in this population. Those carriers of the variant ((287)Thr) had a higher methylation efficiency, excreting 4.63% more MMA in urine (P=0.0007) and presenting a 2.98 times higher odd of excreting levels of MMA over the standard (P=0.011) than the participants homozygous for the normal allele. CONCLUSION: We can conclude that individuals with the (287)Thr variant display increased arsenic methylation; thus, those participants might be at increased risk for the toxic and genotoxic effects of arsenic exposure.

An FB-NOF mediated duplication of the white gene is responsible for the zeste1 phenotype in some Drosophila melanogaster unstable strains.

The males of the Drosophila melanogaster M115 mutant strain and of its spontaneous revertant strain RM115 are phenotypically similar to those carrying the w(+UZ) and w(+UR) alleles. The molecular description of these mutant strains could be extended to the unstable-zeste system, which has been used as a genotoxicity test, and could be of use for a better understanding of the assay. An FB element in the 3' vicinity of the white gene, actually into the second intron of the newly predicted CG32795 gene, was found and precisely located in our M115 and RM115 strains, and also in w(+UZ) as expected. We demonstrate the presence of NOF sequences in the M115 and w(+UZ) insertions. However, we found that the z1 phenotype in these males might not be due to the FB-NOF interference on the zeste-white interaction but to a duplication of the white gene unnoticed in previous studies. The reversion of RM115 correlates with the loss of the duplication, probably by a complex recombination event. Furthermore, a FISH experiment suggests that the two copies of white are nearby or tandemly duplicated.