AOP report: Development of an adverse outcome pathway for oxidative DNA damage leading to mutations and chromosomal aberrations

The Genetic Toxicology Technical Committee (GTTC) of the Health and Environmental Sciences Institute (HESI) is developing adverse outcome pathways (AOPs) that describe modes of action leading to potentially heritable genomic damage. The goal was to enhance the use of mechanistic information in genotoxicity assessment by building empirical support for the relationships between relevant molecular initiating events (MIEs) and regulatory endpoints in genetic toxicology. Herein, we present an AOP network that links oxidative DNA damage to two adverse outcomes (AOs): mutations and chromosomal aberrations. We collected empirical evidence from the literature to evaluate the key event relationships between the MIE and the AOs, and assessed the weight of evidence using the modified Bradford-Hill criteria for causality. Oxidative DNA damage is constantly induced and repaired in cells given the ubiquitous presence of reactive oxygen species and free radicals. However, xenobiotic exposures may increase damage above baseline levels through a variety of mechanisms and overwhelm DNA repair and endogenous antioxidant capacity. Unrepaired oxidative DNA base damage can lead to base substitutions during replication and, along with repair intermediates, can also cause DNA strand breaks that can lead to mutations and chromosomal aberrations if not repaired adequately. This AOP network identifies knowledge gaps that could be filled by targeted studies designed to better define the quantitative relationships between key events, which could be leveraged for quantitative chemical safety assessment. We anticipate that this AOP network will provide the building blocks for additional genotoxicity-associated AOPs and aid in designing novel integrated testing approaches for genotoxicity.

Gene expression changes induced by the human carcinogen aristolochic acid I in renal and hepatic tissue of mice

Aristolochic acid (AA) is the causative agent of urothelial tumors associated with AA nephropathy and is also implicated in the development of Balkan endemic nephropathy-associated urothelial tumors. These tumors contain AA-characteristic TP53 mutations. We examined gene expression changes in Hupki (human TP53 knock-in) mice after treatment with aristolochic acid I (AAI) by gavage (5 mg/kg body weight). After 3, 12 and 21 days of treatment gene expression profiles were investigated using Agilent Whole Mouse 44K Genome Oligo Array. Expression profiles were significantly altered by AAI treatment in both target (kidney) and nontarget (liver) tissue. Renal pathology and DNA adduct analysis confirmed kidney as the target tissue of AAI-induced toxicity. Gene ontology for functional analysis revealed that processes related to apoptosis, cell cycle, stress response, immune system, inflammatory response and kidney development were altered in kidney. Canonical pathway analysis indicated Nfκb, aryl hydrocarbon receptor, Tp53 and cell cycle signaling as the most important pathways modulated in kidney. Expression of Nfκb1 and other Nfκb-target genes was confirmed by quantitative real-time PCR (qRT-PCR) and was consistent with the induction of Nfκb1 protein. Myc oncogene, frequently overexpressed in urothelial tumors, was upregulated by AAI on the microarrays and confirmed by qRT-PCR and protein induction. Collectively we found that microarray gene expression analysis is a useful tool to define tissue-specific responses in AAI-induced toxicity. Several genes identified such as TP53, Rb1, Mdm2, Cdkn2a and Myc are frequently affected in human urothelial cancer, and may be valuable prognostic markers in future clinical studies.

Polo-like kinase 1 reaches beyond mitosis--cytokinesis, DNA damage response, and development

Polo-like kinase 1 (Plk1) is a key regulator of cell division in eukaryotic cells. In this review we focus on recent leaps in our understanding of how Plk1 controls cytokinesis, the final stage of cell division. Furthermore, we will go beyond mitosis to highlight unexpected roles of Plk1 during interphase and during animal development. In vertebrate cells, Plk1 has emerged as a novel player in maintaining genomic stability during DNA replication and as an important modulator of the DNA damage checkpoint. Plk1 functions extend past the 'core' cell cycle. Plk1 acts as a link between developmental processes and the cell cycle machinery during asymmetric cell divisions in flies and worms. The term 'mitotic kinase' might not do justice to Plk1 in the light of these recent results.

Plx1 is required for chromosomal DNA replication under stressful conditions

Polo-like kinase (Plk)1 is required for mitosis progression. However, although Plk1 is expressed throughout the cell cycle, its function during S-phase is unknown. Using Xenopus laevis egg extracts, we demonstrate that Plx1, the Xenopus orthologue of Plk1, is required for DNA replication in the presence of stalled replication forks induced by aphidicolin, etoposide or reduced levels of DNA-bound Mcm complexes. Plx1 binds to chromatin and suppresses the ATM/ATR-dependent intra-S-phase checkpoint that inhibits origin firing. This allows Cdc45 loading and derepression of DNA replication initiation. Checkpoint activation increases Plx1 binding to the Mcm complex through its Polo box domain. Plx1 recruitment to chromatin is independent of checkpoint mediators Tipin and Claspin. Instead, ATR-dependent phosphorylation of serine 92 of Mcm2 is required for the recruitment of Plx1 to chromatin and for the recovery of DNA replication under stress. Depletion of Plx1 leads to accumulation of chromosomal breakage that is prevented by the addition of recombinant Plx1. These data suggest that Plx1 promotes genome stability by regulating DNA replication under stressful conditions.

ATM and ATR promote Mre11 dependent restart of collapsed replication forks and prevent accumulation of DNA breaks

Ataxia-telangiectasia mutated (ATM), ataxia-telangiectasia Rad3-related (ATR) and the Mre11/Rad50/Nbs1 complex ensure genome stability in response to DNA damage. However, their essential role in DNA metabolism remains unknown. Here we show that ATM and ATR prevent accumulation of DNA double-strand breaks (DSBs) during chromosomal replication. Replicating chromosomes accumulate DSBs in Xenopus laevis egg extracts depleted of ATM and ATR. Addition of ATM and ATR proteins to depleted extracts prevents DSB accumulation by promoting restart of collapsed replication forks that arise during DNA replication. We show that collapsed forks maintain MCM complex but lose Pol epsilon, and that Pol epsilon reloading requires ATM and ATR. Replication fork restart is abolished in Mre11 depleted extracts and is restored by supplementation with recombinant human Mre11/Rad50/Nbs1 complex. Using a novel fluorescence resonance energy transfer-based technique, we demonstrate that ATM and ATR induce Mre11/Rad50/Nbs1 complex redistribution to restarting forks. This study provides direct biochemical evidence that ATM and ATR prevent accumulation of chromosomal abnormalities by promoting Mre11/Rad50/Nbs1 dependent recovery of collapsed replication forks.

Radiosensitivity of lymphoblastoid cell lines with a heterozygous BRCA1 mutation is not detected by the comet assay and pulsed field gel electrophoresis

Lymphoblastoid cell lines (LCL) with a heterozygous mutation in the breast cancer susceptibility gene BRCA1 have been repeatedly used to elucidate the biological consequences of such a mutation with respect to radiation sensitivity and DNA repair deficiency. Our previous results indicated that LCL with a BRCA1 mutation do not generally show the same chromosomal mutagen sensitivity in the micronucleus test as lymphocytes with the same BRCA1 mutation. To further study the radiosensitivity of LCL with a BRCA1 mutation, we now performed comparative investigations with the alkaline (pH 13) and the neutral (pH 8.3) comet assay and pulsed field gel electrophoresis (PFGE). These tests are commonly used to determine the repair capacity for DNA double strand breaks (DNA-DSB). Six LCL (three established from women with a heterozygous BRCA1 mutation and three from healthy controls) were investigated. Induction (2 and 5 Gy) of gamma-ray-induced DNA damage and its repair (during 60 min after irradiation) was measured with the alkaline and neutral comet assay. Comparative experiments were performed with PFGE determining the induction of DNA-DSB by 10-50 Gy gamma-irradiation and their repair during 6 h. There was no significant difference between LCL with and without BRCA1 mutation in any of these experiments. Therefore, using these methods, no indication for a delayed repair of DNA-DSB in LCL with a BRCA1 mutation was found. However, these results do not generally exclude DNA-DSB repair deficiency in these cell lines because the methods applied have limited sensitivity and only measure the speed but not the fidelity of the repair process.

Chromosomal mutagen sensitivity associated with mutations in BRCA genes

Chromosomal mutagen sensitivity is a common feature of cells from patients with different kinds of cancer. A portion of breast cancer patients also shows an elevated sensitivity to the induction of chromosome damage in cells exposed to ionizing radiation or chemical mutagens. Segregation analysis in families of patients with breast cancer indicated heritability of mutagen sensitivity. It has therefore been suggested that mutations in low-penetrance genes which are possibly involved in DNA repair predispose a substantial portion of breast cancer patients. Chromosomal mutagen sensitivity has been determined with the G2 chromosome aberration test and the G(0) micronucleus test (MNT). However, there seems to be no clear correlation between the results from the two tests, indicating that the inherited defect leading to enhanced G(0) sensitivity is different from that causing G2 sensitivity. Less than 5% of breast cancer patients have a familial form of the disease due to inherited mutations in the breast cancer susceptibility genes BRCA1 or BRCA2. Heterozygous mutations in BRCA1 or BRCA2 in lymphocytes from women with familial breast cancer are also associated with mutagen sensitivity. Differentiation between mutation carriers and controls seems to be much better with the MNT than with the G2 assay. Mutagen sensitivity was detected with the MNT not only after irradiation but also after treatment with chemical mutagens including various cytostatics. The enhanced formation of micronuclei after exposure of lymphocytes to these substances suggests that different DNA repair pathways are affected by a BRCA1 mutation in accordance with the proposed central role of BRCA1 in maintaining genomic integrity. Mutations in BRCA1 and BRCA2 seem to predispose cells to an increased risk of mutagenesis and transformation after exposure to radiation or cytostatics. This raises a question about potentially increased risks by mammography and cancer therapy in women carrying a mutation in one of the BRCA genes. Lymphoblastoid cell lines (LCLs) from breast cancer patients have been used to study the mechanisms and genetic changes associated with tumorigenesis. With respect to mutagen sensitivity, conflicting results have been reported. In particular enhanced induction of micronuclei does not seem to be a general feature of LCLs with a BRCA1 mutation in contrast to lymphocytes with the same mutation. Therefore, LCLs are of limited utility for studying the mechanisms underlying chromosomal mutagen sensitivity.

Hydrostatic Pressure Induces Apoptosis in the Human Leukaemic T-Cell Line Jurkat Via the Mitochondrial Pathway

We investigated the effect of pressure levels ranging from 80 to 500 bar on the proliferative capacity and viability of Jurkat leukaemic T cells. Pressurization at 360 bar induced apoptotic cell death as shown by apoptotic morphology after Hoechst staining, DNA fragmentation in the TdT-mediated dUTP nick end labelling-assay and cleavage of several caspase substrates. Cell death could be prevented by the general caspase inhibitor zVAD-fmk. Breakdown of the mitochondrial membrane potential and the release of cytochrome c provided strong evidence for an involvement of the mitochondrial pathway, whereas a central role of the death receptor pathway was excluded because caspase-8 was not significantly activated. Pressure incubation led to calcium influx after 5 min, and we hypothesize that calcium influx could be the primary trigger for pressure-induced apoptosis.

Investigations on the effect of cigarette smoking in the comet assay

The comet assay (single-cell gel electrophoresis, SCG) is widely accepted as an in vitro and in vivo genotoxicity test. Because of its demonstrated ability to detect various kinds of DNA damage and its ease of application, the technique is being increasingly used in human biomonitoring. However, the assessment of small genotoxic effects as typically obtained in biomonitoring may be limited by the different sources of assay variability and the lack of an optimal protocol with high sensitivity. To better characterize the suitability of the comet assay for biomonitoring, we are performing a comprehensive investigation on blood samples from smokers and non-smokers. Because tobacco smoke is a well-documented source of a variety of potentially mutagenic and carcinogenic compounds, smokers should be a suitable study group with relevant mutagen exposure. Here, we report our results for the first sample of 20 healthy male smokers and 20 healthy male non-smokers. Baseline and benzo[a]pyrene diolepoxide (BPDE)-induced effects were analysed by two investigators using two image analysis systems. The study was repeated within 4 months. Furthermore, the influence of a repair inhibitor (aphidicolin, APC) on baseline and BPDE-induced DNA damage was comparatively analysed. In all experiments, a reference standard (untreated V79 cells) was included to correct for assay variability. None of these approaches revealed significant differences between smokers and non-smokers. Although more data is needed for a final conclusion, this study indicates some limitations of the comet assay with regard to the detection of DNA damage induced by environmental mutagens in peripheral blood cells.

Enhanced sensitivity of peripheral blood lymphocytes from women carrying a BRCA1 mutation towards the mutagenic effects of various cytostatics

We are studying the induction and repair of DNA damage in lymphocytes of women from families with familial breast cancer and mutations in the breast cancer susceptibility genes BRCA1 and BRCA2. Our previous results indicated a close relationship between the presence of a BRCA1 mutation and sensitivity for the induction of micronuclei by gamma irradiation and hydrogen peroxide (H2O2). To further characterize the mutagen sensitivity and to better understand the underlying mechanisms, we now tested the effect of various cytostatics on the micronucleus frequencies in lymphocytes of women with various BRCA1 mutations in comparison to controls. The results presented here indicate enhanced sensitivity towards bleomycin, cisplatin, cyclophosphamide and bischloroethylnitosurea (BCNU). However, mutagen sensitivity towards cisplatin and BCNU was not accompanied by enhanced induction of sister chromatid exchanges (SCE), suggesting that intrachromosomal recombination is not affected. In contrast to the various DNA-damaging agents, there was no clear difference in the response to vincristine and taxol. FISH analysis revealed that the two aneugens mainly induced centromere-positive micronuclei to a similar extent in lymphocytes with and without a BRCA1 mutation. We conclude that cells containing a heterozygous mutation in BRCA1 are more sensitive towards different kinds of DNA damage in accordance with the proposed central role of BRCA1 in maintaining genomic integrity. Although BRCA1 has been shown to interact with the mitotic spindle, spindle poisons do not cause enhanced induction of micronuclei. Since some of the DNA-damaging mutagens tested here are used as cytostatics in breast cancer chemotherapy, it might be that women with a BRCA1 mutation are at higher risk for the induction of mutations and secondary cancers by standard therapies.

Sensitivity of the FPG protein towards alkylation damage in the comet assay

The comet assay (single cell gel electrophoresis) is widely used for the evaluation of DNA-damaging effects in genotoxicity testing and population monitoring. In its standard version at pH >13, DNA double strand breaks (DSB), DNA single strand breaks (SSB) and alkali-labile sites (ALS) lead to increased DNA migration. At reduced pH (12.5-12.1) the expression of ALS as SSB can be eliminated and the effect of SSB only can be identified. Specific endonucleases have been used to characterize specific classes of DNA damage. The formamido pyrimidine glycosylase (FPG) protein has been used to assess oxidative DNA base damage because it detects 8-OH guanine and other oxidatively damaged purines. Here, we show that the FPG protein also detects alkylation damage with high sensitivity in the comet assay. Human whole blood, isolated lymphocytes and V79 cells were treated with alkylating agents and post-incubated with FPG. FPG strongly enhanced MMS- and EMS-induced DNA damage but had no significant effect on ENU-induced DNA damage, indicating that the amount of N-7 guanine alkylation is responsible for the observed effect. Reducing the pH during alkali unwinding and electrophoresis to 12.5 to avoid the contribution of ALS to the comet assay effects, strongly decreased the sensitivity of the comet assay with and without FPG treatment and prevented DNA migration. We conclude that enhanced DNA effects in the comet assay by FPG after exposure to genotoxins with unknown mode of action should not directly be regarded as evidence for the presence of oxidative damage. Furthermore, reducing the pH leads to a considerable loss in sensitivity and should not be used in biomonitoring and other applications which require a sensitive protocol.

Mutagen sensitivity of human lymphoblastoid cells with a BRCA1 mutation

Previous results indicated that lymphoblastoid cell lines (LCL) with a BRCA1 mutation are hypersensitive to the chromosome-damaging effects of gamma irradiation or hydrogen peroxide as revealed by the micronucleus test. We now investigated six LCL (three with and three without a BRCA1 mutation) in more detail, to see whether LCL represent a useful model for the investigation of mechanisms responsible for the known mutagen sensitivity of lymphocytes from women carrying a BRCA1 mutation. Our results show that there is no systematic difference in radiation sensitivity between LCL with and without a BRCA1 mutation. Spontaneous and gamma radiation-induced micronucleus frequencies were in same range. Furthermore, cytotoxic effects (reduced cell proliferation, reduced viability) induced by gamma radiation were not different. The only difference found was an induction of micronuclei by 10 microM hydrogen peroxide in BRCA1 cell lines while a concentration of 20 microM hydrogen peroxide was necessary to induce micronuclei in control cells. Comet assay experiments did not reveal differences with regard to the induction and removal of primary DNA damage. Furthermore, expression of BRCA1 mRNA after gamma irradiation showed considerable variability and there was no clear difference between cell lines with and without BRCA mutation. These results indicate that LCL with a BRCA1 mutation do not generally show the same mutagen sensitivity as lymphocytes with the same BRCA1 mutation. Therefore, the use of LCL to study the mechanisms underlying mutagen sensitivity due to a heterozygous BRCA1 mutation seems to be limited.

Oxygenated water does not induce genotoxic effects in the comet assay

Drinking of oxygenated water (i.e. water with increased concentration of physically dissolved oxygen) is said to improve oxygen availability of the body and will do the consumer good. However, increased oxygen concentrations can also lead to an increased production of reactive oxygen species (ROS). If antioxidant defences are not completely efficient, ROS can cause cell injury including DNA damage. We therefore investigated whether drinking of oxygenated water can lead to increased DNA damage in peripheral blood cells of test subjects. We also tested whether direct exposure of V79 Chinese hamster cells to oxygenated medium or oxygenated Hank's solution for various time periods induces DNA damage. Induction of DNA damage was measured with the alkaline comet assay (single cell gel electrophoresis). The comet assay, in particular the modification with FPG post-treatment for the determination of oxidative DNA base damage, has been proven to be extremely sensitive for the detection of oxygen-induced DNA damage. However, both the in vivo and the in vitro studies with the comet assay in the absence and presence of FPG post-treatment did not provide evidence for a genotoxic effect of oxygenated water.

Mutagen sensitivity of peripheral blood from women carrying a BRCA1 or BRCA2 mutation

We are studying the induction and repair of DNA damage in lymphocytes of women from families with familial breast cancer and a heterozygous mutation in the breast cancer susceptibility genes BRCA1 or BRCA2. Besides various other functions, BRCA proteins seem to be involved in DNA repair processes like transcription-coupled and double-strand break (dsb) repair. Our previous results indicated a close relationship between the presence of a BRCA1 mutation and sensitivity for the induction of micronuclei (MN) by gamma irradiation and hydrogen peroxide (H2O2). In contrast to the results with the micronucleus assay, we found no significant individual difference between women with and without a BRCA1 mutation with respect to the induction and repair of DNA damage in the alkaline comet assay. We now investigated further cases heterozygous for a BRCA1 mutation and cases heterozygous for a BRCA2 mutation and show that enhanced micronucleus formation after gamma irradiation and H2O2-treatment is also a feature of lymphocytes carrying a BRCA2 mutation. Investigations with the comet assay did not reveal clear differences with regard to the induction of DNA damage on the individual level. There were also no significant differences between blood samples carrying a BRCA1 or BRCA2 mutation and blood samples from normal controls when the repair capacities (i.e. the kinetics of the removal of radiation-induced DNA effects in the comet assay) were compared. Our results indicate that mutagen sensitivity of lymphocytes heterozygous for a BRCA2 mutation is similar to that of cells with a BRCA1 mutation and BRCA1 and BRCA2 cannot be differentiated at present with the micronucleus test (MNT) or the comet assay.

Mutagen sensitivity of human lymphoblastoid cells with a BRCA1 mutation in comparison to ataxia telangiectasia heterozygote cells

Our previous results indicated a close relationship between the presence of a BRCA1 mutation in lymphocytes and hypersensitivity for the induction of micronuclei by gamma irradiation and hydrogen peroxide (H(2)O(2)). Comparative investigations with the comet assay (single-cell gel electrophoresis) suggested a normal rate of damage removal and pointed to a disturbed fidelity of DNA repair as a direct or indirect consequence of a BRCA1 mutation. We now wanted to see whether similar results could be obtained with lymphoblastoid cell lines (LCLs) and whether such permanent cells are suitable as a model for the investigation of mechanisms involved in mutagen sensitivity. Our results show that LCLs with a BRCA1 mutation are also hypersensitive to the chromosome-damaging effects of gamma irradiation or H(2)O(2), as revealed by the micronucleus test. Interestingly, LCLs heterozygous for an ataxia telangiectasia (AT) mutation have similar characteristics as BRCA1 cells with respect to the induction and repair of DNA damage induced by either gamma irradiation or H(2)O(2). However, caffeine enhanced the induction of micronuclei by gamma irradiation only in normal and heterozygous AT cells but not in BRCA1 cells, thus indicating a difference in the pathways leading to mutagen sensitivity in cells with a BRCA1 or an AT mutation. Our results suggest that caffeine could be useful in discriminating AT heterozygotes from carriers of a BRCA1 mutation, as well as BRCA1 mutation carriers from normal individuals.

The influence of temperature during alkaline treatment and electrophoresis on results obtained with the comet assay

The alkaline comet assay (single-cell gel electrophoresis) is becoming established as a genotoxicity test with many fold applications in vitro and in vivo. While the underlying principles are identical, various modifications of the method are in use which clearly affect the sensitivity and resolving power of the assay. One variable of potential importance that has been disregarded until now is temperature during alkaline treatment and electrophoresis. We therefore performed comet assay experiments with human blood and V79 Chinese hamster cells using two different temperatures (4 and 20 degrees C, i.e. room temperature) during alkaline treatment and electrophoresis. DNA damage was induced by the two standard mutagens gamma irradiation and methyl methanesulfonate (MMS). The results clearly indicate significant differences in the detection of background and mutagen-induced DNA damage at these two temperatures. Under otherwise identical test conditions (including the duration of alkaline treatment and electrophoresis), increased temperature during alkaline treatment and electrophoresis strongly enhances DNA migration. Our findings suggest that the comet assay should be performed under strictly controlled and reproducible temperature conditions. In any case the temperature during alkaline treatment and electrophoresis should be stated in a publication to allow for a critical evaluation of results obtained with the comet assay.

Unique double-stranded RNAs responsible for the anti-Candida activity of the yeast Hanseniaspora uvarum

Killer strains of the yeast Hanseniaspora uvarum contain cytoplasmic double-stranded RNAs (dsRNAs) of 4.7-kbp L and 1.0-kbp M species, which were shown to be separately packaged into icosahedral virus-like particles exhibiting RNA-dependent RNA polymerase activity. The L genome of the H. uvarum L-dsRNA virion HuV-L was shown to encode a 77-kDa major capsid protein. Peptide maps of the purified HuV coat protein and the 81-kDa major capsid protein from K1 killer viruses of Saccharomyces cerevisiae revealed distinctly different peptide patterns, suggesting significant sequence divergence at the level of the capsid-coding L-dsRNAs. In vitro transcripts from purified HuV-L particles showed no cross-hybridization to denatured L(A), L(B), or L(C), indicating that L from H. uvarum represents a unique L-dsRNA species. Weak, but clearly detectable cross-hybridization of the 1.0-kb dsRNA of HuV-M, encoding the secreted 18-kDa anti-Candida toxin, to the toxin-coding M genomes of S. cerevisiae K1, K2, and K28 killers indicated partial sequence homology among all of the M-dsRNAs tested.