Quantitative proteomic analysis of rat liver for carcinogenicity prediction in a 28-day repeated dose study

The potential of quantitative proteomic analysis to predict carcinogenicity of chemical compounds was investigated. Using 2D-DIGE, we analyzed the effects of 63 chemical compounds on protein expression in the rat liver after 28 daily doses. Types of carcinogens were categorized depending on the species and organ specificity. The carcinogen characteristic proteins for each classification were identified by Welch's t value. For evaluation of the predictive concordance we used support vector machines. The rat hepatic carcinogen-specific classification gave higher concordance than the other classification. The generalization performance was measured by leave-one-out cross-validation. For genotoxic and non-genotoxic compounds, a concordance of 79.3 and 76.5%, respectively, was obtained by the top 30 ranked proteins with Welch's t value. Furthermore, we found that the increase of the expression level of the stress response proteins as the common feature of poorly predicted chemical compounds in the leave-20%-out cross-validation. Quantitative proteomics could be promising technique for developing biomarker panels that can be used for carcinogenicity prediction. The list of proteins identified in this study and the zoomed gel images of the top ranked proteins in statistic analysis are provided in Supplementary Data.     

Beryllium: genotoxicity and carcinogenicity

Beryllium (Be) has physical-chemical properties, including low density and high tensile strength, which make it useful in the manufacture of products ranging from space shuttles to golf clubs. Despite its utility, a number of standard setting agencies have determined that beryllium is a carcinogen. Only a limited number of studies, however, have addressed the underlying mechanisms of the carcinogenicity and mutagenicity of beryllium. Importantly, mutation and chromosomal aberration assays have yielded somewhat contradictory results for beryllium compounds and whereas bacterial tests were largely negative, mammalian test systems showed evidence of beryllium-induced mutations, chromosomal aberrations, and cell transformation. Although inter-laboratory differences may play a role in the variability observed in genotoxicity assays, it is more likely that the different chemical forms of beryllium have a significant effect on mutagenicity and carcinogenicity. Because workers are predominantly exposed to airborne particles which are generated during the machining of beryllium metal, ceramics, or alloys, testing of the mechanisms of the mutagenic and carcinogenic activity of beryllium should be performed with relevant chemical forms of beryllium.     

DNA damage by ethylbenzenehydroperoxide formed from carcinogenic ethylbenzene by sunlight irradiation

Ethylbenzene, widely used in human life, is a non-mutagenic carcinogen. Sunlight-irradiated ethylbenzene caused DNA damage in the presence of Cu2+, but unirradiated ethylbenzene did not. A Cu+ -specific chelator bathocuproine inhibited DNA damage and catalase showed a little inhibitory effect. The scopoletin assay revealed that peroxides and H(2)O(2) were formed in ethylbenzene exposed to sunlight. These results suggest that Cu+ and alkoxyl radical mainly participate in DNA damage, and H(2)O(2) partially does. When catalase was added, DNA damage at thymine and cytosine was inhibited. Ethylbenzenehydroperoxide, identified by GC/MS analysis, induced the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine and caused DNA damage at consecutive guanines, as observed with cumenehydroperoxide. Equimolar concentrations of H(2)O(2) and acetophenone were produced by the sunlight-irradiation of 1-phenylethanol, a further degraded product of ethylbenzene. These results indicate a novel pathway that oxidative DNA damage induced by the peroxide and H(2)O(2) derived from sunlight-irradiated ethylbenzene may lead to expression of the carcinogenicity.     

Two closely related nickel complexes have different effects on DNA damage and cell viability

Nickel is considered a weak carcinogen. It is known to interact with DNA and DNA-binding proteins. The ability of certain nickel compounds to cleave DNA has been exploited mainly for research purposes and less for developing new anticancer drugs. Here we compare the interactions of two closely related nickel complexes, [NiCR]2+ and [Ni(CR-2H)]2+, with DNA. CR stands for 2,12-dimethyl-3,7,11,17-tetraazabicyclo-[11.3.1]-heptadeca-1(17),2,11,13,15-pentaene. [NiCR]2+ has been used in the past as a structure-specific probe for RNA and DNA oligonucleotides in the presence of oxidizing agent but little is known about the biological effects of either complex. Our results show that [Ni(CR-2H)]2+ can damage DNA in vivo and in vitro in the absence of an added oxidizing agent and has an IC50 of 70 microM in human breast cancer cells whereas [NiCR]2+ and NiCl2 do not exhibit significant cytotoxicity. However, both [NiCR]2+ and [Ni(CR-2H)]2+ bind to the minor groove of double-stranded DNA.     

Distributed structure-searchable toxicity (DSSTox) public database network: a proposal.

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, Structure-Activity Relationship (SAR) model development, or building of chemical relational databases (CRD). The distributed structure-searchable toxicity (DSSTox) public database network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: (1) to adopt and encourage the use of a common standard file format (structure data file (SDF)) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; (2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data sources with potential users of these data from other disciplines (such as chemistry, modeling, and computer science); and (3) to engage public/commercial/academic/industry groups in contributing to and expanding this community-wide, public data sharing and distribution effort. The DSSTox project's overall aims are to effect the closer association of chemical structure information with existing toxicity data, and to promote and facilitate structure-based exploration of these data within a common chemistry-based framework that spans toxicological disciplines.     

Estimation and Testing of Tumor Incidence Rates in Experiments Lacking Cause-of-Death Data

Approximate nonparametric maximum likelihood estimation of the tumor incidence rate and comparison of tumor incidence rates between treatment groups are examined in the context of animal carcinogenicity experiments that have interval sacrifice data but lack cause-of-death information. The estimation procedure introduced by MALANI and VAN RYZIN (1988), which can result in a negative estimate of the tumor incidence rate, is modified by employing a numerical method to maximize the likelihood function iteratively, under the constraint that the tumor incidence rate is nonnegative. With the new procedure, estimates can be obtained even if sacrifices occur anywhere within an interval. The resulting estimates have reduced standard error and give more power to the test of two heterogeneous groups. Furthermore, a linear contrast of more than two groups can be tested using our procedure. The proposed estimation and testing methods are illustrated with an experimental data set.     

Bayesian models for multivariate current status data with informative censoring

Multivariate current status data, consist of indicators of whether each of several events occur by the time of a single examination. Our interest focuses on inferences about the joint distribution of the event times. Conventional methods for analysis of multiple event-time data cannot be used because all of the event times are censored and censoring may be informative. Within a given subject, we account for correlated event times through a subject-specific latent variable, conditional upon which the various events are assumed to occur independently. We also assume that each event contributes independently to the hazard of censoring. Nonparametric step functions are used to characterize the baseline distributions of the different event times and of the examination times. Covariate and subject-specific effects are incorporated through generalized linear models. A Markov chain Monte Carlo algorithm is described for estimation of the posterior distributions of the unknowns. The methods are illustrated through application to multiple tumor site data from an animal carcinogenicity study.     

Benzo [... formula ...] pyrene-induced DNA adducts and gene expression profiles in target and non-target organs for carcinogenesis in mice

Background

Gene expression changes induced by carcinogens may identify differences in molecular function between target and non-target organs. Target organs for benzo[a]pyrene (BaP) carcinogenicity in mice (lung, spleen and forestomach) and three non-target organs (liver, colon and glandular stomach) were investigated for DNA adducts by ³²P-postlabelling, for gene expression changes by cDNA microarray and for miRNA expression changes by miRNA microarray after exposure of animals to BaP.

Results

BaP-DNA adduct formation occurred in all six organs at levels that did not distinguish between target and non-target. cDNA microarray analysis showed a variety of genes modulated significantly by BaP in the six organs and the overall gene expression patterns were tissue specific. Gene ontology analysis also revealed that BaP-induced bioactivities were tissue specific; eight genes (Tubb5, Fos, Cdh1, Cyp1a1, Apc, Myc, Ctnnb1 and Cav) showed significant expression difference between three target and three non-target organs. Additionally, several gene expression changes, such as in Trp53 activation and Stat3 activity suggested some similarities in molecular mechanisms in two target organs (lung and spleen), which were not found in the other four organs. Changes in miRNA expression were generally tissue specific, involving, in total, 21/54 miRNAs significantly up- or down-regulated.

Conclusions

Altogether, these findings showed that DNA adduct levels and early gene expression changes did not fully distinguish target from non-target organs. However, mechanisms related to early changes in p53, Stat3 and Wnt/β-catenin pathways may play roles in defining BaP organotropism.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-880) contains supplementary material, which is available to authorized users.     

Radiofrequency radiations induced genotoxic and carcinogenic effects on chickpea (Cicer arietinum L.) root tip cells

Present study was under taken to predict the possible DNA damages (genotoxicity) and carcinogenicity caused by radiofrequency radiations (RF) to living tissue. Dry seeds of chickpea were treated with GSM cell phone (900 MHz) and laptop (3.31 GHz) as RF source for 24 and 48 h. Untreated seeds were used as (0 h) negative control and Gamma rays (250 Gray) as positive control. Plant chromosomal aberration assay was used as genotoxicity marker. All the treatment of RF inhibits seed germination percentage. 48 h laptop treatment has the most negative effect as compared to untreated control. A decrease was observed in mitotic index (M.I) and increase in abnormality index (A.I) with the increase in exposure duration and frequency in (Hz). Cell membrane damages were also observed only in 48 h exposure of cell phone and laptop (RF). Maximum nuclear membrane damages and ghost cells were again recorded in 48 h exposure of cell phone and laptop. The radiofrequency radiations (900 MHz and 3.31 GHz) are only genotoxic as they induce micronuclei, bi-nuclei, multi-nuclei and scattered nuclei but could be carcinogenic as 48 h incubation of RF induced fragmentation and ghost cells. Therefore cell phones and laptop should not be used unnecessarily to avoid possible genotoxic and carcinogenic effects.     

Risk assessment and the importance of ochratoxins

The multi-faceted and potent toxicity of ochratoxin A to experimental animals, its accepted role as disease determinant in mycotoxic porcine nephropathy, its putative role in the idiopathic human disease Balkan endemic nephropathy and associated urinary tract tumours, and its widespread occurrence usually in trace amounts in foodstuffs is focussing attention on minimising human intake. Conservative risk assessment based on porcine renal disease data has set tolerable intake values rather similar to actual average human intake. However, translating experimental rat tumour data to possible human risk is proving difficult partly because, in the author's view, the finding of a low incidence of DNA adducts could arise from an artificial surge in serum concentration following rapid uptake from aqueous intragastric administration, and this probably exaggerates what would occur during more natural slow uptake from food. The need for experimental data that can assist meaningful evaluation of risk of natural intake of ochratoxin A is emphasised, but prospective legislation should be balanced against socio-economic consequences of setting over-strict limits on contamination of relevant agricultural commodities, particularly in vulnerable specialist sectors such as coffee.