Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes.

In recent decades, our knowledge of the genetics and functional genomics of drug-metabolizing enzymes has increased and a wealth of data on drug-related 'omics' has become available. Despite the availability of large amounts of biological information on xenobiotic biotransformation, the number of available biotransformation pathway maps that can easily be used for visualization of multiple omics data is limited. Here, we created integrated biotransformation pathway maps suitable for multiple omics analysis using PathVisio. The ease of visualizing data on these maps was demonstrated by using published microarray data from human hepatocyte-like cell models, exemplifying - where a sufficient capacity for metabolizing chemicals is a prerequisite for a suited model - how the biotransformation pathway maps can be used for model selection

Prevalence of at-risk genotypes for genotoxic effects decreases with age in a randomly selected population in Flanders: a cross sectional study

Background: We hypothesized that in Flanders (Belgium), the prevalence of at-risk genotypes for genotoxic effects decreases with age due to morbidity and mortality resulting from chronic diseases. Rather than polymorphisms in single genes, the interaction of multiple genetic polymorphisms in low penetrance genes involved in genotoxic effects might be of relevance. Methods: Genotyping was performed on 399 randomly selected adults (aged 50-65) and on 442 randomly selected adolescents. Based on their involvement in processes relevant to genotoxicity, 28 low penetrance polymorphisms affecting the phenotype in 19 genes were selected (xenobiotic metabolism, oxidative stress defense and DNA repair, respectively 13, 6 and 9 polymorphisms). Polymorphisms which, based on available literature, could not clearly be categorized a priori as leading to an 'increased risk' or a 'protective effect' were excluded. Results: The mean number of risk alleles for all investigated polymorphisms was found to be lower in the 'elderly' (17.0 +/- 2.9) than the 'adolescent' (17.6 +/- 3.1) subpopulation (P = 0.002). These results were not affected by gender nor smoking. The prevalence of a high (> 17 = median) number of risk alleles was less frequent in the 'elderly' (40.6%) than the 'adolescent' (51.4%) subpopulation (P = 0.002). In particular for phase II enzymes, the mean number of risk alleles was lower in the 'elderly' (4.3 +/- 1.6) than the 'adolescent' age group (4.8 +/- 1.9) P 4 = median) number of risk alleles was less frequent in the 'elderly' (41.3%) than the adolescent subpopulation (56.3%, P 8 = median) number of risk alleles for DNA repair enzyme-coding genes was lower in the 'elderly' (37,3%) than the 'adolescent' subpopulation (45.6%, P = 0.017). Conclusions: These observations are consistent with the hypothesis that, in Flanders, the prevalence of at-risk alleles in genes involved in genotoxic effects decreases with age, suggesting that persons carrying a higher number of at risk alleles (especially in phase II xenobiotic-metabolizing or DNA repair genes) are at a higher risk of morbidity and mortality from chronic diseases. Our findings also suggest that, regarding risk of disease associated with low penetrance polymorphisms, multiple polymorphisms should be taken into account, rather than single ones

Biological effect markers for exposure to carcinogenic compound and their relevance for risk assessment

In this review data are summarized on biomarkers that are used for biological effect monitoring of human populations exposed to genotoxic carcinogens. The biomarkers are DNA and protein adducts and cytogenetic effects. Most of these biomarkers are relevant for the process of carcinogenesis. Emphasis is on providing information on the properties of the biomarkers and on their relevance for predicting cancer risk. Overviews are presented of: (1) studies on effects of exposure in target tissues of human origin obtained by surgical biopsies or autopsies, (2) epidemiological studies on healthy (cancer-free) individuals, correlating the putative occupational, lifestyle or environmental exposure with increased levels of biomarkers in blood cells, and (3) studies with animal models on the relation between biomarkers and cancer. Finally, on the basis of epidemiological data the possibilities were explored to use biomarker data to estimate the risk of death due to cancer. For several biomarkers the increment of the cancer mortality risk was calculated on the basis of a lifetime doubling of the biomarker level

Lack of clastogenic effects in cultured human lymphocytes treated with hydroquinone

Hydroquinone (HQ) occurs in the environment as a result of manmade processes as well as in natural products from plants and animals. The compound has been reported to produce chromosomal effects in some in vivo and in vitro animal models. However, its potential to produce similar effects in human lymphocytes is less clear. To obtain more information on the clastogenic potential of HQ in human cells, its ability to induce structural chromosomal aberrations in human lymphocytes in vitro has been examined, both in the absence and presence of exogenous metabolic activation. Moreover, the effect of HQ pre-incubation on peroxide induced clastogenicity was studied, because HQ has putative chemopreventive activity as well. It was found that HQ was cytotoxic, but did not induce chromosomal aberrations in human lymphocytes cultured in vitro. Additionally, it was observed that pre-incubation of lymphocytes with HQ resulted in a concentration dependent reduction of the H2O2 induced chromosomal aberrations (P=0.069). However, this effect was present at 12 mM H2O2 only, because of high cytotoxicity at higher dosages. © 2003 Elsevier Ltd. All rights reserved

Modulation of gene expression and DNA adduct formation in HepG2 cells by polycyclic aromatic hydrocarbons with different carcinogenic potencies

Polycyclic aromatic hydrocarbons (PAHs) can occur in relatively high concentrations in the air, and many PAHs are known or suspected carcinogens. In order to better understand differences in carcinogenic potency between PAHs, we investigated modulation of gene expression in human HepG2 cells after 6 h incubation with varying doses of benzo[a]pyrene (B[a]P), benzo[b]fluoranthene (B[b]F), fluoranthene (FA), dibenzo[a,h]anthracene (DB[a,h]A), 1-methylphenanthrene (1-MPA) or dibenzo[a,l]pyrene (DB[a,l]P), by using cDNA microarrays containing 600 toxicologically relevant genes. Furthermore, DNA adduct levels induced by the compounds were assessed with P-32-post-labeling, and carcinogenic potency was determined by literature study. All tested PAHs, except 1-MPA, induced gene expression changes in HepG2 cells, although generally no dose-response relationship could be detected. Clustering and principal component analysis showed that gene expression changes were compound specific, since for each compound all concentrations grouped together. Furthermore, it showed that the six PAHs can be divided into three groups, first FA and 1-MPA, second B[a]P, B[b]F and DB[a,h]A, and third DB[a,l]P. This grouping corresponds with the carcinogenic potencies of the individual compounds. Many of the modulated genes are involved in biological pathways like apoptosis, cholesterol biosynthesis and fatty acid synthesis. The order of DNA adduct levels induced by the PAHs was: B[a]P >> DB[a,l]P > B[b]F > DB[a,h]A > 1-MPA >= FA. When comparing the expression change of individual genes with DNA adduct levels, carcinogenic potency or Ah-receptor antagonicity (the last two were taken from literature), several highly correlated genes were found, of which CYP1A1, PRKCA, SLC22A3, NFKB1A, CYP1A2 and CYP2D6 correlated with all parameters. Our data indicate that discrimination of high and low carcinogenic PAHs by gene expression profiling is feasible. Also, the carcinogenic PAHs induce several pathways that were not affected by the least carcinogenic PAHs