Jos Kleinjans

Publications of Jos Kleinjans

• Comparison of hepatocarcinogen-induced gene expression profiles in conventional primary rat hepatocytes with in vivo rat liver.

  Authors: Tatyana Y Doktorova, Heidrun Ellinger-Ziegelbauer, Mathieu Vinken, Tamara Vanhaecke, Joost van Delft, Jos Kleinjans, Hans-Juergen Ahr, Vera Rogiers

  Archives of toxicology. 04/2012;

  At present, substantial efforts are focused on the development of in vitro assays coupled with "omics" technologies for the identification of carcinogenic substances as an alternative to theAt present, substantial efforts are focused on the development of in vitro assays coupled with "omics" technologies for the identification of carcinogenic substances as an alternative to the classical 2-year rodent carcinogenicity bioassay. A prerequisite for the eventual regulatory acceptance of such assays, however, is the in vivo relevance of the observed in vitro findings. In the current study, hepatocarcinogen-induced gene expression profiles generated after the exposure of conventional cultures of primary rat hepatocytes to three non-genotoxic carcinogens (methapyrilene hydrochloride, piperonyl butoxide, and Wy-14643), three genotoxic carcinogens (aflatoxin B1, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, and 2-nitrofluorene), and two non-carcinogens (nifedipine and clonidine) are compared with previously obtained in vivo data after oral administration for up to 14 days of the same hepatocarcinogens to rats. In addition to the comparison of deregulated genes and functions per compound between in vivo and in vitro models, the major discriminating cellular pathways found in vivo in livers of exposed rats were examined for deregulation in vitro. Further, in vivo-derived gene signatures for the identification of genotoxic versus non-genotoxic carcinogens are used to classify in vitro-tested hepatocarcinogens and non-carcinogens. In the primary hepatocyte cultures, two out of the three tested genotoxic carcinogens mimicked the in vivo-relevant DNA damage response and were correctly assessed. Exposure to the non-genotoxic hepatocarcinogens, however, triggered a relatively weak response in the in vitro system, with no clear similarities to in vivo. This study contributes to the further optimization of toxicogenomics predictive tools when applied in in vitro settings.

• Toward interoperable bioscience data.

  Authors: Susanna-Assunta Sansone, Philippe Rocca-Serra, Dawn Field, Eamonn Maguire, Chris Taylor, Oliver Hofmann, Hong Fang, Steffen Neumann, Weida Tong, Linda Amaral-Zettler [......] Dorothy Reilly, Magali Roux, Caroline E Shamu, Catherine A Shang, Christoph Steinbeck, Anne Trefethen, Bryn Williams-Jones, Katherine Wolstencroft, Ioannis Xenarios, Winston Hide

  Nature genetics. 02/2012; 44(2):121-6.

  To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture.To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.

• Integrating transcriptomics and metabonomics to unravel modes-of-action of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in HepG2 cells.

  Authors: Danyel Jennen, Ainhoa Ruiz-Aracama, Christina Magkoufopoulou, Ad Peijnenburg, Arjen Lommen, Joost van Delft, Jos Kleinjans

  BMC systems biology. 08/2011; 5:139.

  The integration of different 'omics' technologies has already been shown in several in vivo studies to offer a complementary insight into cellular responses to toxic challenges. Being interested inThe integration of different 'omics' technologies has already been shown in several in vivo studies to offer a complementary insight into cellular responses to toxic challenges. Being interested in developing in vitro cellular models as alternative to animal-based toxicity assays, we hypothesize that combining transcriptomics and metabonomics data improves the understanding of molecular mechanisms underlying the effects caused by a toxic compound also in vitro in human cells. To test this hypothesis, and with the focus on non-genotoxic carcinogenesis as an endpoint of toxicity, in the present study, the human hepatocarcinoma cell line HepG2 was exposed to the well-known environmental carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Transcriptomics as well as metabonomics analyses demonstrated changes in TCDD-exposed HepG2 in common metabolic processes, e.g. amino acid metabolism, of which some of the changes only being confirmed if both 'omics' were integrated. In particular, this integrated analysis identified unique pathway maps involved in receptor-mediated mechanisms, such as the G-protein coupled receptor protein (GPCR) signaling pathway maps, in which the significantly up-regulated gene son of sevenless 1 (SOS1) seems to play an important role. SOS1 is an activator of several members of the RAS superfamily, a group of small GTPases known for their role in carcinogenesis. The results presented here were not only comparable with other in vitro studies but also with in vivo studies. Moreover, new insights on the molecular responses caused by TCDD exposure were gained by the cross-omics analysis.

• Human embryonic stem cell derived hepatocyte-like cells as a tool for in vitro hazard assessment of chemical carcinogenicity.

  Authors: Reha Yildirimman, Gabriella Brolén, Mireia Vilardell, Gustav Eriksson, Jane Synnergren, Hans Gmuender, Atanas Kamburov, Magnus Ingelman-Sundberg, José Castell, Agustin Lahoz, Jos Kleinjans, Joost van Delft, Petter Björquist, Ralf Herwig

  Toxicological sciences : an official journal of the Society of Toxicology. 08/2011; 124(2):278-90.

  Hepatocyte-like cells derived from the differentiation of human embryonic stem cells (hES-Hep) have potential to provide a human relevant in vitro test system in which to evaluate the carcinogenicHepatocyte-like cells derived from the differentiation of human embryonic stem cells (hES-Hep) have potential to provide a human relevant in vitro test system in which to evaluate the carcinogenic hazard of chemicals. In this study, we have investigated this potential using a panel of 15 chemicals classified as noncarcinogens, genotoxic carcinogens, and nongenotoxic carcinogens and measured whole-genome transcriptome responses with gene expression microarrays. We applied an ANOVA model that identified 592 genes highly discriminative for the panel of chemicals. Supervised classification with these genes achieved a cross-validation accuracy of > 95%. Moreover, the expression of the response genes in hES-Hep was strongly correlated with that in human primary hepatocytes cultured in vitro. In order to infer mechanistic information on the consequences of chemical exposure in hES-Hep, we developed a computational method that measures the responses of biochemical pathways to the panel of treatments and showed that these responses were discriminative for the three toxicity classes and linked to carcinogenesis through p53, mitogen-activated protein kinases, and apoptosis pathway modules. It could further be shown that the discrimination of toxicity classes was improved when analyzing the microarray data at the pathway level. In summary, our results demonstrate, for the first time, the potential of human embryonic stem cell--derived hepatic cells as an in vitro model for hazard assessment of chemical carcinogenesis, although it should be noted that more compounds are needed to test the robustness of the assay.

• Maternal and gestational factors and micronucleus frequencies in umbilical blood: the NewGeneris Rhea cohort in Crete.

  Authors: Kim Vande Loock, Eleni Fthenou, Ilse Decordier, Georgia Chalkiadaki, Maria Keramarou, Gina Plas, Mathieu Roelants, Jos Kleinjans, Leda Chatzi, Franco Merlo, Manolis Kogevinas, Micheline Kirsch-Volders

  Environmental health perspectives. 05/2011; 119(10):1460-5.

  The use of cancer-related biomarkers in newborns has been very limited. We investigated the formation of micronuclei (MN) in full-term and preterm newborns and their mothers from the Rhea cohortThe use of cancer-related biomarkers in newborns has been very limited. We investigated the formation of micronuclei (MN) in full-term and preterm newborns and their mothers from the Rhea cohort (Crete), applying for the first time in cord blood a validated semiautomated analysis system, in both mono- and binucleated T lymphocytes. We assessed MN frequencies in peripheral blood samples from the mothers and in umbilical cord blood samples. We calculated MN in mononucleated (MNMONO) and binucleated (MNBN) T lymphocytes and the cytokinesis block proliferation index (CBPI) in 251 newborns (224 full term) and 223 mothers, including 182 mother-child pairs. Demographic and lifestyle characteristics were collected. We observed significantly higher MNBN and CBPI levels in mothers than in newborns. In newborns, MNMONO and MNBN were correlated (r = 0.35, p < 0.001), and we found a moderate correlation between MNMONO in mothers and newborns (r = 0.26, p < 0.001). MNMONO frequencies in newborns were positively associated with the mother's body mass index and inversely associated with gestational age and mother's age, but we found no significant predictors of MNBN or CBPI in newborns. Although confirmation is needed by a larger study population, the results indicate the importance of taking into account both mono- and binucleated T lymphocytes for biomonitoring of newborns, because the first reflects damage expressed during in vivo cell division and accumulated in utero, and the latter includes additional damage expressed as MN during the in vitro culture step.

• An untargeted multi-technique metabolomics approach to studying intracellular metabolites of HepG2 cells exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin.

  Authors: Ainhoa Ruiz-Aracama, Ad Peijnenburg, Jos Kleinjans, Danyel Jennen, Joost van Delft, Caroline Hellfrisch, Arjen Lommen

  BMC genomics. 05/2011; 12:251.

  In vitro cell systems together with omics methods represent promising alternatives to conventional animal models for toxicity testing. Transcriptomic and proteomic approaches have been widely appliedIn vitro cell systems together with omics methods represent promising alternatives to conventional animal models for toxicity testing. Transcriptomic and proteomic approaches have been widely applied in vitro but relatively few studies have used metabolomics. Therefore, the goal of the present study was to develop an untargeted methodology for performing reproducible metabolomics on in vitro systems. The human liver cell line HepG2, and the well-known hepatotoxic and non-genotoxic carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), were used as the in vitro model system and model toxicant, respectively. The study focused on the analysis of intracellular metabolites using NMR, LC-MS and GC-MS, with emphasis on the reproducibility and repeatability of the data. State of the art pre-processing and alignment tools and multivariate statistics were used to detect significantly altered levels of metabolites after exposing HepG2 cells to TCDD. Several metabolites identified using databases, literature and LC-nanomate-Orbitrap analysis were affected by the treatment. The observed changes in metabolite levels are discussed in relation to the reported effects of TCDD. Untargeted profiling of the polar and apolar metabolites of in vitro cultured HepG2 cells is a valid approach to studying the effects of TCDD on the cell metabolome. The approach described in this research demonstrates that highly reproducible experiments and correct normalization of the datasets are essential for obtaining reliable results. The effects of TCDD on HepG2 cells reported herein are in agreement with previous studies and serve to validate the procedures used in the present work.

• Alternative (non-animal) methods for cosmetics testing: current status and future prospects-2010.

  Authors: Sarah Adler, David Basketter, Stuart Creton, Olavi Pelkonen, Jan van Benthem, Valérie Zuang, Klaus Ejner Andersen, Alexandre Angers-Loustau, Aynur Aptula, Anna Bal-Price [......] Greet Schoeters, Michael Schwarz, Rositsa Serafimova, Hanna Tähti, Emanuela Testai, Joost van Delft, Henk van Loveren, Mathieu Vinken, Andrew Worth, José-Manuel Zaldivar

  Archives of toxicology. 05/2011; 85(5):367-485.

  The 7th amendment to the EU Cosmetics Directive prohibits to put animal-tested cosmetics on the market in Europe after 2013. In that context, the European Commission invited stakeholder bodiesThe 7th amendment to the EU Cosmetics Directive prohibits to put animal-tested cosmetics on the market in Europe after 2013. In that context, the European Commission invited stakeholder bodies (industry, non-governmental organisations, EU Member States, and the Commission's Scientific Committee on Consumer Safety) to identify scientific experts in five toxicological areas, i.e. toxicokinetics, repeated dose toxicity, carcinogenicity, skin sensitisation, and reproductive toxicity for which the Directive foresees that the 2013 deadline could be further extended in case alternative and validated methods would not be available in time. The selected experts were asked to analyse the status and prospects of alternative methods and to provide a scientifically sound estimate of the time necessary to achieve full replacement of animal testing. In summary, the experts confirmed that it will take at least another 7-9 years for the replacement of the current in vivo animal tests used for the safety assessment of cosmetic ingredients for skin sensitisation. However, the experts were also of the opinion that alternative methods may be able to give hazard information, i.e. to differentiate between sensitisers and non-sensitisers, ahead of 2017. This would, however, not provide the complete picture of what is a safe exposure because the relative potency of a sensitiser would not be known. For toxicokinetics, the timeframe was 5-7 years to develop the models still lacking to predict lung absorption and renal/biliary excretion, and even longer to integrate the methods to fully replace the animal toxicokinetic models. For the systemic toxicological endpoints of repeated dose toxicity, carcinogenicity and reproductive toxicity, the time horizon for full replacement could not be estimated.

• Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining.

  Authors: Kristina M Hettne, Antony J Williams, Erik M van Mulligen, Jos Kleinjans, Valery Tkachenko, Jan A Kors

  Journal of cheminformatics. 01/2010; 2(1):4.

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• A Dictionary to Identify Small Molecules and Drugs in Free Text.

  Authors: Kristina M Hettne, Rob H Stierum, Martijn J Schuemie, Peter JM Hendriksen, Bob Ja Schijvenaars, Erik M van Mulligen, Jos Kleinjans, Jan A Kors

  Bioinformatics (Oxford, England). 09/2009;

  MOTIVATION: From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correctMOTIVATION: From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correct identification of chemical names. Dictionary-based term identification has the power to recognize the diverse representation of chemical information in the literature and map the chemicals to their database identifiers. RESULTS: We developed a dictionary for the identification of small molecules and drugs in text, combining information from UMLS, MeSH, ChEBI, DrugBank, KEGG, HMDB, and ChemIDplus. Rule-based term filtering, manual check of highly frequent terms, and disambiguation rules were applied. We tested the combined dictionary and the dictionaries derived from the individual resources on an annotated corpus, and conclude the following: (1) each of the different processing steps increase precision with a minor loss of recall; (2) the overall performance of the combined dictionary is acceptable (precision 0.67, recall 0.40 (0.80 for trivial names); (3) the combined dictionary performed better than the dictionary in the chemical recognizer OSCAR3; (4) the performance of a dictionary based on ChemIDplus alone is comparable to the performance of the combined dictionary. AVAILABILITY: The combined dictionary is freely available as an XML file in Simple Knowledge Organization System format on the web at http://www.biosemantics.org/chemlist. CONTACT: k.hettne@erasmusmc.nl.

• NewGeneris: A European Study on Maternal Diet during Pregnancy and Child Health.

  Authors: Domenico F Merlo, Christopher P Wild, Manolis Kogevinas, Soterios Kyrtopoulos, Jos Kleinjans

  Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 02/2009; 18(1):5-10.

• The carcinoGENOMICS project: Critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays.

  Authors: Mathieu Vinken, Tatyana Doktorova, Heidrun Ellinger-Ziegelbauer, Hans-Jürgen Ahr, Edward Lock, Paul Carmichael, Erwin Roggen, Joost van Delft, Jos Kleinjans, José Castell [......] Timothy Ebbels, Toby Athersuch, Susanna-Assunta Sansone, Philippe Rocca-Serra, Rob Stierum, Paul Jennings, Walter Pfaller, Hans Gmuender, Tamara Vanhaecke, Vera Rogiers

  Mutation research. 05/2008;

  Recent changes in the European legislation of chemical-related substances have forced the scientific community to speed up the search for alternative methods that could partly or fully replace animalRecent changes in the European legislation of chemical-related substances have forced the scientific community to speed up the search for alternative methods that could partly or fully replace animal experimentation. The Sixth Framework Program project carcinoGENOMICS was specifically raised to develop omics-based in vitro screens for testing the carcinogenic potential of chemical compounds in a pan-European context. This paper provides an in-depth analysis of the complexity of choosing suitable reference compounds used for creating and fine-tuning the in vitro carcinogenicity assays. First, a number of solid criteria for the selection of the model compounds are defined. Secondly, the strategy followed, including resources consulted, is described and the selected compounds are briefly illustrated. Finally, limitations and problems encountered during the selection procedure are discussed. Since selecting an appropriate set of chemicals is a frequent impediment in the early stages of similar research projects, the information provided in this paper might be extremely valuable.

• The CYP1A2-164A-->C polymorphism (CYP1A2*1F) is associated with the risk for colorectal adenomas in humans.

  Authors: Harald Moonen, Leopold Engels, Jos Kleinjans, Theo de Kok

  Cancer letters. 12/2005; 229(1):25-31.

  Colorectal cancer (CRC) is believed to be related to the intake of processed meat and the formed heterocyclic aromatic amines (HCA) herein, which are metabolically activated by the enzymes cytochromeColorectal cancer (CRC) is believed to be related to the intake of processed meat and the formed heterocyclic aromatic amines (HCA) herein, which are metabolically activated by the enzymes cytochrome P4501A2 (CYP1A2) and N-acetyltransferase 2 (NAT2). The influence of genotypic and phenotypic variations for CYP1A2 and NAT2 on the risk for colorectal adenomas was investigated in 94 individuals at different risk of developing CRC. Significant associations were found between the CYP1A2-164A-->C polymorphism (CYP1A2*1F) and the risk of colorectal adenomas, suggesting that the studied polymorphism plays an important role in CRC risk in humans.

• Interaction between cadmium and aromatic DNA adducts in hprt mutagenesis during foetal development.

  Authors: Roger Godschalk, Janneke Hogervorst, Harma Albering, Patricia Mercelina-Roumans, Frederik-Jan van Schooten, Jelte de Haan, Jos Kleinjans

  Mutagenesis. 06/2005; 20(3):181-5.

  The foetus is exposed to multiple xenobiotics through the mother's circulation and this is possibly involved in the development of diseases in later life. Heavy metals and lipophilic genotoxins inThe foetus is exposed to multiple xenobiotics through the mother's circulation and this is possibly involved in the development of diseases in later life. Heavy metals and lipophilic genotoxins in umbilical cord blood of newborns may have synergistic effects on mutagenesis in the hypoxanthine-phosphoribosyltransferase (HPRT) reporter gene. Concentrations of zinc (Zn), lead (Pb) and cadmium (Cd) were determined in the peripheral and cord blood of 16 non-smoking and 9 smoking healthy mothers by atomic absorption spectrometry. Lipophilic DNA adducts in lymphocytes were determined in the same subjects by 32P-postlabelling and the HPRT-variant frequency was assessed by the evaluation of 6-thioguanine resistant cells. Although the Cd/Zn ratio was 2.5-fold higher in the blood of smoking women than in non-smoking women (1.0 +/- 0.2 and 0.4 +/- 0.1, respectively, P = 0.007), this difference could not be observed in umbilical cord blood (0.3 +/- 0.1 and 0.3 +/- 0.1, respectively, P = 0.66). Similarly, mean DNA adduct levels were increased in the lymphocytes of smoking women compared with non-smoking controls (0.99 +/- 0.31 adducts/10(8) nt and 0.43 +/- 0.12, respectively, P = 0.009), but were only marginally higher in the neonates of smokers than in their non-smoking counterparts (0.57 +/- 0.29 and 0.24 +/- 0.09, respectively, P = 0.38). Since Cd is known to effectively inhibit DNA repair, we hypothesized that concomitant exposure of neonates to Cd and genotoxic compounds may result in an increased fixation of DNA damage into somatic mutations. Indeed, the number of HPRT-variants per adduct (i.e. the mutagenic efficiency of adducts) correlated positively with the Cd concentrations in cord blood (r = 0.61, P = 0.001). These data suggest a molecular link between DNA damage, inhibition of DNA repair by Cd and in vivo mutagenesis during foetal development. Thus, exposure to heavy metals may enhance the mutagenic potential of DNA-damaging compounds and results in biologically relevant genotoxic effects in neonates.

• Risk assessment of endogenous formation of carcinogenic N-nitroso compounds in response to intake of NO-aspirin.

  Authors: Jos Kleinjans, Theo de Kok, Leopold Engels

  Gastroenterology. 10/2004; 127(3):1018-9; author reply 1019.

• The carcinoGENOMICS project: Critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays

  Authors: Mathieu Vinken, Tatyana Doktorova, Heidrun Ellinger-Ziegelbauer, Hans-Jürgen Ahr, Edward Lock, Paul Carmichael, Erwin Roggen, Joost van Delft, Jos Kleinjans, José Castell [......] Timothy Ebbels, Toby Athersuch, Susanna-Assunta Sansone, Philippe Rocca-Serra, Rob Stierum, Paul Jennings, Walter Pfaller, Hans Gmuender, Tamara Vanhaecke, Vera Rogiers

  Mutation Research/Reviews in Mutation Research.

  Recent changes in the European legislation of chemical-related substances have forced the scientific community to speed up the search for alternative methods that could partly or fully replace animalRecent changes in the European legislation of chemical-related substances have forced the scientific community to speed up the search for alternative methods that could partly or fully replace animal experimentation. The Sixth Framework Program project carcinoGENOMICS was specifically raised to develop omics-based in vitro screens for testing the carcinogenic potential of chemical compounds in a pan-European context. This paper provides an in-depth analysis of the complexity of choosing suitable reference compounds used for creating and fine-tuning the in vitro carcinogenicity assays. First, a number of solid criteria for the selection of the model compounds are defined. Secondly, the strategy followed, including resources consulted, is described and the selected compounds are briefly illustrated. Finally, limitations and problems encountered during the selection procedure are discussed. Since selecting an appropriate set of chemicals is a frequent impediment in the early stages of similar research projects, the information provided in this paper might be extremely valuable.

• Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution

  Authors: Domenico Franco Merlo, Hans Gmuender, Danitsja van Leeuwen, Fioravante Patrone, Jos Kleinjans, Joost van Delft, Stefano Bonassi, Stefano Moretti

  Background In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, theBackground In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, the interpretation of each single p-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, game theory has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions. Results In this paper we introduce a Bootstrap procedure to test the null hypothesis that each gene has the same relevance between two conditions, where the relevance is represented by the Shapley value of a particular coalitional game defined on a microarray data-set. This method, which is called Comparative Analysis of Shapley value (shortly, CASh), is applied to data concerning the gene expression in children differentially exposed to air pollution. The results provided by CASh are compared with the results from a parametric statistical test for testing differential gene expression. Both lists of genes provided by CASh and t-test are informative enough to discriminate exposed subjects on the basis of their gene expression profiles. While many genes are selected in common by CASh and the parametric test, it turns out that the biological interpretation of the differences between these two selections is more interesting, suggesting a different interpretation of the main biological pathways in gene expression regulation for exposed individuals. A simulation study suggests that CASh offers more power than t-test for the detection of differential gene expression variability. Conclusion CASh is successfully applied to gene expression analysis of a data-set where the joint expression behavior of genes may be critical to characterize the expression response to air pollution. We demonstrate a synergistic effect between coalitional games and statistics that resulted in a selection of genes with a potential impact in the regulation of complex pathways. oui

• Creating and improving detoxification pathways for interpretation of toxicogenomics data

  Authors: Pieter Giesbertz, Jonas Hummel, Stan Gaj, Danyel Jennen, Thomas Kelder, Chris Evelo, Joost van Delft, Jos Kleinjans

  Nature Precedings.

  Current high-throughput technology in genomics creates a large amount of biological data. Bioinformatics approaches are directed towards understanding such data on a systems biology level. AdvancedCurrent high-throughput technology in genomics creates a large amount of biological data. Bioinformatics approaches are directed towards understanding such data on a systems biology level. Advanced mathematical methods like principal component analysis, clustering, neural networks, support vector machine (SVM) approaches and neural networks can help to find patterns in the data. However, to really understand the data the patterns must be combined with existing knowledge. One of the approaches to do so is to associate these data to functional classifications such as can be found in the Gene Ontology. Other methods focus on using biological pathways coming from both public and private pathway databases like KEGG, WikiPathways, Reactome, and MetaCore. Some of these pathway databases contain rather aspecific information about which genes are involved in reactions. A single identifier, like an Enzyme Code, may correspond to a full family of enzymes, whereas only one family member is responsible for the reaction in the given biological context. Another problem arises in the availability of relevant biological pathways for both rodents and humans. This is especially true in the field of toxicology, where many pathways are still lacking. The focus of this project was to create phase I and phase II detoxification pathways using PathVisio, the pathway editor of WikiPathways. New pathway content was generated using information obtained from several trusted resources: a) handbooks, b) manual/automated PubMed literature searches; c) online pathway resources; d) UniProt Knowledgebase; e) EnsEMBL; f) GeneCards. In addition, the content of some existing toxicology pathways was improved. To illustrate the usefulness of the new pathways data from experiments with carcinogenic compounds were retrieved from the main online microarray data repositories Gene Expression Omnibus (GEO) and ArrayExpress. The resulting data were visualized on the new pathways using PathVisio. All these pathways are made available to the community at WikiPathways, where they can be further used for statistical pathway analysis and visualization in the (toxico)genomics field.

• Differences in HPRT mutant frequency among middle-aged Flemish women in association with area of residence and blood lead levels.

  Authors: Nicolas Van Larebeke, Gudrun Koppen, Vera Nelen, Greet Schoeters, Herman Van Loon, Harma Albering, Louk Riga, Robert Vlietinck, Jos Kleinjans

  Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals. 9(1):71-84.

  Biomarkers were measured in residents of Wilrijk and Hoboken, industrial suburbs of the city of Antwerp, and of Peer, a rural municipality in Flanders, Belgium. Persons with known occupationalBiomarkers were measured in residents of Wilrijk and Hoboken, industrial suburbs of the city of Antwerp, and of Peer, a rural municipality in Flanders, Belgium. Persons with known occupational exposures to toxic compounds or commuting over long distances were excluded. Here, we report the hypoxanthine phosphoribosyltransferase gene (HPRT) variant frequencies for 99 non-smoking women aged 50-65 years. HPRT values above the detection limit (V(fpos) values) were observed for 43 subjects (21 from Peer, 22 from Antwerp). The median (10th to 90th percentiles) HPRT variant frequency (V(fpos)) in peripheral lymphocytes was 9.59 (3.44-56.99) for Peer and 3.57 (1.57-13.96) for Antwerp. The V(fpos) value was significantly higher in Peer than in Antwerp, both in terms of crude data (p=0.011) and after correction for age, level of education, smoking status, serum level of selenium and body mass index through analysis of covariance (p=0.011). For the total study population, serum lead concentration showed a non-significant positive correlation with lnV(fpos). In addition, subjects with a blood lead concentration above the median tended to have higher V(fpos) values (9.45x10(-6) for 'high' group versus 5.21x10(-6) for 'low' group; p=0.077 after correction for confounding). Subjects with a serum selenium level above the median tended to have lower V(fpos) values (4.99x10(-6) for 'high' group versus 9.83x10(-6) for 'low' group; p=0.051 after correction for confounding). These data are consistent with an indirect genotoxic effect of lead and with an antimutagenic effect of selenium.