The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Laura Suter - One of the best experts on this subject based on the ideXlab platform.
-
Research Gene Expression Analysis of the Hepatotoxicant Methapyrilene in Primary Rat Hepatocytes: An Interlaboratory Study
2013Co-Authors: Johanna M. Beekman, Franziska Boess, Arno Kalkuhl, Laura Suter, Heinrich Hildebr, F. Hoffmann-laAbstract:Genomics technologies are used in several disciplines, including toxicology. However, these technologies are relatively new, and their applications require further investigations. When investigators apply these technologies to in vitro experiments, two major issues need to be clarified: a) can in vitro toxicity studies, in combination with genomics analyses, be used to predict the toxicity of a compound; and b) are the generated toxicogenomics data reproducible between laboratories? These questions were addressed by an interlaboratory study with laboratories of four pharmaceutical companies. We evaluated gene expression patterns from cultured rat primary hepatocytes after a 24-hr incubation with Methapyrilene (MP). Extensive data analysis showed that comparison of genomics data from different sources is complex because both experimental and statistical variability are important confounding factors. However, appropriate statistical tools allowed us to use gene expression profiles to distinguish high-dose–treated cells from vehicle-treated cells. Moreover, we correctly identified MP in an independently generated in vitro database, underlining that in vitro toxicogenomics could be a predictive tool for toxicity. From a mechanistic point of view, despite the observed site-to-site variability, there was good concordance regarding the affected biologic processes. Several subsets of regulated genes were obtained by analyzing the data sets with one method or using different statistical analysis methods. The identified genes are involved in cellular processes that are associated to the exposure of primary hepatocytes to MP. Whether they are specific for MP and are cause or consequence of the toxicity requires further investigations. Key words: hepatotoxicity, interlaboratory study, Methapyrilene, microarray, rat hepatocytes, toxicogenomics. Environ Health Perspect 114:92–99 (2006). doi:10.1289/ehp.7915 available vi
-
Venn diagram depicting the differentially expressed genes of each company’s experiments determined by its own analysis strategy
2011Co-Authors: Johanna M. Beekman, Franziska Boess, Heinrich Hildebrand, Arno Kalkuhl, Laura SuterAbstract:Copyright information:Taken from "Gene Expression Analysis of the Hepatotoxicant Methapyrilene in Primary Rat Hepatocytes: An Interlaboratory Study"Environmental Health Perspectives 2005;114(1):92-99.Published online 12 Aug 2005PMCID:PMC1332662.This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original DOI.
-
gene expression analysis of the hepatotoxicant Methapyrilene in primary rat hepatocytes an interlaboratory study
Environmental Health Perspectives, 2006Co-Authors: Johanna M. Beekman, Franziska Boess, Heinrich Hildebrand, Arno Kalkuhl, Laura SuterAbstract:Genomics technologies are used in several disciplines, including toxicology. However, these technologies are relatively new, and their applications require further investigations. When investigators apply these technologies to in vitro experiments, two major issues need to be clarified: a) can in vitro toxicity studies, in combination with genomics analyses, be used to predict the toxicity of a compound; and b) are the generated toxicogenomics data reproducible between laboratories? These questions were addressed by an interlaboratory study with laboratories of four pharmaceutical companies. We evaluated gene expression patterns from cultured rat primary hepatocytes after a 24-hr incubation with Methapyrilene (MP). Extensive data analysis showed that comparison of genomics data from different sources is complex because both experimental and statistical variability are important confounding factors. However, appropriate statistical tools allowed us to use gene expression profiles to distinguish high-dose-treated cells from vehicle-treated cells. Moreover, we correctly identified MP in an independently generated in vitro database, underlining that in vitro toxicogenomics could be a predictive tool for toxicity. From a mechanistic point of view, despite the observed site-to-site variability, there was good concordance regarding the affected biologic processes. Several subsets of regulated genes were obtained by analyzing the data sets with one method or using different statistical analysis methods. The identified genes are involved in cellular processes that are associated to the exposure of primary hepatocytes to MP. Whether they are specific for MP and are cause or consequence of the toxicity requires further investigations.
-
interlaboratory evaluation of rat hepatic gene expression changes induced by Methapyrilene
Environmental Health Perspectives, 2004Co-Authors: Jeffrey F Waring, Johanna M. Beekman, Arno Kalkuhl, Roger G Ulrich, Nick Flint, David Morfitt, Frank Staedtler, Michael T Lawton, Laura SuterAbstract:Several studies using microarrays have shown that changes in gene expression provide information about the mechanism of toxicity induced by xenobiotic agents. Nevertheless, the issue of whether gene expression profiles are reproducible across different laboratories remains to be determined. To address this question, several members of the Hepatotoxicity Working Group of the International Life Sciences Institute Health and Environmental Sciences Institute evaluated the liver gene expression profiles of rats treated with Methapyrilene (MP). Animals were treated at one facility, and RNA was distributed to five different sites for gene expression analysis. A preliminary evaluation of the number of modulated genes uncovered striking differences between the five different sites. However, additional data analysis demonstrated that these differences had an effect on the absolute gene expression results but not on the outcome of the study. For all users, unsupervised algorithms showed that gene expression allows the distinction of the high dose of MP from controls and low dose. In addition, the use of a supervised analysis method (support vector machines) made it possible to correctly classify samples. In conclusion, the results show that, despite some variability, robust gene expression changes were consistent between sites. In addition, key expression changes related to the mechanism of MP-induced hepatotoxicity were identified. These results provide critical information regarding the consistency of microarray results across different laboratories and shed light on the strengths and limitations of expression profiling in drug safety analysis.
Igor P Pogribny - One of the best experts on this subject based on the ideXlab platform.
-
effect of aflatoxin b1 benzo a pyrene and Methapyrilene on transcriptomic and epigenetic alterations in human liver heparg cells
Food and Chemical Toxicology, 2018Co-Authors: Volodymyr Tryndyak, Iryna Kindrat, Kostiantyn Dreval, Frederick A Beland, Mona I Churchwell, Igor P PogribnyAbstract:Abstract The increasing number of man-made chemicals in the environment that may pose a carcinogenic risk highlights the need for developing reliable time- and cost-effective approaches for carcinogen detection and identification. To address this issue, we investigated the utility of high-throughput microarray gene expression and next-generation genome-wide DNA methylation sequencing for the in vitro identification of genotoxic and non-genotoxic carcinogens. Terminally differentiated and metabolically competent human liver HepaRG cells were treated at minimally cytotoxic concentrations of (i) the genotoxic human liver carcinogen aflatoxin B1 (AFB1) and its structural non-carcinogenic analog aflatoxin B2 (AFB2); (ii) the genotoxic human lung carcinogen benzo[a]pyrene (B[a]P) and its non-carcinogenic isomer benzo[e]pyrene (B[e]P); and (iii) the non-genotoxic liver carcinogen Methapyrilene for 72 h and transcriptomic and DNA methylation profiles were examined. Treatment of HepaRG cells with the liver carcinogens AFB1 and Methapyrilene generated distinct gene-expression profiles, whereas B[a]P had only a slight effect on gene expression. In contrast to transcriptomic alterations, treatment of HepaRG cells with the carcinogenic and non-carcinogenic chemicals resulted in profound changes in the DNA methylation footprint; however, the correlation between gene-specific DNA methylation and gene expression changes was minimal. Among the carcinogen-altered genes, transferrin (TF) emerged as sensitive marker for an initial screening of chemicals for their potential liver carcinogenicity. Potential liver carcinogens (i.e., chemicals causing altered TF gene expression) could then be subjected to gene-expression analyses to differentiate genotoxic from non-genotoxic liver carcinogens. This approach may substantially enhance the identification and assessment of potential liver carcinogens.
-
effect of Methapyrilene hydrochloride on hepatic intracellular iron metabolism in vivo and in vitro
Toxicology Letters, 2017Co-Authors: Iryna Kindrat, Kostiantyn Dreval, Svitlana Shpyleva, Volodymyr Tryndyak, Aline De Conti, Thilak K Mudalige, Tao Chen, Anna M Erstenyuk, Frederick A Beland, Igor P PogribnyAbstract:The liver, a central detoxification organ and main regulator of systemic iron homeostasis, is prone to damage by xenobiotics. In the present study, we investigated the effect of the hepatotoxicant and hepatocarcinogen Methapyrilene hydrochloride on iron metabolism in rat liver in a repeat-dose in vivo toxicity study and in human HepaRG cells in vitro. Treatment of male Fischer 344 (F344) rats with Methapyrilene at doses 40 and 80mg/kg body weight (bw)/day by gavage for 6 weeks resulted in changes in the expression of classic hepatotoxicity-related marker genes and iron homeostasis-related genes, especially a prominent, dose-dependent down-regulation of the transferrin (Tf) gene and an up-regulation of the ferritin, light chain (Ftl) gene. A decrease in the level of TF and an increase in the level of FTL also occurred in Methapyrilene-treated differentiated HepaRG cells, indicating the existence of interspecies and in vitro-in vivo similarities in the disturbance of cellular iron homeostasis upon liver injury. In contrast, there was minimal overlap in the expression of liver toxicity-marker genes in the livers of rats and in HepaRG cells treated with Methapyrilene. Importantly, the decrease of transferrin at mRNA and protein levels occurred after the treatment with a low dose of Methapyrilene that exhibited minimal cytotoxicity. These results demonstrate the significance of the dysregulation of hepatic iron metabolism in the pathogenesis and mechanism of chemical-induced liver toxicity and suggest that these changes may be sensitive and useful indicators of potentially hepatotoxic chemicals.
-
editor s highlight organ specific epigenetic changes induced by the nongenotoxic liver carcinogen Methapyrilene in fischer 344 rats
Toxicological Sciences, 2016Co-Authors: Svitlana Shpyleva, Iryna Kindrat, Kostiantyn Dreval, Aline De Conti, Tao Chen, Frederick A Beland, Stepan Melnyk, Jian Yan, Igor P PogribnyAbstract:Continuous lifetime exposure to certain natural and man-made chemicals is a major cause of cancers in humans; therefore, evaluating the carcinogenic risks of chemicals remains important. Currently, substantial progress has been made in identification of genotoxic carcinogens; in contrast, predicting the carcinogenic potential of nongenotoxic compounds is a challenge due to many different modes of action that may lead to tumorigenesis. In the present study, we investigated the effects of the nongenotoxic liver carcinogen Methapyrilene and the nongenotoxic noncarcinogen usnic acid, at doses that do not exhibit organ cytotoxicity, on epigenomic alterations in the livers and kidneys of Fischer 344 (F344) rats. We demonstrate that a repeat-dose oral treatment of male F344 rats with Methapyrilene for 6 weeks caused target organ-specific epigenetic alterations in the livers. In contrast, only very slight epigenetic changes were found in the livers of F344 rats treated with hepatotoxicant, but noncarcinogen, usnic acid. The Methapyrilene-induced epigenetic changes consisted of changes in histone lysine acetylation and methylation, with the greatest increase occurring in global and gene-specific histone H3 lysine 9 (H3K9) deacetylation. Importantly, the results of the present study show an association between gene-specific histone H3K9 deacetylation and a reduced expression of critical cancer-related genes, including prospero homeobox 1 (Prox1), HNF1 homebox A (Hnf1a), and peroxisome proliferator activated receptor alpha (Ppara), which provides a mechanistic link between Methapyrilene-induced epigenetic aberrations and liver carcinogenesis.
Johanna M. Beekman - One of the best experts on this subject based on the ideXlab platform.
-
Research Gene Expression Analysis of the Hepatotoxicant Methapyrilene in Primary Rat Hepatocytes: An Interlaboratory Study
2013Co-Authors: Johanna M. Beekman, Franziska Boess, Arno Kalkuhl, Laura Suter, Heinrich Hildebr, F. Hoffmann-laAbstract:Genomics technologies are used in several disciplines, including toxicology. However, these technologies are relatively new, and their applications require further investigations. When investigators apply these technologies to in vitro experiments, two major issues need to be clarified: a) can in vitro toxicity studies, in combination with genomics analyses, be used to predict the toxicity of a compound; and b) are the generated toxicogenomics data reproducible between laboratories? These questions were addressed by an interlaboratory study with laboratories of four pharmaceutical companies. We evaluated gene expression patterns from cultured rat primary hepatocytes after a 24-hr incubation with Methapyrilene (MP). Extensive data analysis showed that comparison of genomics data from different sources is complex because both experimental and statistical variability are important confounding factors. However, appropriate statistical tools allowed us to use gene expression profiles to distinguish high-dose–treated cells from vehicle-treated cells. Moreover, we correctly identified MP in an independently generated in vitro database, underlining that in vitro toxicogenomics could be a predictive tool for toxicity. From a mechanistic point of view, despite the observed site-to-site variability, there was good concordance regarding the affected biologic processes. Several subsets of regulated genes were obtained by analyzing the data sets with one method or using different statistical analysis methods. The identified genes are involved in cellular processes that are associated to the exposure of primary hepatocytes to MP. Whether they are specific for MP and are cause or consequence of the toxicity requires further investigations. Key words: hepatotoxicity, interlaboratory study, Methapyrilene, microarray, rat hepatocytes, toxicogenomics. Environ Health Perspect 114:92–99 (2006). doi:10.1289/ehp.7915 available vi
-
Venn diagram depicting the differentially expressed genes of each company’s experiments determined by its own analysis strategy
2011Co-Authors: Johanna M. Beekman, Franziska Boess, Heinrich Hildebrand, Arno Kalkuhl, Laura SuterAbstract:Copyright information:Taken from "Gene Expression Analysis of the Hepatotoxicant Methapyrilene in Primary Rat Hepatocytes: An Interlaboratory Study"Environmental Health Perspectives 2005;114(1):92-99.Published online 12 Aug 2005PMCID:PMC1332662.This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original DOI.
-
gene expression analysis of the hepatotoxicant Methapyrilene in primary rat hepatocytes an interlaboratory study
Environmental Health Perspectives, 2006Co-Authors: Johanna M. Beekman, Franziska Boess, Heinrich Hildebrand, Arno Kalkuhl, Laura SuterAbstract:Genomics technologies are used in several disciplines, including toxicology. However, these technologies are relatively new, and their applications require further investigations. When investigators apply these technologies to in vitro experiments, two major issues need to be clarified: a) can in vitro toxicity studies, in combination with genomics analyses, be used to predict the toxicity of a compound; and b) are the generated toxicogenomics data reproducible between laboratories? These questions were addressed by an interlaboratory study with laboratories of four pharmaceutical companies. We evaluated gene expression patterns from cultured rat primary hepatocytes after a 24-hr incubation with Methapyrilene (MP). Extensive data analysis showed that comparison of genomics data from different sources is complex because both experimental and statistical variability are important confounding factors. However, appropriate statistical tools allowed us to use gene expression profiles to distinguish high-dose-treated cells from vehicle-treated cells. Moreover, we correctly identified MP in an independently generated in vitro database, underlining that in vitro toxicogenomics could be a predictive tool for toxicity. From a mechanistic point of view, despite the observed site-to-site variability, there was good concordance regarding the affected biologic processes. Several subsets of regulated genes were obtained by analyzing the data sets with one method or using different statistical analysis methods. The identified genes are involved in cellular processes that are associated to the exposure of primary hepatocytes to MP. Whether they are specific for MP and are cause or consequence of the toxicity requires further investigations.
-
interlaboratory evaluation of rat hepatic gene expression changes induced by Methapyrilene
Environmental Health Perspectives, 2004Co-Authors: Jeffrey F Waring, Johanna M. Beekman, Arno Kalkuhl, Roger G Ulrich, Nick Flint, David Morfitt, Frank Staedtler, Michael T Lawton, Laura SuterAbstract:Several studies using microarrays have shown that changes in gene expression provide information about the mechanism of toxicity induced by xenobiotic agents. Nevertheless, the issue of whether gene expression profiles are reproducible across different laboratories remains to be determined. To address this question, several members of the Hepatotoxicity Working Group of the International Life Sciences Institute Health and Environmental Sciences Institute evaluated the liver gene expression profiles of rats treated with Methapyrilene (MP). Animals were treated at one facility, and RNA was distributed to five different sites for gene expression analysis. A preliminary evaluation of the number of modulated genes uncovered striking differences between the five different sites. However, additional data analysis demonstrated that these differences had an effect on the absolute gene expression results but not on the outcome of the study. For all users, unsupervised algorithms showed that gene expression allows the distinction of the high dose of MP from controls and low dose. In addition, the use of a supervised analysis method (support vector machines) made it possible to correctly classify samples. In conclusion, the results show that, despite some variability, robust gene expression changes were consistent between sites. In addition, key expression changes related to the mechanism of MP-induced hepatotoxicity were identified. These results provide critical information regarding the consistency of microarray results across different laboratories and shed light on the strengths and limitations of expression profiling in drug safety analysis.
Frank C Richardson - One of the best experts on this subject based on the ideXlab platform.
-
dose responses in rat hepatic protein modification and expression following exposure to the rat hepatocarcinogen Methapyrilene
Carcinogenesis, 1994Co-Authors: Frank C Richardson, D M Horn, N L AndersonAbstract:Dose-related effects of Methapyrilene (MP) on protein modification and expression were examined using two-dimensional gel electrophoresis (2-D PAGE) coupled with computer analysis. Methapyrilene was administered ad libitum at doses of 0, 62.5, 125, 250 and 1000 p.p.m. to male F-344 rats for 12 weeks beginning at 8 weeks of age. Following treatment, livers were removed and frozen for 2-D PAGE analysis. Separation of hepatic proteins was conducted using ISO-DALT technology. Changes in abundance and modification of hepatic proteins were determined using the Kepler software package. Covalent modifications of three specific mitochondrial proteins were quantified using a charge modification index. Dose-response relationships were analyzed using Tukey's trend test. Results demonstrated that covalent modification of the three mitochondrial proteins was linearly related to dose and that a dose effect could be found at all dose levels in 2 out of 3 proteins. Two forms of change in protein expression were observed: (i) a dose-dependent change with effects at all doses and (ii) a change only at the toxic dose of 1000 p.p.m. MP. These results demonstrate a molecular effect of MP at doses that do not produce cellular responses including toxicity or increases in cell replication suggesting that these specific mitochondrial modifications are molecular dosimeters but are probably not direct factors and/or sufficient factors in carcinogenesis. This study also demonstrates the potential use of 2-D PAGE electrophoresis to delineate the effect of dose on expression of specific proteins.
-
effects of Methapyrilene on dna synthesis in mice and rats following continuous dietary exposure
Carcinogenesis, 1992Co-Authors: Frank C Richardson, Deborah M Copple, P I EachoAbstract:The effects of the antihistamine Methapyrilene (MP) on DNA synthesis in rats and mice were investigated. Previous studies have demonstrated a dose response for tumor induction in the rat but no carcinogenic effect in the mouse. To study the role of DNA synthesis in MP carcinogenesis, rats and mice were administered MP at doses of 0, 62.5, 125, 250 or 1000 p.p.m. in the diet for a period of 1-12 weeks. Bromodeoxyuridine was administered continuously using an osmotic minipump during the last week of treatment to provide an index of DNA synthesis. Results demonstrated that in the rat 250 and 1000 p.p.m. MP increased DNA synthesis in a dose-dependent manner that correlated with the tumor response in previous oncogenic studies. MP at 62.5 p.p.m. did not increase DNA synthesis, indicating a no effect level for cell proliferation and suggesting a no effect level for carcinogenicity by this compound in the rat. MP did not induce DNA synthesis in mice after exposure to 1000 p.p.m. for 12 weeks, nor did it induce changes in serum chemistries or liver histopathology suggestive of overt toxicity as was seen in the rat at 1000 p.p.m. The correlations between labeling index and tumorigenicity in the rat and mouse strongly support a role of cell proliferation in the carcinogenic mechanism of MP.
-
effects of methrpyrilene measured in mitochondria isolated from naive and Methapyrilene treated rat and mouse hepatocytes
Toxicology and Applied Pharmacology, 1992Co-Authors: Deborah M Copple, Glenn F Rush, Frank C RichardsonAbstract:Methapyrilene (MP) is a rat-specific liver carcinogen that alters mitochondrial number and morphology both in vivo and in vitro. This biological phenomenon may be due to the effects of MP on mitochondrial function. To test this hypothesis, studies were conducted to examine the effects of MP on DNA and protein synthesis and respiration in isolated mitochondria. DNA and protein synthesis activities were measured using [3H]thymidine and [3H]leucine incorporation. Mouse liver mitochondria were also examined for comparison since no tumor formation or alterations in mitochondrial morphology have been associated with MP treatment in mice. A signicant decrease in basal DNA and protein synthesis levels was observed in mitochondria isolated from rats and mice following in vivo MP treatment. This effect could not be reproduced when mitochondria were exposed to 0 or 100 μm MP following isolation, despite the presence of an S9 activation system. Electron microscopic examinations were performed on isolated rat mitochondria and revealed morphologic differences between mitochondria from naive and MP-treated rats. Although significant differences in State 3 and State 4 respiratory rates were noted, the respiratory control ratio, ADPO ratio, and uncoupler-stimulated respiratory rates were unaffected. Results demonstrate that: (1) MP irreversibly depresses DNA and protein synthesis in a majority of mitochondria, despite only localized morphologic changes; (2) these changes are not reflected by a decrease in respiratory function; and (3) depression of DNA and protein synthesis does not correlate with carcinogenic susceptibility.
Arno Kalkuhl - One of the best experts on this subject based on the ideXlab platform.
-
Research Gene Expression Analysis of the Hepatotoxicant Methapyrilene in Primary Rat Hepatocytes: An Interlaboratory Study
2013Co-Authors: Johanna M. Beekman, Franziska Boess, Arno Kalkuhl, Laura Suter, Heinrich Hildebr, F. Hoffmann-laAbstract:Genomics technologies are used in several disciplines, including toxicology. However, these technologies are relatively new, and their applications require further investigations. When investigators apply these technologies to in vitro experiments, two major issues need to be clarified: a) can in vitro toxicity studies, in combination with genomics analyses, be used to predict the toxicity of a compound; and b) are the generated toxicogenomics data reproducible between laboratories? These questions were addressed by an interlaboratory study with laboratories of four pharmaceutical companies. We evaluated gene expression patterns from cultured rat primary hepatocytes after a 24-hr incubation with Methapyrilene (MP). Extensive data analysis showed that comparison of genomics data from different sources is complex because both experimental and statistical variability are important confounding factors. However, appropriate statistical tools allowed us to use gene expression profiles to distinguish high-dose–treated cells from vehicle-treated cells. Moreover, we correctly identified MP in an independently generated in vitro database, underlining that in vitro toxicogenomics could be a predictive tool for toxicity. From a mechanistic point of view, despite the observed site-to-site variability, there was good concordance regarding the affected biologic processes. Several subsets of regulated genes were obtained by analyzing the data sets with one method or using different statistical analysis methods. The identified genes are involved in cellular processes that are associated to the exposure of primary hepatocytes to MP. Whether they are specific for MP and are cause or consequence of the toxicity requires further investigations. Key words: hepatotoxicity, interlaboratory study, Methapyrilene, microarray, rat hepatocytes, toxicogenomics. Environ Health Perspect 114:92–99 (2006). doi:10.1289/ehp.7915 available vi
-
Venn diagram depicting the differentially expressed genes of each company’s experiments determined by its own analysis strategy
2011Co-Authors: Johanna M. Beekman, Franziska Boess, Heinrich Hildebrand, Arno Kalkuhl, Laura SuterAbstract:Copyright information:Taken from "Gene Expression Analysis of the Hepatotoxicant Methapyrilene in Primary Rat Hepatocytes: An Interlaboratory Study"Environmental Health Perspectives 2005;114(1):92-99.Published online 12 Aug 2005PMCID:PMC1332662.This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original DOI.
-
gene expression analysis of the hepatotoxicant Methapyrilene in primary rat hepatocytes an interlaboratory study
Environmental Health Perspectives, 2006Co-Authors: Johanna M. Beekman, Franziska Boess, Heinrich Hildebrand, Arno Kalkuhl, Laura SuterAbstract:Genomics technologies are used in several disciplines, including toxicology. However, these technologies are relatively new, and their applications require further investigations. When investigators apply these technologies to in vitro experiments, two major issues need to be clarified: a) can in vitro toxicity studies, in combination with genomics analyses, be used to predict the toxicity of a compound; and b) are the generated toxicogenomics data reproducible between laboratories? These questions were addressed by an interlaboratory study with laboratories of four pharmaceutical companies. We evaluated gene expression patterns from cultured rat primary hepatocytes after a 24-hr incubation with Methapyrilene (MP). Extensive data analysis showed that comparison of genomics data from different sources is complex because both experimental and statistical variability are important confounding factors. However, appropriate statistical tools allowed us to use gene expression profiles to distinguish high-dose-treated cells from vehicle-treated cells. Moreover, we correctly identified MP in an independently generated in vitro database, underlining that in vitro toxicogenomics could be a predictive tool for toxicity. From a mechanistic point of view, despite the observed site-to-site variability, there was good concordance regarding the affected biologic processes. Several subsets of regulated genes were obtained by analyzing the data sets with one method or using different statistical analysis methods. The identified genes are involved in cellular processes that are associated to the exposure of primary hepatocytes to MP. Whether they are specific for MP and are cause or consequence of the toxicity requires further investigations.
-
interlaboratory evaluation of rat hepatic gene expression changes induced by Methapyrilene
Environmental Health Perspectives, 2004Co-Authors: Jeffrey F Waring, Johanna M. Beekman, Arno Kalkuhl, Roger G Ulrich, Nick Flint, David Morfitt, Frank Staedtler, Michael T Lawton, Laura SuterAbstract:Several studies using microarrays have shown that changes in gene expression provide information about the mechanism of toxicity induced by xenobiotic agents. Nevertheless, the issue of whether gene expression profiles are reproducible across different laboratories remains to be determined. To address this question, several members of the Hepatotoxicity Working Group of the International Life Sciences Institute Health and Environmental Sciences Institute evaluated the liver gene expression profiles of rats treated with Methapyrilene (MP). Animals were treated at one facility, and RNA was distributed to five different sites for gene expression analysis. A preliminary evaluation of the number of modulated genes uncovered striking differences between the five different sites. However, additional data analysis demonstrated that these differences had an effect on the absolute gene expression results but not on the outcome of the study. For all users, unsupervised algorithms showed that gene expression allows the distinction of the high dose of MP from controls and low dose. In addition, the use of a supervised analysis method (support vector machines) made it possible to correctly classify samples. In conclusion, the results show that, despite some variability, robust gene expression changes were consistent between sites. In addition, key expression changes related to the mechanism of MP-induced hepatotoxicity were identified. These results provide critical information regarding the consistency of microarray results across different laboratories and shed light on the strengths and limitations of expression profiling in drug safety analysis.