A long-term goal of numerous research projects is to identify biomarkers for in vitro systems predicting toxicity in vivo. Often, transcriptomics data are used to identify candidates for further evaluation. However, a systematic directory summarizing key features of chemically influenced genes in human hepatocytes is not yet available. To bridge this gap, we used the Open TG-GATES database with Affymetrix files of cultivated human hepatocytes incubated with chemicals, further sets of gene array data with hepatocytes from human donors generated in this study, and publicly available genome-wide datasets of human liver tissue from patients with non-alcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular cancer (HCC). After a curation procedure, expression data of 143 chemicals were included into a comprehensive biostatistical analysis. The results are summarized in the publicly available toxicotranscriptomics directory (http://wiki.toxbank.net/toxicogenomics-map/) which provides information for all genes whether they are up- or downregulated by chemicals and, if yes, by which compounds. The directory also informs about the following key features of chemically influenced genes: (1) Stereotypical stress response. When chemicals induce strong expression alterations, this usually includes a complex but highly reproducible pattern named 'stereotypical response.' On the other hand, more specific expression responses exist that are induced only by individual compounds or small numbers of compounds. The directory differentiates if the gene is part of the stereotypical stress response or if it represents a more specific reaction. (2) Liver disease-associated genes. Approximately 20 % of the genes influenced by chemicals are up- or downregulated, also in liver disease. Liver disease genes deregulated in cirrhosis, HCC, and NASH that overlap with genes of the aforementioned stereotypical chemical stress response include CYP3A7, normally expressed in fetal liver; the phase II metabolizing enzyme SULT1C2; ALDH8A1, known to generate the ligand of RXR, one of the master regulators of gene expression in the liver; and several genes involved in normal liver functions: CPS1, PCK1, SLC2A2, CYP8B1, CYP4A11, ABCA8, and ADH4. (3) Unstable baseline genes. The process of isolating and the cultivation of hepatocytes was sufficient to induce some stress leading to alterations in the expression of genes, the so-called unstable baseline genes. (4) Biological function. Although more than 2,000 genes are transcriptionally influenced by chemicals, they can be assigned to a relatively small group of biological functions, including energy and lipid metabolism, inflammation and immune response, protein modification, endogenous and xenobiotic metabolism, cytoskeletal organization, stress response, and DNA repair. In conclusion, the introduced toxicotranscriptomics directory offers a basis for a rationale choice of candidate genes for biomarker evaluation studies and represents an easy to use source of background information on chemically infl...

The undecapeptide ciclosporin is used as immunosuppressant after organ transplantation and for therapy of immune diseases. Low and variable bioavailability of ciclosporin has been attributed to its metabolism in the small intestine. The aim of the present study was to investigate drug interactions and interindividual variability of ciclosporin metabolism in the small intestine. Ciclosporin metabolism was studied in vitro using microsomes isolated from the small intestine of humans and pigs. The metabolites generated were quantified by HPLC and identified by mass spectrometry. Using specific antibodies and inhibitors, we showed that, as in the liver, cytochrome P450 3A (CYP 3A) enzymes are responsible for ciclosporin metabolism in the human small intestine. Of the 28 xenobiotics included in the study, 16 drugs, all well-known CYP 3A inhibitors, inhibited ciclosporin metabolism in the small intestine. In the small intestine of different patients, the rate of metabolism varied by a factor of 10. Ciclosporin was metabolized faster by small intestine microsomes from female (n = 4) than from male (n = 10) patients (p < 0.009).

1. Certain chemicals and drugs in addition to metabolically activated carcinogens are substrates for intestinal cytochrome P450s (CYPs) and a number of cell lines are available which could be used in metabolism studies. These include the rat duodenal cell line IEC 6, rat ileal IEC 18, foetal human HuTu 80, foetal human small intestinal FHS 74, human duodenal HCT 8 and human colon CaCo-2 cells, but they lack thorough biochemical characterization. 2. The aim of the present study was therefore to investigate the mRNA and protein expression of CYP1A1, CYP1A2, CYP2C9/10, CYP2E1 and CYP3A. In addition, the metabolism of the immunosuppressant drug tacrolimus and of the procarcinogen 7,12-dimethyl-benz[a]anthracene (DMBA) was studied to obtain information on the functional activity on these cell lines. 3. Of all the cell lines tested only CaCo-2 cells expressed CYP1A1 at the protein and mRNA level, but the CYP2E1 and CYP3A protein was also detected in CaCo-2 and FHS 74 cells. It is of considerable interest that none of the other cell lines expressed CYP1A1, CYP1A2, CYP2C9/10 or CYP3A4 at the protein and mRNA level. 4. When the metabolism of DMBA (a model carcinogen) was studied, CaCo-2 cells produced the following metabolites: 7,12-dihydroxymethylbenz[a]anthracene, 7,12-dimethylbenz-[a]anthracene-di-hydrodiol, 7-methyl-12-hydroxymethylbenz[a]anthracene, 7-hydroxy-methyl-12-benz[a]anthracene and possibly the dihydrated product of the latter two derivatives. 5. CaCo-2 cells also catalysed the metabolism of the immunosuppressant drug tacrolimus resulting in the formation of 13-O-demethyl-tacrolimus bisdemethyl-hydroxy-tacrolimus and demethyl-dihydroxy-tacrolimus. Neither the foetal human small intestinal FHS 74 cell line nor any of the other cell lines were able to catalyse the biotransformation of tacrolimus. 6. In conclusion, only CaCo-2 cells were able to produce metabolites similar to those observed in in vivo metabolism studies, whereas all other cell lines were metabolically incompetent. Therefore, this cell line may be used in studies of intestinal biotransformation.