Tessa E. Pronk

Exploring the zebrafish embryo as an alternative model for the evaluation of liver toxicity by histopathology and expression profiling

The whole zebrafish embryo model (ZFE) has proven its applicability in developmental toxicity testing. Since functional hepatocytes are already present from 36 h post fertilization onwards, whole ZFE have been proposed as an attractive alternative to mammalian in vivo models in hepatotoxicity testing. The goal of the present study is to further underpin the applicability of whole ZFE for hepatotoxicity testing by combining histopathology and next-generation sequencing-based gene expression profiling. To this aim, whole ZFE and adult zebrafish were exposed to a set of hepatotoxic reference compounds. Histopathology revealed compound and life-stage-specific effects indicative of toxic injury in livers of whole ZFE and adult zebrafish. Next-generation sequencing (NGS) was used to compare transcript profiles in pooled individual RNA samples of whole ZFE and livers of adult zebrafish. This revealed that hepatotoxicity-associated expression can be detected beyond the overall transcription noise in the whole embryo. In situ hybridization verified liver specificity of selected highly expressed markers in whole ZFE. Finally, cyclosporine A (CsA) was used as an illustrative case to support applicability of ZFE in hepatotoxicity testing by comparing CsA-induced gene expression between ZFE, in vivo mouse liver and HepaRG cells on the levels of single genes, pathways and transcription factors. While there was no clear overlap on single gene level between the whole ZFE and in vivo mouse liver, strong similarities were observed between whole ZFE and in vivo mouse liver in regulated pathways related to hepatotoxicity, as well as in relevant overrepresented transcription factors. In conclusion, both the use of NGS of pooled RNA extracts analysis combined with histopathology and traditional microarray in single case showed the potential to detect liver-related genes and processes within the transcriptome of a whole zebrafish embryo. This supports the applicability of the whole ZFE model for compound-induced hepatotoxicity screening.

Applicability of a keratinocyte gene signature to predict skin sensitizing potential

There is a need to replace animal tests for the identification of skin sensitizers and currently many alternative assays are being developed that have very promising results. In this study a gene signature capable of very accurate identification of sensitizers was established in the HaCaT human keratinocyte cell line. This signature was evaluated in a separate study using six chemicals that are either local lymph node (LLNA) false-positive or false-negative chemicals in addition to nine sensitizers and four non-sensitizers. Similar studies do not apply these more difficult to classify chemicals, which show the true potential for human predictions of an assay. Although the gene signature has improved prediction accuracy compared to the LLNA, the misclassified compounds were comparable between the two assays. Gene profiling also showed a sensitizer specific response of the Nrf2-keap1 and Toll-like receptor signaling pathways. After exposure to non-sensitizing chemicals that induce either of the pathways the signature misclassified all Nrf2-inducers, while the Toll-like receptor ligands were correctly classified. In conclusion, we confirm that keratinocyte based prediction assays may provide essential information on the properties of compounds. Furthermore, chemical selection is critical for assessment of the performance of in vitro alternative assays.

Concentration-Response Analysis of Differential Gene Expression in the Zebrafish Embryotoxicity Test Following Flusilazole Exposure

The zebrafish embryotoxicity test (ZET) is considered a promising alternative model in predictive toxicology. Currently, morphological assessment of the embryo is the main readout for this assay. However, implementation of transcriptomics may help to detect more subtle effects, which may increase the sensitivity and predictability of the test. In this study, we tested a concentration response of flusilazole in the ZET. After exposure for 24 h postfertilization, microarray analysis revealed a number of processes to be regulated in a concentration-dependent way. We identified development related processes, retinol metabolism and transcription, as well as processes corresponding to the antifungal mechanism of action, steroid biosynthesis, and fatty acid metabolism, to be differentially regulated. Retinol metabolism and transcription were already significantly altered at concentrations that were not inducing morphological effects. Differential expression of genes related to steroid biosynthesis and fatty acid metabolism showed a concentration response similar to morphological response. An increase in concentration was also positively associated with an increase in magnitude of expression for individual genes within functional processes. Our study shows that transcriptomics analysis in the ZET is a more sensitive readout of compound-induced effects than morphological assessment. However, the interpretation of differential gene expression in terms of predicting morphological effects is not straightforward and requires further study.

Chemical class-specific gene expression changes in the zebrafish embryo after exposure to glycol ether alkoxy acids and 1,2,4-triazole antifungals.

The zebrafish embryotoxicity test (ZET) is an alternative test to predict embryotoxicity of substances based on morphological assessment. Implementing transcriptomics may increase sensitivity and objectivity of the test system. We applied the category approach to compare effects of compounds from two chemical classes, the glycol ethers and 1,2,4-triazoles, on the embryo. At 24h post fertilization, microarray analysis revealed several thousands of responsive genes after glycol ether exposure, whereas the triazoles significantly regulated only several hundreds of genes. Principal component analysis of the genes commonly regulated per chemical class demonstrated that the two classes can be distinguished. Gene set enrichment analysis showed that after glycol ether exposure mainly gene sets related to development were downregulated. After triazole exposure, gene sets corresponding to previously described mechanisms of action, such as glycolysis and fatty acid metabolism were regulated. Our results demonstrate that transcriptomics in the ZET provides a more sensitive endpoint than standard morphological assessment. In addition, information about mechanisms of action of substances may become available, thereby facilitating the extrapolation of findings to mammalian species including man.

A Comparison of Gene Expression Responses in Rat Whole Embryo Culture and In Vivo: Time-Dependent Retinoic Acid-Induced Teratogenic Response

The whole embryo culture (WEC) model serves as a potential alternative for classical in vivo developmental toxicity testing. In the WEC, cultured rat embryos are exposed during neurulation and early organogenesis and evaluated for morphological effects. Toxicogenomic-based approaches may improve the predictive ability of WEC by providing molecular-based markers associated with chemical exposure, which can be compared across multiple parameters (e.g., exposure duration, developmental time, experimental model). Additionally, comparisons between in vitro and in vivo models may identify objective relevant molecular responses linked with developmental toxicity endpoints in vivo. In this study, using a transcriptomic approach, we compared all-trans retinoic acid (RA)-exposed and nonexposed Wistar rat embryos derived using WEC (RA, 0.5 μg/ml) or in vivo (RA, 50 mg/kg, oral gavage) to identify overlapping and nonoverlapping effects of RA on RNA expression in parallel with morphological changes. Across six time points (gestational day 10 + 2-48 h), we observed strong similarities in RA response at the gene (directionality, significance) and functional (e.g., embryonic development, cell differentiation) level which associated with RA-induced adverse morphological effects, including growth reduction as well as alterations in neural tube, limb, branchial, and mandible development. We observed differences between models in the timing of RA-induced effects on genes related to embryonic development and RA metabolism. These observations on the gene expression level were associated with specific differential morphological outcomes. This study supports the use of WEC to examine compound-induced molecular responses relative to in vivo and, furthermore, assists in defining the applicability domain of the WEC in determining complementary windows of sensitivity for developmental toxicological investigations.

Gene set assembly for quantitative prediction of developmental toxicity in the embryonic stem cell test.

The embryonic stem cell test (EST) is an in vitro method for predicting developmental toxicity based on compound-induced inhibition of embryonic stem cell (ESC) differentiation. We previously described how gene expression analysis in the EST can be used to describe normal ESC differentiation as well as identify compound developmental toxicity, by means of our differentiation track algorithm. In this study, we combined raw data from our three previous studies in a new integrated analysis, to identify a gene set that allows for improved prediction. By evaluating predictions of 100,000 randomly selected gene sets, we identified which genes contribute significantly to the prediction reliability. By additional cross-validation, we identified a set of 52 genes that allows for improved prediction of toxicity. The correlation between the predictions using this gene set and the magnitude of the EST endpoint was 0.85, and the gene set predicted developmental toxicity with 83% accuracy (area under the curve 89%). If compounds with ineffective data because of a too low tested concentration or too much variation between samples were excluded, even 100% accuracy could be reached based on 15 compounds. This novel gene set consists mainly of genes involved in the stem cell differentiation or other developmental processes. We expect that this set can be of use in future studies aimed at improving the EST for risk assessment, thus making a next step towards regulatory implementation of this method.

Transcriptomic analysis in the developing zebrafish embryo after compound exposure: Individual gene expression and pathway regulation

The zebrafish embryotoxicity test is a promising alternative assay for developmental toxicity. Classically, morphological assessment of the embryos is applied to evaluate the effects of compound exposure. However, by applying differential gene expression analysis the sensitivity and predictability of the test may be increased. For defining gene expression signatures of developmental toxicity, we explored the possibility of using gene expression signatures of compound exposures based on commonly expressed individual genes as well as based on regulated gene pathways. Four developmental toxic compounds were tested in concentration-response design, caffeine, carbamazepine, retinoic acid and valproic acid, and two non-embryotoxic compounds, d-mannitol and saccharin, were included. With transcriptomic analyses we were able to identify commonly expressed genes, which were mostly development related, after exposure to the embryotoxicants. We also identified gene pathways regulated by the embryotoxicants, suggestive of their modes of action. Furthermore, whereas pathways may be regulated by all compounds, individual gene expression within these pathways can differ for each compound. Overall, the present study suggests that the use of individual gene expression signatures as well as pathway regulation may be useful starting points for defining gene biomarkers for predicting embryotoxicity.

Triazole-induced gene expression changes in the zebrafish embryo

The zebrafish embryo is considered to provide a promising alternative test model for developmental toxicity testing. Most systems use morphological assessment of the embryos, however, microarray analyses may increase sensitivity and predictability of the test by detecting more subtle and detailed responses. In this study, we investigated the possibility of relating gene expression profiles of structurally similar chemicals tested in a single concentration, to a complete transcriptomic concentration-response of flusilazole (FLU). We tested five other triazoles, hexaconazole (HEX), cyproconazole (CYP), triadimefon (TDF), myclobutanil (MYC), and triticonazole (TTC) at equipotent concentrations based on morphological evaluation. Results showed that every compound had a different degree of regulation within their anti-fungal and developmental toxicity pathways, steroid biosynthesis and retinol metabolism, respectively. Assuming that the ratio between these pathways is relevant for efficacy compared to developmental toxicity, we found TTC was more efficient and CYP was more toxic compared to the other triazoles. With the approach used in this study we demonstrated that gene expression data allow more comprehensive assessment of compound effects by discriminating relative potencies using these specific gene sets. The zebrafish embryo model can therefore be considered a useful vertebrate model providing information of relevant pathways related to anti-fungal mechanism of action and toxicological activity.

Cyclosporine A treated in vitro models induce cholestasis response through comparison of phenotype-directed gene expression analysis of in vivo Cyclosporine A-induced cholestasis.

In vitro models for hepatotoxicity testing are a necessity for advancement of toxicological research. Assessing the in vitro response requires in vivo validated gene sets reflective of the hepatotoxic phenotype. Cholestasis, the impairment of bile flow, is induced in C57BL/6J mice treated with cyclosporine A (CsA) to identify phenotype reflective gene sets. CsA treatment through oral gavage for 25 days induced cholestasis, as confirmed by histopathology and serum chemistry. Over 1, 4, and 11 days of CsA exposure gradual increases in serum markers were correlated to gene expression. This phenotype-directed analysis identified gene sets specific to the onset and progression of cholestasis, such as PPAR related processes and drug metabolism, by circumventing other effects of CsA, such as immunosuppression, found in dose*time group analysis. In vivo gene sets are enriched in publicly available data sets of CsA-treated HepaRG and primary mouse hepatocytes. However, genes identified within these gene sets did not overlap between in vivo and in vitro. In vitro regulated genes represent the initial response to cholestasis, whereas in vivo genes represent the later adaptive response. We conclude that the applicability of in vitro models for hepatotoxicity testing fully depends on a solid in vivo phenotype anchored analysis.

Gene expression markers in the zebrafish embryo reflect a hepatotoxic response in animal models and humans

The zebrafish embryo (ZFE) is a promising non-rodent model in toxicology, and initial studies suggested its applicability in detecting hepatotoxic responses. Here, we hypothesize that the detailed analysis of underlying mechanisms of hepatotoxicity in ZFE contributes to the improved identification of hepatotoxic properties of new compounds and to the reduction of rodents used for screening. ZFEs were exposed to nine reference hepatotoxicants, targeted at induction of cholestasis, steatosis and necrosis, and two non-hepatotoxic controls. Histopathology revealed various specific morphological changes in the ZFE hepatocytes indicative of cell injury. Gene expression profiles of the individual compounds were generated using microarrays. Regulation of single genes and of pathways could be linked to hepatotoxic responses in general, but phenotype-specific responses could not be distinguished. Hepatotoxicity-associated pathways included xenobiotic metabolism and oxidoreduction related pathways. Overall analysis of gene expression identified a limited set of potential biomarkers specific for a common hepatotoxicity response. This set included several cytochrome P450 genes (cyp2k19, cyp4v7, cyp2aa3), genes related to liver development (pklr) and genes important in oxidoreduction processes (zgc:163022, zgc:158614, zgc:101858 and sqrdl). In conclusion, the ZFE model allows for identification of hepatotoxicants, without discrimination into specific phenotypes.