Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach

Abstract

Developmental neurotoxicity (DNT) and many forms of reproductive toxicity (RT) often manifest themselves in functional deficits that are not necessarily based on cell death, but rather on minor changes relating to cell differentiation or communication. The fields of DNT/RT would greatly benefit from in vitro tests that allow the identification of toxicant-induced changes of the cellular proteostasis, or of its underlying transcriptome network. Therefore, the ‘human embryonic stem cell (hESC)-derived novel alternative test systems (ESNATS)’ European commission research project established RT tests based on defined differentiation protocols of hESC and their progeny. Valproic acid (VPA) and methylmercury (MeHg) were used as positive control compounds to address the following fundamental questions: (1) Does transcriptome analysis allow discrimination of the two compounds? (2) How does analysis of enriched transcription factor binding sites (TFBS) and of individual probe sets (PS) distinguish between test systems? (3) Can batch effects be controlled? (4) How many DNA microarrays are needed? (5) Is the highest non-cytotoxic concentration optimal and relevant for the study of transcriptome changes? VPA triggered vast transcriptional changes, whereas MeHg altered fewer transcripts. To attenuate batch effects, analysis has been focused on the 500 PS with highest variability. The test systems differed significantly in their responses (<20 % overlap). Moreover, within one test system, little overlap between the PS changed by the two compounds has been observed. However, using TFBS enrichment, a relatively large ‘common response’ to VPA and MeHg could be distinguished from ‘compound-specific’ responses. In conclusion, the ESNATS assay battery allows classification of human DNT/RT toxicants on the basis of their transcriptome profiles.Electronic supplementary materialThe online version of this article (doi:10.1007/s00204-012-0967-3) contains supplementary material, which is available to authorized users.

Toxicogenomics directory of chemically exposed human hepatocytes

“…Gene array analysis performed on the livers of rats facilitated the differentiation between genotoxic and non-genotoxic carcinogens (Ellinger-Ziegelbauer et al 2008;. These successful toxicogenomics studies in vivo prompted several ambitious research programs, including the EU-funded SEURAT-1 network and the ESNATs project Krug et al 2013;Schug et al 2013;Weng et al 2014;Balmer et al 2014;Campos et al 2014), with the aim to identify biomarkers of toxicity in vitro. One long-term goal of these projects is to identify biomarkers in the in vitro systems that can predict certain mechanisms of toxicity in vivo.…”

Highlight report: acetaminophen hepatotoxicity

“…Currently, intensive research activities are ongoing to establish in vitro systems particularly for hepatotoxicity (Grinberg et al 2014;Ramaiahgari et al 2014;Rodrigues et al 2013;Schug et al 2013), nephrotoxicity (Sanchez-Niño et al 2014;Fujiki et al 2013;, neurotoxicity (Barbosa et al 2014;Sisnaiske et al 2014;Frimat et al 2010) and developmental toxicity (Krug et al 2013;Rempel et al 2015;Balmer et al 2014;Zimmer et al 2014). For validation of in vitro systems with hepatocytes APAP represents a popular reference compound (Jennings et al 2014;Hengstler et al 2014).…”

Highlight report: perspectives in stem cell research—unbiased quantification of the similarity between in vitro generated and primary hepatocytes

“…Particularly, in the fields of liver (Godoy et al 2013;Zellmer et al 2010;Godoy and Bolt 2012), kidney (Faiz et al 2015;Yang et al 2014), and neurotoxicity (Zimmer et al 2014;Waldmann et al 2014;Krug et al 2013), in vitro systems are frequently used. Primary human cells still represent a gold standard in toxicological research (Heise et al 2012;Ghallab 2013Ghallab , 2014a.…”