Protein biomarkers for in vitro testing of toxicology.

The vision of the toxicology in the 21st century movement is to overcome the currently used animal tests and identify molecular pathways of toxicity, using human in vitro systems with the aim to provide the most relevant mechanistic information for human risk assessment. It is expected to translate key surrogate biomarkers to novel types of toxicity-related high throughput screening of the many thousands of compounds which need to be tested during development phases of the pharmaceutical industry and with regard to the REACH legislation in Europe. Systems biology, an emerging and increasingly popular field of research, appears to be the discipline of choice to integrate results from transcriptomics, proteomics, epigenomics and metabonomics technologies used to analyze samples from toxicological models. The challenges, however, with respect to data generation, statistical treatment, bioinformatic integration and interpretation or in silico modeling remain formidable. One of the main difficulties is the fact that the sheer number of molecular species is inflated enormously in the course of translation from genes to proteins due to post-translational modifications. Moreover, at the level of proteins, time scales of cellular reactions to toxic insults can be very fast, ranging from milliseconds to seconds. Linear dynamic ranges of concentration differences between conditions can also differ by several orders of magnitude. So, the search for protein biomarkers of toxicity requires sophisticated strategies for time-resolved quantitative differential approaches. The statistical principles, normalization of primary data and principal component and cluster analysis have been well developed for genomics/transcriptomics and partly for proteomics, but have not been widely adapted to technologies like metabonomics. Also, the integration of functional data, in particular data from mass spectrometry, with the aim of modeling pathways of toxicity for human risk assessment, is still at an infant stage.

Protein biomarkers for in vitro testing of embryotoxicity.

There are new challenges for hazard and risk assessment in the chemical industry with regard to REACH legislation in Europe and related activities in the U.S. and Japan, which require the development of novel in vitro models for the molecular characterization of drug- or chemical-related effects replacing conventional animal testing. In the frame of a European FP6 project on reproductive toxicology ( www.reprotect.eu ), we prepared protein samples from mouse embryonic stem cells differentiated into contracting cardiomyocytes according to the validated embryonic stem cell test (EST) protocol, which had been exposed to toxic substances selected by an expert committee from different in vivo categories of embryotoxicity. Lysates were used to carry out the following investigations: (i) identify optimal dose range conditions in the EST that are suitable for (ii) performing a differential quantitative proteomic study of underlying molecular pathways, (iii) define classes of substances with similar proteomic response patterns, (iv) relate these classes to the traditional in vivo categories of embryotoxicity with (v) the final goal to identify novel surrogate protein biomarker candidates for embryo toxicity. We found two distinct classes of toxic substances (Dinoseb, Ochratoxin-A, and Nitrofen vs ß-aminoproprionitril, Metoclopramide, Doxylamine succinate, and d-penicillamine) with clear pathway-related differences in their proteomic patterns. Most notably, different responses to cluster 1 and cluster 2 substances were observed for Heat shock protein ß-1, Ras-GTPase-activating protein SH3-domain binding protein, Ran binding protein 5, and Calreticulin, Dihydropyrimidinase-like 2 (Ulip2 protein). On the other hand, Heat shock protein 8 and Fscn1 protein were down-regulated by all compounds from both clusters.

Unexpected common mechanistic pathways for embryotoxicity of warfarin and lovastatin.

Novel molecular content for fast in vitro strategies in the context of safety tests concerning developmental toxicity has a potential to substantially reduce animal experiments according to the "3R" concept (Reduce/Refine/Replace). Here we present and discuss data from a differential proteomic profiling of samples generated using embryonic stem cell derived in vitro models treated with a set of model substances. Among substance-dependent proteomic changes, potential surrogate markers were some isoforms of heat shock proteins and a component of the Ras pathway, present in several redundant isoforms due to posttranslational modifications. Both proteins are implicated in cell migration, cell survival, growth and embryonic development. Using the examples of warfarin and lovastatin, two substances with entirely different primary targets, the surrogate marker signature nevertheless indicates a common embryotoxic mode of action. We discuss these findings observed in in vitro toxicity tests, in a context of clinical validation and evidence-based toxicology.

Age-dependent posttranslational modifications of voltage-dependent anion channel 1.

The accumulation of oxidative damage in mitochondrial proteins, membranes and DNA during ageing is supposed to lead to mitochondrial inactivation, downstream molecular impairments and subsequent decline of biological systems. In a quantitative study investigating the age-related changes of mitochondrial proteins on the level of oxidative posttranslational modifications, we previously found a set of conserved biomarkers across ageing models in five species with consistent oxidative break-up of tryptophan residues and formation of N-formyl kynurenine. In an additional proteomic profiling of a long-living Drosophila mutant overexpressing mitochondrial Hsp22 and controls, we found age-related redundant isoforms of voltage-dependent anion channel 1 (VDAC-1). A re-examination of data from human umbilical vein endothelial cells (with normal and chemically accelerated in vitro ageing), revealed similar age-dependent alterations of voltage-dependent anion channel isoforms. Building on these results, we examined the expression of VDAC-1 in an in vitro model of excitotoxicity. We show that glutamate-induced calcium toxicity in neurons induces changes of voltage-dependent anion channel 1 related to downstream events of mitochondrial apoptosis like poly-ADP-ribosylation.