Report of a symposium on the use of genomics and proteomics in toxicology

Toxicogenomics: regulatory perspective on current position

Published studies on the utility of toxicogenomic approaches (transcriptomics, proteomics and metabonomics) in screening for toxicological mechanisms and evaluation of dose response effects have been reviewed. The information supports the use of transcriptomics to screen for specific toxicological mechanisms for which there is an a priori hypothesis, although in some areas such as mutagenicity testing, toxicogenomics appear to have limited value for identifying mutagens. Data from such screening approaches cannot be used to exclude the possibility of toxicity. Targeted transcriptomics might be valuable for screening for specific mechanisms of toxicity considered to be irrelevant for assessing risk to humans, which would help to reduce the need for detailed testing of some chemicals. An integrated approach is suggested where data from more than one toxicogenomic approach could be used as an adjunct to conventional toxicology to assess dose-response in toxicological tests. An outline preliminary proposal for use by regulators is suggested although it is noted that more data are required before this could be formally used in a decision-making process.

Transcriptional analysis of rat piriform cortex following exposure to the organophosphonate anticholinesterase sarin and induction of seizures

Background

Organophosphorus nerve agents irreversibly inhibit acetylcholinesterase, causing a toxic buildup of acetylcholine at muscarinic and nicotinic receptors. Current medical countermeasures to nerve agent intoxication increase survival if administered within a short period of time following exposure but may not fully prevent neurological damage. Therefore, there is a need to discover drug treatments that are effective when administered after the onset of seizures and secondary responses that lead to brain injury.

Methods

To determine potential therapeutic targets for such treatments, we analyzed gene expression changes in the rat piriform cortex following sarin (O-isopropyl methylphosphonofluoridate)-induced seizure. Male Sprague-Dawley rats were challenged with 1 × LD₅₀ sarin and subsequently treated with atropine sulfate, 2-pyridine aldoxime methylchloride (2-PAM), and the anticonvulsant diazepam. Control animals received an equivalent volume of vehicle and drug treatments. The piriform cortex, a brain region particularly sensitive to neural damage from sarin-induced seizures, was extracted at 0.25, 1, 3, 6, and 24 h after seizure onset, and total RNA was processed for microarray analysis. Principal component analysis identified sarin-induced seizure occurrence and time point following seizure onset as major sources of variability within the dataset. Based on these variables, the dataset was filtered and analysis of variance was used to determine genes significantly changed in seizing animals at each time point. The calculated p-value and geometric fold change for each probeset identifier were subsequently used for gene ontology analysis to identify canonical pathways, biological functions, and networks of genes significantly affected by sarin-induced seizure over the 24-h time course.

Results

A multitude of biological functions and pathways were identified as being significantly altered following sarin-induced seizure. Inflammatory response and signaling pathways associated with inflammation were among the most significantly altered across the five time points examined.

Conclusions

This analysis of gene expression changes in the rat brain following sarin-induced seizure and the molecular pathways involved in sarin-induced neurodegeneration will facilitate the identification of potential therapeutic targets for the development of effective neuroprotectants to treat nerve agent exposure.

Toxicogenomics in the assessment of immunotoxicity

Microarray analysis is used for simultaneous measurement of expression of thousands of genes in a given sample and as such extends and deepens our understanding of biological processes. Application of the technique in toxicology is referred to as toxicogenomics. The examples of assessment of immunotoxicity by gene expression profiling presented and discussed here, show that microarray analysis is able to detect known and novel effects of a wide range of immunomodulating agents. Besides the elucidation of mechanisms of action, toxicogenomics is also applied to predict consequences of exposing biological systems to toxic agents. Successful attempts to classify compounds using signature gene expression profiles have been reported. These did, however, not specifically focus on immunotoxicity. Databases containing expression profiles can facilitate the applications of toxicogenomics. Platforms and methodologies for gene expression profiling may vary, however, hampering data compiling across different laboratories. Therefore, attention is paid to standardization of the generation, reporting, and management of microarray data. Obtained gene expression profiles should be anchored to pathological and functional endpoints for correct interpretation of results. These issues are also important when using toxicogenomics in risk assessment. The application of toxicogenomics in evaluation of immunotoxicity is thus not yet without challenges. It already contributes to the understanding of immunotoxic processes and the development of in vitro screening assays, though, and is therefore expected to be of value for mechanistic insight into immunotoxicity and hazard identification of existing and novel compounds.

Microbial genotoxicity as an environmental indicator for near-coastal sediment pore waters

The genotoxic potential of sediment pore water collected from coastal areas in the Gulf of Mexico has not been reported frequently in the literature. This report summarizes a study of the microbial mutagenicity of 31 pore water samples obtained from sediment affected by non-point source runoff and compares the results with those for more traditional chemical and biological indicators of sediment quality. Genotoxicity was determined pre- and post-enzyme activation using a proprietary short-term microbial assay for pore water centrifuged from sediment collected adjacent to a Florida coastal golf complex and from an urbanized bayou-estuary. Sediment and the associated pore water also were analyzed for acute toxicity to Hyallela azteca, Palaemonetes pugio, or Americamysis bahia and for benthic macroinvertebrate diversity (sediment only). Genotoxicity (direct and enzyme-activated) was detected in 4 of 17 (golf complex) and in 10 of 14 (urbanized bayou) pore water samples. The lowest toxic pore water concentrations were between 1.8% and 44.4% (direct) and between 2.6% and 25% (enzyme-activated). The results of the genotoxic assay paralleled those based on exceedance of proposed sediment quality guidelines, pore water acute toxicity and Shannon-Wiener diversity index values for 81%, 58%, and 65% of the comparisons, respectively.