T2 AM 'Omic' Technologies: Current and Future Application to Environmental Toxicology (Part 1)|
Tuesday, 15 November 2005: 8:00 AM - 11:40 AM in Ballroom 2
214 (WAT-1117-851039) Advancing Environmental Toxicogenomics.
Start time: 8:00 AM
Waters, M.1, 1 National Center for Toxicogenomics, NIEHS, NIH, DHHS, Research Triangle Park, NC, USA
Toxicogenomics is just beginning to integrate the multiple data streams derived from transcriptomics, proteomics and metabonomics with traditional toxicological endpoint evaluation. This integration has the potential to synergize our understanding of environmental toxicology at the systems level. The integration of multiple domain data for knowledge discovery about animal models and mechanisms in toxicology is an important goal of the Chemical Effects in Biological Systems knowledgebase. CEBS (http://cebs.niehs.nih.gov, http://www.niehs.nih.gov/cebs-df/) is being developed to meet the information needs of systems toxicology. Systems toxicology involves the study of environmental stressor-induced perturbations, monitoring changes in molecular expression, and iteratively integrating biological response data to describe the functioning organism. Environmental toxicology and toxicogenomics are progressively developing from studies done predominantly on individual chemicals and stressors into a knowledge-based science. However, the evolution of a truly predictive toxicology wherein knowledge of toxicogenomic responses of a prototypic agent in one species and strain is used to predict the mode-of-action of a similar agent in a related strain or another species will require that the results of numerous toxicogenomics investigations across genotypes and species be assimilated into a multi-domain, multi-genome, knowledgebase. This knowledgebase must be searchable by chemical formula/stressor-type, by gene/protein/metabolite molecular signature, or by phenotypic outcome, among other entities, to find results analogous to those observed with a newly tested agent. Toxicology will then have become an information science, and environmental health and risk assessment will be the beneficiaries. CEBS will become a public resource late in 2005.
215 (ZAC-1117-821525) Incorporation of Toxicogenomics into Quantitative Risk Assessment.
Start time: 8:20 AM
Zacharewski, T1, 1 Michigan State University, East Lansing, MI, USA
In order to fully assess the potential adverse health effects of chronic and subchronic exposure to environmental contaminants and commerce chemicals, as well as their mixtures, a more comprehensive understanding of their molecular, cellular and physiological effects is required within the context of the exposed organism, its genome, proteome and metabolome. Emerging omic technologies, novel computational approaches, and the availability of genome sequence information for a variety of species, including environmentally relevant models, has provided unprecedented opportunities to further elucidate mechanisms of toxicity and identify mechanistically-based biomarkers. However, our ability to extract meaningful biological information from toxicogenomic data to support quantitative risk assessment has been elusive. This presentation will attempt to separate hype from reality by describing the resources, infrastructure and technical skills that toxicologists, risk/hazard assessors and policy analysts will require to facilitate the incorporation of toxicogenomic data into regulatory decision-making. More specifically, the development of dbZach (http://dbzach.fst.msu.edu) a MIAME compliant toxicogenomic supportive relational database, the construction of orthologous human, mouse and rat cDNA microarrays, study design issues, and approaches for comprehensive data analysis and interpretation will be described. Examples from the systematic integration of computational, microarray, and histopathology data from comparative in vitro and in vivo dose response and time course studies examining the mechanisms of toxicity of dioxin and estrogenic endocrine disruptors will be used to demonstrate the support toxicogenomics can provide to mechanistically-based risk assessment. Moreover, factors impeding the incorporation of toxicogenomic data into mechanistically-based ecologically relevant quantitative risk assessment will also be presented. This work is supported by the United States Environmental Protection Agency (826301), the National Institutes of Health (ES11271 and ES12245) and the Superfund Program (ES 4911).
216 (GOO-1117-573373) Toxicogenomics in the identification of biomarkers of nephrotoxicity for multiple species.
Start time: 8:40 AM
Goodsaid, F1, 1 Genomics, Office of Clinical Pharmacology and Biopharmaceutics, CDER, US Food and Drug Administration, Rockville, Maryland, USA
Results from toxicogenomic studies provide a common lexicon in the search for biomarkers of toxicity across multiple species. One of the best examples of this application of toxicogenomics has been the identification of genomic biomarkers of nephrotoxicity. Genomic and proteomic biomarkers for nephrotoxicity have been identified in rats, monkeys and humans on the basis of results from several studies in these species. The value of these biomarkers is clear for each species in which they have been identified, but the common language provided by toxicogenomic markers has also helped understand similarities and differences in toxicity between species. These studies have also shown a close relationship between the detection of transcriptomic and proteomic versions of these markers, leading to their potential use in clinical applications.
217 (HEL-1117-832050) Making ′omics′ tools work for sentinel species — a lesson from frogs.
Start time: 9:00 AM
Helbing, Caren1, 1 University of Victoria, Victoria, BC, Canada
Despite the number of genome sequences available, only a minute fraction of the diversity of life on our planet is represented. Sentinel species for which substantial toxicological data exist are largely underrepresented in the genomics arena. Yet ′omics′ tools still have promise for use in these less genetically-characterized species. There are over 5,000 species of frogs and toads worldwide that represent a variety of life strategies, ecological niches and susceptibilities to environmental contaminants and several of these species have been used in toxicology. However, only one frog genome sequence (Xenopus tropicalis) is known and the bulk of genetic information available through expressed sequence tags (ESTs) is from Xenopus laevis. Both of these species are useful as laboratory models, but fall short as useful sentinel species outside of the laboratory due to their limited natural range. Can their genetic information be directly applied to other frog species? Yes and no. Careful design of genomics tools can by-pass the pitfalls and generate valuable information that can be applied to the production of species-specific quantitative real time polymerase chain reaction (QPCR) gene expression biomarkers for indigenous frog species. Using examples from my laboratory, I will address the challenges and successes of applying ′omics′ tools to the study of thyroid hormones and disruptors of hormone action in North American frog species.
Start time: 9:20 AM
218 (CHI-1118-083046) Biomarkers from (eco)toxicogenomics : the European flounder as a non-model organism and the distinction between compensatory versus toxic responses.
Start time: 10:00 AM
Chipman, J K1, George, S G 2, Williams, T D1, Diab, A.M. 2, Sabine, V2, Godfrey, R E1, Minchin, S D1, 1 School of Biosciences, University of Birmingham, Birmingham, UK2 University of Stirling, Stirling, Scotland
There is increasing interest in gaining information on altered gene expression in response to exposure to toxic chemicals. These studies will aid identification of toxic mechanisms and the development of novel, sensitive and early biomarkers for use in screening and in environmental monitoring. Information is relatively forthcoming in model organisms for which adequate databases are available. However, toxicogenomics in organisms of environmental relevance is more difficult. We initiated studies in the flounder by designing degenerate primers for a range of genes of toxicological interest. In addition, subtractive suppressive hybridisations (SSH) between flounder collected from the Alde (reference) and Tyne (polluted) estuaries provided clones of differentially expressed genes, as did SSH between flounder treated with benzo(a)pyrene or cadmium in comparison to controls. These clones were combined with clones from a liver cDNA library to produce a 13,000 cDNA microarray for the flounder (EU-GENIPOL Project). Proof of principle has been achieved by comparing the differences in gene expression between flounder sampled from estuaries of different pollution status and also between flounder treated in the laboratory with model toxicants. We have detected induction of known biomarker genes, eg. CYP1A with PAH treatments, metallothionein with cadmium, vitellogenin and choriogenin with estradiol and ethinyl-estradiol. Importantly, interactive effects have been discovered e.g. between PAH and metals. Bioinformatics analyses including gene ontology have been initiated as more complete sequencing of clones is being achieved. Activated processes are being identified and correlations are emerging between laboratory and field responses e.g. induction of CYP1A, Cu/Zn SOD. Potential novel biomarkers have been indicated such as HSP 30B, fatty acid binding protein and other, yet to be characterised, ESTs. A major challenge is the integration of such studies into risk assessment for example in the derivation of novel batteries of biomarkers. However, to achieve this, it is necessary to distinguish between compensatory and toxic responses and these issues will be illustrated with reference to CYP and HSP induction. This work was funded by the NERC, CEFAS and EU and has involved GENIPOL collaborations.
219 (PER-1118-091610) Does Toxicogenomics Have Any Practical Use? - Assessing Presence and Population Level Impacts of Contaminants.
Start time: 10:20 AM
Perkins, E1, Steevens, J1, 1 U.S. Army Engineer Research and Development Center, Vicksburg, MS, 39180
The Department of Defense is responsible for stewardship of more than 25 million acres of land used primarily for military training and testing. Current approaches employed by the military to assess the impact of military training and testing on the environment include more traditional environmental assessment tools within the risk assessment paradigm (e.g., bioassays, chemistry, and surveys). For the most part toxicogenomics has not been utilized within ecological risk assessments and has provided little value in making resource management decisions. While proposed as a screening tool in human health, drug development, and ecological assessments the principle goals of contaminant risk assessment and resource management require strong linkage of toxicogenomic studies to management objectives. In addition to development of screening tools, our laboratory has focused on toxicogenomics as a tool to link molecular level events to individual and population level effects of military unique contaminants (i.e., metals and explosives). These studies have been conducted in the laboratory using a wide variety of species (e.g., rats, quail, fish, soil and aquatic invertebrates) to understand the impact of military contaminants in different environments and scale differences between species for use in cross species extrapolation. A critical component of the effort is to scale whole organism effects (growth, reproduction) that can be quantified and used for population modeling. For example, in linking toxicogenomics to a measured dose of TNT (i.e., tissue residues), we found no correlation between TNT exposure levels and gene expression but a high correlation between expression, tissue residues and lethality in the benthic invertebrate Leptocheirus plumulosus. Similar studies are being conducted with the earthworm Eisenia fetida, and fathead minnow Pimephales promelas with DNT, TNT, and RDX to further understand exposure-dose-effect relationships. Given the likely variability in contaminant dose, biological diversity, and sensitivity, toxicogenomics is limited to its use as a tool within the greater context of improving methods for assessing exposure and ecological effects of contaminants.
220 (DEV-1117-208677) Can microbial community analyses effectively contribute to ecological assessments?
Start time: 10:40 AM
Devereux, R.1, Fisher, W.1, 1 US EPA NHEERL Gulf Ecology Divsion, Gulf Breeze, FL, USA
Microbial communities respond rapidly to environmental changes including stressors such as hydrocarbon pollutants, heavy metals and nutrient enrichment. They therefore have potential value in ecological assessments. Bacteria are widely used as indicators of fecal pollution and chlorophyll concentrations may be used to assess water quality relative to nutrient loadings. Can microorganisms tell us more about environmental condition? Over the last 20 years, microbial community ecology has been strengthened as a discipline by technological progress that provides community information in greater detail than was previously possible using traditional cultivation-dependent approaches. These advances, based on retrieval of genetic information (i.e., DNA sequences) directly from microorganisms in environmental samples, allow determinations of microbial community composition, diversity, and genetic potential independent of any need to culture them in the laboratory. The first complete genome sequences obtained were from bacteria and subsequent advances have been rapid. It can be expected that genomic-enabled technology will ultimately translate into efficient and useful methods for microbial ecology and potentially ecological assessments. Microarray technology, for example, is an attractive tool for ecological assessments because it can be used to characterize bacterial communities in terms of taxonomic composition, heavy metal resistance, hydrocarbon degradation, or nutrient cycling. However, the utility of microbial community measurements for ecological assessment remains an open question. Useful ecological indicators require that measurements are relevant to an assessment question, feasible to implement, transportable among different environments, and sufficiently straightforward that interpretations can be embraced by resource managers, lawmakers and the public. Moreover, development of a useful tool requires validation and technical transfer to State and Federal regulatory departments. Development of ecological indicators from measurements of microbial communities requires a strong understanding of the assessment needs; application to an assessment will require a comprehensive strategy to address the needs of the stakeholders.
221 (ANK-1117-823187) Role of genomics in regulatory ecotoxicology: overview of a Pellston workshop.
Start time: 11:00 AM
Ankley, G1, Daston, G2, Hodson, P3, Hoke, R4, Miracle, A5, Perkins, E6, Snape, J7, Tyler, C8, 1 US Environmental Protection Agency, Duluth, MN, USA2 Proctor and Gamble, Cincinnati, OH, USA3 Queens University, Kingston, ON, Canada4 DuPont, Newark, DE, USA5 Pacific Northwest National Laboratories, Richland, WA, USA6 US Army Corps of Engineers, Vicksburg, MS, USA7 AstraZeneca, Brixham, UK8 University of Exeter, Exeter, UK
A variety of new techniques have emerged to examine responses of organisms to internal and external stimuli at the molecular level. Approaches to evaluate gene, protein and metabolite expression/production (collectively referred to as toxicogenomics) promise to impact the field of toxicology in several respects, including: (a) identification of mechanisms/modes of action to help define toxicity pathways, (b) providing a basis for extrapolation of chemical effects across species, (c) development of techniques for dealing with chemical mixtures, and (d) identification of biomarkers of exposure, bioaccumulation and effects for use in both lab and field (monitoring) studies. Much of this potential, however, has been discussed in the literature and at technical meetings only in relatively broad terms, making it difficult to assess exactly how data generated from new genomics technologies might impact/benefit different types of risk assessments. This challenge has started to be recognized by scientists and regulators involved in human health assessments; however, ecotoxicologists have yet to address the issue in a systematic fashion. There are critical differences between human health and ecological risk assessments that render a one size fits all fix problematic with respect to generation and application of genomic data. Hence it is important (and timely) to develop a conceptual framework concerning how genomics data can most effectively impact current approaches for ecological risk assessments. Given the long history of SETAC Pellston workshops in aligning science and regulation, it was felt that this was an ideal forum for addressing the issue. To this end, a Pellston workshop, Molecular Biology and Risk Assessment: Evaluation of the Potential Role of Genomics in Regulatory Ecotoxicology, with about 40 international participants from industry, government and academia, was held in September, 2005, in North America. Our presentation will highlight outcomes of that Pellston meeting.
222 (58188) Panel Discussion.
Start time: 11:20 AM