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ADAPTING MICROARRAY TECHNOLOGY FOR USE IN ECOTOXICOGENOMICS
Citation:
Miracle, A L., D L. Lattier, R Flick, T V. Reddy, AND G P. Toth. ADAPTING MICROARRAY TECHNOLOGY FOR USE IN ECOTOXICOGENOMICS. Presented at Third International Conference on Pharmaceuticals and Endocrine Disrupting Chemicals, Minneapolis, MN, March 19-21, 2003.
Impact/Purpose:
The indeterminate condition of exposure indicator research stands to change markedly with the ability to connect molecular biological technologies with cellular or tissue effects and outcomes. Three focal areas of ecological research aim to develop a sequence of approaches where "the earliest recognizable signatures of exposure" (i.e., unique patterns of up- and down-regulated genes and proteins) are identified for numerous stressors, demonstrable in case studies and incorporated into Agency, State and Regional studies supported by EMAP and other programs.
Area 1, Computational Toxicology Research: Exposure assessment has historically been based on use of chemical analysis data to generate exposure models. While biological activity of chemicals has been recognized to be important for exposure risk assessments, measurement of such activity has been limited to whole organism toxicity tests. Use of molecular approaches will:
improve extrapolation between components of source-to-outcome continuum (source , exposure , dose , effect , outcome)
Using a systems modeling approach, gene and protein expression data, in small fish models (fathead minnow and zebrafish), will be integrated with metabolomic and histopathological data. This will assist in prediction of environmental transformation and chemical effects based on structural characteristics, and enhance quantitative risk assessments, including areas of uncertainty such as a basis for extrapolation of effects of endocrine disrupting chemicals, interspecies extrapolation, complex chemical mixtures and dose-response assessment.
Area 2, Ecological Research-Environmental Diagnostics: Development of molecular diagnostic indicators contributes to several of the GPRA Diagnostic Research Goals. Methods will employ DNA microarray technology and expression proteomics, focusing on species of relevance to aquatic ecosystem risk assessment. Significantly, these diagnostic indicators will open the door to understanding subcellular interactions resulting from exposure to complex chemical mixtures.
define relationship between genetic disposition of populations and degree/specificity of stressor-specific gene transcriptional response in aquatic organisms (fish and invertebrates)
identify of chemical mixture induced transcriptional "patterns" using microarrays and hyperspectral scanning - via collaboration with DOE Sandia National Labs
apply molecular indicators to watershed level stressor study, including pilot studies with targeted pesticides and toxins indicators
develop molecular indicators of exposure for invertebrates (Daphnia, Lumbriculus, Chironomus)
Area 3, Exposure Research in Endocrine Disruptors:
Subobjective 1: Develop exposure methods, measurement protocols, and models for assessment of risk management practices of endocrine disrupting compounds. As risk management approaches are identified and developed, there will be a need to identify, adapt and develop bioassay screening tools and other analytical methods to assess their efficacy. Measurements research will be performed to define management needs. This effort will entail cross-lab participation from NRMRL, NERL and NHEERL.
Subobjective 2: Determine extent of environmental and human exposures to EDCs, characterize sources and factors influencing these exposures, develop and evaluate risk management strategies to reduce exposures. In order to develop effective risk management strategies, it is important to understand the extent of exposures to endocrine disrupting compounds and factors influencing source-to-exposure-to-dose relationships.
apply molecular indicators of exposure to estrogenic compounds in selected wastewater treatment plants located in ten USEPA Regions
identify differential gene expression following exposure of fathead minnows to environmental androgens and androgen-like compounds
apply molecular indicators of exposu
Description:
Ecotoxicogenomics includes research to identify differential gene expression in laboratory and field animals exposed to toxicants, and ultimately, to link the earliest indicators of exposure to adverse effects in organisms and populations. The USEPA National Exposure Research Laboratory has started to develop a multiple aquatic stressor diagnostic exposure model using fathead minnow (Pimephales promelas) gene sequences in a microarray platform. Because there is very little gene sequence information for the target organism, an approach involving several different methodologies has been developed to examine specific gene expression and to identify stressor-specific patterns of expression over a portion of the expressed genome. Single exposure-specific subtractive cDNA libraries were constructed from adult liver, fry, and embryos to identify differentially expressed genes in minnows exposed to low levels of endocrine disruptor compounds. To complement genes isolated in subtractive arrays, other P. promelas gene sequences were identified by differential display PCR to isolate EDC sensitive genes. In addition, PCR primers based on close relatives of the fathead minnow, the common carp and goldfish, were used to identify homologs of known carp or goldfish genes. By combining these methods for identifying fathead minnow specific sequences, different functional classes of protein-encoding genes are used to build an oligo microarray that encompasses a sampling of the expressed genome. Single and multiple exposures are assessed at the oligo microarray level to gain a better understanding of relative bioavailability of environmental stressors present in mixtures. Thus, the use of microarray technology to examine gene expression promises to be a powerful tool in understanding environmental exposures and their impacts.