Superfund Research Program
Microarrays in Fathead Minnows and Bass
Program Director: Barbara J. Carter
Grant Number: R44ES011882
Funding Period: Phase II: 2006-2008
Microarrays are a powerful way to measure the biological impact of contaminants in the environment. Because they are used to test changes in expression of many genes in parallel, they provide data on the mechanisms by which compounds affect health more quickly than methods now in use, which makes them much less expensive than current tests. Today, gene chips (microarrays) are an established technology in human disease research. The purpose of this project is to bring their power and precision to environmental toxicology. By understanding how contaminants affect gene expression in fish and other wildlife, we can begin to link environmental exposures to adverse health effects in these animals, and by extrapolation, to humans.
EcoArray intends to develop, validate and begin to market large oligonucleotide-based glass microarrays for fathead minnows and largemouth bass and to develop the backbone of a powerful database. Later, EcoArray will use knowledge obtained in this research project to finalize its product offering of a suite of general- and special-purpose microarrays for research and environmental monitoring by academia, government and industry. Previously, these researchers validated the use of arrays for a small set of environmental contaminants, which resulted in prototype arrays for the two species, as described in EcoArray's publications, presentations and posters. The goal for this work is to expand the current arrays to a larger, more robust format, resulting in a 10,000+-gene fathead minnow microarray and 2,000+ gene largemouth bass microarray. We have engaged five collaborators, all of whom are experts in fish biology, to carry out exposures and field analysis in fathead minnows or largemouth bass. For the fathead minnow studies, we will use the microarrays that we will develop to identify and characterize the genetic signatures for 14 different compounds commonly found at superfund sites, and that are known to have distinct modes of action. Many of these compounds are on the 2003 Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) Priority list. We are currently involved in a collaboration (CRADA) with the EPA to pick the best microarray platform and validate its use, and this commercial platform will be the basis for our enhanced microarrays. We will incorporate the gene expression data into a relational database that will also include other parameters such as water chemistry data and biological and physiological endpoints in the treatment species. We will conduct similar laboratory and field studies, but on a smaller scale, in largemouth bass and identify and characterize the genetic signatures for 5 different compounds. We have begun our marketing plan, and have had early success in selling laboratory services associated with gene discovery. We expect to offer an oligonucleotide-based chip developed with the EPA in late 2005 and then begin our marketing launch of the chips developed in this grant, as well as several other complementary products, in late 2006.