Peering into molecular mechanisms of action with frogSCOPE

Abstract

Exposure of critical life stages to harmful chemicals at low, environmentally-relevant concentrations can alter how hormones function, and change metabolic pathways or developmental processes that impact reproduction, behavior, or susceptibility to disease later in life. These alterations can be captured through evaluation of changes to transcriptomes, proteomes, and metabolomes occurring at those critical life stages thereby enabling more effective and earlier identification of mechanism of action, individual susceptibilities and adaptation, and prediction of detrimental sublethal effects. Amphibians are “wet canaries in the coalmine” as indicators for environmental health. There are more than 6000 species living in a variety of ecological niches worldwide yet limited ‘omics resources and approaches exist. To provide for a means of addressing this challenge, frogSCOPE (frog Sentinel species Comparative “ Omics” for the Environment) combines transcriptomics, proteomics, and metabolomics together to form the foundation for the identification of biological response indicators of harmful effects on a species of wild frog ( Rana catesbeiana) at a sensitive tadpole stage. Various exposure and sampling methodologies are possible including standard in vivo exposures, tail fin biopsies, and the C-fin assay. frogSCOPE establishes methodological and analytical approaches applicable to wildlife by using a uniquely-designed frog cDNA array developed to accommodate cross-species hybridization and quantitative real-time polymerase chain reaction (QPCR) assays on poorly genetically-characterized wildlife species. Combination with proteomics (isobaric tags for relative and absolute protein quantitation; iTRAQ) and metabolomics (mass spectrometry) enable the generation of molecular fingerprints to identify mechanisms of action in a more comprehensive fashion to better define suitable indicators of deleterious biological outcomes to wildlife.