Development and initial testing of EcoToxChip, a novel toxicogenomics tool for environmental management and chemical risk assessment.

Abstract

New approach methods (NAMs) are increasingly important to help accelerate the pace of ecological risk assessment and offer more ethical, affordable, and efficient alternatives to traditional toxicity tests. In the present study, we describe the development, technical characterization and initial testing of a toxicogenomics tool, EcoToxChip (384-well qPCR array), to support chemical management and environmental monitoring for three laboratory model species - fathead minnow (Pimephales promelas), African clawed frog (Xenopus laevis), and Japanese quail (Coturnix japonica). Chip design, including gene selection, was informed by a diverse end-user group and quality control metrics (e.g. primer assay, reverse transcription and PCR efficiency) performed well based on a priori established criteria. Correlation with RNAseq data provided additional confidence in this novel toxicogenomics tool. While the present study represents an initial testing of only 24 EcoToxChips for each of the model species, the results provide increased confidence in the robustness/reproducibility of EcoToxChips for evaluating perturbations in gene expression associated with chemical exposure and thus, this NAM, combined with early-life stage toxicity testing, could augment current efforts for chemical prioritization and environmental management.