Experimental reporting of fish transcriptomic responses in environmental toxicology and ecotoxicology.

Abstract

Due to its increasing affordability and efforts to understand transcriptional responses of organisms to biotic and abiotic stimuli, transcriptomics has become an important tool with significant impact on toxicological investigations and hazard and risk assessments, especially during development and application of new approach methodologies (NAMs). Data generated using transcriptomic methodologies have directly informed adverse outcome pathway frameworks, chemical and biological read across, and aided in the identification of points of departure. Using data reporting frameworks for transcriptomics data offers improved transparency and reproducibility of research and an opportunity to identify barriers to adoption of these NAMs, especially in environmental toxicology and ecotoxicology with aquatic models. Improved reporting also allows for reexamination of existing data, limiting needs for experiment replication and further reducing animal experimentation. Here, we use a standardized form of data reporting for omics-based studies, the Organisation for Economic Co-operation and Development omics reporting framework, which specifically reports on a list of parameters that should be included in transcriptomics studies used in a regulatory context. We focused specifically on fish studies using RNA- Sequencing (Seq)/microarray technologies within a toxicology context. Inconsistencies in reporting and methodologies among the experimental designs (toxicology vs. molecular characterization) were observed in addition to foundational differences in reporting of sample concentration or preparation or quality assessments, which can affect reproducibility and read across, confidence in results, and contribute substantially to understanding molecular mechanisms of toxicants and toxins. Our findings present an opportunity for improved research reporting. We also provide several recommendations as logical steps to reduce barriers to adoption of transcriptomics within environmental toxicology and ecotoxicology.