Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay.
Daniel L Villeneuve1, Michelle Le2, Monique Hazemi2
1US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA.
Current Research in Toxicology
|January 9, 2023
Summary
Pilot testing of transcriptomics-based points of departure (tPODs) in larval fathead minnows revealed that tPODs derived from fewer than 15 differentially expressed genes are unreliable for ecological hazard screening. Interindividual gene expression variability significantly impacts tPOD reliability.
Area of Science:
- Environmental toxicology
- Ecotoxicogenomics
- Aquatic toxicology
Background:
- Global gene expression profiles can indicate toxicity.
- Transcriptomics-based points of departure (tPODs) are proposed for hazard assessment.
- High-throughput transcriptomics assays are needed for ecological screening.
Purpose of the Study:
- Pilot test a high-throughput transcriptomics assay using larval fathead minnows.
- Evaluate assay design and acceptance criteria for reliable tPOD estimation.
- Assess the influence of gene expression variability on tPODs.
Main Methods:
- Exposed larval fathead minnows to metals, SSRIs, and neonicotinoid-like compounds.
- Applied concentration-response modeling to whole-body gene expression data.
- Used in silico subsampling to evaluate assay parameters.
Main Results:
- tPODs were consistently lower than apical effect concentrations in fish.
- Larval fathead minnow tPODs were not always lower than toxicity values in other aquatic species.
- Reliable tPOD estimates required concentration-response relationships for at least 15 differentially expressed genes.
- Interindividual gene expression variability was a major driver of tPOD variability.
Conclusions:
- Current assay design and analysis pipeline require >15 differentially expressed genes for reliable screening tPODs.
- Interindividual variability in gene expression is a critical factor influencing tPOD reliability.
- Further development of high-throughput transcriptomics assays is needed for ecological hazard screening.
Keywords:
BMD, Benchmark doseBenchmark doseComputational toxicologyDEGs, Differentially expressed genesECOTOX knowledgebaseFishHTTr, High throughput transcriptomicsRIN, RNA integrity numberRNA sequencingRNAseq, RNA sequencingSSRI, Selective serotonin reuptake inhibitorToxCast, US EPA Toxicity ForecasterTranscriptomics-based point of departurecDNA, Complementary DNAeco-HTTr, Ecological high throughput transcriptomicstPOD, Transcriptomics-based point of departure
