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Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout
Sophie Depiereux1, Bertrand De Meulder2, Eric Bareke3
1Unit of research in Environmental and Evolutionary Biology (URBE-NARILIS), Laboratory of Ecophysiology and Ecotoxicology, University of Namur, Namur, Belgium.
Plos One
|July 18, 2015
Summary
This study identifies potential biomarkers for ovotestis development in rainbow trout exposed to ethynylestradiol (EE2). The research highlights molecular responses and pathways affected by feminizing contaminants, offering tools for environmental monitoring.
Area of Science:
- Environmental toxicology
- Fish reproductive biology
- Genomics and bioinformatics
Background:
- Sex steroids are crucial for fish sex differentiation, and environmental exposure can cause adverse effects like ovotestis development and reproductive failure.
- Genomic technologies offer insights into mechanisms of action and biomarkers for toxic compounds, but require robust bioinformatics tools and species-specific resources.
- Rainbow trout (Oncorhynchus mykiss) is a key aquaculture species susceptible to endocrine-disrupting compounds.
Purpose of the Study:
- To investigate the molecular responses in rainbow trout gonads following chronic exposure to various doses of ethynylestradiol (EE2).
- To identify potential gene biomarkers indicative of ovotestis development caused by EE2 exposure.
- To adapt and validate a bioinformatics workflow for toxicogenomic analysis in a non-model fish species.
Main Methods:
- Chronic exposure of rainbow trout fry to four doses of EE2 (0.01, 0.1, 1, and 10 μg/L).
- Adaptation of a human-derived bioinformatics microarray analysis workflow for rainbow trout toxicogenomics.
- Differential gene expression analysis and over-representation analysis (ORA) to identify enriched pathways and gene ontologies.
- Selection of potential ovotestis biomarker gene sets based on pathway relevance and statistical significance.
Main Results:
- The adapted bioinformatics workflow successfully identified differentially expressed genes (DEGs) in response to EE2 exposure.
- ORA revealed significant enrichment of pathways related to cell division, metabolism, sexual reproduction, and steroid production.
- Two sets of potential ovotestis biomarkers were identified: specific biomarkers including the ovarian differentiation gene foxl2a, and sensitive but non-specific DEGs with high fold changes and low p-values.
Conclusions:
- The study provides valuable insights into the molecular mechanisms of EE2-induced feminization in fish.
- Identified gene sets serve as potential biomarkers for detecting ovotestis development and assessing the impact of endocrine-disrupting compounds in aquatic environments.
- The validated bioinformatics methodology is applicable to other non-model species and microarray platforms, advancing toxicogenomic research.
