Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2015 Jul 18

PMID 26186543

Citations 3

Authors

Sophie Depiereux

Bertrand De Meulder

Eric Bareke

Fabrice Berger

Florence Le Gac

Eric Depiereux

Patrick Kestemont

Affiliations

Soon will be listed here.

Abstract

Sex steroids play a key role in triggering sex differentiation in fish, the use of exogenous hormone treatment leading to partial or complete sex reversal. This phenomenon has attracted attention since the discovery that even low environmental doses of exogenous steroids can adversely affect gonad morphology (ovotestis development) and induce reproductive failure. Modern genomic-based technologies have enhanced opportunities to find out mechanisms of actions (MOA) and identify biomarkers related to the toxic action of a compound. However, high throughput data interpretation relies on statistical analysis, species genomic resources, and bioinformatics tools. The goals of this study are to improve the knowledge of feminisation in fish, by the analysis of molecular responses in the gonads of rainbow trout fry after chronic exposure to several doses (0.01, 0.1, 1 and 10 μg/L) of ethynylestradiol (EE2) and to offer target genes as potential biomarkers of ovotestis development. We successfully adapted a bioinformatics microarray analysis workflow elaborated on human data to a toxicogenomic study using rainbow trout, a fish species lacking accurate functional annotation and genomic resources. The workflow allowed to obtain lists of genes supposed to be enriched in true positive differentially expressed genes (DEGs), which were subjected to over-representation analysis methods (ORA). Several pathways and ontologies, mostly related to cell division and metabolism, sexual reproduction and steroid production, were found significantly enriched in our analyses. Moreover, two sets of potential ovotestis biomarkers were selected using several criteria. The first group displayed specific potential biomarkers belonging to pathways/ontologies highlighted in the experiment. Among them, the early ovarian differentiation gene foxl2a was overexpressed. The second group, which was highly sensitive but not specific, included the DEGs presenting the highest fold change and lowest p-value of the statistical workflow output. The methodology can be generalized to other (non-model) species and various types of microarray platforms.

Citing Articles

Tandem Mass Tag-Based Quantitative Proteomics Analysis of Gonads Reveals New Insight into Sexual Reversal Mechanism in Chinese Soft-Shelled Turtles.

Zhou T, Chen G, Chen M, Wang Y, Zou G, Liang H Biology (Basel). 2022; 11(7).

PMID: 36101459 PMC: 9312195. DOI: 10.3390/biology11071081.

Twenty years of transcriptomics, 17alpha-ethinylestradiol, and fish.

Martyniuk C, Feswick A, Munkittrick K, Dreier D, Denslow N Gen Comp Endocrinol. 2019; 286:113325.

PMID: 31733209 PMC: 6961817. DOI: 10.1016/j.ygcen.2019.113325.

Meta-Analysis of Microarray Data of Rainbow Trout Fry Gonad Differentiation Modulated by Ethynylestradiol.

Depiereux S, Le Gac F, De Meulder B, Pierre M, Helaers R, Guiguen Y PLoS One. 2015; 10(9):e0135799.

PMID: 26379055 PMC: 4574709. DOI: 10.1371/journal.pone.0135799.

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