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Cell cycle. In our study, the Cell Cycle is an example of a significantly enriched pathway resulting from the DAVID analysis. Red stars indicate genes belonging to the list of DEG submitted to the program. The background was made up of 16,977 Ensembl IDs (corresponding to the total number of identifiers on the Agilent 60K platform).
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Sex differentiation in fish is a highly labile process easily reversed by the use of exogenous hormonal treatment and has led to environmental concerns since low doses of estrogenic molecules can adversely impact fish reproduction. The goal of this study was to identify pathways altered by treatment with ethynylestradiol (EE2) in developing fish an...
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In non-mammalian vertebrates, estrogens and expressions of cyp19a1 and foxl2 play critical roles in maintaining ovary differentiation and development, while dmrt1 and sox9 are male-specific genes in testicular differentiation and are highly conserved. In order to deeply understand the morphological change, sex steroids level and molecular mechanism...
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... As an analog of E2, EE2 provides a clear example of how a XE can alter reproductive processes. An in vivo study in the fry of rainbow trout revealed that exposure up to 10 µg/L EE2 enriched pathways related to the cell cycle and DNA replication, and demonstrated the ability of EE2 to disrupt gonad differentiation [100]. While sex differentiation in fish is more labile than in mammals, the ability of EE2 to alter transcriptional patterns during female gonad differentiation in male fish demonstrates the estrogenic effects of EE2 [100]. ...
... An in vivo study in the fry of rainbow trout revealed that exposure up to 10 µg/L EE2 enriched pathways related to the cell cycle and DNA replication, and demonstrated the ability of EE2 to disrupt gonad differentiation [100]. While sex differentiation in fish is more labile than in mammals, the ability of EE2 to alter transcriptional patterns during female gonad differentiation in male fish demonstrates the estrogenic effects of EE2 [100]. ...
Exposure to Endocrine Disrupting Chemicals (EDC) has been linked with several adverse outcomes. In this review, we examine EDCs that are pervasive in the environment and are of concern in the context of human, animal, and environmental health. We explore the consequences of EDC exposure on aquatic life, terrestrial animals, and humans. We focus on the exploitation of genomics technologies and in particular whole transcriptome sequencing. Genome-wide analyses using RNAseq provides snap shots of cellular, tissue and whole organism transcriptomes under normal physiological and EDC perturbed conditions. A global view of gene expression provides highly valuable information as it uncovers gene families or more specifically, pathways that are affected by EDC exposures, but also reveals those that are unaffected. Hypotheses about genes with unknown functions can also be formed by comparison of their expression levels with genes of known function. Risk assessment strategies leveraging genomic technologies and the development of toxicology databases are explored. Finally, we review how the Adverse Outcome Pathway (AOP) has exploited this high throughput data to provide a framework for toxicology studies.
... Au vu de ces résultats, il nous paraît primordial de caractériser les acteurs moléculaires responsables de la différenciation gonadique, en particulier celle des ovaires chez A. mexicanus. Pour cela, il existe des approches méthodologiques plus puissantes voire "exhaustives", qui ont été utilisées chez d'autres espèces, permettant de quantifier de manière simultanée l'expression de nombreux gènes à différents stades gonadiques telles que les microarray (Depiereux et al., 2015;Douglas, 2006) ou encore les techniques de séquençage type RNA-seq Tao et al., 2018;Zhang et al., 2019). L'utilisation d'une telle démarche serait très intéressante afin de valider nos résultats surprenants avec une autre approche, et aussi Notons tout de même que malgré ces divergences observées par rapport aux autres espèces de vertébrés, l'ensemble de nos résultats (Article 1) nous ont permis de proposer un schéma illustrant les grandes étapes de la différenciation histologique mâle et femelle ainsi que l'expression concomitante des principaux marqueurs moléculaires explorés dans la présente étude ( Figure 9). ...
L’évolution des mécanismes de détermination du sexe (SD), qui a souvent été abordée principalement dans un contexte macro-évolutif chez les poissons, montre une variabilité saisissante des gènes SD et de leurs chromosomes sexuels associés. En plus des chromosomes de type A, certaines espèces de poissons téléostéens contiennent des chromosomes B (Bs), qui sont parfois considérés comme des chromosomes sexuels. À ce titre, mon projet de thèse avait pour objectif d’explorer l’évolution des systèmes SD en lien avec les Bs chez le tétra Mexicain, Astyanax mexicanus, qui comporte de nombreuses populations cavernicoles (CF) ayant évoluées à partir d'une population ancestrale de surface (SF) il y a moins de 20 000 ans. Nos travaux apportent des preuves fonctionnelles de l’existence d’un système de SD “original” reposant uniquement sur des chromosomes “B-sexuels” à dominance mâle avec gdf6b-B comme potentiel gène déterminant majeur du sexe chez les CF de la grotte Pachón. En parallèle, nous apportons des résultats qui suggèrent qu’il pourrait exister une transition évolutive rapide entre un système de type B-sex chromosome à dominance mâle fixe chez certaines populations vers un système plus complexe (probablement polygénique) ne reposant que partiellement sur le chromosome “B-sexuel” et ses loci gdf6b-B chez d’autres populations.
... Disruptions to gonadal development in fish exposed to estrogenic EDCs, including EE 2 , have been widely reported (Bhandari et al., 2015). The feminization process observed in EE 2 exposed juvenile fish is observed both morphologically (differentiation of the ovary in exposed individuals) and molecularly (cyp19a1, 11βhsd and other target genes; Pérez et al., 2012, Depiereux et al., 2015. Female-skewed sex ratios have been found in zebrafish and fathead minnow exposed to environmentally-relevant concentrations of EE 2 (5 ng/L or less; Fenske et al., 2005;Leet et al., 2015;Luzio et al., 2016a,b;Örn et al., 2016;Parrott and Wood, 2002). ...
The environmental estrogen 17α-ethinylestradiol (EE2) will depress or completely inhibit egg production in many common model teleosts at low concentrations (≤ 0.5 ng/L; Runnals et al., 2015). This inhibition is not seen in the estuarine killifish, or mummichog (Fundulus heteroclitus), even when exposed to 100 ng/L EE2. This relative insensitivity to EE2 exposure indicates species-specific mechanisms for compensating for exogenous estrogenic exposure. This review compares various reproductive responses elicited by EE2 in mummichog to other common model teleosts, such as zebrafish (Danio rerio) and fathead minnow (Pimephales promelas), identifying key endpoints where mummichog differ from other studied fish. For example, EE2 accumulates primarily in the liver/gall bladder of mummichog, which is different than zebrafish and fathead minnow in which accumulation is predominantly in the carcass. Despite causing species-specific differences in fecundity, EE2 has been shown to consistently induce hepatic vitellogenin in males and cause feminization/sex reversal during gonadal differentiation in larval mummichog, similar to other species. In addition, while gonadal steroidogenesis and plasma steroid levels respond to exogenous EE2, it is generally at higher concentrations than observed in other species. In mummichog, production of 17β-estradiol (E2) by full grown ovarian follicles remains high; unlike other teleost models where E2 synthesis decreases as 17α,20β-dihydroxy-4-prenen-3-on levels increase to induce oocyte maturation. New evidence in mummichog indicates some dissimilarity in gonadal steroidogenic gene expression responses compared to gene expression responses in zebrafish and fathead minnow exposed to EE2. The role of ovarian physiology continues to warrant investigation regarding the tolerance of mummichog to exogenous EE2 exposure. Here we present a comprehensive review, highlighting key biological differences in response to EE2 exposure between mummichog and other commonly used model teleosts.
... Proteomics and other omic techniques can facilitate the understanding of key molecular-level changes and toxicity pathways underlying responses to chemicals, namely within the framework of adverse outcome pathways (AOPs) [13,14]. In the past years, most studies have used transcriptomics to investigate the toxicological response to EE2, in fish brain [15][16][17][18][19], liver [20][21][22][23][24][25][26] and gonads [27][28][29][30][31][32]. In comparison, few studies have used proteomics [22,33]. ...
Early-life represents a critically sensitive window to endocrine disrupting chemicals, potentially leading to long-term repercussions on the phenotype later in life. The mechanisms underlying this phenomenon, referred to as the Developmental Origins of Health and Disease (DOHaD), are still poorly understood. To gain molecular understanding of these effects, we exposed mangrove rivulus (Kryptolebias marmoratus) for 28 days post hatching (dph) to 4 and 120 ng/L 17-α-ethinylestradiol, a model xenoestrogen. After 28 days, fish were raised for 140 days in clean water and we performed quantitative label-free proteomics on brain, liver and ovotestis of 168 dph adults. A total of 820, 888 and 420 proteins were robustly identified in the brain, liver and ovotestis, respectively. Effects of 17-α-ethinylestradiol were tissue and dose-dependent: a total of 31, 51 and 18 proteins were differentially abundant at 4 ng/L in the brain, liver and ovotestis, respectively, compared to 20, 25 and 39 proteins at 120 ng/L. Our results suggest that estrogen-responsive pathways, such as lipid metabolism, inflammation, and the innate immune system were affected months after the exposure. In addition, the potential perturbation of S-adenosylmethionine metabolism encourages future studies to investigate the role of DNA methylation in mediating the long-term effects of early-life exposures.
... In medaka some cyst germ cells were germline stem cells with bipotential activity that differentiate in to oogonia but in the absence of E2 are capable to differentiate into spermatogonia [Paul-Prasanth et al., 2013]. The mode of action of feminizing EE2 (ethinylestradiol) treatment was studied in rainbow trout fry/juveniles with a meta-analysis of microarray data showing a rapid and strong decrease of key testis genes, notably those involved in androgen synthesis [Depiereux et al., 2015]. It highlighted new pathways such as the progesterone-oocyte maturation pathway with several genes of the germline, cell division and oocyte meiosis represented and the peroxisome proliferator-activated receptor (PPAR) signaling pathway containing genes from the nuclear hormone (steroid/thyroid/retinoid) receptor family that perhaps regulate aromatase levels. ...
Fish sex reversal is a means to understand sex determination and differentiation, but it is also used to control sex in aquaculture. This review discusses sex reversal in gonochoristic fish, with the coexistence of genetic and environmental influences. The different periods of fish sensitivity to sex reversal treatments are presented with the mechanisms implicated. The old players of sex differentiation are revisited with transcriptome data and loss of function studies following hormone- or temperature-induced sex reversal. We also discuss whether cortisol is the universal mediator of sex reversal in fish due to its implication in ovarian meiosis and 11KT increase. The large plasticity in fish for sex reversal is also evident in the brain, with a reversibility existing even in adulthood. Studies on epigenetics are presented, since it links the environment, gene expression, and sex reversal, notably the association of DNA methylation in sex reversal. Manipulations with exogenous factors reverse the primary sex in many fish species under controlled conditions, but several questions arise on whether this can occur under wild conditions and what is the ecological significance. Cases of sex reversal in wild fish populations are shown and their fitness and future perspectives are discussed.
... Several studies have shown the benefits of meta-analysis in terms of both higher statistical power and precision in detecting differentially expressed genes (DEGs) in different complex traits including infectious disease (Song et al., 2014;Camacho-Cáceres et al., 2015;Sharma et al., 2015;Yin et al., 2015;Wang C.-Y. et al., 2015;Wang X. et al., 2015). Further, data integration approaches at a higher level try to map multiple biological data levels into one mechanistic network to improve representativeness of data (Chen et al., 2008;Bowick and McAuley, 2011;Amiri et al., 2013;Depiereux et al., 2015;Paraboschi et al., 2015). The generated multi-dimensional network is likely to be more useful in inferring universally involved processes or pathways regardless of inter-studies differences (Azimzadeh Jamalkandi et al., 2015). ...
The prototypical neurotropic virus, rabies, is a member of the Rhabdoviridae family that causes lethal encephalomyelitis. Although there have been a plethora of studies investigating the etiological mechanism of the rabies virus and many precautionary methods have been implemented to avert the disease outbreak over the last century, the disease has surprisingly no definite remedy at its late stages. The psychological symptoms and the underlying etiology, as well as the rare survival rate from rabies encephalitis, has still remained a mystery. We, therefore, undertook a systems biomedicine approach to identify the network of gene products implicated in rabies. This was done by meta-analyzing whole-transcriptome microarray datasets of the CNS infected by strain CVS-11, and integrating them with interactome data using computational and statistical methods. We first determined the differentially expressed genes (DEGs) in each study and horizontally integrated the results at the mRNA and microRNA levels separately. A total of 61 seed genes involved in signal propagation system were obtained by means of unifying mRNA and microRNA detected integrated DEGs. We then reconstructed a refined protein-protein interaction network (PPIN) of infected cells to elucidate the rabies-implicated signal transduction network (RISN). To validate our findings, we confirmed differential expression of randomly selected genes in the network using Real-time PCR. In conclusion, the identification of seed genes and their network neighborhood within the refined PPIN can be useful for demonstrating signaling pathways including interferon circumvent, toward proliferation and survival, and neuropathological clue, explaining the intricate underlying molecular neuropathology of rabies infection and thus rendered a molecular framework for predicting potential drug targets.
Collichthys lucidus (C. lucidus) is an economically important fish species, exhibiting sexual dimorphism in its growth rate. However, there is a lack of research on its underlying sex-related mechanisms. Therefore, small RNA sequencing was performed to better comprehend these sex-related molecular mechanisms. In total, 171 differentially expressed miRNAs (DE-miRNAs) were identified between the ovaries and testes. Functional enrichment analysis revealed that the target genes of DE-miRNAs were considerably enriched in the p53 signaling, PI3K–Akt signaling, and TGF-beta signaling pathways. In addition, sex-related miRNAs were identified, and the expression of miR-430c-3p and miR-430f-3p was specifically observed in the gonads compared with other organs and their expression was markedly upregulated in the testes relative to the ovaries. Bmp15 was a target of miR-430c-3p and was greatly expressed in the ovaries compared with the testes. Importantly, miR-430c-3p and bmp15 co-expressed in the ovaries and testes. This research provides the first detailed miRNA profiles for C. lucidus concerning sex, likely laying the basis for further studies on sex differentiation in C. lucidus.
The prototypical neurotropic virus, rabies, is a member of the Rhabdoviridae family that causes lethal encephalomyelitis. Although there have been a plethora of studies investigating the etiological mechanism of the rabies virus and many precautionary methods have been implemented to avert the disease outbreak over the last century, the disease has surprisingly no definite remedy at its late stages. The psychological symptoms and the underlying etiology, as well as the rare survival rate from rabies encephalitis, has still remained a mystery. We, therefore, undertook a systems biomedicine approach to identify the network of gene products implicated in rabies. This was done by meta-analyzing whole-transcriptome microarray datasets of the CNS infected by strain CVS-11, and integrating them with interactome data using computational and statistical methods. We first determined the differentially expressed genes (DEGs) in each study and horizontally integrated the results at the mRNA and microRNA levels separately. A total of 61 seed genes involved in signal propagation system were obtained by means of unifying mRNA and microRNA detected integrated DEGs. We then reconstructed a refined protein-protein interaction network (PPIN) of infected cells to elucidate biological signaling transduction pathways affected by rabies virus. To validate our findings, we confirmed differential expression of randomly selected genes in the network using Real-time PCR. In conclusion, the identification of seed genes and their network neighborhood within the refined PPIN can be useful for demonstrating signaling pathways including interferon circumvent, toward proliferation and survival, and neuropathological clue, explaining the intricate underlying molecular neuropathology of rabies infection and thus rendered a molecular framework for predicting potential drug targets.
Blotched snakehead (Channa maculata) is an economically important freshwater fish in China, of which males grow much faster than females. To illuminate the molecular mechanism of sex differentiation and gonad development, RNA-Sequencing was performed to identify sex-related genes and pathway in gonads of 6-month-old normal XX females (XX-F), normal XY males (XY-M), XY sex reversal females (XY-F) and YY super-males (YY-M). The analysis showed that many differentially expressed genes (DEGs) had similar expression patterns in XY-F and XX-F, which were different from XY-M and YY-M. qRT-PCR indicated that Amh, Dmrt1, and Sox9 had relatively high expression in testes of XY-M and YY-M. Taking Amh as an example, there was a relative fold change of 1.0 in XX-F, 2.1 fold change in XY-F, 36.1 fold change in XY-M, and 26.0 fold change in YY-M. Cyp19a1a, Figla, and Foxl2 were highly expressive in ovaries of XX-F and XY-F. Taking Figla as an example, there was a relative fold change of 557 in XX-F, 304.5 fold change in XY-F, 5.6 fold change in XY-M, and 4.4 fold change in YY-M. KEGG analysis revealed many DEGs distributed in pathways related to sex differentiation, steroid hormone synthesis and growth, etc. Significant variation and trends in relative expression levels tested by qRT-PCR were consistent with those recorded by RNA-Sequencing. This is the first time that transcriptome of snakehead has been investigated systematically and in an integrated way. Large quantities of candidate genes involved in sex differentiation, gonad development and growth dimorphism were identified. The study provides useful resources for understanding sex differentiation and growth dimorphism, potentially assisting mono-sex production of snakehead in aquaculture.
In aquatic toxicology, perhaps no pharmaceutical has been investigated more intensely than 17alpha-ethinylestradiol (EE2), the active ingredient of the birth control pill. At the turn of the century, the fields of comparative endocrinology and endocrine disruption research witnessed the emergence of omics technologies, which were rapidly adapted to characterize potential hazards associated with exposures to environmental estrogens, such as EE2. Since then, significant advances have been made by the scientific community, and as a result, much has been learned about estrogen receptor signaling in fish from environmental xenoestrogens. Vitellogenin, the egg yolk precursor protein, was identified as a major estrogen-responsive gene, establishing itself as the premier biomarker for estrogenic exposures. Omics studies have identified a plethora of estrogen responsive genes, contributing to a wealth of knowledge on estrogen-mediated regulatory networks in teleosts. There have been ∼40 studies that report on transcriptome responses to EE2 in a variety of fish species (e.g., zebrafish, fathead minnows, rainbow trout, pipefish, mummichog, stickleback, cod, and others). Data on the liver and testis transcriptome dominate in the literature and have been the subject of many EE2 studies, yet there remain knowledge gaps for other tissues, such as the spleen, kidney, and pituitary. Inter-laboratory genomics studies have revealed transcriptional networks altered by EE2 treatment in the liver; networks related to amino acid activation and protein folding are increased by EE2 while those related to xenobiotic metabolism, immune system, circulation, and triglyceride storage are suppressed. EE2-responsive networks in other tissues are not as comprehensively defined which is a knowledge gap as regulated networks are expected to be tissue-specific. On the horizon, omics studies for estrogen-mediated effects in fish include: (1) Establishing conceptual frameworks for incorporating estrogen-responsive networks into environmental monitoring programs; (2) Leveraging in vitro and computational toxicology approaches to identify chemicals associated with estrogen receptor-mediated effects in fish (e.g., male vitellogenin production); (3) Discovering new tissue-specific estrogen receptor signaling pathways in fish; and (4) Developing quantitative adverse outcome pathway predictive models for estrogen signaling. As we look ahead, research into EE2 over the past several decades can serve as a template for the array of hormones and endocrine active substances yet to be fully characterized or discovered.
