Hepatic Transcriptomic Responses to Ethinylestradiol in Embryonic Japanese Quail and Double-crested Cormorant
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ABSTRACT:
PROVIDER: PRJNA886409 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21781142_1.fastq.gz | Fastqsanger.gz | |||
| SRR21781142_2.fastq.gz | Fastqsanger.gz | |||
| SRR21781143_1.fastq.gz | Fastqsanger.gz | |||
| SRR21781143_2.fastq.gz | Fastqsanger.gz | |||
| SRR21781144_1.fastq.gz | Fastqsanger.gz |
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Project description:Species difference in susceptibility to toxicants is a critical issue in ecotoxicology. Transcriptomics is being proposed as a strategy to improve toxicity testing for regulatory risk assessment; however, different responses among species have not been extensively explored using this approach. In the present study, we identified dysregulated genes and pathways in Japanese quail (JQ) and double-crested cormorant (DCCO) embryos following exposure to ethinylestradiol (EE2). The objectives were to evaluate unique and overlapping transcriptomic responses to estrogenic exposure in the two species, and to determine whether these responses correspond to previously reported sensitivity difference at the organismal level. Exposures were conducted according to an avian egg injection protocol that we have proposed for standardization. EE2 was dissolved in dimethyl sulfoxide and injected into the air cell of eggs prior to incubation at nominal concentrations of 0, 3.33, and 33.3 µg/g egg weight. After 9-days (JQ) or 16-days (DCCO) of incubation (representing mid-incubation stage), liver tissues were collected from 5 embryos per treatment group for RNA-sequencing. Data were processed and analyzed using EcoOmicsAnalyst (www.ecoomicsanalyst.ca) and ExpressAnalyst (www.expressanalyst.ca). Following exposure to EE2, JQ and DCCO had 238 and 1987 differentially expressed genes, respectively, having 78 of them in common. The results of this study will contribute to a better understanding of the estrogenic effects of contaminants in birds, the expansion of taxonomic coverage in chemical risk assessment from model to non-model species, and the evaluation of transcriptomics and early-life stage tests as alternative toxicity testing methods. This study was conducted as a part of a large-scale Genome Canada-funded project, EcoToxChip project (www.ecotoxchip.ca).
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Project description:Modern 21st century toxicity testing makes use of omics technologies to address critical questions in toxicology and chemical management. Of interest are questions relating to chemical mechanisms of toxicity, differences in species sensitivity, and translation of molecular effects to observable apical endpoints. Our study addressed these questions by comparing apical outcomes and multiple omics responses in early-life stage exposure studies with Japanese quail (JQ; Coturnix japonica) and double crested cormorant (DCCO; Phalacrocorax auritus), representing a model and ecological species, respectively. Specifically, we investigated the dose-dependent response of apical outcomes, transcriptomics, and metabolomics in the liver in each species exposed to chlorpyrifos (CPF), a widely used organophosphate pesticide. Our results revealed a clear pattern of dose-dependent disruption of gene expression and metabolic profiles in JQ but not DCCO at similar CPF exposure concentrations. The difference in effect sensitivity between species was likely due to higher metabolic transformation of CPF in the precocial JQ compared to the more altricial DCCO. The most impacted biological pathways after CPF exposure in JQ included hepatic metabolism, oxidative stress, endocrine disruption (steroid and non-steroid hormones), and metabolic disease (lipid and fatty acid metabolism). Importantly, we show consistent responses across biological scales, suggesting that significant disruption at the level of gene expression and metabolite profiles leads to observable apical responses at the organism level. Our study demonstrates the utility of evaluating effects at multiple biological levels of organization to understand how modern toxicity testing relates to outomes of regulatory relevance, while also highlighting important, yet poorly understood, species differences in sensitivity to chemical exposure.
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Project description:Chemical risk assessment for avian species typically depends on information from toxicity tests performed in adult birds. Early-life stage (ELS) toxicity tests have been proposed as an attractive alternative, but incorporation of these data into existing frameworks will require knowledge about the similarities/differences between ELS and adult responses. The present study uses transcriptomics to assess hepatic gene expression in ELS and adult Japanese quail following exposure to ethinylestradiol (EE2). ELS quail were dosed with 0, 3.33, and 33.3 µg EE2/g egg via air cell injection prior to incubation. Adult quail were fed a single dose of EE2 at 0, 0.5, and 5 mg/kg body weight by gavage. Liver tissue was collected from 5-6 individuals per dose group at mid-incubation for ELS quail, and 4 days after dosing for adult birds. A total of 283 and 111 differentially expressed genes (DEGs) were detected in ELS and adult quail, respectively, 16 of which were shared across life stages. Shared DEGs included estrogenic biomarkers such as vitellogenin genes and Apovitellenin-1. For the dose groups that resulted in the highest number of DEGs (ELS [3.3 µg/g]; adult [5 mg/kg]), 21 and 35 KEGG pathways were enriched, respectively. Ten of these pathways were shared between life stages, including pathways involved with signaling molecules and interaction, and endocrine system. Taken together, our results suggest conserved mechanisms of action following estrogenic exposure across two life stages, with evidence from differentially expressed genes and enriched pathways. This study contributes to the development and evaluation of toxicogenomic and ELS approaches as alternative toxicity testing methods and supports the use of the ELS test for screening estrogenic chemicals.
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Project description:Chemical risk assessment for avian species typically depends on information from toxicity tests performed in adult birds. Early-life stage (ELS) toxicity tests have been proposed as an attractive alternative, but incorporation of these data into existing frameworks will require knowledge about the similarities/differences between ELS and adult responses. The present study uses transcriptomics to assess hepatic gene expression in ELS and adult Japanese quail following exposure to ethinylestradiol (EE2). ELS quail were dosed with 0, 3.33, and 33.3 µg EE2/g egg via air cell injection prior to incubation. Adult quail were fed a single dose of EE2 at 0, 0.5, and 5 mg/kg body weight by gavage. Liver tissue was collected from 5-6 individuals per dose group at mid-incubation for ELS quail, and 4 days after dosing for adult birds. A total of 283 and 111 differentially expressed genes (DEGs) were detected in ELS and adult quail, respectively, 16 of which were shared across life stages. Shared DEGs included estrogenic biomarkers such as vitellogenin genes and Apovitellenin-1. For the dose groups that resulted in the highest number of DEGs (ELS [3.3 µg/g]; adult [5 mg/kg]), 21 and 35 KEGG pathways were enriched, respectively. Ten of these pathways were shared between life stages, including pathways involved with signaling molecules and interaction, and endocrine system. Taken together, our results suggest conserved mechanisms of action following estrogenic exposure across two life stages, with evidence from differentially expressed genes and enriched pathways. This study contributes to the development and evaluation of toxicogenomic and ELS approaches as alternative toxicity testing methods and supports the use of the ELS test for screening estrogenic chemicals.
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Project description:Hepatic Transcriptomic Responses to Ethinylestradiol in Two Life Stages of Japanese Quail
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Project description:Since Japanese quail and chicken belong to the same order Galliforms, DNA sequence of both species are highly conserved and proved to be applicable for various analyses each other. Quail are commonly used to address physiological questions for reasons of economy. To test whether chicken microarrays are useful to quail samples, we compared hybridization signals of chicken and quail genomic DNA on Affymetrix chicken genome array. Keywords: comparative genomic hybridization
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Project description:To understand molecular mechanism of stripe patterning in the embryonic skin of Japanese quail, we compared gene expression profile between black stripe and yelllow stripe by using RNA seq method. Most of differential expression genes were known pigmentation-related genes, but some are unknown role in pigment pattern formation.
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Project description:Since Japanese quail and chicken belong to the same order Galliforms, DNA sequence of both species are highly conserved and proved to be applicable for various analyses each other. Quail are commonly used to address physiological questions for reasons of economy. To test whether chicken microarrays are useful to quail samples, we compared hybridization signals of chicken and quail genomic DNA on Affymetrix chicken genome array. Experiment Overall Design: Genomic DNA of female chicken and quail were extracted individually from liver of three birds and hybridized on Affymetrix microarrays. Samples were analyzed in triplicate set of array (three biological replicates).
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Project description:In this study, we used RNA-seq to identify differences in gene expression patterns in ovarian follicles of female Japanese quail (Coturnix coturnix japonica) that produce large versus small eggs relative to their body size. A high quality reference genome is currently under construction by the Quail Genome Consortium (BioProject ID: PRJNA292031).
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