Unknown,Transcriptomics,Genomics,Proteomics

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Ethynylestradiol (EE2) effect on global gene expression in primary rainbow trout (Oncorhynchus mykiss) hepatocytes

ABSTRACT: To study short term (48h) hepatic transcriptional changes and identify potential modes of action in primary rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to 0.03, 0.3, 3 and 30nM EE2. The transcriptional gene expression analysis involved a high density (60k) custom designed oligonucleotide salmonid microarray in combination with quantitative real-time polymerase chain reaction (qPCR). Differently expressed genes (DEGs) were obtained after application of a one-way analysis of variance (ANOVA) and Tukey posthoc test. Enrichment analysis was performed based on Gene Ontology (GO) to determine the biological roles of the DEGs. The obtained DEGs were further mapped against mammalian orthologs. The successfully mapped DEGs were further subjected to a gene network analysis based on well-curated mammalian protein -protein interactions, followed by a canonical and toxicity pathway analysis. The pathways and network analysis were performed in order to link DEGs to specific and toxicological/biological functions. Isolated primary rainbow trout hepatocytes were exposed to 0.03-30nM ethynylestradiol for 48h. The cells were sampled and used for gene expression analysis. A total of 4 biological replicates were analyzed for each concentration, including solvent (DMSO) control.

ORGANISM(S): Oncorhynchus mykiss

SUBMITTER: Maria Hultman

PROVIDER: E-GEOD-68335 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Purpose: The goal of this study is to identify the difference of immunity between wild-type and yellow mutant rainbow trout in natural flowing water pond culture environment. Methods: The transcriptomic profiles of the skin were generated by using the Hiseq™4000 sequencing platform. Results: A total of 557,976,332 clean reads were yielded from six libraries and then assembled into 38,226 genes. Using P-value of 0.05 as the threshold, 3373 differentially expressed genes (DEGs) were obtained between WR_S and YR_S rainbow trout skin including the members of HSP90, V-ATPases, GST, SUGT1, NLRP3, NOD1, TLR3, IFR3, DHX58, IFIH1, JAK1, JAK2, STAT1 and NAMPT (|log2 fold-change| ranged from 1 to 4). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were performed. A majority of DEGs were enriched in innate immune-related GO terms and pathways, such as activation of innate immune response, inflammatory response, innate immune response, NAD+ADP-ribosyltransferase activity and NAD biosynthetic process in sub-categories of GO terms, and RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, Phagosome, Jak-STAT signaling pathway in KEGG enrichment pathways. Meanwhile, several immune-related metabolic pathways were also identified including metabolism of Xenobiotics by cytochrome P450, Glutathione metabolism, Nicotinate and nicotinamide metabolism. Additionally, 15 DEGs were selected and validated their expression level by qRT-PCR to confirm accuracy of the RNA-seq. Conclusions: Our study is the first time to clarify the skin innate immunity difference between wild-type and yellow mutant rainbow trout in the natural flowing water pond culture environment. Our results show that the expression of most immune-related genes in the corresponding pathways were up-regulated in WR_S rainbow trout. We presumed that the disease resistance of WR_S rainbow trout might be stronger than YR_S rainbow trout.

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Ethynylestradiol (EE2) effect on global gene expression in primary rainbow trout (Oncorhynchus mykiss) hepatocytes

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