Zebrafish embryos exposed to the model hedgehog pathway inhibitor cyclopamine, as well as to the potential hedghog pathway disrupters SANT-2 and GANT-61.
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
SUBMITTER: Wibke Busch
PROVIDER: E-GEOD-29357 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The hedgehog (Hh) signaling pathway is important for various developmental processes during embryogenesis and for homeostasis of adult tissue in vertebrates. Aberrant signaling results in severe birth defects and malignancies, respectively. The small molecules SANT-2 and GANT-61 were identified as potential Hh-pathway inhibitors in a reporter gene assay (Shh-light II cells). We aimed to analyze the effects of these compounds on the gene expression level in zebrafish embryos in comparison with the well known Hh-pathway inhibitor cyclopamine.
2011-10-01 | GSE29357 | GEO
Project description:Acetylcholinesterase (AChE) inhibitors are widely used as pesticides and drugs. Their primary effect is the overstimulation of muscular activity. Whether AChE inhibitors and related neurotoxic compound also provoke specific changes in gene transcription patterns that allow to establish a mechanistic link useful for diagnostic purposes has, however, yet not been investigated. Therefore, as a proof of principle, we examined the transcriptomic response of a known AChE inhibitor, the organophosphate azinphos-methyl (APM), in zebrafish embryos and compared the response with two non-AChE inhibiting control compounds, 1,4-dimethoxybenzene (DMB) and 2,4-dinitrophenol (DNP). A highly specific cluster of APM induced gene transcripts was identified and a subset of strongly regulated genes was analyzed in more detail. The small heat shock protein hspb11 was found to be the most sensitive gene in response to AChE inhibitors. Comparison of expression in wild-type, ache and fixe mutant embryos revealed that hspb11 expression was dependent on the nicotinic acetylcholine receptor (nAChR) activity. Furthermore, modulators of intracellular calcium levels led to an hspb11 transcriptional up-regulation which suggest that elevated intracellular calcium levels and the resulting increase in muscular activity triggering hspb11 up-regulation. During early zebrafish development, hspb11 was specifically expressed in muscle pioneers and morpholino-knockdown resulted in defects in slow muscle myosin organization. These findings demonstrate that a combination of transcriptome and functional analyzes in the zebrafish embryo is able to correlate gene expression changes to the mechanism of action of neurotoxic compounds. Zebrafish embryos were exposed for 24 h and 48 h (26-50 and 2-50 hpf) to 5,83 µM of azinphos-methyl (APM), 509 µM of 1,4-dimethoxybenzene (DMB) and 14,2 µM 2,4-dinitrophenol (DNP), the respective LC10 of each compound, in order to determine mode of action specific responding genes, or not exposed and parallel treated as controls. 50 zebrafish embryos were used per treatment, and 4 biological independent replicates were analysed, respectively.
2011-12-01 | E-GEOD-27680 | biostudies-arrayexpress
Project description:We have employed the Zebrafish gene expression microarray (MZH_Zebrafish_16k_v1.0) as a discovery platform to analyze the trancriptome of 108hpf (hours post fertilization) embryos exposed from the 96hpf to 108hpf to 100µM of diethylmaleate (DEM). Four two-color microarray studies for measuring expression levels of zebrafish embryos treated with 100µM of diethylmaleate (DEM) were performed. 8 samples were analyzed in total. Four samples were treated with 0.1% DMSO as a control; four samples were treated with 100 µM of DEM and 0.1% DMSO.
2011-09-23 | E-GEOD-32267 | biostudies-arrayexpress
Project description:The zebrafish (Danio rerio) is a popular animal model in studies of vertebrate development and organogenesis. Recent research has shown a similarity of approximately 70% between the human and zebrafish genomes and of 84% in human disease-causing genes, specifically. Zebrafish embryos have a number of desirable features, including transparency, a large size, and rapid embryogenesis. Protein phosphorylation is a well-known post-translational modification (PTM), which performs various biological functions. Recent mass spectrometry (MS) developments have enabled the study of global phosphorylation patterns by using MS-based proteomics coupled with TiO2 phosphopeptide enrichment. In the present study, we identified 3,500 non-redundant phosphorylation sites on 2,166 phosphoproteins and 1,564 quantified phosphoproteins in zebrafish embryos.
2015-10-14 | PXD002232 | Pride
Project description:The morphogen Sonic H edgehog governs a wide range of developmental processes. The zebrafish genetic mutant iguana has vascular stability defects due to decreased Shh signaling. Using iguana mutant embryos and embryos treated with the Hedgehog pathway inhibitor cyclopamine, we conducted a microarray to determine genes that are specifically regulated by Shh signaling, and that might mediate vascular stability. We populate a list of 40 genes to have significantly altered expression in both conditions. Using in situ hybridization and quantitative real-time PCR, we verify the expression changes seen in a subset of genes from the list and determine their localization during embryonic development. We then assay the functional relevance of one of the array hits, the cell-cycle regulator pim1, which was upregulated on the microarray. By overexpressing pim1, we observe a loss of vascular stability, similar to that of iguana mutants. Furthermore, chemical inhibition of pim1 in iguana mutant embryos or cyclopamine treated embryos rescues vascular stability. We conclude that the microarray identified a set of genes that are differentially expressed in two distinct modes of Shh signaling interference. Furthermore, this set of genes contains a high proportion of factors potentially involved in vascular stabilization. The identification of these genes is the first step in defining the molecular mechanism by which Shh promotes vascular stability. 3 biological cyclopamine treated samples plus 3 biological DMSO treated controls, plus 3 biological replicates of iguana mutants plus 3 wild type sibling controls, all collected at 30 hpf
2014-06-30 | E-GEOD-48335 | biostudies-arrayexpress
Project description:Background. Primary cilia (PC) are solitary antennae present at the cell surface. These non-motile cilia play an important role in organ development and tissue homeostasis through the transduction of the Hedgehog (Hh) signaling pathway. We recently revealed the presence of PC in the epithelium of the developing epididymis, an organ of the male reproductive system whose dysfunction triggers male infertility. Acknowledging that systemic blockade of the Hh pathway trigger epididymal dysfunctions in vivo, our main goals were 1) to portray the epididymal Hh environment, 2) to determine the direct responsiveness of epididymal epithelial cells to Hh, and 3) to define the contribution of PC to the transduction of this pathway. Results. The Hh ligands Indian and Sonic hedgehog (Ihh and Shh) were respectively located in principal and clear cells of the mouse epididymis by immunofluorescent staining. The propensity of epididymal principal cells to respond to Hh signaling was assessed on immortalized epididymal DC2 cells by western-blot, confocal imaging and 3D-reconstruction. Our results indicate that epididymal principal cells secrete Ihh and expose PC that co-localize with the conventional acetylated tubulin/Arl13b ciliary markers, as well as with GLI3 Hh signaling factor. Gene expression microarray profiling indicated that the expression of 43 and 248 genes was respectively and significantly modified following pharmacological treatment of DC2 cells with the Hh agonist SAG (250 nM) or the Hh antagonist cyclopamine (20 µM) compared with the control. Among Hh target genes identified, 6.7 % presented perfect matches for GLI-transcription factor consensus sequences, and the majority belonged to interferon-dependent immune response and lipocalin 2 pathways. Finally, the contribution of epididymal PC to the transduction of canonical Hh pathway was validated by ciliobrevinD treatment, which induced a significant decrease of PC length and the expressional reduction of Hh signalling targets. Conclusions. All together our data indicate that PC from epithelial principal cells regulate gene expression profile through a possible autocrine Hh signaling. This provides new hypotheses regarding the potential contribution of PC and Hh signaling in intercellular cross-talk and immunological regulation of the epididymis.
2020-04-17 | GSE143829 | GEO
Project description:Introduction and objectives: Proper In utero Wolffian duct (WD) development requires androgens and is essential to epididymis formation and male fertility. However, non-hormonal factors that control WD homeostasis and development remain largely unknown. In this study, we investigated the contribution of Hedgehog signaling pathway to Wolffian duct development by combining pharmacological approaches on organotypic cultures of WD with microarray profiling. Methods: WD were collected from embryos isolated from 16.5 days post-coitum pregnant mice and cultured in air-liquid condition at 37oC during 72 hours in the presence of either: 1) Cyclopamine (25 µM): Hh inhibitor; 2) Smoothened agonist (0.5 µM ; SAG): Hh activator; 3) Culture media (control). WD pictures were taken and analyzed on ImageJ. At the end of the culture, WD were snap-frozen to perform transcriptomic microarray analyses. Three to four biological replicates per condition, i.e. control (n=3), SAG (n=4) and cyclopamine (n=3), were used for microarray analyses. The quality of the RNA was determined using an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and displayed a RIN ranging from 9.10 to 9.60 out of 10 for the different samples. Microarray analyses were carried out on Affymetrix Mouse Clariom S arrays (Thermofisher) according to the Affymetrix standard protocol. In brief, 100 ng total RNA samples were labeled using the GeneChip® WT Plus Reagent Kit protocol and hybridized to the arrays as described by the manufacturer (Affymetrix, Thermofisher). The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After a 16-h hybridization period, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol. The arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Command Console Software (AGCC) (Affymetrix, Thermofisher) to produce the probe cell intensity data (CEL). The imaged data were then analyzed using the Affymetrix Expression Console Software to perform the quality control, background subtraction and normalization of probe set intensities using Robust Multiarray Analysis (RMA). Microarray processing was performed by the Gene Expression Core facility of the Genomic platform of the Centre Hospitalier Universitaire de Quebec Research Center. The microarray CEL files were imported and analyzed with Transcriptome Analysis Console (TAC) Software 4.0.2 (Applied Biosystems), and submitted to RMA normalization. Samples were included within three different treatment groups (control, SAG and cyclopamine) and compared by Analysis of Variance. Principal Component Analysis and heat maps were performed with Partek Pathway (Partek Incorporated). Biological pathways analyses were performed by using 5 distinct algorithms (i.e. DAVID, STRING, GOrilla, Metascape, GSEA and BLAST2GO). Conclusion: The data made available on GEO repository provide new insights regarding the mechanisms that control epididymis morphogenesis and male fertility. Financially supported by a CIHR grant to CB.
2022-02-21 | GSE145816 | GEO
Project description:Zebrafish (Danio rerio) model system have used widespread vertebrate investigations for genetic and cell biological analyses, and is suitable for small molecular screens such as chemical, toxicity and drug in order to use for human diseases and drug discovery . Recently, These powerful zebrafish model increasingly apply to human metabolic disease such as obesity and diabetes and toxicology. Despite a lot of advantages, proteomics research at zebrafish has received little interest in comparison with genetic and biological research using histology and in situ hybridization. Protein lysine acetylation is one of the most known post-translational modifications with dynamic and reversibly controlled by lysine acetyltransferase such as histone acetyltransferases and lysine deacetylase such as histone deacetylases and sirtuins family.Also, during the past year, global lysine acetylome studies using MS-based proteomics approach was in diverse species such as human, mouse, E. coli, Yeast and plants. Based on global acetylome data, our understanding of the roles of lysine acetylation in various cellular processes has increased. . The aim of this study was to identify Lysine acetylation in zebrafish embryos and determine the homology from Human at modified site level. Here we showed the global lysine acetylation study in Zebrafish embryos using MS-based zebrafish embryos.
2016-10-10 | PXD003455 | Pride
Project description:T helper 17 (Th17) cells play a key role in barrier protection against fungal and bacterial pathogens but are also pathological drivers of many inflammatory diseases. We find that Hh signaling inhibition through Smoothened inhibitor cyclopamine selectively inhibits Th17 lineage differentiation but not the development of Th1, Th2, or iTreg CD4+ Th cells. In these experiments we analysed the transcriptomes of Th17 cells that had been polarized in the presence of cyclopamine or carrier control to profile the global transcriptome of Th17 cells in which the Hh pathway had been blocked. The aim of this analysis was to identify the target genes downstream of Smo that may be important for Th17 polarisation.
2022-06-13 | GSE205848 | GEO
Project description:Zebrafish embryos exposed to the model hedgehog pathway inhibitor cyclopamine, as well as to the potential hedghog pathway disrupters SANT-2 and GANT-61.
| PRJNA140187 | ENA