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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Upregulated Hedgehog Signaling Promotes Zebrafish CNS Tumorigenesis

ABSTRACT: Using a cytokeratin 5 gene promoter, we ectopically expressed a constitutively active zebrafish smoothened (smoa1) in presumably glial progenitor cells of zebrafish CNS. Stable transgenic zebrafish developed retinal tumors and low grade glioma of the optic nerve. Microarray analysis showed upregulation of Hh downstream targets of ptc1, gli1 and gli2a in tumors. Immunofluorescence studies confirmed overexpression of Pax2, GFAP, S100 and Sox2, specifically in gliomas. We also detected upregulated expression of phosphorylated pRb and Mdm2 associated with gliomagenesis. Our results suggest that dysregulated Hh signaling initiates tumorigenesis in zebrafish CNS. Zebrafish optic nerve maintains phosphorylated pRb expression, therefore provides a unique niche for pathogenesis of glioma. RNAs from 4 gross eye tumors (from fish of 4 months of age) and 4 normal eyes from wil-type control fish were extracted and used for array analysis

ORGANISM(S): Danio rerio

SUBMITTER: Yong-Dong Wang

PROVIDER: E-GEOD-40761 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Upregulated Hedgehog Signaling Promotes Zebrafish CNS Tumorigenesis

Project description:Using a cytokeratin 5 gene promoter, we ectopically expressed a constitutively active zebrafish smoothened (smoa1) in presumably glial progenitor cells of zebrafish CNS. Stable transgenic zebrafish developed retinal tumors and low grade glioma of the optic nerve. Microarray analysis showed upregulation of Hh downstream targets of ptc1, gli1 and gli2a in tumors. Immunofluorescence studies confirmed overexpression of Pax2, GFAP, S100 and Sox2, specifically in gliomas. We also detected upregulated expression of phosphorylated pRb and Mdm2 associated with gliomagenesis. Our results suggest that dysregulated Hh signaling initiates tumorigenesis in zebrafish CNS. Zebrafish optic nerve maintains phosphorylated pRb expression, therefore provides a unique niche for pathogenesis of glioma.

2013-09-07 | GSE40761 | GEO

Differential gene expression in Danio rerio during optic nerve regeneration

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2010-05-16 | E-GEOD-17854 | biostudies-arrayexpress

Differential gene expression in Danio rerio during optic nerve regeneration

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Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line

Project description:Heterozygous adults of the zebrafish transgenic line Tg(flk1:RFP)is18 develop tumors in the retina, optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 month old sibling wild type and Tg(flk1:RFP)is18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT (wild type); 3 grossly normal retina from Tg(flk1:RFP)is18/+ were pooled to create Sample PT (pre tumor) and 2 large tumors from Tg(flk1:RFP)is18/+ were pooled to create Sample T (tumor). Each sample was run in an individual lane on the HiSeq system.

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RNA-sequencing of tumor-associated microglia reveals Ccl5 as a stromal chemokine critical for neurofibromatosis-1 glioma growth

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Integrated analyses of zebrafish miRNA and mRNA expression profiles identify miR-29b and miR-223 as potential regulators of optic nerve regeneration

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Zebrafish Optic Nerve Regeneration Metabolomics - 3 Days Post Crush

Project description:Zebrafish (Danio Rerio) have the capacity for successful adult optic nerve regeneration. In contrast, mammals lack this intrinsic ability and undergo irreversible neurodegeneration seen in glaucoma and other optic neuropathies. Optic nerve regeneration is often studied using optic nerve crush, a mechanical neurodegenerative model. Untargeted metabolomic studies within successful regenerative models are deficient. Evaluation of tissue metabolomic changes in active zebrafish optic nerve regeneration can elucidate prioritized metabolite pathways that can be targeted in mammalian systems for therapeutic development. Female and male (6 month to 1 year old) right Zebrafish (Tg(gap43:GFP)) optic nerves were crushed and collected three days after. Contralateral, uninjured optic nerves were collected as controls. The tissue was dissected from euthanized fish and frozen on dry ice. Samples were pooled for each category (female crush, female control, male crush, male control) and pooled at n = 31 to obtain sufficient metabolite concentrations for analysis. Optic nerve regeneration was verified by microscope visualization of GFP fluorescence. Metabolites were extracted using a Precellys Homogenizer and a serial extraction method: (1) 1:1 Methanol/Water and (2) 8:1:1 Acetonitrile/Methanol/Acetone. Metabolites were analyzed by untargeted liquid chromatography-mass spectrometry (LC MS-MS) profiling using a Q-Exactive Orbitrap instrument coupled with Vanquish Horizon Binary UHPLC LC-MS system. Metabolites were identified and quantified using Compound Discoverer 3.3 and isotopic internal metabolites standards.

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Gene expression timecourse in zebrafish whole eye in response to optic nerve crush

Project description:It is well-established that neurons in the adult mammalian central nervous system are terminally differentiated and, if injured, will be unable to regenerate their connections. In contrast to mammals, zebrafish and other teleosts display a robust neuroregenerative response. Following optic nerve crush (ONX), retinal ganglion cells (RGC) regrow their axons to synapse with topographically correct targets in the optic tectum, such that vision is restored in ~21 days. What accounts for these differences between teleostean and mammalian responses to neural injury is not fully understood. A time course analysis of global gene expression patterns in the zebrafish eye after optic nerve crush can help to elucidate cellular and molecular mechanisms that contribute to a successful neuroregeneration. We used microarrays to detail the global gene expression patterns underlying a successful regeneration or the optic nerve following injury. Experiment Overall Design: Microarray analysis was performed on total RNA extracted from whole eye following optic nerve crush (ONX) or sham surgery at defined intervals (4, 12, & 21 days).

2010-02-21 | E-GEOD-19298 | biostudies-arrayexpress

Expression data from P4 and P10 mouse optic nerves

2011-05-16 | GSE24513 | GEO

Expression data from P4 and P10 mouse optic nerves

Project description:Optic nerves are an accessible part of the CNS, providing a source of glia without the presence of neuronal cell bodies. Therefore, an analysis was carried out of gene expression in optic nerves at P4, before myelination begins and at P10, when myelination is very actively proceeding. The goal was to obtain a profile of the changing gene expression that accompanies this transition from unmyelinated CNS nerve to myelinated nerve. Two microarray experiments were combined here. In the first, RNA was prepared from the optic nerves of 75 P4 C57BL/6J mice and 70 P10 C57BL/6J mice. In the second experiment, RNA was prepared from the optic nerves of 55 P4 C57BL/6J mice and two groups of 50 P10 C57Bl/6J mice. In total, there are 2 P4 RNA samples and 3 P10 RNA samples being hybridized to Affymetrix GeneChip 430A for Mouse Expression.

2011-05-16 | E-GEOD-24513 | biostudies-arrayexpress

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