Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of wild type and Rpe65-/- mouce retinae to characterize gene response in Rpe65-/- mouse model of Lebers congenital amaurosis during progression of the disease.

ABSTRACT: To characterize gene response in RPE65-/- mouse model of Leber's congenital amaurosis during progression of the disease, we analyzed differential gene expression in retinae early in the development of the disease, namely before and at the onset of photoreceptor cell death in knock-out mice of 2, 4 and 6 months of age. Experiment Overall Design: We compared gene expression in wild type and RPE65-/- retinae at 2, 4 and 6 months of age. Three biological replicates were performed for each of the six conditions analyzed; this series hence contains 18 samples.

ORGANISM(S): Mus musculus

SUBMITTER: Lydia Michaut

PROVIDER: E-GEOD-3249 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Biological characterization of gene response in Rpe65-/- mouse model of Leber's congenital amaurosis during progression of the disease.

Cottet Sandra S Michaut Lydia L Boisset Gaëlle G Schlecht Ulrich U Gehring Walter W Schorderet Daniel F DF

FASEB journal : official publication of the Federation of American Societies for Experimental Biology 20061001 12

RPE65 is the retinal isomerase essential for conversion of all-trans-retinyl ester to 11-cis-retinol in the visual cycle. Leber's congenital amaurosis (LCA), an autosomal recessive form of RP resulting in blindness, is commonly caused by mutations in the Rpe65 gene. Whereas the molecular mechanisms by which these mutations contribute to retinal disease remain largely unresolved, affected patients show marked RPE damage and photoreceptor degeneration. We evaluated gene expression in Rpe65-/- mous ...[more]

PMID: 17012256

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Project description:Congenital glioblastoma multiforme (cGBM) historically has been considered an aggressive tumor of infancy requiring extensive chemotherapy to achieve cure. We report on 4 patients at our institution with cGBMs who were treated with surgery and chemotherapy (carboplatin and etoposide every 21 days for 2-6 cycles). Four of four patients are progression free at a median time of 27.5 months (22-103 months). To characterize the molecular biology of cGBM, we compared the gene expression profiles of 3 cGBMs to 12 pediatric and 6 primary adult glioblastomas collected at our institution. Unsupervised hierarchical clustering showed cGBMs grouped together with other high-grade gliomas. cGBMs demonstrated marked similarity to both pediatric and adult GBMs, with only a total of 31 differentially expressed genes identified (FDR < 0.05). Unique molecular features of congenital GBMs identified included over-expression of multiple genes involved in glucose metabolism and tissue hypoxia pathways. Four tyrosine kinases were also mong the up-regulated genes (RET, RASGRF2, EFNA5, ALK). Thus, at our institution congenital GBMs, while similar both histologically and molecularly to other GBMs, appear to have a good prognosis with surgery in combination with relatively moderate chemotherapy. Further study is needed to determine if the few gene expression differences that were identified may contribute to the better survival seen in these tumors compared to pediatric or adult GBMs. Key Words: glioblastoma; congenital; pediatric; gene expression; microarray Molecular profiling of 18 AT/RT patient tumor samples was performed using Affymetrix U133 Plus2 GeneChips. Data were background corrected and normalized using gcRMA (as implemented in Bioconductor). Unsupervised agglomerative hierarchical clustering was performed to identify subsets of AT/RTs with similar gene expression. Limma (moderated t-tests; Bioconductor) was used to identify signature genes for each cluster. Bioinformatics web tool DAVID was used to identify enriched biological processes for each cluster. Survival was analyzed using Kaplan-Meier curves and Cox Hazard Ratio. Bioinformatics tools Gene Set Enrichment (GSEA) and Ingenuity Pathways Analysis were also used to gain further insight into cluster differences.

Dataset Information

Transcription profiling of wild type and Rpe65-/- mouce retinae to characterize gene response in Rpe65-/- mouse model of Lebers congenital amaurosis during progression of the disease.

Publications

Biological characterization of gene response in Rpe65-/- mouse model of Leber's congenital amaurosis during progression of the disease.

Similar Datasets

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