Expression data from GFAP-negative LC cells exposed to 24 hours of hypoxia
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE26820 | GEO | 2012/03/01
SECONDARY ACCESSION(S): PRJNA136019
REPOSITORIES: GEO
Similar Datasets
Project description:Vascular hypoperfusion is a pathological phenomenon in the glaucomatous optic nerve head. We report transcriptional responses in GFAP-negative LC cells exposed to in-vitro hypoxic stress (1%O2). The study design was as follows: For GSM659595: "human donor 1" LC cells were passaged into three p100 plates of cells and then exposed to normoxia for 24 hours. The RNA from each of these three plates was then extracted, pooled and hybridised to the microarray "normoxia_1". For GSM659592: "human donor 1" LC cells were passaged into three p100 plates of cells and then exposed to hypoxia for 24 hours. The RNA from each of these three plates was then extracted, pooled and hybridised to the microarray "hypoxia_1". "hypoxia_1" and "normoxia_1" microarray data were then compared to calculate differential gene expression in response to hypoxia. This experiment (same design) was then conducted a second and third time using biologically independent "human donor 2" and "human donor 3" cell lines respectively.
2012-03-01 | E-GEOD-26820 | biostudies-arrayexpress
Project description:Primary open angle glaucoma (POAG) is a progressive optic neuropathy, which is a major cause of worldwide visual impairment and blindness. Pathological hallmarks of the glaucomatous optic nerve head include retinal ganglion cell axon loss and extracellular matrix (ECM) remodeling of the lamina cribrosa layer. TGF-beta is an important pro-fibrotic modulator of ECM metabolism, whose levels are elevated in human POAG lamina cribrosa tissue compared with non-glaucomatous controls. We treated human lamina cribrosa (LC) cells with TGF-beta1 (10ng/ml) for 24 hours in order to examine differential gene expression patterns in repsonse to this cytokine. In particular we focused on ECM and fibrotic genes. We found that TGF-beta1 induces expression and release of ECM components in LC cells, which may be important in regulating matrix remodeling in the lamina cribrosa. In disease states such as POAG, the LC cell may represent an important pro-fibrotic cell type and an attractive target for novel therapeutic strategies.
2008-06-12 | E-GEOD-2705 | biostudies-arrayexpress
Project description:Primary open angle glaucoma (POAG) is a progressive optic neuropathy, which is a major cause of worldwide visual impairment and blindness. Pathological hallmarks of the glaucomatous optic nerve head include retinal ganglion cell axon loss and extracellular matrix (ECM) remodeling of the lamina cribrosa layer. TGF-beta is an important pro-fibrotic modulator of ECM metabolism, whose levels are elevated in human POAG lamina cribrosa tissue compared with non-glaucomatous controls. We treated human lamina cribrosa (LC) cells with TGF-beta1 (10ng/ml) for 24 hours in order to examine differential gene expression patterns in repsonse to this cytokine. In particular we focused on ECM and fibrotic genes. We found that TGF-beta1 induces expression and release of ECM components in LC cells, which may be important in regulating matrix remodeling in the lamina cribrosa. In disease states such as POAG, the LC cell may represent an important pro-fibrotic cell type and an attractive target for novel therapeutic strategies. Keywords: other
2005-08-05 | GSE2705 | GEO
Project description:Purpose: Marked extracellular matrix (ECM) remodeling occurs in the human optic nerve head in primary open angle glaucoma (POAG). The glial fibrillary acid protein (GFAP) negative lamina cribrosa cell may play an important role in this remodeling process. The authors report the first study of global and ECM-focused gene transcription differentials between GFAP-negative negative lamina cribrosa (LC) cells from normal and POAG human donors. Methods: GFAP-negative LC cell lines were generated from the optic nerve tissue of three normal (n=3) and three POAG (n=3) human donors. Using Affymetrix U133A arrays the transcriptional profile between the normal and diseased groups were compared. Bioinformatic analysis was carried out using robust multichip average (RMA Express) and EASE/David. Real time TaqMan PCR and immunohistochemistry analyses were performed to validate the microarray data. Results: 285 genes were up regulated by greater than 1.5 fold and 413 were down regulated by greater than 1.5 fold in the POAG LC cells versus normal controls. Upregulated genes in POAG LC cells included, SPARC, periostin, thrombospondin, CRTL-1, CTGF and collagen types I, III, V and VIII. Downregulated ECM genes in POAG included MMP-1, fibulin, decorin and tenacsin XB. All TaqMan PCR validation assays were significant (*p<0.05) and consistent with the array data. Immunohistochemistry of one target (periostin) confirmed its differential expression at the protein level in POAG optic nerve head tissue compared with non-glaucomatous controls. Functional annotation and over-representation analysis identified ECM genes as a statistically over-represented class of genes in POAG LC cells compared with normal LC cells. Conclusions: This study reports for the first time that POAG LC cells in-vitro demonstrate up regulated ECM and pro-fibrotic gene expression compared with normal LC cells. This may be a pathological characteristic of this cell type in POAG in-vivo. We believe that the LC cell may be a pivotal regulator of optic nerve head ECM remodeling and an attractive target for future therapeutic strategies in POAG.
2009-01-06 | GSE13534 | GEO
Project description:Chromatium okenii LC strain:LC Genome sequencing
| PRJNA230878 | ENA
Project description:Various retinal disorder such as glaucomatous, retinal ischemia reperfusion, and traumatic optic neuropathy, are involved in the pathogenesis of neurodegeneration via glutamate exicitotoxicity. However, the proteomic characteristics and modulation of the neural-microenvironment with NMDA-induced neurodegeneration in retina and optic nerve remain partly understood. We established a protein sketch of NMDA-induced injury by comparing the proteomes of the PBS-operated, NMDA-operated and control groups. We carried out mass spectrometry-based label-free quantitative proteomics to investigate the exicitotoxic neurodegeneration mechanisms and identify key proteins that regulated neural cell death related signaling pathway in retina and optic nerve spatially. Using LC-MS/MS proteomics analysis, in total, we identified 3532 proteins in retina, 2593 proteins in optic nerve. According to Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), the protein changes and energy metabolism in retina and optic nerve tissue were comprehensively evaluated.
2021-12-30 | PXD022729 | Pride
Project description:Various retinal disorder such as glaucomatous, retinal ischemia reperfusion, and traumatic optic neuropathy, are involved in the pathogenesis of neurodegeneration via glutamate exicitotoxicity. However, the proteomic characteristics and modulation of the neural-microenvironment with NMDA-induced neurodegeneration in retina and optic nerve remain partly understood. We established a protein sketch of NMDA-induced injury by comparing the proteomes of the PBS-operated, NMDA-operated and control groups. We carried out mass spectrometry-based label-free quantitative proteomics to investigate the exicitotoxic neurodegeneration mechanisms and identify key proteins that regulated neural cell death related signaling pathway in retina and optic nerve spatially. Using LC-MS/MS proteomics analysis, in total, we identified 3532 proteins in retina, 2593 proteins in optic nerve. According to Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), the protein changes and energy metabolism in retina and optic nerve tissue were comprehensively evaluated.
2021-12-30 | PXD022466 | Pride
Project description:Olfactory bulb transcript levels for GFAP transgenic mice compared to wildtype at 3wks and 4mos Keywords = GFAP Keywords = Rosenthal fibers Keywords = Alexander disease Keywords: other
2005-07-20 | GSE977 | GEO
Project description:Modulation of the GFAP cytoskeleton in astrocytoma cells alters processes involved in extracellular matrix remodelling and cell-cell signalling – a transcriptome analysis Astrocytomas grade IV are malignant brain tumours with no effective treatment and a five year survival rate of only 5%. Expression of Glial Fibrillary Acidic Protein (GFAP) is lower in high astrocytoma grade, but the expression of the splice isoform GFAPδ is similar in low and high-grade astrocytomas. Thus the ratio of GFAPδ/α is increased in high-grade astrocytomas. We studied transcriptome changes in astrocytoma cell lines resulting from an induced alteration of GFAP isoform expression. GFAPα or GFAPδ were increased or decreased by recombinant expression or shRNA mediated knockdown of GFAPpan or GFAPα. We find that the most prominent effects are induced by the modulations where the GFAPδ/GFAPα ratio is increased. Gene ontology analysis revealed that the main effects of GFAP modulation take place in the extracellular matrix remodelling and cellular signalling clusters, with possible implications in astrocytoma invasive behaviour and angiogenesis.
2017-07-03 | GSE74567 | GEO